Atomistic simulation of defect formation and structure transitions in U-Mo alloys in swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Kolotova, L. N.; Starikov, S. V.

2017-11-01

In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy transfer into the electronic subsystem and relaxations processes lead to the formation of structural defects and cause specific effects, such as the track formation. There is a large interest to understanding of the mechanisms of defects/tracks formation due to the heating of the electron subsystem. In this work, the atomistic simulation of defects formation and structure transitions in U-Mo alloys in irradiation of swift heavy ions has been carried out. We use the two-temperature atomistic model with explicit account of electron pressure and electron thermal conductivity. This two-temperature model describes ionic subsystem by means of molecular dynamics while the electron subsystem is considered in the continuum approach. The various mechanisms of structure changes in irradiation are examined. In particular, the simulation results indicate that the defects formation may be produced without melting and subsequent crystallization. Threshold stopping power of swift ions for the defects formation in irradiation in the various conditions are calculated.

Simulation of Electron Scattering in Complex Nanostructures: Lithography, Metrology, and Characterization.

NASA Astrophysics Data System (ADS)

Johnson, Sylvester, IV

A CAE (Computer Aided Engineering) tool called SEEL (Simulation of Electron Energy Loss) is described in detail. SEEL simulates in any material the energy loss and trajectories of electrons in the complex, multilayered nanostructures typical of ULSI, at beam energies from 1 to 50 keV. Structures and materials are defined in the input file rather than in the source code of the program, for which flowcharts are included in addition to an explanation of the algorithms implemented. Satisfactory comparisons of simulated with experimental results are made of both secondary electron (SE) and backscattered electron (BSE) linescans across an array of MOS gate structures capped by rough oxide. Many other comparisons are made. The effects of varying line edge slopes on SE linescan peak shape are simulated and analyzed. A data library containing the simulated variation of the FWHM, peak height, and peak location with slope for different materials, line heights or trench depths, widths, beam energies, and nominal diameters could be used to find the edge location relative to the peak for improvement of the accuracy of linewidth measurement algorithms. An investigation indicates that the use of such a library would be complicated by the effect of surface roughness on the SE signal at the edge of a feature. SEEL can be used as the first module in a series of programs that simulate energy deposition in resist structures and correct the exposure of a circuit pattern. Pixel by pixel convolution for prediction of the proximity effect is time-consuming. Another method of proximity effect prediction based on the reciprocity of the RED is described. Such programs could be used to reduce the number of iterations in the lab required to optimize resist structures and exposure parameters. For both smooth and rough interfaces between a bottom layer of PMMA in a multilayer resist structure and a W film, the simulated exposure contrast declines from that with an oxide film beneath the structure. A comparison of Auger peak to background ratios resulting from simulation of smooth and rough surfaces indicates that roughening of an Al surface on a small scale could result in a smaller ratio.

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

NASA Astrophysics Data System (ADS)

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-04-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices.We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr00459g

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.

SU-E-T-489: Quantum versus Classical Trajectory Monte Carlo Simulations of Low Energy Electron Transport.

PubMed

Thomson, R; Kawrakow, I

2012-06-01

Widely-used classical trajectory Monte Carlo simulations of low energy electron transport neglect the quantum nature of electrons; however, at sub-1 keV energies quantum effects have the potential to become significant. This work compares quantum and classical simulations within a simplified model of electron transport in water. Electron transport is modeled in water droplets using quantum mechanical (QM) and classical trajectory Monte Carlo (MC) methods. Water droplets are modeled as collections of point scatterers representing water molecules from which electrons may be isotropically scattered. The role of inelastic scattering is investigated by introducing absorption. QM calculations involve numerically solving a system of coupled equations for the electron wavefield incident on each scatterer. A minimum distance between scatterers is introduced to approximate structured water. The average QM water droplet incoherent cross section is compared with the MC cross section; a relative error (RE) on the MC results is computed. RE varies with electron energy, average and minimum distances between scatterers, and scattering amplitude. The mean free path is generally the relevant length scale for estimating RE. The introduction of a minimum distance between scatterers increases RE substantially (factors of 5 to 10), suggesting that the structure of water must be modeled for accurate simulations. Inelastic scattering does not improve agreement between QM and MC simulations: for the same magnitude of elastic scattering, the introduction of inelastic scattering increases RE. Droplet cross sections are sensitive to droplet size and shape; considerable variations in RE are observed with changing droplet size and shape. At sub-1 keV energies, quantum effects may become non-negligible for electron transport in condensed media. Electron transport is strongly affected by the structure of the medium. Inelastic scatter does not improve agreement between QM and MC simulations of low energy electron transport in condensed media. © 2012 American Association of Physicists in Medicine.

Propagation of localized structures in relativistic magnetized electron-positron plasmas using particle-in-cell simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

López, Rodrigo A.; Muñoz, Víctor; Viñas, Adolfo F.

2015-09-15

We use a particle-in-cell simulation to study the propagation of localized structures in a magnetized electron-positron plasma with relativistic finite temperature. We use as initial condition for the simulation an envelope soliton solution of the nonlinear Schrödinger equation, derived from the relativistic two fluid equations in the strongly magnetized limit. This envelope soliton turns out not to be a stable solution for the simulation and splits in two localized structures propagating in opposite directions. However, these two localized structures exhibit a soliton-like behavior, as they keep their profile after they collide with each other due to the periodic boundary conditions.more » We also observe the formation of localized structures in the evolution of a spatially uniform circularly polarized Alfvén wave. In both cases, the localized structures propagate with an amplitude independent velocity.« less

Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors

NASA Astrophysics Data System (ADS)

Ryu, Hoon; Jeong, Yosang; Kang, Ji-Hoon; Cho, Kyu Nam

2016-12-01

Modelling of multi-million atomic semiconductor structures is important as it not only predicts properties of physically realizable novel materials, but can accelerate advanced device designs. This work elaborates a new Technology-Computer-Aided-Design (TCAD) tool for nanoelectronics modelling, which uses a sp3d5s∗ tight-binding approach to describe multi-million atomic structures, and simulate electronic structures with high performance computing (HPC), including atomic effects such as alloy and dopant disorders. Being named as Quantum simulation tool for Advanced Nanoscale Devices (Q-AND), the tool shows nice scalability on traditional multi-core HPC clusters implying the strong capability of large-scale electronic structure simulations, particularly with remarkable performance enhancement on latest clusters of Intel Xeon PhiTM coprocessors. A review of the recent modelling study conducted to understand an experimental work of highly phosphorus-doped silicon nanowires, is presented to demonstrate the utility of Q-AND. Having been developed via Intel Parallel Computing Center project, Q-AND will be open to public to establish a sound framework of nanoelectronics modelling with advanced HPC clusters of a many-core base. With details of the development methodology and exemplary study of dopant electronics, this work will present a practical guideline for TCAD development to researchers in the field of computational nanoelectronics.

Electron Acceleration in the Magnetotail during Substorms in Semi-Global PIC Simulations

NASA Astrophysics Data System (ADS)

Richard, R. L.; Schriver, D.; Ashour-Abdalla, M.; El-Alaoui, M.; Lapenta, G.; Walker, R. J.

2015-12-01

To understand the acceleration of electrons during a substorm reconnection event we have applied a semi-global particle in cell (PIC) simulation box embedded within a global magnetohydrodynamic (MHD) simulation of Earth's magnetosphere for an event on February 15, 2008. The MHD results were used to populate the PIC simulation and to set the boundary conditions. In the magnetotail we found that a series of dipolarizations formed due to unsteady reconnection. We also found that the most energetic electrons were in the separatrices far from the x-point. We attributed the acceleration to a streaming instability in the separatrices. To further understand electron acceleration we have applied the large scale kinetic (LSK) technique in which tens- to hundreds- of thousands of electrons are followed within the electric and magnetic fields from the PIC simulations., Electrons are already included in the PIC simulation, but the LSK simulations will allow selected individual particles to be followed and analyzed. Initially we performed electron LSK calculations in a two dimensional version of the PIC simulation in which electrons were allowed to move in the ignorable cross tail direction. These LSK calculations showed that electrons gained energy primarily for two reasons: (1) acceleration by the average dawn to dusk electric field and (2) acceleration by intense but localized electric field structures. The overall electron transport was more dawnward than duskward due to the average electric field. At the same time electrons typically moved away from the reconnection region in both the earthward and tailward directions. Superimposed on this large-scale transport was motion in both the dusk and dawn directions across the tail because of the electric field structures, which were particularly intense in the separatrices. LSK calculations are now being carried out by using the full three-dimensional magnetic and electric fields from the PIC simulation and these results will be compared with the two-dimensional results for the same substorm event.

Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum.

PubMed

Padula, Daniele; Jurinovich, Sandro; Di Bari, Lorenzo; Mennucci, Benedetta

2016-11-14

We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Particle Acceleration and Magnetic Field Generation in Electron-Positron Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, K.-L.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G. J.

2004-01-01

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic electron-positron jet front propagating into an ambient electron-positron plasma with and without initial magnetic fields. We find small differences in the results for no ambient and modest ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. The non-linear fluctuation amplitudes of densities, currents, electric, and magnetic fields in the electron-positron shock are larger than those found in the electron-ion shock studied in a previous paper at the comparable simulation time. This comes from the fact that both electrons and positrons contribute to generation of the Weibel instability. Additionally, we have performed simulations with different electron skin depths. We find that growth times scale inversely with the plasma frequency, and the sizes of structures created by the Weibel instability scale proportional to the electron skin depth. This is the expected result and indicates that the simulations have sufficient grid resolution. While some Fermi acceleration may occur at the jet front, the majority of electron and positron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying nonuniform: small-scale magnetic fields which contribute to the electron's (positron's) transverse deflection behind the jet head. This small scale magnetic field structure is appropriate to the generation of jitter radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation has different properties than synchrotron radiation calculated assuming a a uniform magnetic field. The jitter radiation resulting from small scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.

Particle Acceleration and Magnetic Field Generation in Electron-Positron Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G. J.

2005-01-01

Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel, and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a three-dimensional relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic electron-positron jet front propagating into an ambient electron-positron plasma with and without initial magnetic fields. We find small differences in the results for no ambient and modest ambient magnetic fields. New simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. Furthermore, the nonlinear fluctuation amplitudes of densities, currents, and electric and magnetic fields in the electron-positron shock are larger than those found in the electron-ion shock studied in a previous paper at a comparable simulation time. This comes from the fact that both electrons and positrons contribute to generation of the Weibel instability. In addition, we have performed simulations with different electron skin depths. We find that growth times scale inversely with the plasma frequency, and the sizes of structures created by tine Weibel instability scale proportionally to the electron skin depth. This is the expected result and indicates that the simulations have sufficient grid resolution. While some Fermi acceleration may occur at the jet front, the majority of electron and positron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying nonuniform, small-scale magnetic fields, which contribute to the electron s (positron s) transverse deflection behind the jet head. This small- scale magnetic field structure is appropriate to the generation of "jitter" radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation has different properties than synchrotron radiation calculated assuming a uniform magnetic field. The jitter radiation resulting from small-scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.

Dynamical simulation of electron transfer processes in self-assembled monolayers at metal surfaces using a density matrix approach.

PubMed

Prucker, V; Bockstedte, M; Thoss, M; Coto, P B

2018-03-28

A single-particle density matrix approach is introduced to simulate the dynamics of heterogeneous electron transfer (ET) processes at interfaces. The characterization of the systems is based on a model Hamiltonian parametrized by electronic structure calculations and a partitioning method. The method is applied to investigate ET in a series of nitrile-substituted (poly)(p-phenylene)thiolate self-assembled monolayers adsorbed at the Au(111) surface. The results show a significant dependence of the ET on the orbital symmetry of the donor state and on the molecular and electronic structure of the spacer.

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry

DOE PAGES

Ophus, Colin; Ciston, Jim; Pierce, Jordan; ...

2016-02-29

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, makingmore » it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Ultimately, simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals.« less

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry.

PubMed

Ophus, Colin; Ciston, Jim; Pierce, Jordan; Harvey, Tyler R; Chess, Jordan; McMorran, Benjamin J; Czarnik, Cory; Rose, Harald H; Ercius, Peter

2016-02-29

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, making it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals.

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry

PubMed Central

Ophus, Colin; Ciston, Jim; Pierce, Jordan; Harvey, Tyler R.; Chess, Jordan; McMorran, Benjamin J.; Czarnik, Cory; Rose, Harald H.; Ercius, Peter

2016-01-01

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, making it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals. PMID:26923483

Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Graph-based linear scaling electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Electronic structure and simulated STM images of non-honeycomb phosphorene allotropes

NASA Astrophysics Data System (ADS)

Kaur, Sumandeep; Kumar, Ashok; Srivastava, Sunita; Tankeshwar, K.

2018-04-01

We have investigated the electronic structure and simulated STM images of various non-honeycomb allotropes of phosphorene namely ɛ - P, ζ - P, η - P and θ - P, within combined density functional theory and Tersoff-Hamman approach. All these allotropes are found to be energetically stable and electronically semiconductingwith bandgap ranging between 0.5-1.2 eV. Simulated STM images show distinctly different features in terms of the topography. Different maximas in the distance-height profile indicates the difference in buckling of atoms in these allotropes. Distinctly different images obtained in this study may be useful to differentiate various allotropes that can serve as fingerprints to identify various allotropes during the synthesis of phosphorene.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Scattering of an electronic wave packet by a one-dimensional electron-phonon-coupled structure

NASA Astrophysics Data System (ADS)

Brockt, C.; Jeckelmann, E.

2017-02-01

We investigate the scattering of an electron by phonons in a small structure between two one-dimensional tight-binding leads. This model mimics the quantum electron transport through atomic wires or molecular junctions coupled to metallic leads. The electron-phonon-coupled structure is represented by the Holstein model. We observe permanent energy transfer from the electron to the phonon system (dissipation), transient self-trapping of the electron in the electron-phonon-coupled structure (due to polaron formation and multiple reflections at the structure edges), and transmission resonances that depend strongly on the strength of the electron-phonon coupling and the adiabaticity ratio. A recently developed TEBD algorithm, optimized for bosonic degrees of freedom, is used to simulate the quantum dynamics of a wave packet launched against the electron-phonon-coupled structure. Exact results are calculated for a single electron-phonon site using scattering theory and analytical approximations are obtained for limiting cases.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Haishuang; Krysiak, Yaşar; Hoffmann, Kristin

The crystal structure and disorder phenomena of Al{sub 4}B{sub 2}O{sub 9}, an aluminum borate from the mullite-type family, were studied using automated diffraction tomography (ADT), a recently established method for collection and analysis of electron diffraction data. Al{sub 4}B{sub 2}O{sub 9}, prepared by sol-gel approach, crystallizes in the monoclinic space group C2/m. The ab initio structure determination based on three-dimensional electron diffraction data from single ordered crystals reveals that edge-connected AlO{sub 6} octahedra expanding along the b axis constitute the backbone. The ordered structure (A) was confirmed by TEM and HAADF-STEM images. Furthermore, disordered crystals with diffuse scattering along themore » b axis are observed. Analysis of the modulation pattern implies a mean superstructure (AAB) with a threefold b axis, where B corresponds to an A layer shifted by ½a and ½c. Diffraction patterns simulated for the AAB sequence including additional stacking disorder are in good agreement with experimental electron diffraction patterns. - Graphical abstract: Crystal structure and disorder phenomena of B-rich Al{sub 4}B{sub 2}O{sub 9} studied by automated electron diffraction tomography (ADT) and described by diffraction simulation using DISCUS. - Highlights: • Ab-initio structure solution by electron diffraction from single nanocrystals. • Detected modulation corresponding mainly to three-fold superstructure. • Diffuse diffraction streaks caused by stacking faults in disordered crystals. • Observed streaks explained by simulated electron diffraction patterns.« less

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Simulation study on the effects of chemical structure and molecular size on the acceptor strength in poly(3-hexylthiophene)-based copolymer with alternating donor and acceptor for photovoltaic applications

NASA Astrophysics Data System (ADS)

Rassamesard, Areefen; Pengpan, Teparksorn

2017-02-01

This research assessed the effects of various chemical structures and molecular sizes on the simulated geometric parameters, electron structures, and spectroscopic properties of single-chain complex alternating donor-acceptor (D-A) monomers and copolymers that are intended for use as photoactive layer in a polymer solar cell by using Kohn-Sham density functional theory with B3LYP exchange-correlation functional. The 3-hexylthiophene (3HT) was selected for electron donor, while eight chemicals, namely thiazole (Z), thiadiazole (D), thienopyrazine (TP), thienothiadiazole (TD), benzothiadiazole (BT), thiadiazolothieno-pyrazine (TPD), oxadiazole (OXD) and 5-diphenyl-1,2,4-triazole (TAZ), were employed as electron acceptor functional groups. The torsional angle, bridge bond length, intramolecular charge transfer, energy levels, and molecular orbitals were analyzed. The simulation results reveal that the geometry and electron structure of donor-acceptor monomer and copolymer are significantly impacted by heterocyclic rings, heteroatoms, fused rings, degree of steric hindrance and coplanarity of the acceptor molecular structure. Planar conformation was obtained from the D copolymer, and a pseudo-planar structure with the TD copolymer. The TAZ acceptor exhibited strong steric hindrance due to its bulky structure and non-planarity of its structure. An analysis of the electron structures indicated that the degree of intramolecular electron-withdrawing capability had the rank order TAZ  <  Z  <  D  <  TPD  <  OXD  <  TP  <  BT  <  TD. The TD is indicated as the most effective acceptor among those that were simulated. However, the small energy gaps of TD as well as TPD copolymer indicate that these two copolymers can be used in transparent conducting materials. The copolymer based on BT acceptor exhibited good intramolecular charge transfer and absorbed at 656 nm wavelength which is close to the maximum flux of solar spectrum. Hence, the BT acceptor functional group provides a compromise in the characteristics of a donor-acceptor copolymer, useful in a polymeric candidate material for the photoactive layer in a polymer solar cell.

Particle Acceleration and Magnetic Field Generation in Electron-Positron Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G. J.

2004-01-01

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic electron-positron jet front propagating into an ambient electron-positron plasma with and without initial magnetic fields. We find small differences in the results for no ambient and modest ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. The non-linear fluctuation amplitudes of densities, currents, electric, and magnetic fields in the electron-positron shock are larger than those found in the electron-ion shock studied in a previous paper. This comes from the fact that both electrons and positrons contribute to generation of the Weibel instability. Additionally, we have performed simulations with different electron skin depths. We find that growth times scale inversely with the plasma frequency, and the sizes of structures created by the Weibel instability scale proportional to the electron skin depth. This is the expected result and indicates that the simulations have sufficient grid resolution. While some Fermi acceleration may occur at the jet front, the majority of electron and positron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying nonuniform, small-scale magnetic fields which contribute to the electron's (positron's) transverse deflection behind the jet head. This small scale magnetic field structure is appropriate to the generation of "jitter" radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation has different properties than synchrotron radiation calculated assuming a a uniform magnetic field. The jitter radiation resulting from small scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.

Mechanism of vacuum breakdown in radio-frequency accelerating structures

NASA Astrophysics Data System (ADS)

Barengolts, S. A.; Mesyats, V. G.; Oreshkin, V. I.; Oreshkin, E. V.; Khishchenko, K. V.; Uimanov, I. V.; Tsventoukh, M. M.

2018-06-01

It has been investigated whether explosive electron emission may be the initiating mechanism of vacuum breakdown in the accelerating structures of TeV linear electron-positron colliders (Compact Linear Collider). The physical processes involved in a dc vacuum breakdown have been considered, and the relationship between the voltage applied to the diode and the time delay to breakdown has been found. Based on the results obtained, the development of a vacuum breakdown in an rf electric field has been analyzed and the main parameters responsible for the initiation of explosive electron emission have been estimated. The formation of craters on the cathode surface during explosive electron emission has been numerically simulated, and the simulation results are discussed.

Electrically induced spontaneous emission in open electronic system

NASA Astrophysics Data System (ADS)

Wang, Rulin; Zhang, Yu; Yam, Chiyung; Computation Algorithms Division (CSRC) Team; Theoretical; Computational Chemistry (HKU) Collaboration

A quantum mechanical approach is formulated for simulation of electroluminescence process in open electronic system. Based on nonequilibrium Green's function quantum transport equations and combining with photon-electron interaction, this method is used to describe electrically induced spontaneous emission caused by electron-hole recombination. The accuracy and reliability of simulation depends critically on correct description of the electronic band structure and the electron occupancy in the system. In this work, instead of considering electron-hole recombination in discrete states in the previous work, we take continuous states into account to simulate the spontaneous emission in open electronic system, and discover that the polarization of emitted photon is closely related to its propagation direction. Numerical studies have been performed to silicon nanowire-based P-N junction with different bias voltage.

Assigning crystallographic electron densities with free energy calculations—The case of the fluoride channel Fluc

PubMed Central

2018-01-01

Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious. In this study, we suggest the use of molecular dynamics (MD) simulations and free energy calculations, which are well-established computational methods, to aid in the assignment of ambiguous disconnected electron densities. Specifically, estimates of (i) relative binding affinities, for instance between an ion and water, (ii) absolute binding free energies, i.e., free energies for transferring a solute from bulk solvent to a binding site, and (iii) stability assessments during equilibrium simulations may reveal the most plausible assignments. We illustrate this strategy using the crystal structure of the fluoride specific channel (Fluc), which contains five disconnected electron densities previously interpreted as four fluoride and one sodium ion. The simulations support the assignment of the sodium ion. In contrast, calculations of relative and absolute binding free energies as well as stability assessments during free MD simulations suggest that four of the densities represent water molecules instead of fluoride. The assignment of water is compatible with the loss of these densities in the non-conductive F82I/F85I mutant of Fluc. We critically discuss the role of the ion force fields for the calculations presented here. Overall, these findings indicate that MD simulations and free energy calculations are helpful tools for modeling water and ions into crystallographic density maps. PMID:29771936

Droplet Epitaxy Image Contrast in Mirror Electron Microscopy

NASA Astrophysics Data System (ADS)

Kennedy, S. M.; Zheng, C. X.; Jesson, D. E.

2017-01-01

Image simulation methods are applied to interpret mirror electron microscopy (MEM) images obtained from a movie of GaAs droplet epitaxy. Cylindrical symmetry of structures grown by droplet epitaxy is assumed in the simulations which reproduce the main features of the experimental MEM image contrast, demonstrating that droplet epitaxy can be studied in real-time. It is therefore confirmed that an inner ring forms at the droplet contact line and an outer ring (or skirt) occurs outside the droplet periphery. We believe that MEM combined with image simulations will be increasingly used to study the formation and growth of quantum structures.

Development of the field of structural physiology

PubMed Central

FUJIYOSHI, Yoshinori

2015-01-01

Electron crystallography is especially useful for studying the structure and function of membrane proteins — key molecules with important functions in neural and other cells. Electron crystallography is now an established technique for analyzing the structures of membrane proteins in lipid bilayers that closely simulate their natural biological environment. Utilizing cryo-electron microscopes with helium-cooled specimen stages that were developed through a personal motivation to understand the functions of neural systems from a structural point of view, the structures of membrane proteins can be analyzed at a higher than 3 Å resolution. This review covers four objectives. First, I introduce the new research field of structural physiology. Second, I recount some of the struggles involved in developing cryo-electron microscopes. Third, I review the structural and functional analyses of membrane proteins mainly by electron crystallography using cryo-electron microscopes. Finally, I discuss multifunctional channels named “adhennels” based on structures analyzed using electron and X-ray crystallography. PMID:26560835

Simulation of Mirror Electron Microscopy Caustic Images in Three-Dimensions

NASA Astrophysics Data System (ADS)

Kennedy, S. M.; Zheng, C. X.; Jesson, D. E.

A full, three-dimensional (3D) ray tracing approach is developed to simulate the caustics visible in mirror electron microscopy (MEM). The method reproduces MEM image contrast resulting from 3D surface relief. To illustrate the potential of the simulation methods, we study the evolution of crater contrast associated with a movie of GaAs structures generated by the droplet epitaxy technique. Specifically, we simulate the image contrast resulting from both a precursor stage and the final crater morphology which is consistent with an inverted pyramid consisting of (111) facet walls. The method therefore facilities the study of how self-assembled quantum structures evolve with time and, in particular, the development of anisotropic features including faceting.

Simulating Pressure Profiles for the Free-Electron Laser Photoemission Gun Using Molflow+

NASA Astrophysics Data System (ADS)

Song, Diego; Hernandez-Garcia, Carlos

2012-10-01

The Jefferson Lab Free Electron Laser (FEL) generates tunable laser light by passing a relativistic electron beam generated in a high-voltage DC electron gun with a semiconducting photocathode through a magnetic undulator. The electron gun is in stringent vacuum conditions in order to guarantee photocathode longevity. Considering an upgrade of the electron gun, this project consists of simulating pressure profiles to determine if the novel design meets the electron gun vacuum requirements. The method of simulation employs the software Molflow+, developed by R. Kersevan at the Organisation Europ'eene pour la Recherche Nucl'eaire (CERN), which uses the test-particle Monte Carlo method to simulate molecular flows in 3D structures. Pressure is obtained along specified chamber axes. Results are then compared to measured pressure values from the existing gun for validation. Outgassing rates, surface area, and pressure were found to be proportionally related. The simulations indicate that the upgrade gun vacuum chamber requires more pumping compared to its predecessor, while it holds similar vacuum conditions. The ability to simulate pressure profiles through tools like Molflow+, allows researchers to optimize vacuum systems during the engineering process.

Electronic structure and STM images simulation of defects on hBN/ black-phosphorene heterostructures: A theoretical study

NASA Astrophysics Data System (ADS)

Ospina, D. A.; Cisternas, E.; Duque, C. A.; Correa, J. D.

2018-03-01

By first principles calculations which include van der Waals interactions, we studied the electronic structure of hexagonal boron-nitride/black-phosphorene heterostructures (hBN/BP). In particular the role of several kind of defects on the electronic properties of black-phosphorene monolayer and hBN/BP heterostructure was analyzed. The defects under consideration were single and double vacancies, as well Stone-Wale type defects, all of them present in the phosphorene layer. In this way, we found that the electronic structure of the hBN/BP is modified according the type of defect that is introduced. As a remarkable feature, our results show occupied states at the Fermi Level introduced by a single vacancy in the energy gap of the hBN/BP heterostructure. Additionally, we performed simulations of scanning tunneling microscopy images. These simulations show that is possible to discriminate the kind of defect even when the black-phosphorene monolayer is part of the heterostructure hBN/BP. Our results may help to discriminate among several kind of defects during experimental characterization of these novel materials.

On the generation of double layers from ion- and electron-acoustic instabilities

NASA Astrophysics Data System (ADS)

Fu, Xiangrong; Cowee, Misa M.; Gary, S. Peter; Winske, Dan

2016-03-01

A plasma double layer (DL) is a nonlinear electrostatic structure that carries a uni-polar electric field parallel to the background magnetic field due to local charge separation. Past studies showed that DLs observed in space plasmas are mostly associated with the ion acoustic instability. Recent Van Allen Probes observations of parallel electric field structures traveling much faster than the ion acoustic speed have motivated a computational study to test the hypothesis that a new type of DLs—electron acoustic DLs—generated from the electron acoustic instability are responsible for these electric fields. Nonlinear particle-in-cell simulations yield negative results, i.e., the hypothetical electron acoustic DLs cannot be formed in a way similar to ion acoustic DLs. Linear theory analysis and the simulations show that the frequencies of electron acoustic waves are too high for ions to respond and maintain charge separation required by DLs. However, our results do show that local density perturbations in a two-electron-component plasma can result in unipolar-like electric field structures that propagate at the electron thermal speed, suggesting another potential explanation for the observations.

Modeling and simulation of electronic structure, material interface and random doping in nano electronic devices

PubMed Central

Chen, Duan; Wei, Guo-Wei

2010-01-01

The miniaturization of nano-scale electronic devices, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. Modeling and simulation of this class of problems have emerged as an important topic in applied and computational mathematics. This work presents mathematical models and computational algorithms for the simulation of nano-scale MOSFETs. We introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential of the nano-electronic device. This framework enables us to put microscopic and macroscopic descriptions in an equal footing at nano scale. By optimization of the energy functional, we derive consistently-coupled Poisson-Kohn-Sham equations. Additionally, layered structures are crucial to the electrostatic and transport properties of nano transistors. A material interface model is proposed for more accurate description of the electrostatics governed by the Poisson equation. Finally, a new individual dopant model that utilizes the Dirac delta function is proposed to understand the random doping effect in nano electronic devices. Two mathematical algorithms, the matched interface and boundary (MIB) method and the Dirichlet-to-Neumann mapping (DNM) technique, are introduced to improve the computational efficiency of nano-device simulations. Electronic structures are computed via subband decomposition and the transport properties, such as the I-V curves and electron density, are evaluated via the non-equilibrium Green's functions (NEGF) formalism. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our three-dimensional numerical simulations. For these devices, the current fluctuation and voltage threshold lowering effect induced by the discrete dopant model are explored. Numerical convergence and model well-posedness are also investigated in the present work. PMID:20396650

Demonstration of Anisotropic Fluid Closure Capturing the Kinetic Structure of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Ohia, Obioma

2012-10-01

Magnetic reconnection in collisionless plasmas plays an important role in space and laboratory plasmas. Allowing magnetic stress to be reduced by a rearrangement of magnetic line topology, this process is often accompanied by a large release of magnetic field energy, which can heat the plasma, drive large scale flows, or accelerate particles. Reconnection has been widely studied through fluid models and kinetic simulations. While two-fluid models often reproduce the fast reconnection that is observed in nature and seen in kinetic simulations, it is found that the structure surrounding the electron diffusion region and the electron current layer differ vastly between fluid models and kinetic simulations [1]. Recently, using an adiabatic solution of the Vlasov equation, a new fluid closure has been obtained for electrons that relate parallel and perpendicular pressures to the density and magnetic field [2]. Here we present the results of fluid simulation, developed using the HiFi framework [3], that implements new equations of state for guide-field reconnection. The new fluid closure accurately accounts for the anisotropic electron pressure that builds in the reconnection region due to electric and magnetic trapping of electrons. In contrast to previous fluid models, our fluid simulation reproduces the detailed reconnection region as observed in fully kinetic simulations [4]. We hereby demonstrate that the new fluid closure self-consistently captures all the physics relevant to the structure of the reconnection region, providing a gateway to a renewed and deeper theoretical understanding for reconnection in weakly collisional regimes.[4pt] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0pt] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0pt] [3] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011). [0pt] [4] Ohia O, et al., Phys. Rev. Lett. In Press (2012).

Three-Dimensional Electron Optics Model Developed for Traveling-Wave Tubes

NASA Technical Reports Server (NTRS)

Kory, Carol L.

2000-01-01

A three-dimensional traveling-wave tube (TWT) electron beam optics model including periodic permanent magnet (PPM) focusing has been developed at the NASA Glenn Research Center at Lewis Field. This accurate model allows a TWT designer to develop a focusing structure while reducing the expensive and time-consuming task of building the TWT and hot-testing it (with the electron beam). In addition, the model allows, for the first time, an investigation of the effect on TWT operation of the important azimuthally asymmetric features of the focusing stack. The TWT is a vacuum device that amplifies signals by transferring energy from an electron beam to a radiofrequency (RF) signal. A critically important component is the focusing structure, which keeps the electron beam from diverging and intercepting the RF slow wave circuit. Such an interception can result in excessive circuit heating and decreased efficiency, whereas excessive growth in the beam diameter can lead to backward wave oscillations and premature saturation, indicating a serious reduction in tube performance. The most commonly used focusing structure is the PPM stack, which consists of a sequence of cylindrical iron pole pieces and opposite-polarity magnets. Typically, two-dimensional electron optics codes are used in the design of magnetic focusing devices. In general, these codes track the beam from the gun downstream by solving equations of motion for the electron beam in static-electric and magnetic fields in an azimuthally symmetric structure. Because these two-dimensional codes cannot adequately simulate a number of important effects, the simulation code MAFIA (solution of Maxwell's equations by the Finite-Integration-Algorithm) was used at Glenn to develop a three-dimensional electron optics model. First, a PPM stack was modeled in three dimensions. Then, the fields obtained using the magnetostatic solver were loaded into a particle-in-cell solver where the fully three-dimensional behavior of the beam was simulated in the magnetic focusing field. For the first time, the effects of azimuthally asymmetric designs and critical azimuthally asymmetric characteristics of the focusing stack (such as shunts, C-magnets, or magnet misalignment) on electron beam behavior have been investigated. A cutaway portion of a simulated electron beam focused by a PPM stack is illustrated.

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

NASA Astrophysics Data System (ADS)

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-04-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation

NASA Astrophysics Data System (ADS)

Del Ben, Mauro; Hutter, Jürg; VandeVondele, Joost

2015-08-01

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water. Isobaric-isothermal (NpT) ensemble simulations based on the Random Phase Approximation (RPA) yield excellent density (0.994 g/ml) and fair radial distribution functions, while various other density functional approximations produce scattered results (0.8-1.2 g/ml). Molecular dynamics simulation in the microcanonical (NVE) ensemble based on Møller-Plesset perturbation theory (MP2) yields dynamical properties in the condensed phase, namely, the infrared spectrum and diffusion constant. At the MP2 and RPA levels of theory, ice is correctly predicted to float on water, resolving one of the anomalies as resulting from a delicate balance between van der Waals and hydrogen bonding interactions. For several properties, obtaining quantitative agreement with experiment requires correction for nuclear quantum effects (NQEs), highlighting their importance, for structure, dynamics, and electronic properties. A computed NQE shift of 0.6 eV for the band gap and absorption spectrum illustrates the latter. Giving access to both structure and dynamics of condensed phase systems, non-local electron correlation will increasingly be used to study systems where weak interactions are of paramount importance.

Fully kinetic simulations of collisionless, mesothermal plasma emission: Macroscopic plume structure and microscopic electron characteristics

NASA Astrophysics Data System (ADS)

Hu, Yuan; Wang, Joseph

2017-03-01

This paper presents a fully kinetic particle particle-in-cell simulation study on the emission of a collisionless plasma plume consisting of cold beam ions and thermal electrons. Results are presented for both the two-dimensional macroscopic plume structure and the microscopic electron kinetic characteristics. We find that the macroscopic plume structure exhibits several distinctive regions, including an undisturbed core region, an electron cooling expansion region, and an electron isothermal expansion region. The properties of each region are determined by microscopic electron kinetic characteristics. The division between the undisturbed region and the cooling expansion region approximately matches the Mach line generated at the edge of the emission surface, and that between the cooling expansion region and the isothermal expansion region approximately matches the potential well established in the beam. The interactions between electrons and the potential well lead to a new, near-equilibrium state different from the initial distribution for the electrons in the isothermal expansion region. The electron kinetic characteristics in the plume are also very anisotropic. As the electron expansion process is mostly non-equilibrium and anisotropic, the commonly used assumption that the electrons in a collisionless, mesothermal plasma plume may be treated as a single equilibrium fluid in general is not valid.

The influence of structure depth on image blurring of micrometres-thick specimens in MeV transmission electron imaging.

PubMed

Wang, Fang; Sun, Ying; Cao, Meng; Nishi, Ryuji

2016-04-01

This study investigates the influence of structure depth on image blurring of micrometres-thick films by experiment and simulation with a conventional transmission electron microscope (TEM). First, ultra-high-voltage electron microscope (ultra-HVEM) images of nanometer gold particles embedded in thick epoxy-resin films were acquired in the experiment and compared with simulated images. Then, variations of image blurring of gold particles at different depths were evaluated by calculating the particle diameter. The results showed that with a decrease in depth, image blurring increased. This depth-related property was more apparent for thicker specimens. Fortunately, larger particle depth involves less image blurring, even for a 10-μm-thick epoxy-resin film. The quality dependence on depth of a 3D reconstruction of particle structures in thick specimens was revealed by electron tomography. The evolution of image blurring with structure depth is determined mainly by multiple elastic scattering effects. Thick specimens of heavier materials produced more blurring due to a larger lateral spread of electrons after scattering from the structure. Nevertheless, increasing electron energy to 2MeV can reduce blurring and produce an acceptable image quality for thick specimens in the TEM. Copyright © 2016 Elsevier Ltd. All rights reserved.

Simulation of transmission electron microscope images of biological specimens.

PubMed

Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

2011-09-01

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Simulation of the photodetachment spectrum of HHfO- using coupled-cluster calculations

NASA Astrophysics Data System (ADS)

Mok, Daniel K. W.; Dyke, John M.; Lee, Edmond P. F.

2016-12-01

The photodetachment spectrum of HHfO- was simulated using restricted-spin coupled-cluster single-double plus perturbative triple {RCCSD(T)} calculations performed on the ground electronic states of HHfO and HHfO-, employing basis sets of up to quintuple-zeta quality. The computed RCCSD(T) electron affinity of 1.67 ± 0.02 eV at the complete basis set limit, including Hf 5s25p6 core correlation and zero-point energy corrections, agrees well with the experimental value of 1.70 ± 0.05 eV from a recent photodetachment study [X. Li et al., J. Chem. Phys. 136, 154306 (2012)]. For the simulation, Franck-Condon factors were computed which included allowances for anharmonicity and Duschinsky rotation. Comparisons between simulated and experimental spectra confirm the assignments of the molecular carrier and electronic states involved but suggest that the experimental vibrational structure has suffered from poor signal-to-noise ratio. An alternative assignment of the vibrational structure to that suggested in the experimental work is presented.

Electron Holes in phase-space: what they are and why they matter

NASA Astrophysics Data System (ADS)

Hutchinson, I. H.

2016-10-01

Plasma electron holes are soliton-like electric potential structures sustained self-consistently by a deficit of phase-space density on trapped orbits. They are a class of Bernstein Green and Kruskal (BGK)-mode phase-space vortices, long studied in basic analytic and computational theory and observed in some experiments. Recently it has become clear from space-craft observations that isolated potential structures with the character of electron holes constitute an important component of space-plasma turbulence. Modern computational simulations of collisionless plasmas also often observe electron holes to form as a nonlinear consequence of kinetic electron instabilities. This tutorial will explain the basic theory of electron hole structure, trace the development of the understanding of electron holes, and survey some of the observational evidence for their significance. It was found early on that unmagnetized multidimensional simulations of electron two-stream instabilities do not show the long lived holes that appear in one dimension. Deliberately-created 1-D slab holes in multiple dimensions experience a transverse instability unless the guiding magnetic field is strong enough. Analysis has yet to identify unequivocally the instability mechanism and threshold; but it can show that spherically symmetric holes in 3-D without magnetic field are essentially impossible. Recent simulations have studied holes' formation, self-acceleration, merging, splitting, and growth. Analytic understanding of many of these phenomena is gained from the kinematics of the hole regarded as a coherent entity, accounting for the plasma momentum changes it induces, and especially the interaction with the ions. Electron holes can travel at up to approximately the electron thermal speed, but not slower (relative to ions) than several times the ion acoustic speed. Some notable current research questions will be described.

Study of strain boundary conditions and GaAs buffer sizes in InGaAs quantum dots

NASA Technical Reports Server (NTRS)

Oyafuso, F.; Klimeck, G.; Boykin, T. B.; Bowen, R. C.; Allmen, P. von

2003-01-01

NEMO 3-D has been developed for the simulation of electronic structure in self-assembled InGaAs quantum dots on GaAs substrates. Typical self-assembled quantum dots in that material system contain about 0.5 to 1 million atoms. Effects of strain by the surrounding GaAs buffer modify the electronic structure inside the quantum dot significantly and a large GaAs buffer must be included in the strain and electronic structure.

Electronic structure and nature of the color centers in MgF2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freidman, S.P.; Golota, A.F.; Galakhov, V.R.

1986-09-01

The electronic structure and spectroscopic properties of samples of magnesium fluoride with different numbers of defects have been investigated with the use of the methods of x-ray photoelectron, x-ray emission, ESR, and optical spectroscopy. Nonempirical self-consistent calculations of the electronic structure of clusters which simulate stoichiometric and defective MgF2 have been carried out. The color centers in the approx. 5-eV energy range are attributed to the presence of vacancies in the anionic sublattice.

Comprehensive photonics-electronics convergent simulation and its application to high-speed electronic circuit integration on a Si/Ge photonic chip

NASA Astrophysics Data System (ADS)

Takeda, Kotaro; Honda, Kentaro; Takeya, Tsutomu; Okazaki, Kota; Hiraki, Tatsurou; Tsuchizawa, Tai; Nishi, Hidetaka; Kou, Rai; Fukuda, Hiroshi; Usui, Mitsuo; Nosaka, Hideyuki; Yamamoto, Tsuyoshi; Yamada, Koji

2015-01-01

We developed a design technique for a photonics-electronics convergence system by using an equivalent circuit of optical devices in an electrical circuit simulator. We used the transfer matrix method to calculate the response of an optical device. This method used physical parameters and dimensions of optical devices as calculation parameters to design a device in the electrical circuit simulator. It also used an intermediate frequency to express the wavelength dependence of optical devices. By using both techniques, we simulated bit error rates and eye diagrams of optical and electrical integrated circuits and calculated influences of device structure change and wavelength shift penalty.

Monte Carlo simulations of disorder in ZnSn N 2 and the effects on the electronic structure

DOE PAGES

Lany, Stephan; Fioretti, Angela N.; Zawadzki, Paweł P.; ...

2017-08-10

In multinary compound semiconductors, cation disorder can decisively alter the electronic properties and impact potential applications. ZnSnN 2 is a ternary nitride of interest for photovoltaics, which forms in a wurtzite-derived crystal structure. In the ground state, every N anion is coordinated by two Zn and two Sn cations, thereby observing the octet rule locally. Using a motif-based model Hamiltonian, we performed Monte Carlo simulations that provide atomistic representations of ZnSnN 2 with varying degrees of cation disorder. Subsequent electronic structure calculations describe the evolution of band gaps, optical properties, and carrier localization effects as a function of the disorder.more » We find that octet-rule conserving disorder is practically impossible to avoid but perfectly benign, with hardly any effects on the electronic structure. In contrast, a fully random cation distribution would be very detrimental, but fortunately it is energetically highly unfavorable. A degree of disorder that can realistically be expected for nonequilibrium thin-film deposition leads to a moderate band-gap reduction and to moderate carrier localization effects. Comparing the simulated structures with experimental samples grown by sputtering, we find evidence that these samples indeed incorporate a certain degree of octet-rule violating disorder, which is reflected in the x-ray diffraction and in the optical absorption spectra. This study demonstrates that the electronic properties of ZnSnN 2 are dominated by changes of the local coordination environments rather than long-range ordering effects.« less

Monte Carlo simulations of disorder in ZnSn N 2 and the effects on the electronic structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lany, Stephan; Fioretti, Angela N.; Zawadzki, Paweł P.

In multinary compound semiconductors, cation disorder can decisively alter the electronic properties and impact potential applications. ZnSnN 2 is a ternary nitride of interest for photovoltaics, which forms in a wurtzite-derived crystal structure. In the ground state, every N anion is coordinated by two Zn and two Sn cations, thereby observing the octet rule locally. Using a motif-based model Hamiltonian, we performed Monte Carlo simulations that provide atomistic representations of ZnSnN 2 with varying degrees of cation disorder. Subsequent electronic structure calculations describe the evolution of band gaps, optical properties, and carrier localization effects as a function of the disorder.more » We find that octet-rule conserving disorder is practically impossible to avoid but perfectly benign, with hardly any effects on the electronic structure. In contrast, a fully random cation distribution would be very detrimental, but fortunately it is energetically highly unfavorable. A degree of disorder that can realistically be expected for nonequilibrium thin-film deposition leads to a moderate band-gap reduction and to moderate carrier localization effects. Comparing the simulated structures with experimental samples grown by sputtering, we find evidence that these samples indeed incorporate a certain degree of octet-rule violating disorder, which is reflected in the x-ray diffraction and in the optical absorption spectra. This study demonstrates that the electronic properties of ZnSnN 2 are dominated by changes of the local coordination environments rather than long-range ordering effects.« less

Aerodynamic Simulation Analysis of Unmanned Airborne Electronic Bomb

NASA Astrophysics Data System (ADS)

Yang, Jiaoying; Guo, Yachao

2017-10-01

For microelectronic bombs for UAVs, on the basis of the use of rotors to lift the insurance on the basis of ammunition, increased tail to increase stability. The aerodynamic simulation of the outer structure of the ammunition was carried out by FLUENT software. The resistance coefficient, the lift coefficient and the pitch moment coefficient under different angle of attack and Mach number were obtained, and the aerodynamic characteristics of the electronic bomb were studied. The pressure line diagram and the velocity line diagram of the flow around the bomb are further analyzed, and the rationality of the external structure is verified, which provides a reference for the subsequent design of the electronic bomb.

Window for Optimal Frequency Operation and Reliability of 3DEG and 2DEG Channels for Oxide Microwave MESFETs and HFETs

DTIC Science & Technology

2016-04-01

noise, and energy relaxation for doped zinc-oxide and structured ZnO transistor materials with a 2-D electron gas (2DEG) channel subjected to a strong...function on the time delay. Closed symbols represent the Monte Carlo data with hot-phonon effect at different electron gas density: 1•1017 cm-3...Monte Carlo simulation is performed for electron gas density of 1•1018 cm-3. Figure 18. Monte Carlo simulation of density-dependent hot-electron energy

Divide and conquer approach to quantum Hamiltonian simulation

NASA Astrophysics Data System (ADS)

Hadfield, Stuart; Papageorgiou, Anargyros

2018-04-01

We show a divide and conquer approach for simulating quantum mechanical systems on quantum computers. We can obtain fast simulation algorithms using Hamiltonian structure. Considering a sum of Hamiltonians we split them into groups, simulate each group separately, and combine the partial results. Simulation is customized to take advantage of the properties of each group, and hence yield refined bounds to the overall simulation cost. We illustrate our results using the electronic structure problem of quantum chemistry, where we obtain significantly improved cost estimates under very mild assumptions.

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

PubMed Central

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-01-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design. PMID:27109208

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

DOE PAGES

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; ...

2016-04-25

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

Rationalizing the role of structural motif and underlying electronic structure in the finite temperature behavior of atomic clusters

NASA Astrophysics Data System (ADS)

Susan, Anju; Joshi, Kavita

2014-04-01

Melting in finite size systems is an interesting but complex phenomenon. Many factors affect melting and owing to their interdependencies it is a challenging task to rationalize their roles in the phase transition. In this work, we demonstrate how structural motif of the ground state influences melting transition in small clusters. Here, we report a case with clusters of aluminum and gallium having same number of atoms, valence electrons, and similar structural motif of the ground state but drastically different melting temperatures. We have employed Born-Oppenheimer molecular dynamics to simulate the solid-like to liquid-like transition in these clusters. Our simulations have reproduced the experimental trends fairly well. Further, the detailed analysis of isomers has brought out the role of the ground state structure and underlying electronic structure in the finite temperature behavior of these clusters. For both clusters, isomers accessible before cluster melts have striking similarities and does have strong influence of the structural motif of the ground state. Further, the shape of the heat capacity curve is similar in both the cases but the transition is more spread over for Al36 which is consistent with the observed isomerization pattern. Our simulations also suggest a way to characterize transition region on the basis of accessibility of the ground state at a specific temperature.

The structure of the electron diffusion region during asymmetric anti-parallel magnetic reconnection

NASA Astrophysics Data System (ADS)

Swisdak, M.; Drake, J. F.; Price, L.; Burch, J. L.; Cassak, P.

2017-12-01

The structure of the electron diffusion region during asymmetric magnetic reconnection is ex- plored with high-resolution particle-in-cell simulations that focus on an magnetopause event ob- served by the Magnetospheric Multiscale Mission (MMS). A major surprise is the development of a standing, oblique whistler-like structure with regions of intense positive and negative dissipation. This structure arises from high-speed electrons that flow along the magnetosheath magnetic sepa- ratrices, converge in the dissipation region and jet across the x-line into the magnetosphere. The jet produces a region of negative charge and generates intense parallel electric fields that eject the electrons downstream along the magnetospheric separatrices. The ejected electrons produce the parallel velocity-space crescents documented by MMS.

Measurements and modeling of radio frequency field structures in a helicon plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, C. A.; Chen, Guangye; Arefiev, A. V.

2011-01-01

Measurements of the radio frequency (rf) field structure, plasma density, and electron temperature are presented for a 1 kW argon helicon plasma source. The measured profiles change considerably when the equilibrium magnetic field is reversed. The measured rf fields are identified as fields of radially localized helicon waves, which propagate in the axial direction. The rf field structure is compared to the results of two-dimensional cold plasma full-wave simulations for the measured density profiles. Electron collision frequency is adjusted in the simulations to match the simulated and measured field profiles. The resulting frequency is anomalously high, which is attributed tomore » the excitation of an ion-acoustic instability. The calculated power deposition is insensitive to the collision frequency and accounts for most of the power supplied by the rf-generator.« less

Transition in discharge plasma of Hall thruster type in presence of secondary electron emissive surface

NASA Astrophysics Data System (ADS)

Schweigert, I. V.; Yadrenkin, M. A.; Fomichev, V. P.

2017-11-01

Modification of the sheath structure near the emissive plate placed in magnetized DC discharge plasma of Hall thruster type was studied in the experiment and in kinetic simulations. The plate is made from Al2O3 which has enhanced secondary electron emission yield. The energetic electrons emitted by heated cathode provide the volume ionization and the secondary electron emission from the plate. An increase of the electron beam energy leads to an increase of the secondary electron generation, which initiates the transition in sheath structure over the emissive plate.

Low energy electrons and swift ion track structure in PADC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.

The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particularmore » incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.« less

Low energy electrons and swift ion track structure in PADC

DOE PAGES

Fromm, Michel; Quinto, Michele A.; Weck, Philippe F.; ...

2015-05-27

The current work aims at providing an accurate description of the ion track-structure in poly-allyl dyglycol carbonate (PADC) by using an up-to-date Monte-Carlo code-called TILDA-V (a French acronym for Transport d’Ions Lourds Dans l’Aqua & Vivo). In this simulation the ion track-structure in PADC is mainly described in terms of ejected electrons with a particular attention done to the Low Energy Electrons (LEEs). After a brief reminder of the most important channels through which LEEs are prone to break a chemical bond, we will report on the simulated energetic distributions of LEEs along an ion track in PADC for particularmore » incident energies located on both sides of the Bragg-peak position. Lastly, based on the rare data dealing with LEEs interaction with polymers or organic molecules, we will emphasise the role played by the LEEs in the formation of a latent track in PADC, and more particularly the one played by the sub-ionization electrons.« less

Violation of Field Line Conservation and Associated Spatial Scales in Particle-in-Cell Simulations and MMS Data

NASA Astrophysics Data System (ADS)

Wendel, D. E.; Liu, Y. H.; Giles, B. L.; Torbert, R. B.

2017-12-01

For the first time, space flight technology exists to detect, in situ, violation of magnetic field line conservation. The violation of magnetic line conservation on scales smaller than the system size is a necessary and sufficient condition for magnetic reconnection. We demonstrate that violation of line conservation produces a detectable, structured signature in both particle-in-cell simulations of reconnection and in data from the Magnetospheric Multi-Scale mission. In particle-in-cell simulations of asymmetric reconnection, the quantity-which we call M-that identifies this violation achieves a significant value in electron skin depth-scale layers that extend from the electron diffusion region along the separatrices, with higher values emerging on the low density, high magnetic field side of the current sheet. In two MMS burst data intervals associated with detection of the electron diffusion region—one interval with antiparallel reconnecting fields and the other with a guide field-we determine the location and scale of M and of the diffusion region relative to electron outflows and the magnetic separatrices. We find that M exceeds measurement uncertainties both at the diffusion region and near the separatrices, where it attains its highest values in layered structures. The observed magnitude scales as the simulated magnitude after adjusting for the artificial parameters of the simulation. Bipolar forms of the quantity also appear further from the diffusion region, possibly associated with electron holes. The measure serves not only as a powerful diagnostic for magnetic reconnection, but reveals that electrons transport this signature of reconnection away from the x-line.

Result of Monte-Carlo simulation of electron-photon cascades in lead and layers of lead-scintillator

NASA Technical Reports Server (NTRS)

Wasilewski, A.; Krys, E.

1985-01-01

Results of Monte-Carlo simulation of electromagnetic cascade development in lead and lead-scintillator sandwiches are analyzed. It is demonstrated that the structure function for core approximation is not applicable in the case in which the primary energy is higher than 100 GeV. The simulation data has shown that introducing an inhomogeneous chamber structure results in subsequent reduction of secondary particles.

Correlative SEM SERS for quantitative analysis of dimer nanoparticles.

PubMed

Timmermans, F J; Lenferink, A T M; van Wolferen, H A G M; Otto, C

2016-11-14

A Raman microscope integrated with a scanning electron microscope was used to investigate plasmonic structures by correlative SEM-SERS analysis. The integrated Raman-SEM microscope combines high-resolution electron microscopy information with SERS signal enhancement from selected nanostructures with adsorbed Raman reporter molecules. Correlative analysis is performed for dimers of two gold nanospheres. Dimers were selected on the basis of SEM images from multi aggregate samples. The effect of the orientation of the dimer with respect to the polarization state of the laser light and the effect of the particle gap size on the Raman signal intensity is observed. Additionally, calculations are performed to simulate the electric near field enhancement. These simulations are based on the morphologies observed by electron microscopy. In this way the experiments are compared with the enhancement factor calculated with near field simulations and are subsequently used to quantify the SERS enhancement factor. Large differences between experimentally observed and calculated enhancement factors are regularly detected, a phenomenon caused by nanoscale differences between the real and 'simplified' simulated structures. Quantitative SERS experiments reveal the structure induced enhancement factor, ranging from ∼200 to ∼20 000, averaged over the full nanostructure surface. The results demonstrate correlative Raman-SEM microscopy for the quantitative analysis of plasmonic particles and structures, thus enabling a new analytical method in the field of SERS and plasmonics.

On the generation of double layers from ion- and electron-acoustic instabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Xiangrong, E-mail: xrfu@lanl.gov; Cowee, Misa M.; Winske, Dan

2016-03-15

A plasma double layer (DL) is a nonlinear electrostatic structure that carries a uni-polar electric field parallel to the background magnetic field due to local charge separation. Past studies showed that DLs observed in space plasmas are mostly associated with the ion acoustic instability. Recent Van Allen Probes observations of parallel electric field structures traveling much faster than the ion acoustic speed have motivated a computational study to test the hypothesis that a new type of DLs—electron acoustic DLs—generated from the electron acoustic instability are responsible for these electric fields. Nonlinear particle-in-cell simulations yield negative results, i.e., the hypothetical electronmore » acoustic DLs cannot be formed in a way similar to ion acoustic DLs. Linear theory analysis and the simulations show that the frequencies of electron acoustic waves are too high for ions to respond and maintain charge separation required by DLs. However, our results do show that local density perturbations in a two-electron-component plasma can result in unipolar-like electric field structures that propagate at the electron thermal speed, suggesting another potential explanation for the observations.« less

Finite element analyses of a linear-accelerator electron gun

NASA Astrophysics Data System (ADS)

Iqbal, M.; Wasy, A.; Islam, G. U.; Zhou, Z.

2014-02-01

Thermo-structural analyses of the Beijing Electron-Positron Collider (BEPCII) linear-accelerator, electron gun, were performed for the gun operating with the cathode at 1000 °C. The gun was modeled in computer aided three-dimensional interactive application for finite element analyses through ANSYS workbench. This was followed by simulations using the SLAC electron beam trajectory program EGUN for beam optics analyses. The simulations were compared with experimental results of the assembly to verify its beam parameters under the same boundary conditions. Simulation and test results were found to be in good agreement and hence confirmed the design parameters under the defined operating temperature. The gun is operating continuously since commissioning without any thermal induced failures for the BEPCII linear accelerator.

Finite element analyses of a linear-accelerator electron gun.

PubMed

Iqbal, M; Wasy, A; Islam, G U; Zhou, Z

2014-02-01

Thermo-structural analyses of the Beijing Electron-Positron Collider (BEPCII) linear-accelerator, electron gun, were performed for the gun operating with the cathode at 1000 °C. The gun was modeled in computer aided three-dimensional interactive application for finite element analyses through ANSYS workbench. This was followed by simulations using the SLAC electron beam trajectory program EGUN for beam optics analyses. The simulations were compared with experimental results of the assembly to verify its beam parameters under the same boundary conditions. Simulation and test results were found to be in good agreement and hence confirmed the design parameters under the defined operating temperature. The gun is operating continuously since commissioning without any thermal induced failures for the BEPCII linear accelerator.

Hybrid simulations of magnetic reconnection with kinetic ions and fluid electron pressure anisotropy

DOE PAGES

Le, A.; Daughton, W.; Karimabadi, H.; ...

2016-03-16

We present the first hybrid simulations with kinetic ions and recently developed equations of state for the electron fluid appropriate for reconnection with a guide field. The equations of state account for the main anisotropy of the electron pressure tensor.Magnetic reconnection is studied in two systems, an initially force-free current sheet and a Harris sheet. The hybrid model with the equations of state is compared to two other models, hybrid simulations with isothermal electrons and fully kinetic simulations. Including the anisotropicequations of state in the hybrid model provides a better match to the fully kinetic model. In agreement with fullymore » kinetic results, the main feature captured is the formation of an electron current sheet that extends several ion inertial lengths. This electron current sheet modifies the Hall magnetic field structure near the X-line, and it is not observed in the standard hybrid model with isotropic electrons. The saturated reconnection rate in this regime nevertheless remains similar in all three models. Here, implications for global modeling are discussed.« less

Ab initio simulations of the dynamic ion structure factor of warm dense lithium

DOE PAGES

Witte, B. B. L.; Shihab, M.; Glenzer, S. H.; ...

2017-04-06

Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less

Ab initio simulations of the dynamic ion structure factor of warm dense lithium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, B. B. L.; Shihab, M.; Glenzer, S. H.

Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less

Electron Energization and Structure of the Diffusion Region During Asymmetric Reconnection

NASA Technical Reports Server (NTRS)

Chen, Li-Jen; Hesse, Michael; Wang, Shan; Bessho, Naoki; Daughton, William

2016-01-01

Results from particle-in-cell simulations of reconnection with asymmetric upstream conditions are reported to elucidate electron energization and structure of the electron diffusion region (EDR). Acceleration of unmagnetized electrons results in discrete structures in the distribution functions and supports the intense current and perpendicular heating in the EDR. The accelerated electrons are cyclotron turned by the reconnected magnetic field to produce the outflow jets, and as such, the acceleration by the reconnection electric field is limited, leading to resistivity without particle-particle or particle-wave collisions. A map of electron distributions is constructed, and its spatial evolution is compared with quantities previously proposed to be EDR identifiers to enable effective identifications of the EDR in terrestrial magnetopause reconnection.

Phase-space dynamics of runaway electrons in magnetic fields

DOE PAGES

Guo, Zehua; McDevitt, Christopher Joseph; Tang, Xian-Zhu

2017-02-16

Dynamics of runaway electrons in magnetic fields are governed by the competition of three dominant physics: parallel electric field acceleration, Coulomb collision, and synchrotron radiation. Examination of the energy and pitch-angle flows reveals that the presence of local vortex structure and global circulation is crucial to the saturation of primary runaway electrons. Models for the vortex structure, which has an O-point to X-point connection, and the bump of runaway electron distribution in energy space have been developed and compared against the simulation data. Lastly, identification of these velocity-space structures opens a new venue to re-examine the conventional understanding of runawaymore » electron dynamics in magnetic fields.« less

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations

PubMed Central

Bachega, José Fernando R.; Timmers, Luís Fernando S.M.; Assirati, Lucas; Bachega, Leonardo R.; Field, Martin J.; Wymore, Troy

2014-01-01

Hybrid quantum chemical (QC)/molecular mechanical (MM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions, that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use we have developed an open-source graphical plug-in, GTKDynamo, that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. PMID:24137667

Silicon-carbon bond inversions driven by 60-keV electrons in graphene.

PubMed

Susi, Toma; Kotakoski, Jani; Kepaptsoglou, Demie; Mangler, Clemens; Lovejoy, Tracy C; Krivanek, Ondrej L; Zan, Recep; Bangert, Ursel; Ayala, Paola; Meyer, Jannik C; Ramasse, Quentin

2014-09-12

We demonstrate that 60-keV electron irradiation drives the diffusion of threefold-coordinated Si dopants in graphene by one lattice site at a time. First principles simulations reveal that each step is caused by an electron impact on a C atom next to the dopant. Although the atomic motion happens below our experimental time resolution, stochastic analysis of 38 such lattice jumps reveals a probability for their occurrence in a good agreement with the simulations. Conversions from three- to fourfold coordinated dopant structures and the subsequent reverse process are significantly less likely than the direct bond inversion. Our results thus provide a model of nondestructive and atomically precise structural modification and detection for two-dimensional materials.

The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

NASA Astrophysics Data System (ADS)

Oliveira, Micael

The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

THz emission of donor and acceptor doped GaAs/AlGaAs quantum well structures with inserted thin AlAs monolayer

NASA Astrophysics Data System (ADS)

van Dommelen, Paphavee; Daengngam, Chalongrat; Kalasuwan, Pruet

2018-04-01

In this paper, we explore THz range optical intersubband transition energies in a donor doped quantum well of a GaAs/AlGaAs system as a function of the insertion position of an AlAs monolayer in the GaAs quantum well. In simulated models, the optical transition energies between electron subband levels 1 and 2 were higher in the doped structure than in the undoped structure. This may be because the envelope wave function of the second electron subband strongly overlapped the envelope wave function of the first electron subband and influenced the optical intersubband transition between the two levels in the THz range. At different levels of bias voltage at the Schottky barrier on the donor doped structure, the electric field in the growth direction of the structure linearly increased the further away the AlAs monolayer was placed from the reference position. We also simulated the optical transition energies between acceptor energy levels of the acceptor doped structure as a function of the insertion position of the AlAs monolayer. The acceptor doped structure induced THz range emission whereas the undoped structure induced mid-IR emission.

Synergic Investigation Of The Self-Assembly Structure And Mechanism Of Retroviral Capsid Proteins By Solid State NMR, Transmission Electron Microscopy And Multiscale simulation

DTIC Science & Technology

2017-03-29

310 helix. Green: this work. Cyans: solution NMR RSV CA structure in PDB entry 1D1D.[18] Magentas: X-ray crystallography structure of flat hexameric...to combine cryo-electron microscopy and X-ray crystallography , Methods, 49 (2009) 174-180. [8] K.Y. Chan, J. Gumbart, R. McGreevy, J.M. Watermeyer

Simulation of the β-voltaic effect in silicon pin structures irradiated with electrons from a nickel-63 β source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagornov, Yu. S., E-mail: Nagornov.Yuri@gmail.com; Murashev, V. N.

2016-01-15

The prospects of β voltaics as electric-power sources for semiconductor circuits are considered. Experimental studies show that charging of the surface and a decrease in the electrovoltaic power are important. Simulation of the β-voltaic effect induced by electrons from a nickel-63 source on silicon pin structures is performed; it is shown that the coefficient of the collection of generated charge carriers can be as high as 13%. The dose dependences of the performance efficiency of silicon β-voltaic structures are determined for the case of irradiation with α particles and γ-ray photons; it is shown that 1.3 × 10{sup 14} andmore » 10{sup 20} cm{sup –2}, respectively, are the threshold doses, above which a rapid decrease in efficiency occurs. The optimal parameters of microchannel structures in β-voltaic electronics, in which the width of the channels and the distance between them correspond to 3 and 10 μm, are determined.« less

Structural and electron diffraction scaling of twisted graphene bilayers

NASA Astrophysics Data System (ADS)

Zhang, Kuan; Tadmor, Ellad B.

2018-03-01

Multiscale simulations are used to study the structural relaxation in twisted graphene bilayers and the associated electron diffraction patterns. The initial twist forms an incommensurate moiré pattern that relaxes to a commensurate microstructure comprised of a repeating pattern of alternating low-energy AB and BA domains surrounding a high-energy AA domain. The simulations show that the relaxation mechanism involves a localized rotation and shrinking of the AA domains that scales in two regimes with the imposed twist. For small twisting angles, the localized rotation tends to a constant; for large twist, the rotation scales linearly with it. This behavior is tied to the inverse scaling of the moiré pattern size with twist angle and is explained theoretically using a linear elasticity model. The results are validated experimentally through a simulated electron diffraction analysis of the relaxed structures. A complex electron diffraction pattern involving the appearance of weak satellite peaks is predicted for the small twist regime. This new diffraction pattern is explained using an analytical model in which the relaxation kinematics are described as an exponentially-decaying (Gaussian) rotation field centered on the AA domains. Both the angle-dependent scaling and diffraction patterns are in quantitative agreement with experimental observations. A Matlab program for extracting the Gaussian model parameters accompanies this paper.

Simulation of plasma double-layer structures

NASA Technical Reports Server (NTRS)

Borovsky, J. E.; Joyce, G.

1982-01-01

Electrostatic plasma double layers are numerically simulated by means of a magnetized 2 1/2 dimensional particle in cell method. The investigation of planar double layers indicates that these one dimensional potential structures are susceptible to periodic disruption by instabilities in the low potential plasmas. Only a slight increase in the double layer thickness with an increase in its obliqueness to the magnetic field is observed. Weak magnetization results in the double layer electric field alignment of accelerated particles and strong magnetization results in their magnetic field alignment. The numerical simulations of spatially periodic two dimensional double layers also exhibit cyclical instability. A morphological invariance in two dimensional double layers with respect to the degree of magnetization implies that the potential structures scale with Debye lengths rather than with gyroradii. Electron beam excited electrostatic electron cyclotron waves and (ion beam driven) solitary waves are present in the plasmas adjacent to the double layers.

High quantum efficiency photocathode simulation for the investigation of novel structured designs

DOE PAGES

MacPhee, A. G.; Nagel, S. R.; Bell, P. M.; ...

2014-09-02

A computer model in CST Studio Suite has been developed to evaluate several novel geometrically enhanced photocathode designs. This work was aimed at identifying a structure that would increase the total electron yield by a factor of two or greater in the 1–30 keV range. The modeling software was used to simulate the electric field and generate particle tracking for several potential structures. The final photocathode structure has been tailored to meet a set of detector performance requirements, namely, a spatial resolution of <40 μm and a temporal spread of 1–10 ps. As a result, we present the details ofmore » the geometrically enhanced photocathode model and resulting static field and electron emission characteristics.« less

Electronic doping of transition metal oxide perovskites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cammarata, Antonio, E-mail: cammaant@fel.cvut.cz; Rondinelli, James M.

2016-05-23

CaFeO{sub 3} is a prototypical negative charge transfer oxide that undergoes electronic metal-insulator transition concomitant with a dilation and contraction of nearly rigid octahedra. Altering the charge neutrality of the bulk system destroys the electronic transition, while the structure is significantly modified at high charge content. Using density functional theory simulations, we predict an alternative avenue to modulate the structure and the electronic transition in CaFeO{sub 3}. Charge distribution can be modulated using strain-rotation coupling and thin film engineering strategies, proposing themselves as a promising avenue for fine tuning electronic features in transition metal-oxide perovskites.

Investigation of Local Ordering in Amorphous Materials.

NASA Astrophysics Data System (ADS)

Fan, Gary Guoyou

The intent of the research described in this dissertation, as indicated by the title, is to provide a better understanding of the structure of amorphous material. The possibility of using electron microscopy to study the amorphous structure is investigated. Chapter 1 gives a brief introduction to the understanding and modeling of the amorphous structure, electron microscopy and the image analysis in general. The difficulty of using 2-D images to infer 3-D structures information is illustrated in Chapter 2, where it is shown that some high resolution images are not qualitatively different from images of white -noises weak-phase objects or those of random atomic arrangements. The means of obtaining statistical information from these images is given in Chapters 3 and 5, where the quantitative differences between experimental images and simulated white-noise or simulated images corresponding to random arrangements are revealed. The use of image processing techniques in electron microscopy and the possible artifacts are presented in Chapter 4. The pattern recognition technique outlined in Chapter 6 demonstrates a feasible mode of scanning transition electron microscope operation. Statistical analysis can be effectively performed on a large number of nano-diffraction patterns from, for example, locally ordered samples. Some recent developments in physics as well as in electron microscopy are briefly reviewed, and their possible applications in the study of amorphous structures are discussed in Chapter 7.

Front surface structured targets for enhancing laser-plasma interactions

NASA Astrophysics Data System (ADS)

Snyder, Joseph; George, Kevin; Ji, Liangliang; Yalamanchili, Sasir; Simonoff, Ethan; Cochran, Ginevra; Daskalova, Rebecca; Poole, Patrick; Willis, Christopher; Lewis, Nathan; Schumacher, Douglass

2016-10-01

We present recent progress made using front surface structured interfaces for enhancing ultrashort, relativistic laser-plasma interactions. Structured targets can increase laser absorption and enhance ion acceleration through a number of mechanisms such as direct laser acceleration and laser guiding. We detail experimental results obtained at the Scarlet laser facility on hollow, micron-scale plasma channels for enhancing electron acceleration. These targets show a greater than three times enhancement in the electron cutoff energy as well as an increased slope temperature for the electron distribution when compared to a flat interface. Using three-dimensional particle-in-cell (PIC) simulations, we have modeled the interaction to give insight into the physical processes responsible for the enhancement. Furthermore, we have used PIC simulations to design structures that are more advantageous for ion acceleration. Such targets necessitate advanced target fabrication methods and we describe techniques used to manufacture optimized structures, including vapor-liquid-solid growth, cryogenic etching, and 3D printing using two-photon-polymerization. This material is based upon work supported by the Air Force Office of Scientific Research under Award Number FA9550-14-1-0085.

Atomic and electronic structure of Pd40Ni40P20 bulk metallic glass from ab initio simulations

NASA Astrophysics Data System (ADS)

Kumar, Vijay; Fujita, T.; Konno, K.; Matsuura, M.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

2011-10-01

The atomic structure of Pd40Ni40P20 bulk metallic glass has been simulated using an ab initio molecular dynamics method with projector-augmented wave pseudopotentials for electron-ion interaction and generalized gradient approximation for exchange-correlation energy. The calculated extended x-ray absorption fine structure (EXAFS) spectra of Pd-K and Ni-K edges, the mass density, and the electronic structure agree remarkably well with the available experimental data and the EXAFS spectra measured at the SPring-8 synchrotron radiation facility. Our results show that the atomic structure can be described in terms of P-centered polyhedra. There are no two P atoms that are nearest neighbors at this composition, and this could be a reason for the observed optimal P concentration of about 20 at.%. The neighboring polyhedra share metal (M) atoms and form a polar covalently bonded random network of P-M-P favoring certain angles. The remaining M atoms act as metallic glue with a tendency of nanoscale clustering of Pd-Pd and Ni-Ni atoms.

Simulation of electron transport during electron-beam-induced deposition of nanostructures

PubMed Central

Jeschke, Harald O; Valentí, Roser

2013-01-01

Summary We present a numerical investigation of energy and charge distributions during electron-beam-induced growth of tungsten nanostructures on SiO2 substrates by using a Monte Carlo simulation of the electron transport. This study gives a quantitative insight into the deposition of energy and charge in the substrate and in the already existing metallic nanostructures in the presence of the electron beam. We analyze electron trajectories, inelastic mean free paths, and the distribution of backscattered electrons in different compositions and at different depths of the deposit. We find that, while in the early stages of the nanostructure growth a significant fraction of electron trajectories still interacts with the substrate, when the nanostructure becomes thicker the transport takes place almost exclusively in the nanostructure. In particular, a larger deposit density leads to enhanced electron backscattering. This work shows how mesoscopic radiation-transport techniques can contribute to a model that addresses the multi-scale nature of the electron-beam-induced deposition (EBID) process. Furthermore, similar simulations can help to understand the role that is played by backscattered electrons and emitted secondary electrons in the change of structural properties of nanostructured materials during post-growth electron-beam treatments. PMID:24367747

Finite element analyses of a linear-accelerator electron gun

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iqbal, M., E-mail: muniqbal.chep@pu.edu.pk, E-mail: muniqbal@ihep.ac.cn; Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049; Wasy, A.

Thermo-structural analyses of the Beijing Electron-Positron Collider (BEPCII) linear-accelerator, electron gun, were performed for the gun operating with the cathode at 1000 °C. The gun was modeled in computer aided three-dimensional interactive application for finite element analyses through ANSYS workbench. This was followed by simulations using the SLAC electron beam trajectory program EGUN for beam optics analyses. The simulations were compared with experimental results of the assembly to verify its beam parameters under the same boundary conditions. Simulation and test results were found to be in good agreement and hence confirmed the design parameters under the defined operating temperature. The gunmore » is operating continuously since commissioning without any thermal induced failures for the BEPCII linear accelerator.« less

Contrast of Backscattered Electron SEM Images of Nanoparticles on Substrates with Complex Structure

PubMed Central

Müller, Erich; Fritsch-Decker, Susanne; Hettler, Simon; Störmer, Heike; Weiss, Carsten; Gerthsen, Dagmar

2017-01-01

This study is concerned with backscattered electron scanning electron microscopy (BSE SEM) contrast of complex nanoscaled samples which consist of SiO2 nanoparticles (NPs) deposited on indium-tin-oxide covered bulk SiO2 and glassy carbon substrates. BSE SEM contrast of NPs is studied as function of the primary electron energy and working distance. Contrast inversions are observed which prevent intuitive interpretation of NP contrast in terms of material contrast. Experimental data is quantitatively compared with Monte-Carlo- (MC-) simulations. Quantitative agreement between experimental data and MC-simulations is obtained if the transmission characteristics of the annular semiconductor detector are taken into account. MC-simulations facilitate the understanding of NP contrast inversions and are helpful to derive conditions for optimum material and topography contrast. PMID:29109816

Contrast of Backscattered Electron SEM Images of Nanoparticles on Substrates with Complex Structure.

PubMed

Kowoll, Thomas; Müller, Erich; Fritsch-Decker, Susanne; Hettler, Simon; Störmer, Heike; Weiss, Carsten; Gerthsen, Dagmar

2017-01-01

This study is concerned with backscattered electron scanning electron microscopy (BSE SEM) contrast of complex nanoscaled samples which consist of SiO 2 nanoparticles (NPs) deposited on indium-tin-oxide covered bulk SiO 2 and glassy carbon substrates. BSE SEM contrast of NPs is studied as function of the primary electron energy and working distance. Contrast inversions are observed which prevent intuitive interpretation of NP contrast in terms of material contrast. Experimental data is quantitatively compared with Monte-Carlo- (MC-) simulations. Quantitative agreement between experimental data and MC-simulations is obtained if the transmission characteristics of the annular semiconductor detector are taken into account. MC-simulations facilitate the understanding of NP contrast inversions and are helpful to derive conditions for optimum material and topography contrast.

Electron cloud simulations for the main ring of J-PARC

NASA Astrophysics Data System (ADS)

Yee-Rendon, Bruce; Muto, Ryotaro; Ohmi, Kazuhito; Satou, Kenichirou; Tomizawa, Masahito; Toyama, Takeshi

2017-07-01

The simulation of beam instabilities is a helpful tool to evaluate potential threats against the machine protection of the high intensity beams. At Main Ring (MR) of J-PARC, signals related to the electron cloud have been observed during the slow beam extraction mode. Hence, several studies were conducted to investigate the mechanism that produces it, the results confirmed a strong dependence on the beam intensity and the bunch structure in the formation of the electron cloud, however, the precise explanation of its trigger conditions remains incomplete. To shed light on the problem, electron cloud simulations were done using an updated version of the computational model developed from previous works at KEK. The code employed the signals of the measurements to reproduce the events seen during the surveys.

Study of structural colour of Hebomoia glaucippe butterfly wing scales

NASA Astrophysics Data System (ADS)

Shur, V. Ya; Kuznetsov, D. K.; Pryakhina, V. I.; Kosobokov, M. S.; Zubarev, I. V.; Boymuradova, S. K.; Volchetskaya, K. V.

2017-10-01

Structural colours of Hebomoia glaucippe butterfly wing scales have been studied experimentally using high resolution scanning electron microscopy. Visualization of scales structures and computer simulation allowed distinguishing correlation between nanostructures on the scales and their colour.

Physical Processes and Applications of the Monte Carlo Radiative Energy Deposition (MRED) Code

NASA Astrophysics Data System (ADS)

Reed, Robert A.; Weller, Robert A.; Mendenhall, Marcus H.; Fleetwood, Daniel M.; Warren, Kevin M.; Sierawski, Brian D.; King, Michael P.; Schrimpf, Ronald D.; Auden, Elizabeth C.

2015-08-01

MRED is a Python-language scriptable computer application that simulates radiation transport. It is the computational engine for the on-line tool CRÈME-MC. MRED is based on c++ code from Geant4 with additional Fortran components to simulate electron transport and nuclear reactions with high precision. We provide a detailed description of the structure of MRED and the implementation of the simulation of physical processes used to simulate radiation effects in electronic devices and circuits. Extensive discussion and references are provided that illustrate the validation of models used to implement specific simulations of relevant physical processes. Several applications of MRED are summarized that demonstrate its ability to predict and describe basic physical phenomena associated with irradiation of electronic circuits and devices. These include effects from single particle radiation (including both direct ionization and indirect ionization effects), dose enhancement effects, and displacement damage effects. MRED simulations have also helped to identify new single event upset mechanisms not previously observed by experiment, but since confirmed, including upsets due to muons and energetic electrons.

Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

PubMed

Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

2018-03-01

Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

Acceleration and Pickup Ring of Energetic Electrons Observed in Relativistic Magnetic Reconnection Simulations

NASA Astrophysics Data System (ADS)

Ping, Y. L.; Zhong, J. Y.; Wang, X. G.; Sheng, Z. M.; Zhao, G.

2017-11-01

Pickup ring of energetic electrons found in relativistic magnetic reconnection (MR) driven by two relativistic intense femtosecond laser pulses is investigated by particle simulation in 3D geometry. Magnetic reconnection processes and configurations are characterized by plasma current density distributions at different axial positions. Two helical structures associated with the circular polarization of laser pulses break down in the reconnection processes to form a current sheet between them, where energetic electrons are found to pile up and the outflow relativistic electron jets are observed. In the field line diffusion region, electrons are accelerated to multi-MeV with a flatter power-law spectrum due to MR. The development of the pickup ring of energetic electrons is strongly dependent upon laser peak intensities.

Superlattice structure modeling and simulation of High Electron Mobility Transistor for improved performance

NASA Astrophysics Data System (ADS)

Munusami, Ravindiran; Yakkala, Bhaskar Rao; Prabhakar, Shankar

2013-12-01

Magnetic tunnel junction were made by inserting the magnetic materials between the source, channel and the drain of the High Electron Mobility Transistor (HEMT) to enhance the performance. Material studio software package was used to design the superlattice layers. Different cases were analyzed to optimize the performance of the device by placing the magnetic material at different positions of the device. Simulation results based on conductivity reveals that the device has a very good electron transport due to the magnetic materials and will amplify very low frequency signals.

Particle-in-cell simulations of anomalous transport in a Penning discharge

NASA Astrophysics Data System (ADS)

Carlsson, Johan; Kaganovich, Igor; Powis, Andrew; Raitses, Yevgeny; Romadanov, Ivan; Smolyakov, Andrei

2018-06-01

Electrostatic particle-in-cell simulations of a Penning discharge are performed in order to investigate azimuthally asymmetric, spoke-like structures previously observed in experiments. Two-dimensional simulations show that for Penning-discharge conditions, a persistent nonlinear spoke-like structure forms readily and rotates in the direction of E × B and electron diamagnetic drifts. The azimuthal velocity is within about a factor of 2 of the ion acoustic speed. The spoke frequency follows the experimentally observed scaling with ion mass, which indicates the importance of ion inertia in spoke formation. The spoke provides enhanced (anomalous) radial electron transport, and the effective cross-field conductivity is several times larger than the classical (collisional) value. The level of anomalous current obtained in the simulations is in good agreement with the experimental data. The rotating spoke channels most of the radial current, observable by an edge probe as short pulses.

Rotational and fine structure of open-shell molecules in nearly degenerate electronic states

NASA Astrophysics Data System (ADS)

Liu, Jinjun

2018-03-01

An effective Hamiltonian without symmetry restriction has been developed to model the rotational and fine structure of two nearly degenerate electronic states of an open-shell molecule. In addition to the rotational Hamiltonian for an asymmetric top, this spectroscopic model includes the energy separation between the two states due to difference potential and zero-point energy difference, as well as the spin-orbit (SO), Coriolis, and electron spin-molecular rotation (SR) interactions. Hamiltonian matrices are computed using orbitally and fully symmetrized case (a) and case (b) basis sets. Intensity formulae and selection rules for rotational transitions between a pair of nearly degenerate states and a nondegenerate state have also been derived using all four basis sets. It is demonstrated using real examples of free radicals that the fine structure of a single electronic state can be simulated with either a SR tensor or a combination of SO and Coriolis constants. The related molecular constants can be determined precisely only when all interacting levels are simulated simultaneously. The present study suggests that analysis of rotational and fine structure can provide quantitative insights into vibronic interactions and related effects.

Simulation of cooling efficiency via miniaturised channels in multilayer LTCC for power electronics

NASA Astrophysics Data System (ADS)

Pietrikova, Alena; Girasek, Tomas; Lukacs, Peter; Welker, Tilo; Müller, Jens

2017-03-01

The aim of this paper is detailed investigation of thermal resistance, flow analysis and distribution of coolant as well as thermal distribution inside multilayer LTCC substrates with embedded channels for power electronic devices by simulation software. For this reason four various structures of internal channels in the multilayer LTCC substrates were designed and simulated. The impact of the volume flow, structures of channels, and power loss of chip was simulated, calculated and analyzed by using the simulation software Mentor Graphics FloEFDTM. The structure, size and location of channels have the significant impact on thermal resistance, pressure of coolant as well as the effectivity of cooling power components (chips) that can be placed on the top of LTCC substrate. The main contribution of this paper is thermal analyze, optimization and impact of 4 various cooling channels embedded in LTCC multilayer structure. Paper investigate, the effect of volume flow in cooling channels for achieving the least thermal resistance of LTCC substrate that is loaded by power thermal chips. Paper shows on the impact of the first chips thermal load on the second chip as well as. This possible new technology could ensure in the case of practical realization effective cooling and increasing reliability of high power modules.

A Monte Carlo method using octree structure in photon and electron transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogawa, K.; Maeda, S.

Most of the early Monte Carlo calculations in medical physics were used to calculate absorbed dose distributions, and detector responses and efficiencies. Recently, data acquisition in Single Photon Emission CT (SPECT) has been simulated by a Monte Carlo method to evaluate scatter photons generated in a human body and a collimator. Monte Carlo simulations in SPECT data acquisition are generally based on the transport of photons only because the photons being simulated are low energy, and therefore the bremsstrahlung productions by the electrons generated are negligible. Since the transport calculation of photons without electrons is much simpler than that withmore » electrons, it is possible to accomplish the high-speed simulation in a simple object with one medium. Here, object description is important in performing the photon and/or electron transport using a Monte Carlo method efficiently. The authors propose a new description method using an octree representation of an object. Thus even if the boundaries of each medium are represented accurately, high-speed calculation of photon transport can be accomplished because the number of voxels is much fewer than that of the voxel-based approach which represents an object by a union of the voxels of the same size. This Monte Carlo code using the octree representation of an object first establishes the simulation geometry by reading octree string, which is produced by forming an octree structure from a set of serial sections for the object before the simulation; then it transports photons in the geometry. Using the code, if the user just prepares a set of serial sections for the object in which he or she wants to simulate photon trajectories, he or she can perform the simulation automatically using the suboptimal geometry simplified by the octree representation without forming the optimal geometry by handwriting.« less

GeV ion irradiation of NiFe and NiCo: Insights from MD simulations and experiments

DOE PAGES

Leino, Aleksi A.; Samolyuk, German D.; Sachan, Ritesh; ...

2018-03-31

Concentrated solid solution alloys have attracted rapidly increasing attention due to their potential for designing materials with high tolerance to radiation damage. To tackle the effects of chemical complexity in defect dynamics and radiation response, we present in this paper a computational study on swift heavy ion induced effects in Ni and equiatomic Ni -based alloys (Ni 50Fe 50, Ni 50Co 50) using two-temperature molecular dynamics simulations (2T-MD). The electronic heat conductivity in the two-temperature equations is parameterized from the results of first principles electronic structure calculations. A bismuth ion (1.542 GeV) is selected and single impact simulations performed inmore » each target. We study the heat flow in the electronic subsystem and show that alloying Ni with Co or Fe reduces the heat dissipation from the impact by the electronic subsystem. Simulation results suggest no melting or residual damage in pure Ni while a cylindrical region melts along the ion propagation path in the alloys. In Ni 50Co 50 the damage consists of a dislocation loop structure (d = 2 nm) and isolated point defects, while in Ni 50Fe 50, a defect cluster (d = 4 nm) along the ion path is, in addition, formed. The simulation results are supported by atomic-level structural and defect characterizations in bismuth-irradiated Ni and Ni 50Fe 50. Finally, the significance of the 2T-MD model is demonstrated by comparing the results to those obtained with an instantaneous energy deposition model without consideration of e-ph interactions in pure Ni and by showing that it leads to a different qualitative behavior.« less

GeV ion irradiation of NiFe and NiCo: Insights from MD simulations and experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leino, Aleksi A.; Samolyuk, German D.; Sachan, Ritesh

Concentrated solid solution alloys have attracted rapidly increasing attention due to their potential for designing materials with high tolerance to radiation damage. To tackle the effects of chemical complexity in defect dynamics and radiation response, we present in this paper a computational study on swift heavy ion induced effects in Ni and equiatomic Ni -based alloys (Ni 50Fe 50, Ni 50Co 50) using two-temperature molecular dynamics simulations (2T-MD). The electronic heat conductivity in the two-temperature equations is parameterized from the results of first principles electronic structure calculations. A bismuth ion (1.542 GeV) is selected and single impact simulations performed inmore » each target. We study the heat flow in the electronic subsystem and show that alloying Ni with Co or Fe reduces the heat dissipation from the impact by the electronic subsystem. Simulation results suggest no melting or residual damage in pure Ni while a cylindrical region melts along the ion propagation path in the alloys. In Ni 50Co 50 the damage consists of a dislocation loop structure (d = 2 nm) and isolated point defects, while in Ni 50Fe 50, a defect cluster (d = 4 nm) along the ion path is, in addition, formed. The simulation results are supported by atomic-level structural and defect characterizations in bismuth-irradiated Ni and Ni 50Fe 50. Finally, the significance of the 2T-MD model is demonstrated by comparing the results to those obtained with an instantaneous energy deposition model without consideration of e-ph interactions in pure Ni and by showing that it leads to a different qualitative behavior.« less

Ionic structures and transport properties of hot dense W and U plasmas

NASA Astrophysics Data System (ADS)

Hou, Yong; Yuan, Jianmin

2016-10-01

We have combined the average-atom model with the hyper-netted chain approximation (AAHNC) to describe the electronic and ionic structure of uranium and tungsten in the hot dense matter regime. When the electronic structure is described within the average-atom model, the effects of others ions on the electronic structure are considered by the correlation functions. And the ionic structure is calculated though using the hyper-netted chain (HNC) approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution in the temperature-depended density functional theory. And electronic and ionic structures are determined self-consistently. On the basis of the ion-ion pair potential, we perform the classical (CMD) and Langevin (LMD) molecular dynamics to simulate the ionic transport properties, such as ionic self-diffusion and shear viscosity coefficients, through the ionic velocity correlation functions. Due that the free electrons become more and more with increasing the plasma temperature, the influence of the electron-ion collisions on the transport properties become more and more important.

Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice.

PubMed

Henderson, Richard; McMullan, Greg

2013-02-01

Theoretical considerations together with simulations of single-particle electron cryomicroscopy images of biological assemblies in ice demonstrate that atomic structures should be obtainable from images of a few thousand asymmetric units, provided the molecular weight of the whole assembly being studied is greater than the minimum needed for accurate position and orientation determination. However, with present methods of specimen preparation and current microscope and detector technologies, many more particles are needed, and the alignment of smaller assemblies is difficult or impossible. Only larger structures, with enough signal to allow good orientation determination and with enough images to allow averaging of many hundreds of thousands or even millions of asymmetric units, have successfully produced high-resolution maps. In this review, we compare the contrast of experimental electron cryomicroscopy images of two smaller molecular assemblies, namely apoferritin and beta-galactosidase, with that expected from perfect simulated images calculated from their known X-ray structures. We show that the contrast and signal-to-noise ratio of experimental images still require significant improvement before it will be possible to realize the full potential of single-particle electron cryomicroscopy. In particular, although reasonably good orientations can be obtained for beta-galactosidase, we have been unable to obtain reliable orientation determination from experimental images of apoferritin. Simulations suggest that at least 2-fold improvement of the contrast in experimental images at ~10 Å resolution is needed and should be possible.

Decomposition of L a2 -xS rxCu O4 into several L a2O3 phases at elevated temperatures in ultrahigh vacuum inside a transmission electron microscope

NASA Astrophysics Data System (ADS)

Jeong, Jong Seok; Wu, Wangzhou; Topsakal, Mehmet; Yu, Guichuan; Sasagawa, Takao; Greven, Martin; Mkhoyan, K. Andre

2018-05-01

We report the decomposition of L a2 -xS rxCu O4 into L a2O3 and Cu nanoparticles in ultrahigh vacuum, observed by in situ heating experiments in a transmission electron microscope. The analysis of electron diffraction data reveals that the phase decomposition process starts at about 150 °C and is considerably expedited in the temperature range of 350 °C-450 °C. Two major resultant solid phases are identified as metallic Cu and L a2O3 by electron diffraction, simulation, and electron energy-loss spectroscopy (EELS) analyses. With the aid of calculations, L a2O3 phases are further identified to be derivatives of a fluorite structure—fluorite, pyrochlore, and (distorted) bixbyite—characterized by different oxygen-vacancy order. Additionally, the bulk plasmon energy and the fine structures of the O K and La M4 ,5 EELS edges are reported for these structures, along with simulated O K x-ray absorption near-edge structure. The resultant Cu nanoparticles and L a2O3 phases remain unchanged after cooling to room temperature.

Simulations of nanocrystals under pressure: combining electronic enthalpy and linear-scaling density-functional theory.

PubMed

Corsini, Niccolò R C; Greco, Andrea; Hine, Nicholas D M; Molteni, Carla; Haynes, Peter D

2013-08-28

We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure. Based on a definition of the system volume as that enclosed within an electronic density isosurface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)], it supports both geometry optimizations and molecular dynamics simulations. We introduce an approach for calibrating the parameters defining the volume in the context of geometry optimizations and discuss their significance. Results in good agreement with simulations using explicit solvents are obtained, validating our approach. Size-dependent pressure-induced structural transformations and variations in the energy gap of hydrogenated silicon nanocrystals are investigated, including one comparable in size to recent experiments. A detailed analysis of the polyamorphic transformations reveals three types of amorphous structures and their persistence on depressurization is assessed.

Simulations of nanocrystals under pressure: Combining electronic enthalpy and linear-scaling density-functional theory

NASA Astrophysics Data System (ADS)

Corsini, Niccolò R. C.; Greco, Andrea; Hine, Nicholas D. M.; Molteni, Carla; Haynes, Peter D.

2013-08-01

We present an implementation in a linear-scaling density-functional theory code of an electronic enthalpy method, which has been found to be natural and efficient for the ab initio calculation of finite systems under hydrostatic pressure. Based on a definition of the system volume as that enclosed within an electronic density isosurface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)], 10.1103/PhysRevLett.94.145501, it supports both geometry optimizations and molecular dynamics simulations. We introduce an approach for calibrating the parameters defining the volume in the context of geometry optimizations and discuss their significance. Results in good agreement with simulations using explicit solvents are obtained, validating our approach. Size-dependent pressure-induced structural transformations and variations in the energy gap of hydrogenated silicon nanocrystals are investigated, including one comparable in size to recent experiments. A detailed analysis of the polyamorphic transformations reveals three types of amorphous structures and their persistence on depressurization is assessed.

Simulating pump-probe photoelectron and absorption spectroscopy on the attosecond timescale with time-dependent density functional theory.

PubMed

De Giovannini, Umberto; Brunetto, Gustavo; Castro, Alberto; Walkenhorst, Jessica; Rubio, Angel

2013-05-10

Molecular absorption and photoelectron spectra can be efficiently predicted with real-time time-dependent density functional theory. We show herein how these techniques can be easily extended to study time-resolved pump-probe experiments, in which a system response (absorption or electron emission) to a probe pulse is measured in an excited state. This simulation tool helps with the interpretation of fast-evolving attosecond time-resolved spectroscopic experiments, in which electronic motion must be followed at its natural timescale. We show how the extra degrees of freedom (pump-pulse duration, intensity, frequency, and time delay), which are absent in a conventional steady-state experiment, provide additional information about electronic structure and dynamics that improve characterization of a system. As an extension of this approach, time-dependent 2D spectroscopy can also be simulated, in principle, for large-scale structures and extended systems. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-million atom electronic structure calculations for quantum dots

NASA Astrophysics Data System (ADS)

Usman, Muhammad

Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined stark shift, coherent coupling of electronic states in a quantum dot molecule etc.; (3) to assess the potential use of the quantum dots in real device implementation and to provide physical insight to the experimentalists. Full three dimensional strain and electronic structure simulations of quantum dot structures containing multi-million atoms are done using NEMO 3-D. Both single and vertically stacked quantum dot structures are analyzed in detail. The results show that the strain and the piezoelectricity significantly impact the electronic structure of these devices. This work shows that the InAs quantum dots when placed in the InGaAs quantum well red shifts the emission wavelength. Such InAs/GaAs-based optical devices can be used for optical-fiber based communication systems at longer wavelengths (1.3um -- 1.5um). Our atomistic simulations of InAs/InGaAs/GaAs quantum dots quantitatively match with the experiment and give the critical insight of the physics involved in these structures. A single quantum dot molecule is studied for coherent quantum coupling of electronic states under the influence of static electric field applied in the growth direction. Such nanostructures can be used in the implementation of quantum information technologies. A close quantitative match with the experimental optical measurements allowed us to get a physical insight into the complex physics of quantum tunnel couplings of electronic states as the device operation switches between atomic and molecular regimes. Another important aspect is to design the quantum dots for a desired isotropic polarization of the optical emissions. Both single and coupled quantum dots are studied for TE/TM ratio engineering. The atomistic study provides a detailed physical analysis of these computationally expensive large nanostructures and serves as a guide for the experimentalists for the design of the polarization independent devices for the optical communication systems.

Electron Scale Structures and Magnetic Reconnection Signatures in the Turbulent Magnetosheath

NASA Technical Reports Server (NTRS)

Yordanova, E.; Voros, Z.; Varsani, A.; Graham, D. B.; Norgren, C.; Khotyaintsev, Yu. V.; Vaivads, A.; Eriksson, E.; Nakamura, R.; Lindqvist, P.-A.;

Lattice and Valence Electronic Structures of Crystalline Octahedral Molybdenum Halide Clusters-Based Compounds, Cs2[Mo6X14] (X = Cl, Br, I), Studied by Density Functional Theory Calculations.

PubMed

Saito, Norio; Cordier, Stéphane; Lemoine, Pierric; Ohsawa, Takeo; Wada, Yoshiki; Grasset, Fabien; Cross, Jeffrey S; Ohashi, Naoki

2017-06-05

The electronic and crystal structures of Cs 2 [Mo 6 X 14 ] (X = Cl, Br, I) cluster-based compounds were investigated by density functional theory (DFT) simulations and experimental methods such as powder X-ray diffraction, ultraviolet-visible spectroscopy, and X-ray photoemission spectroscopy (XPS). The experimentally determined lattice parameters were in good agreement with theoretically optimized ones, indicating the usefulness of DFT calculations for the structural investigation of these clusters. The calculated band gaps of these compounds reproduced those experimentally determined by UV-vis reflectance within an error of a few tenths of an eV. Core-level XPS and effective charge analyses indicated bonding states of the halogens changed according to their sites. The XPS valence spectra were fairly well reproduced by simulations based on the projected electron density of states weighted with cross sections of Al K α , suggesting that DFT calculations can predict the electronic properties of metal-cluster-based crystals with good accuracy.

Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory

DOE PAGES

Tait, E. W.; Ratcliff, L. E.; Payne, M. C.; ...

2016-04-20

Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree withmore » those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. As a result, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable.« less

Reversible electron heating vs. wave-particle interactions in quasi-perpendicular shocks

NASA Technical Reports Server (NTRS)

Veltri, P.; Mangeney, A.; Scudder, J. D.

1992-01-01

The energy necessary to explain the electron heating in quasi-perpendicular collisionless shocks can be derived either from the electron acceleration in the d.c. cross shock electric potential, or by the interactions between the electrons and the waves existing in the shock. A Monte Carlo simulation has been performed to study the electron distribution function evolution through the shock structure, with and without particle diffusion on waves. This simulation has allowed us to clarify the relative importance of the two possible energy sources; in particular it has been shown that the electron parallel temperature is determined by the d.c. electromagnetic field and not by any wave-particle-induced heating. Wave particle interactions are effective in smoothing out the large gradients in phase space produced by the 'reversible' motion of the electrons, thus producing a 'cooling' of the electrons.

Full 3D opto-electronic simulation tool for nanotextured solar cells (Conference Presentation)

NASA Astrophysics Data System (ADS)

Michallon, Jérôme; Collin, Stéphane

2017-04-01

Increasing efforts on the photovoltaics research have recently been devoted to material savings, leading to the emergence of new designs based on nanotextured and nanowire-based solar cells. The use of small absorber volumes, light-trapping nanostructures and unconventional carrier collection schemes (radial nanowire junctions, point contacts in planar structures,…) increases the impact of surfaces recombination and induces homogeneity in the photogenerated carrier concentrations. The investigation of their impacts on the device performances need to be addressed using full 3D coupled opto-electrical modeling. In this context, we have developed a new tool for full 3D opto-electrical simulation using the most advanced optical and electrical simulation techniques. We will present an overview of its simulation capabilities and the key issues that have been solved to make it fully operational and reliable. We will provide various examples of opto-electronic simulation of (i) nanostructured solar cells with localized contacts and (ii) nanowire solar cells. We will also show how opto-electronic simulation can be used to simulate light- and electron-beam induced current (LBIC/EBIC) experiments, targeting quantitative analysis of the passivation properties of surfaces.

Preface: Special Topic: From Quantum Mechanics to Force Fields.

PubMed

Piquemal, Jean-Philip; Jordan, Kenneth D

2017-10-28

This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

Preface: Special Topic: From Quantum Mechanics to Force Fields

NASA Astrophysics Data System (ADS)

Piquemal, Jean-Philip; Jordan, Kenneth D.

2017-10-01

This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

Nonlinear Evolution of Counter-Propagating Whistler Mode Waves Excited by Anisotropic Electrons Within the Equatorial Source Region: 1-D PIC Simulations

NASA Astrophysics Data System (ADS)

Chen, Huayue; Gao, Xinliang; Lu, Quanming; Sun, Jicheng; Wang, Shui

2018-02-01

Nonlinear physical processes related to whistler mode waves are attracting more and more attention for their significant role in reshaping whistler mode spectra in the Earth's magnetosphere. Using a 1-D particle-in-cell simulation model, we have investigated the nonlinear evolution of parallel counter-propagating whistler mode waves excited by anisotropic electrons within the equatorial source region. In our simulations, after the linear phase of whistler mode instability, the strong electrostatic standing structures along the background magnetic field will be formed, resulting from the coupling between excited counter-propagating whistler mode waves. The wave numbers of electrostatic standing structures are about twice those of whistler mode waves generated by anisotropic hot electrons. Moreover, these electrostatic standing structures can further be coupled with either parallel or antiparallel propagating whistler mode waves to excite high-k modes in this plasma system. Compared with excited whistler mode waves, these high-k modes typically have 3 times wave number, same frequency, and about 2 orders of magnitude smaller amplitude. Our study may provide a fresh view on the evolution of whistler mode waves within their equatorial source regions in the Earth's magnetosphere.

Simulation-Guided 3D Nanomanufacturing via Focused Electron Beam Induced Deposition

DOE PAGES

Fowlkes, Jason D.; Winkler, Robert; Lewis, Brett B.; ...

2016-06-10

Focused electron beam induced deposition (FEBID) is one of the few techniques that enables direct-write synthesis of free-standing 3D nanostructures. While the fabrication of simple architectures such as vertical or curving nanowires has been achieved by simple trial and error, processing complex 3D structures is not tractable with this approach. This is due, inpart, to the dynamic interplay between electron–solid interactions and the transient spatial distribution of absorbed precursor molecules on the solid surface. Here, we demonstrate the ability to controllably deposit 3D lattice structures at the micro/nanoscale, which have received recent interest owing to superior mechanical and optical properties.more » Moreover, a hybrid Monte Carlo–continuum simulation is briefly overviewed, and subsequently FEBID experiments and simulations are directly compared. Finally, a 3D computer-aided design (CAD) program is introduced, which generates the beam parameters necessary for FEBID by both simulation and experiment. In using this approach, we demonstrate the fabrication of various 3D lattice structures using Pt-, Au-, and W-based precursors.« less

Nanoscale inhomogeneity and photoacid generation dynamics in extreme ultraviolet resist materials

NASA Astrophysics Data System (ADS)

Wu, Ping-Jui; Wang, Yu-Fu; Chen, Wei-Chi; Wang, Chien-Wei; Cheng, Joy; Chang, Vencent; Chang, Ching-Yu; Lin, John; Cheng, Yuan-Chung

2018-03-01

The development of extreme ultraviolet (EUV) lithography towards the 22 nm node and beyond depends critically on the availability of resist materials that meet stringent control requirements in resolution, line edge roughness, and sensitivity. However, the molecular mechanisms that govern the structure-function relationships in current EUV resist systems are not well understood. In particular, the nanoscale structures of the polymer base and the distributions of photoacid generators (PAGs) should play a critical roles in the performance of a resist system, yet currently available models for photochemical reactions in EUV resist systems are exclusively based on homogeneous bulk models that ignore molecular-level details of solid resist films. In this work, we investigate how microscopic molecular organizations in EUV resist affect photoacid generations in a bottom-up approach that describes structure-dependent electron-transfer dynamics in a solid film model. To this end, molecular dynamics simulations and stimulated annealing are used to obtain structures of a large simulation box containing poly(4-hydroxystyrene) (PHS) base polymers and triphenylsulfonium based PAGs. Our calculations reveal that ion-pair interactions govern the microscopic distributions of the polymer base and PAG molecules, resulting in a highly inhomogeneous system with nonuniform nanoscale chemical domains. Furthermore, the theoretical structures were used in combination of quantum chemical calculations and the Marcus theory to evaluate electron transfer rates between molecular sites, and then kinetic Monte Carlo simulations were carried out to model electron transfer dynamics with molecular structure details taken into consideration. As a result, the portion of thermalized electrons that are absorbed by the PAGs and the nanoscale spatial distribution of generated acids can be estimated. Our data reveal that the nanoscale inhomogeneous distributions of base polymers and PAGs strongly affect the electron transfer and the performance of the resist system. The implications to the performances of EUV resists and key engineering requirements for improved resist systems will also be discussed in this work. Our results shed light on the fundamental structure dependence of photoacid generation and the control of the nanoscale structures as well as base polymer-PAG interactions in EVU resist systems, and we expect these knowledge will be useful for the future development of improved EUV resist systems.

Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

DOE PAGES

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

2014-10-29

We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fathany, Maulana Yusuf, E-mail: myfathany@gmail.com; Fuada, Syifaul, E-mail: fsyifaul@gmail.com; Lawu, Braham Lawas, E-mail: bram-labs@rocketmail.com

2016-04-19

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.

Simulation of Relativistic Shocks and Associated Self-Consistent Radiation

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Niemiec, J.; Medvedev, M.; Zhang, B.; Hardee, P.; Mizuno, Y.; Nordlund, A.; Frederiksen, J.; Sol, H.; Pohl, M.;

Simulation of Relativistic Shocks and Associated Radiation from Turbulent Magnetic Fields

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Mizuno, Y.; Niemiec, J.; Medvedev, M.; Zhang, B.; Hardee, P.; Frederiksen, J.; Sol, H.; Pohl, M.; Hartmann, D. H.;

Modeling of electron-specimen interaction in scanning electron microscope for e-beam metrology and inspection: challenges and perspectives

NASA Astrophysics Data System (ADS)

Suzuki, Makoto; Kameda, Toshimasa; Doi, Ayumi; Borisov, Sergey; Babin, Sergey

2018-03-01

The interpretation of scanning electron microscopy (SEM) images of the latest semiconductor devices is not intuitive and requires comparison with computed images based on theoretical modeling and simulations. For quantitative image prediction and geometrical reconstruction of the specimen structure, the accuracy of the physical model is essential. In this paper, we review the current models of electron-solid interaction and discuss their accuracy. We perform the comparison of the simulated results with our experiments of SEM overlay of under-layer, grain imaging of copper interconnect, and hole bottom visualization by angular selective detectors, and show that our model well reproduces the experimental results. Remaining issues for quantitative simulation are also discussed, including the accuracy of the charge dynamics, treatment of beam skirt, and explosive increase in computing time.

Predicting mesoscale microstructural evolution in electron beam welding

DOE PAGES

Rodgers, Theron M.; Madison, Jonathan D.; Tikare, Veena; ...

2016-03-16

Using the kinetic Monte Carlo simulator, Stochastic Parallel PARticle Kinetic Simulator, from Sandia National Laboratories, a user routine has been developed to simulate mesoscale predictions of a grain structure near a moving heat source. Here, we demonstrate the use of this user routine to produce voxelized, synthetic, three-dimensional microstructures for electron-beam welding by comparing them with experimentally produced microstructures. When simulation input parameters are matched to experimental process parameters, qualitative and quantitative agreement for both grain size and grain morphology are achieved. The method is capable of simulating both single- and multipass welds. As a result, the simulations provide anmore » opportunity for not only accelerated design but also the integration of simulation and experiments in design such that simulations can receive parameter bounds from experiments and, in turn, provide predictions of a resultant microstructure.« less

Bridging the gap between atomic microstructure and electronic properties of alloys: The case of (In,Ga)N

NASA Astrophysics Data System (ADS)

Chan, J. A.; Liu, J. Z.; Zunger, Alex

2010-07-01

The atomic microstructure of alloys is rarely perfectly random, instead exhibiting differently shaped precipitates, clusters, zigzag chains, etc. While it is expected that such microstructural features will affect the electronic structures (carrier localization and band gaps), theoretical studies have, until now, been restricted to investigate either perfectly random or artificial “guessed” microstructural features. In this paper, we simulate the alloy microstructures in thermodynamic equilibrium using the static Monte Carlo method and study their electronic structures explicitly using a pseudopotential supercell approach. In this way, we can bridge atomic microstructures with their electronic properties. We derive the atomic microstructures of InGaN using (i) density-functional theory total energies of ˜50 ordered structures to construct a (ii) multibody cluster expansion, including strain effects to which we have applied (iii) static Monte Carlo simulations of systems consisting of over 27000 atoms to determine the equilibrium atomic microstructures. We study two types of alloy thermodynamic behavior: (a) under lattice incoherent conditions, the formation enthalpies are positive and thus the alloy system phase-separates below the miscibility-gap temperature TMG , (b) under lattice coherent conditions, the formation enthalpies can be negative and thus the alloy system exhibits ordering tendency. The microstructure is analyzed in terms of structural motifs (e.g., zigzag chains and InnGa4-nN tetrahedral clusters). The corresponding electronic structure, calculated with the empirical pseudopotentials method, is analyzed in terms of band-edge energies and wave-function localization. We find that the disordered alloys have no electronic localization but significant hole localization, while below the miscibility gap under the incoherent conditions, In-rich precipitates lead to strong electron and hole localization and a reduction in the band gap.

Effects of whistler mode hiss waves on the radiation belts structure during quiet times

NASA Astrophysics Data System (ADS)

Ripoll, J. F.; Santolik, O.; Reeves, G. D.; Kurth, W. S.; Denton, M.; Loridan, V.; Thaller, S. A.; Cunningham, G.; Kletzing, C.; Turner, D. L.; Henderson, M. G.; Ukhorskiy, S.; Drozdov, A.; Cervantes Villa, J. S.; Shprits, Y.

2017-12-01

We present dynamic Fokker-Planck simulations of the electron radiation belts and slot formation during the quiet days that can follow a storm. Simulations are made for all energies and L-shells between 2 and 6 in the view of recovering the observations of two particular events. Pitch angle diffusion is essential to energy structure of the belts and slot region. Pitch angle diffusion is computed from data-driven spatially and temporally-resolved whistler mode hiss wave and ambient plasma observations from the Van Allen Probes satellites. The simulations are performed either with a 3D formulation that uses pitch angle diffusion coefficients or with a simpler 1D Fokker-Planck equation based on losses computed from a lifetime. Validation is carried out globally against Magnetic Electron and Ion Spectrometer observations of the belts at all energy. Results are complemented with a sensitivity study involving different radial diffusion coefficients, electron lifetimes, and pitch angle diffusion coefficients. We discuss which models allow to recover the observed "S-shaped" energy-dependent inner boundary to the outer zone that results from the competition between diffusive radial transport and losses. Periods when the plasmasphere extends beyond L 5 favor long-lasting hiss losses from the outer belt. Through these simulations, we explain the full structure in energy and L-shell of the belts and the slot formation by hiss scattering during quiet storm recovery.

Black Box Real-Time Transient Absorption Spectroscopy and Electron Correlation

NASA Astrophysics Data System (ADS)

Parkhill, John

2017-06-01

We introduce an atomistic, all-electron, black-box electronic structure code to simulate transient absorption (TA) spectra and apply it to simulate pyrazole and a GFP- chromophore derivative1. The method is an application of OSCF2, our dissipative exten- sion of time-dependent density-functional theory. We compare our simulated spectra directly with recent ultra-fast spectroscopic experiments. We identify features in the TA spectra to Pauli-blocking which may be missed without a first-principles model. An important ingredient in this method is the stationary-TDDFT correction scheme recently put forwards by Fischer, Govind, and Cramer which allows us to overcome a limitation of adiabatic TDDFT. We demonstrate that OSCF2 is able to reproduce the energies of bleaches and induced absorptions, as well as the decay of the transient spectrum, with only the molecular structure as input. We show that the treatment of electron correlation is the biggest hurdle for TA simulations, which motivates the second half of the talk a new method for realtime electron correlation. We continue to derive and propagate self-consistent electronic dynamics. Extending our derivation of OSCF2 to include electron correlation we obtain a non-linear correlated one-body equation of motion which corrects TDHF. Similar equations are known in quantum kinetic theory, but rare in electronic structure. We introduce approximations that stabilize the theory and reduce its computational cost. We compare the resulting dynamics with well-known exact and approximate theories showing improvements over TDHF. When propagated EE2 changes occupation numbers like exact theory, an important feature missing from TDHF or TDDFT. We introduce a rotating wave approximation to reduce the scaling of the model to O(N^4), and enable propagation on realistically large systems. The equation-of-motion does not rely on a pure-state model for the electronic state, and could be used to study the relationship between electron correlation and relaxation/dephasing or as a non-adiabatic kernel for TDDFT. We show that a quasi-thermal Fermi-Dirac population of one-particle states is a stationary state of the method reached as the endpoint of propagation in some limits. We discuss this 'thermalization' of an isolated quantum many-body system in the context of the eigenstate thermalization hypothesis.

Ultrastructure Processing and Environmental Stability of Advanced Structural and Electronic Materials.

DTIC Science & Technology

1983-03-01

network dissolution, electron beam simulated desorption, electron signal decay, oxidation, oxide layer , growth kinetics, silicon carbide, assivation...surface layers on silicate glasses are reviewed. A type IIIB glass surface is proposed. The mechanisms of hydrothermal attack of two phase lithia...method to make reliable lifetime predictions. Use of electron beam techniques is essential for understanding surface layers formed on glasses (Section III

Electron holes observed in the Moon Plasma Wake

NASA Astrophysics Data System (ADS)

Hutchinson, I. H.; Malaspina, D.; Zhou, C.

2017-10-01

Electrostatic instabilities are predicted in the magnetized wake of plasma flowing past a non-magnetic absorbing object such as a probe or the moon. Analysis of the data from the Artemis satellites, now orbiting the moon at distances ten moon radii and less, shows very clear evidence of fast-moving isolated solitary potential structures causing bipolar electric field excursions as they pass the satellite's probes. These structures have all the hallmarks of electron holes: BGK solitons typically a few Debye-lengths in size, self-sustaining by a deficit of phase-space density on trapped orbits. Electron holes are now observed to be widespread in space plasmas. They have been observed in PIC simulations of the moon wake to be the non-linear consequence of the predicted electron instabilities. Simulations document hole prevalence, speed, length, and depth; and theory can explain many of these features from kinetic analysis. The solar wind wake is certainly the cause of the overwhelming majority of the holes observed by Artemis, because we observe almost all holes to be in or very near to the wake. We compare theory and simulation of the hole generation, lifetime, and transport mechanisms with observations. Work partially supported by NASA Grant NNX16AG82G.

Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3.

PubMed

Stashans, Arvids; Chamba, Gaston; Pinto, Henry

2008-02-01

The electronic structure, chemical bonding, geometry, and effects produced by Sr-doping in CaCO(3) have been studied on the basis of density-functional theory using the VASP simulation package and molecular-orbital theory utilizing the CLUSTERD computer code. Two calcium carbonate structures which occur naturally in anhydrous crystalline forms, calcite and aragonite, were considered in the present investigation. The obtained diagrams of density of states show similar patterns for both materials. The spatial structures are computed and analyzed in comparison to the available experimental data. The electronic properties and atomic displacements because of the trace element Sr-incorporation are discussed in a comparative manner for the two crystalline structures. (c) 2007 Wiley Periodicals, Inc.

Systematic research on Ag2X (X = O, S, Se, Te) as visible and near-infrared light driven photocatalysts and effects of their electronic structures

NASA Astrophysics Data System (ADS)

Jiang, Wei; Wu, Zhaomei; Zhu, Yingming; Tian, Wen; Liang, Bin

2018-01-01

Four silver chalcogen compounds, Ag2O, Ag2S, Ag2Se and Ag2Te, can be utilized as visible-light-driven photocatalysts. In this research, the electronic structures of these compounds were analyzed by simulation and experiments to systematically reveal the relationship between photocatalytic performance and energetic structure. All four chalcogenides exhibited interesting photocatalytic activities under ultraviolet, visible and near-infrared light. However, their photocatalytic performances and stability significantly depended on the band gap width, and the valence band and conduct band position, which was determined by their composition. Increasing the X atomic number from O to Te resulted in the upward movement of the valence band top and the conduct band bottom, which resulted in narrower band gaps, a wider absorption spectrum, a weaker photo-oxidization capacity, a higher recombination probability of hole and electron pairs, lower quantum efficiency, and worse stability. Among them, Ag2O has the highest photocatalytic performance and stability due to its widest band gap and lowest position of VB and CB. The combined action of photogenerated holes and different radicals, depending on the different electronic structures, including anion ozone radical, hydroxide radical, and superoxide radical, was observed and understood. The results of experimental observations and simulations of the four silver chalcogen compounds suggested that a proper electronic structure is necessary to obtain a balance between photocatalytic performance and absorbable light region in the development of new photocatalysts.

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

2015-08-01

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Fluid theory and simulations of instabilities, turbulent transport and coherent structures in partially-magnetized plasmas of \\mathbf{E}\\times \\mathbf{B} discharges

NASA Astrophysics Data System (ADS)

Smolyakov, A. I.; Chapurin, O.; Frias, W.; Koshkarov, O.; Romadanov, I.; Tang, T.; Umansky, M.; Raitses, Y.; Kaganovich, I. D.; Lakhin, V. P.

2017-01-01

Partially-magnetized plasmas with magnetized electrons and non-magnetized ions are common in Hall thrusters for electric propulsion and magnetron material processing devices. These plasmas are usually in strongly non-equilibrium state due to presence of crossed electric and magnetic fields, inhomogeneities of plasma density, temperature, magnetic field and beams of accelerated ions. Free energy from these sources make such plasmas prone to various instabilities resulting in turbulence, anomalous transport, and appearance of coherent structures as found in experiments. This paper provides an overview of instabilities that exist in such plasmas. A nonlinear fluid model has been developed for description of the Simon-Hoh, lower-hybrid and ion-sound instabilities. The model also incorporates electron gyroviscosity describing the effects of finite electron temperature. The nonlinear fluid model has been implemented in the BOUT++ framework. The results of nonlinear simulations are presented demonstrating turbulence, anomalous current and tendency toward the formation of coherent structures.

Switch-off slow shock/rotational discontinuity structures in collisionless magnetic reconnection: What to look for in satellite observations

NASA Astrophysics Data System (ADS)

Innocenti, M. E.; Cazzola, E.; Mistry, R.; Eastwood, J. P.; Goldman, M. V.; Newman, D. L.; Markidis, S.; Lapenta, G.

2017-04-01

In Innocenti et al. (2015) we have observed and characterized for the first time Petschek-like switch-off slow shock/rotational discontinuity (SO-SS/RD) compound structures in a 2-D fully kinetic simulation of collisionless magnetic reconnection. Observing these structures in the solar wind or in the magnetotail would corroborate the possibility that Petschek exhausts develop in collisionless media as a result of single X point collisionless reconnection. Here we highlight their signatures in simulations with the aim of easing their identification in observations. The most notable signatures include a four-peaked ion current profile in the out-of-plane direction, associated ion distribution functions, increased electron and ion anisotropy downstream the SS, and increased electron agyrotropy downstream the RDs.

Temperature dependence of the hydrated electron's excited-state relaxation. I. Simulation predictions of resonance Raman and pump-probe transient absorption spectra of cavity and non-cavity models

NASA Astrophysics Data System (ADS)

Zho, Chen-Chen; Farr, Erik P.; Glover, William J.; Schwartz, Benjamin J.

2017-08-01

We use one-electron non-adiabatic mixed quantum/classical simulations to explore the temperature dependence of both the ground-state structure and the excited-state relaxation dynamics of the hydrated electron. We compare the results for both the traditional cavity picture and a more recent non-cavity model of the hydrated electron and make definite predictions for distinguishing between the different possible structural models in future experiments. We find that the traditional cavity model shows no temperature-dependent change in structure at constant density, leading to a predicted resonance Raman spectrum that is essentially temperature-independent. In contrast, the non-cavity model predicts a blue-shift in the hydrated electron's resonance Raman O-H stretch with increasing temperature. The lack of a temperature-dependent ground-state structural change of the cavity model also leads to a prediction of little change with temperature of both the excited-state lifetime and hot ground-state cooling time of the hydrated electron following photoexcitation. This is in sharp contrast to the predictions of the non-cavity model, where both the excited-state lifetime and hot ground-state cooling time are expected to decrease significantly with increasing temperature. These simulation-based predictions should be directly testable by the results of future time-resolved photoelectron spectroscopy experiments. Finally, the temperature-dependent differences in predicted excited-state lifetime and hot ground-state cooling time of the two models also lead to different predicted pump-probe transient absorption spectroscopy of the hydrated electron as a function of temperature. We perform such experiments and describe them in Paper II [E. P. Farr et al., J. Chem. Phys. 147, 074504 (2017)], and find changes in the excited-state lifetime and hot ground-state cooling time with temperature that match well with the predictions of the non-cavity model. In particular, the experiments reveal stimulated emission from the excited state with an amplitude and lifetime that decreases with increasing temperature, a result in contrast to the lack of stimulated emission predicted by the cavity model but in good agreement with the non-cavity model. Overall, until ab initio calculations describing the non-adiabatic excited-state dynamics of an excess electron with hundreds of water molecules at a variety of temperatures become computationally feasible, the simulations presented here provide a definitive route for connecting the predictions of cavity and non-cavity models of the hydrated electron with future experiments.

Radiation from Accelerated Particles in Shocks and Reconnections

NASA Technical Reports Server (NTRS)

Nishikawa, K. I.; Choi, E. J.; Min, K. W.; Niemiec, J.; Zhang, B.; Hardee, P.; Mizuno, Y.; Medvedev, M.; Nordlund, A.; Frederiksen, J.;

Multicomponent kinetic simulation of Bernstein–Greene–Kruskal modes associated with ion acoustic and dust-ion acoustic excitations in electron-ion and dusty plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hosseini Jenab, S. M., E-mail: mehdi.jenab@yahoo.com; Kourakis, I., E-mail: IoannisKourakisSci@gmail.com

2014-04-15

A series of numerical simulations based on a recurrence-free Vlasov kinetic algorithm presented earlier [Abbasi et al., Phys. Rev. E 84, 036702 (2011)] are reported. Electron-ion plasmas and three-component (electron-ion-dust) dusty, or complex, plasmas are considered, via independent simulations. Considering all plasma components modeled through a kinetic approach, the nonlinear behavior of ionic scale acoustic excitations is investigated. The focus is on Bernstein–Greene–Kruskal (BGK) modes generated during the simulations. In particular, we aim at investigating the parametric dependence of the characteristics of BGK structures, namely of their time periodicity (τ{sub trap}) and their amplitude, on the electron-to-ion temperature ratio andmore » on the dust concentration. In electron-ion plasma, an exponential relation between τ{sub trap} and the amplitude of BGK modes and the electron-to-ion temperature ratio is observed. It is argued that both characteristics, namely, the periodicity τ{sub trap} and amplitude, are also related to the size of the phase-space vortex which is associated with BGK mode creation. In dusty plasmas, BGK modes characteristics appear to depend on the dust particle density linearly.« less

Effect of the lattice dynamics on the electronic structure of paramagnetic NiO within the disordered local moment picture

NASA Astrophysics Data System (ADS)

Mozafari, Elham; Alling, Björn; Belov, Maxim P.; Abrikosov, Igor A.

2018-01-01

Using the disordered local moments approach in combination with the ab initio molecular dynamics method, we simulate the behavior of a paramagnetic phase of NiO at finite temperatures to investigate the effect of magnetic disorder, thermal expansion, and lattice vibrations on its electronic structure. In addition, we study its lattice dynamics. We verify the reliability of our theoretical scheme via comparison of our results with available experiment and earlier theoretical studies carried out within static approximations. We present the phonon dispersion relations for the paramagnetic rock-salt (B1) phase of NiO and demonstrate that it is dynamically stable. We observe that including the magnetic disorder to simulate the paramagnetic phase has a small yet visible effect on the band gap. The amplitude of the local magnetic moment of Ni ions from our calculations for both antiferromagnetic and paramagnetic phases agree well with other theoretical and experimental values. We demonstrate that the increase of temperature up to 1000 K does not affect the electronic structure strongly. Taking into account the lattice vibrations and thermal expansion at higher temperatures have a major impact on the electronic structure, reducing the band gap from ˜3.5 eV at 600 K to ˜2.5 eV at 2000 K. We conclude that static lattice approximations can be safely employed in simulations of the paramagnetic state of NiO up to relatively high temperatures (˜1000 K), but as we get closer to the melting temperature vibrational effects become quite large and therefore should be included in the calculations.

Dynamics of Secondary Large-Scale Structures in ETG Turbulence Simulations

NASA Astrophysics Data System (ADS)

Li, Jiquan; Y, Kishimoto; Dong, Jiaqi; N, Miyato; T, Matsumoto

2006-01-01

The dynamics of secondary large-scale structures in electron-temperature-gradient (ETG) turbulence is investigated based on gyrofluid simulations in sheared slab geometry. It is found that structural bifurcation to zonal flow dominated or streamer-like states depends on the spectral anisotropy of turbulent ETG fluctuation, which is governed by the magnetic shear. The turbulent electron transport is suppressed by enhanced zonal flows. However, it is still low even if the streamer is formed in ETG turbulence with strong shears. It is shown that the low transport may be related to the secondary excitation of poloidal long-wavelength mode due to the beat wave of the most unstable components or a modulation instability. This large-scale structure with a low frequency and a long wavelength may saturate, or at least contribute to the saturation of ETG fluctuations through a poloidal mode coupling. The result suggests a low fluctuation level in ETG turbulence.

Effect of Structure and Disorder on the Charge Transport in Defined Self-Assembled Monolayers of Organic Semiconductors.

PubMed

Schmaltz, Thomas; Gothe, Bastian; Krause, Andreas; Leitherer, Susanne; Steinrück, Hans-Georg; Thoss, Michael; Clark, Timothy; Halik, Marcus

2017-09-26

Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising type of organic electronic device but also allow detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-π-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations allows us to characterize self-assembled monolayer (SAM) based devices in great detail. For this purpose, we have constructed transistors based on SAMs of two molecules that consist of the organic p-type semiconductor benzothieno[3,2-b][1]benzothiophene (BTBT), linked to a C 11 or C 12 alkylphosphonic acid. Both molecules form ordered SAMs; however, our experiments show that the size of the crystalline domains and the charge-transport properties vary considerably in the two systems. These findings were confirmed by molecular dynamics (MD) simulations and semiempirical molecular-orbital electronic-structure calculations, performed on snapshots from the MD simulations at different times, revealing, in atomistic detail, how the charge transport in organic semiconductors is influenced and limited by dynamic disorder.

Analysis of the structural, electronic and optic properties of Ni doped MgSiP{sub 2} semiconductor chalcopyrite compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kocak, Belgin, E-mail: koakbelgin@gmail.com; Ciftci, Yasemin Oztekin, E-mail: yasemin@gazi.edu.tr

2016-03-25

The structural, electronic band structure and optic properties of the Ni doped MgSiP{sub 2} chalcopyrite compound have been performed by using first-principles method in the density functional theory (DFT) as implemented in Vienna Ab-initio Simulation Package (VASP). The generalized gradient approximation (GGA) in the scheme of Perdew, Burke and Ernzerhof (PBE) is used for the exchange and correlation functional. The present lattice constant (a) follows generally the Vegard’s law. The electronic band structure, total and partial density of states (DOS and PDOS) are calculated. We present data for the frequency dependence of imaginary and real parts of dielectric functions ofmore » Ni doped MgSiP{sub 2}. For further investigation of the optical properties the reflectivity, refractive index, extinction coefficient and electron energy loss function are also predicted. Our obtained results indicate that the lattice constants, electronic band structure and optical properties of this compound are dependent on the substitution concentration of Ni.« less

Numerical simulation of current-free double layers created in a helicon plasma device

NASA Astrophysics Data System (ADS)

Rao, Sathyanarayan; Singh, Nagendra

2012-09-01

Two-dimensional simulations reveal that when radially confined source plasma with magnetized electrons and unmagnetized ions expands into diverging magnetic field B, a current-free double layer (CFDL) embedded in a conical density structure forms, as experimentally measured in the Australian helicon plasma device (HPD). The magnetized electrons follow the diverging B while the unmagnetized ions tend to flow directly downstream of the source, resulting in a radial electric field (E⊥) structure, which couples the ion and electron flows. Ions are transversely (radially) accelerated by E⊥ on the high potential side of the double layer in the CFDL. The accelerated ions are trapped near the conical surface, where E⊥ reverses direction. The potential structure of the CFDL is U-shaped and the plasma density is enhanced on the conical surface. The plasma density is severely depleted downstream of the parallel potential drop (φ||o) in the CFDL; the density depletion and the potential drop are related by quasi-neutrality condition, including the divergence in the magnetic field and in the plasma flow in the conical structure. The potential and density structures, the CFDL spatial size, its electric field strengths and the electron and ion velocities and energy distributions in the CFDL are found to be in good agreements with those measured in the Australian experiment. The applicability of our results to measured axial potential profiles in magnetic nozzle experiments in HPDs is discussed.

Acceleration of on-axis and ring-shaped electron beams in wakefields driven by Laguerre-Gaussian pulses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Guo-Bo; Key Laboratory for Laser Plasmas; Chen, Min, E-mail: minchen@sjtu.edu.cn, E-mail: yanyunma@126.com

2016-03-14

The acceleration of electron beams with multiple transverse structures in wakefields driven by Laguerre-Gaussian pulses has been studied through three-dimensional (3D) particle-in-cell simulations. Under different laser-plasma conditions, the wakefield shows different transverse structures. In general cases, the wakefield shows a donut-like structure and it accelerates the ring-shaped hollow electron beam. When a lower plasma density or a smaller laser spot size is used, besides the donut-like wakefield, a central bell-like wakefield can also be excited. The wake sets in the center of the donut-like wake. In this case, both a central on-axis electron beam and a ring-shaped electron beam aremore » simultaneously accelerated. Further, reducing the plasma density or laser spot size leads to an on-axis electron beam acceleration only. The research is beneficial for some potential applications requiring special pulse beam structures, such as positron acceleration and collimation.« less

Effects of front-surface target structures on properties of relativistic laser-plasma electrons.

PubMed

Jiang, S; Krygier, A G; Schumacher, D W; Akli, K U; Freeman, R R

2014-01-01

We report the results of a study of the role of prescribed geometrical structures on the front of a target in determining the energy and spatial distribution of relativistic laser-plasma electrons. Our three-dimensional particle-in-cell simulation studies apply to short-pulse, high-intensity laser pulses, and indicate that a judicious choice of target front-surface geometry provides the realistic possibility of greatly enhancing the yield of high-energy electrons while simultaneously confining the emission to narrow (<5°) angular cones.

Decomposition of L a 2 – x S r x Cu O 4 into several L a 2 O 3 phases at elevated temperatures in ultrahigh vacuum inside a transmission electron microscope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeong, Jong Seok; Wu, Wangzhou; Topsakal, Mehmet

Here, we report the decomposition of La 2–xSr xCuO 4 into La 2O 3 and Cu nanoparticles in ultrahigh vacuum, observed by in situ heating experiments in a transmission electron microscope. The analysis of electron diffraction data reveals that the phase decomposition process starts at about 150°C and is considerably expedited in the temperature range of 350°C–450°C. Two major resultant solid phases are identified as metallic Cu and La 2O 3 by electron diffraction, simulation, and electron energy-loss spectroscopy (EELS) analyses. With the aid of calculations, La 2O 3 phases are further identified to be derivatives of a fluorite structure—fluorite,more » pyrochlore, and (distorted) bixbyite—characterized by different oxygen-vacancy order. Additionally, the bulk plasmon energy and the fine structures of the O K and LaM 4,5 EELS edges are reported for these structures, along with simulated O K x-ray absorption near-edge structure. The resultant Cu nanoparticles and La 2O 3 phases remain unchanged after cooling to room temperature.« less

Decomposition of L a 2 – x S r x Cu O 4 into several L a 2 O 3 phases at elevated temperatures in ultrahigh vacuum inside a transmission electron microscope

DOE PAGES

Jeong, Jong Seok; Wu, Wangzhou; Topsakal, Mehmet; ...

2018-05-15

Here, we report the decomposition of La 2–xSr xCuO 4 into La 2O 3 and Cu nanoparticles in ultrahigh vacuum, observed by in situ heating experiments in a transmission electron microscope. The analysis of electron diffraction data reveals that the phase decomposition process starts at about 150°C and is considerably expedited in the temperature range of 350°C–450°C. Two major resultant solid phases are identified as metallic Cu and La 2O 3 by electron diffraction, simulation, and electron energy-loss spectroscopy (EELS) analyses. With the aid of calculations, La 2O 3 phases are further identified to be derivatives of a fluorite structure—fluorite,more » pyrochlore, and (distorted) bixbyite—characterized by different oxygen-vacancy order. Additionally, the bulk plasmon energy and the fine structures of the O K and LaM 4,5 EELS edges are reported for these structures, along with simulated O K x-ray absorption near-edge structure. The resultant Cu nanoparticles and La 2O 3 phases remain unchanged after cooling to room temperature.« less

Nightside Structure of the Venusian Ionosphere

NASA Astrophysics Data System (ADS)

Ledvina, S. A.; Brecht, S. H.

2017-12-01

The Pioneer Venus Orbiter, PVO, was the first mission to detect large-scale structure in the nightside region of Venus. This structure is often referred to as "tail rays." Since this discovery, there has been continuous discussion as to the cause of the structure. There have been theoretical attempts to explain the structure but no definitive determination of the mechanism. Typically, the wavelengths of the structure were not always consistent with the theory. Three-dimensional hybrid simulations are reported that produce structure on the nightside of Venus. The structure seems consistent with the data. This paper will present the results of the simulations as well as a variety of numerical tests that offer some insight into the mechanism driving the development of the structure. The tests reveal that the ambipolar electric fields as produced by the gradient of the electron pressure seems to be the root cause of the structure. It will be shown that different realizations of the neutral wind modify the structure. The hybrid simulations are three dimensional with neutral winds included in the simulations. The resolution of the simulation is 50 km/cell and lower. The spherical grid used in the simulations to handle chemistry and collisions has a resolution of 5 km radially and under 50 km in the angular directions. It is these high resolution simulations that produce the structure to be discussed in this paper.

The Radiation Belt Electron Scattering by Magnetosonic Wave: Dependence on Key Parameters

NASA Astrophysics Data System (ADS)

Lei, Mingda; Xie, Lun; Li, Jinxing; Pu, Zuyin; Fu, Suiyan; Ni, Binbin; Hua, Man; Chen, Lunjin; Li, Wen

2017-12-01

Magnetosonic (MS) waves have been found capable of creating radiation belt electron butterfly distributions in the inner magnetosphere. To investigate the physical nature of the interactions between radiation belt electrons and MS waves, and to explore a preferential condition for MS waves to scatter electrons efficiently, we performed a comprehensive parametric study of MS wave-electron interactions using test particle simulations. The diffusion coefficients simulated by varying the MS wave frequency show that the scattering effect of MS waves is frequency insensitive at low harmonics (f < 20 fcp), which has great implications on modeling the electron scattering caused by MS waves with harmonic structures. The electron scattering caused by MS waves is very sensitive to wave normal angles, and MS waves with off 90° wave normal angles scatter electrons more efficiently. By simulating the diffusion coefficients and the electron phase space density evolution at different L shells under different plasma environment circumstances, we find that MS waves can readily produce electron butterfly distributions in the inner part of the plasmasphere where the ratio of electron plasma-to-gyrofrequency (fpe/fce) is large, while they may essentially form a two-peak distribution outside the plasmapause and in the inner radiation belt where fpe/fce is small.

Theory and simulation of an inverse free-electron laser experiment

NASA Astrophysics Data System (ADS)

Gou, S. K.; Bhattacharjee, A.; Fang, J.-M.; Marshall, T. C.

1997-03-01

An experimental demonstration of the acceleration of electrons using a high-power CO2 laser interacting with a relativistic electron beam moving along a wiggler has been carried out at the Accelerator Test Facility of the Brookhaven National Laboratory [Phys. Rev. Lett. 77, 2690 (1996)]. The data generated by this inverse free-electron-laser (IFEL) experiment are studied by means of theory and simulation. Included in the simulations are such effects as: a low-loss metallic waveguide with a dielectric coating on the walls; multi-mode coupling due to self-consistent interaction between the electrons and the optical wave; space charge; energy spread of the electrons; and arbitrary wiggler-field profile. Two types of wiggler profile are considered: a linear taper of the period, and a step-taper of the period. (The period of the wiggler is ˜3 cm, its magnetic field is ˜1 T, and the wiggler length is 0.47 m.) The energy increment of the electrons (˜1-2%) is analyzed in detail as a function of laser power, wiggler parameters, and the initial beam energy (˜40 MeV). At a laser power level ˜0.5 Gw, the simulation results on energy gain are in reasonable agreement with the experimental results. Preliminary results on the electron energy distribution at the end of the IFEL are presented. Whereas the experiment produces a near-monotone distribution of electron energies with the peak shifted to higher energy, the simulation shows a more structured and non-monotonic distribution at the end of the wiggler. Effects that may help reconcile these differences are considered.

Kinetic simulation of edge instability in fusion plasmas

NASA Astrophysics Data System (ADS)

Fulton, Daniel Patrick

In this work, gyrokinetic simulations in edge plasmas of both tokamaks and field reversed. configurations (FRC) have been carried out using the Gyrokinetic Toroidal Code (GTC) and A New Code (ANC) has been formulated for cross-separatrix FRC simulation. In the tokamak edge, turbulent transport in the pedestal of an H-mode DIII-D plasma is. studied via simulations of electrostatic driftwaves. Annulus geometry is used and simulations focus on two radial locations corresponding to the pedestal top with mild pressure gradient and steep pressure gradient. A reactive trapped electron instability with typical ballooning mode structure is excited in the pedestal top. At the steep gradient, the electrostatic instability exhibits unusual mode structure, peaking at poloidal angles theta=+- pi/2. Simulations find this unusual mode structure is due to steep pressure gradients in the pedestal but not due to the particular DIII-D magnetic geometry. Realistic DIII-D geometry has a stabilizing effect compared to a simple circular tokamak geometry. Driftwave instability in FRC is studied for the first time using gyrokinetic simulation. GTC. is upgraded to treat realistic equilibrium calculated by an MHD equilibrium code. Electrostatic local simulations in outer closed flux surfaces find ion-scale modes are stable due to the large ion gyroradius and that electron drift-interchange modes are excited by electron temperature gradient and bad magnetic curvature. In the scrape-off layer (SOL) ion-scale modes are excited by density gradient and bad curvature. Collisions have weak effects on instabilities both in the core and SOL. Simulation results are consistent with density fluctuation measurements in the C-2 experiment using Doppler backscattering (DBS). The critical density gradients measured by the DBS qualitatively agree with the linear instability threshold calculated by GTC simulations. One outstanding critical issue in the FRC is the interplay between turbulence in the FRC. core and SOL regions. While the magnetic flux coordinates used by GTC provide a number of computational advantages, they present unique challenges at the magnetic field separatrix. To address this limitation, a new code, capable of coupled core-SOL simulations, is formulated, implemented, and successfully verified.

Structural analysis, electronic properties, and band gaps of a graphene nanoribbon: A new 2D materials

NASA Astrophysics Data System (ADS)

Dass, Devi

2018-03-01

Graphene nanoribbon (GNR), a new 2D carbon nanomaterial, has some unique features and special properties that offer a great potential for interconnect, nanoelectronic devices, optoelectronics, and nanophotonics. This paper reports the structural analysis, electronic properties, and band gaps of a GNR considering different chirality combinations obtained using the pz orbital tight binding model. In structural analysis, the analytical expressions for GNRs have been developed and verified using the simulation for the first time. It has been found that the total number of unit cells and carbon atoms within an overall unit cell and molecular structure of a GNR have been changed with the change in their chirality values which are similar to the values calculated using the developed analytical expressions thus validating both the simulation as well as analytical results. Further, the electronic band structures at different chirality values have been shown for the identification of metallic and semiconductor properties of a GNR. It has been concluded that all zigzag edge GNRs are metallic with very small band gaps range whereas all armchair GNRs show both the metallic and semiconductor nature with very small and high band gaps range. Again, the total number of subbands in each electronic band structure is equal to the total number of carbon atoms present in overall unit cell of the corresponding GNR. The semiconductors GNRs can be used as a channel material in field effect transistor suitable for advanced CMOS technology whereas the metallic GNRs could be used for interconnect.

LIGHT SOURCE: Physical design of a 10 MeV LINAC for polymer radiation processing

NASA Astrophysics Data System (ADS)

Feng, Guang-Yao; Pei, Yuan-Ji; Wang, Lin; Zhang, Shan-Cai; Wu, Cong-Feng; Jin, Kai; Li, Wei-Min

2009-06-01

In China, polymer radiation processing has become one of the most important processing industries. The radiation processing source may be an electron beam accelerator or a radioactive source. Physical design of an electron beam facility applied for radiation crosslinking is introduced in this paper because of it's much higher dose rate and efficiency. Main part of this facility is a 10 MeV travelling wave electron linac with constant impedance accelerating structure. A start to end simulation concerning the linac is reported in this paper. The codes Opera-3d, Poisson-superfish and Parmela are used to describe electromagnetic elements of the accelerator and track particle distribution from the cathode to the end of the linac. After beam dynamic optimization, wave phase velocities in the structure have been chosen to be 0.56, 0.9 and 0.999 respectively. Physical parameters about the main elements such as DC electron gun, iris-loaded periodic structure, solenoids, etc, are presented. Simulation results proves that it can satisfy the industrial requirement. The linac is under construction. Some components have been finished. Measurements proved that they are in a good agreement with the design values.

Perspective: Machine learning potentials for atomistic simulations

NASA Astrophysics Data System (ADS)

Behler, Jörg

2016-11-01

Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of the investigated problems, there is a constantly increasing need for simulations of more realistic, i.e., larger, model systems with improved accuracy. In many cases, the availability of sufficiently efficient interatomic potentials providing reliable energies and forces has become a serious bottleneck for performing these simulations. To address this problem, currently a paradigm change is taking place in the development of interatomic potentials. Since the early days of computer simulations simplified potentials have been derived using physical approximations whenever the direct application of electronic structure methods has been too demanding. Recent advances in machine learning (ML) now offer an alternative approach for the representation of potential-energy surfaces by fitting large data sets from electronic structure calculations. In this perspective, the central ideas underlying these ML potentials, solved problems and remaining challenges are reviewed along with a discussion of their current applicability and limitations.

Simulation of the 3-D Evolution of Electron Scale Magnetic Reconnection - Motivated by Laboratory Experiments Predictions for MMS

NASA Astrophysics Data System (ADS)

Buechner, J.; Jain, N.; Sharma, A.

2013-12-01

The four s/c of the Magnetospheric Multiscale (MMS) mission, to be launched in 2014, will use the Earth's magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes. One of them is magnetic reconnection, an essentially multi-scale process. While laboratory experiments and past theoretical investigations have shown that important processes necessary to understand magnetic reconnection take place at electron scales the MMS mission for the first time will be able to resolve these scales by in space observations. For the measurement strategy of MMS it is important to make specific predictions of the behavior of current sheets with a thickness of the order of the electron skin depth which play an important role in the evolution of collisionless magnetic reconnection. Since these processes are highly nonlinear and non-local numerical simulation is needed to specify the current sheet evolution. Here we present new results about the nonlinear evolution of electron-scale current sheets starting from the linear stage and using 3-D electron-magnetohydrodynamic (EMHD) simulations. The growth rates of the simulated instabilities compared well with the growth rates obtained from linear theory. Mechanisms and conditions of the formation of flux ropes and of current filamentation will be discussed in comparison with the results of fully kinetic simulations. In 3D the X- and O-point configurations of the magnetic field formed in reconnection planes alternate along the out-of-reconnection-plane direction with the wavelength of the unstable mode. In the presence of multiple reconnection sites, the out-of-plane magnetic field can develop nested structure of quadrupoles in reconnection planes, similar to the 2-D case, but now with variations in the out-of-plane direction. The structures of the electron flow and magnetic field in 3-D simulations will be compared with those in 2-D simulations to discriminate the essentially 3D features. We also discuss the influence of guide fields, as in the magnetopause case and show how the 3-D evolution of an electron current sheet is influenced the strength of the guide field. This is unlike the 2-D case where reconnection takes place only in a plane. This work was partially funded by the Max-Planck/Princeton Center for Plasma Physics and the National Science Foundation.

Investigations of glass structure using fluorescence line narrowing and moleuclar dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, M.J.; Brawer, S.A.

1982-07-02

The local structure at individual ion sites in simple and multicomponent glasses is simulated using methods of molecular dynamics. Computer simulations of fluoroberyllate glasses predict a range of ion separations and coordination numbers that increases with increasing complexity of the glass composition. This occurs at both glass forming and glass modifying cation sites. Laser-induced fluorescence line-narrowing techniques provide a unique probe of the local environments of selected subsets of ions and are used to measure site to site variations in the electronic energy levels and transition probabilities of rare earth ions. These and additional results from EXAFS, neutron and x-raymore » diffraction, and NMR experiments are compared with simulated glass structures.« less

Entire plasmas can be restructured when electrons are emitted from the boundaries

DOE PAGES

Campanell, M. D.

2015-04-14

It is well known that electron emission can restructure the thin sheaths at plasma-facing surfaces. But conventional models assume that the plasma's structure negligibly changes (the “presheath” is still thought to be governed by ion acceleration to the Bohm speed). Here, it is shown by theory and simulation that the presheath can take a fundamentally different structure where the emitted electrons entering the quasineutral region cause numerous changes. As a result, gradients of total plasma density, ion and electron pressures, and electric potential throughout the “inverted” presheath can carry different magnitudes, and opposite signs, from Bohm presheaths.

Output power fluctuations due to different weights of macro particles used in particle-in-cell simulations of Cerenkov devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Rong; Li, Yongdong; Liu, Chunliang

2016-07-15

The output power fluctuations caused by weights of macro particles used in particle-in-cell (PIC) simulations of a backward wave oscillator and a travelling wave tube are statistically analyzed. It is found that the velocities of electrons passed a specific slow-wave structure form a specific electron velocity distribution. The electron velocity distribution obtained in PIC simulation with a relative small weight of macro particles is considered as an initial distribution. By analyzing this initial distribution with a statistical method, the estimations of the output power fluctuations caused by different weights of macro particles are obtained. The statistical method is verified bymore » comparing the estimations with the simulation results. The fluctuations become stronger with increasing weight of macro particles, which can also be determined reversely from estimations of the output power fluctuations. With the weights of macro particles optimized by the statistical method, the output power fluctuations in PIC simulations are relatively small and acceptable.« less

Magnetic field enhanced resonant tunneling in a silicon nanowire single-electron-transistor.

PubMed

Aravind, K; Lin, M C; Ho, I L; Wu, C S; Kuo, Watson; Kuan, C H; Chang-Liao, K S; Chen, C D

2012-03-01

We report fabrication, measurement and simulation of silicon single-electron-transistors made on silicon-on-insulator wafers. At T-2 K, these devices showed clear Coulomb blockade structures. An external perpendicular magnetic field was found to enhance the resonant tunneling peak and was used to predict the presence of two laterally coupled quantum dots in the narrow constriction between the source-drain electrodes. The proposed model and measured experimental data were consistently explained using numerical simulations.

Analyzing indirect secondary electron contrast of unstained bacteriophage T4 based on SEM images and Monte Carlo simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogura, Toshihiko, E-mail: t-ogura@aist.go.jp

2009-03-06

The indirect secondary electron contrast (ISEC) condition of the scanning electron microscopy (SEM) produces high contrast detection with minimal damage of unstained biological samples mounted under a thin carbon film. The high contrast image is created by a secondary electron signal produced under the carbon film by a low acceleration voltage. Here, we show that ISEC condition is clearly able to detect unstained bacteriophage T4 under a thin carbon film (10-15 nm) by using high-resolution field emission (FE) SEM. The results show that FE-SEM provides higher resolution than thermionic emission SEM. Furthermore, we investigated the scattered electron area within themore » carbon film under ISEC conditions using Monte Carlo simulation. The simulations indicated that the image resolution difference is related to the scattering width in the carbon film and the electron beam spot size. Using ISEC conditions on unstained virus samples would produce low electronic damage, because the electron beam does not directly irradiate the sample. In addition to the routine analysis, this method can be utilized for structural analysis of various biological samples like viruses, bacteria, and protein complexes.« less

Structural optimization of structured carbon-based energy-storing composite materials used in space vehicles.

PubMed

Yu, Jia; Yu, Zhichao; Tang, Chenlong

2016-07-04

The hot work environment of electronic components in the instrument cabin of spacecraft was researched, and a new thermal protection structure, namely graphite carbon foam, which is an impregnated phase-transition material, was adopted to implement the thermal control on the electronic components. We used the optimized parameters obtained from ANSYS to conduct 2D optimization, 3-D modeling and simulation, as well as the strength check. Finally, the optimization results were verified by experiments. The results showed that after optimization, the structured carbon-based energy-storing composite material could reduce the mass and realize the thermal control over electronic components. This phase-transition composite material still possesses excellent temperature control performance after its repeated melting and solidifying.

DIFFUSIVE SHOCK ACCELERATION SIMULATIONS OF RADIO RELICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Hyesung; Ryu, Dongsu; Jones, T. W., E-mail: kang@uju.es.pusan.ac.kr, E-mail: ryu@canopus.cnu.ac.kr, E-mail: twj@msi.umn.edu

2012-09-01

Recent radio observations have identified a class of structures, so-called radio relics, in clusters of galaxies. The radio emission from these sources is interpreted as synchrotron radiation from GeV electrons gyrating in {mu}G-level magnetic fields. Radio relics, located mostly in the outskirts of clusters, seem to associate with shock waves, especially those developed during mergers. In fact, they seem to be good structures to identify and probe such shocks in intracluster media (ICMs), provided we understand the electron acceleration and re-acceleration at those shocks. In this paper, we describe time-dependent simulations for diffusive shock acceleration at weak shocks that aremore » expected to be found in ICMs. Freshly injected as well as pre-existing populations of cosmic-ray (CR) electrons are considered, and energy losses via synchrotron and inverse Compton are included. We then compare the synchrotron flux and spectral distributions estimated from the simulations with those in two well-observed radio relics in CIZA J2242.8+5301 and ZwCl0008.8+5215. Considering that CR electron injection is expected to be rather inefficient at weak shocks with Mach number M {approx}< a few, the existence of radio relics could indicate the pre-existing population of low-energy CR electrons in ICMs. The implication of our results on the merger shock scenario of radio relics is discussed.« less

3-D RPIC Simulations of Relativistic Jets: Particle Acceleration, Magnetic Field Generation, and Emission

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Mizuno, Y.; Hardee, P.; Hededal, C. B.; Fishman, G. J.

2006-01-01

Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets into ambient plasmas show that acceleration occurs in relativistic shocks. The Weibel instability created in shocks is responsible for particle acceleration, and generation and amplification of highly inhomogeneous, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection in relativistic jets. The "jitter" radiation from deflected electrons has different properties than the synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understand the complex time evolution and spectral structure in relativistic jets and gamma-ray bursts. We will present recent PIC simulations which show particle acceleration and magnetic field generation. We will also calculate associated self-consistent emission from relativistic shocks.

Secondary signal imaging (SSI) electron tomography (SSI-ET): A new three-dimensional metrology for mesoscale specimens in transmission electron microscope.

PubMed

Han, Chang Wan; Ortalan, Volkan

2015-09-01

We have demonstrated a new electron tomography technique utilizing the secondary signals (secondary electrons and backscattered electrons) for ultra thick (a few μm) specimens. The Monte Carlo electron scattering simulations reveal that the amount of backscattered electrons generated by 200 and 300keV incident electrons is a monotonic function of the sample thickness and this causes the thickness contrast satisfying the projection requirement for the tomographic reconstruction. Additional contribution of the secondary electrons emitted from the edges of the specimens enhances the visibility of the surface features. The acquired SSI tilt series of the specimen having mesoscopic dimensions are successfully reconstructed verifying that this new technique, so called the secondary signal imaging electron tomography (SSI-ET), can directly be utilized for 3D structural analysis of mesoscale structures. Published by Elsevier Ltd.

Optical bistability and second-harmonic generation in thin film coupled cavity photonic crystal structures

NASA Astrophysics Data System (ADS)

Diao, Liyong

This thesis deals with design, fabrication and modeling of bistable and multi-stable switching dynamics and second-harmonic generation in two groups of thin film coupled cavity photonic crystal structures. The first component studies optical bistability and multistability in such structures. Optical bistability and multistability are modelled by a nonlinear transfer matrix method. The second component is focused on the modelling and experimental measurement of second-harmonic generation in such structures. It is found that coupled cavity structures can reduce the threshold and index change for bistable operation, but single cavity structures can do the same. However, there is a clear advantage in using coupled cavity structures for multistability in that the threshold for multistability can be reduced. Second-harmonic generation is enhanced by field localization due to the resonant effect at the fundamental wavelength in single and coupled cavity structures by simulated and measured results. The work in this thesis makes three significant contributions. First, in the successful fabrication of thin film coupled cavity structures, the simulated linear transmissions of such structures match those of the fabricated structures almost exactly. Second, the newly defined figure of merit at the maximum transmission point on the bistable curve can be used to compare the material damage tolerance to any other Kerr effect nonlinear gate. Third, the simulated second-harmonic generation agrees excellently with experimental results. More generally optical thin film fabrication has commercial applications in many industry sections, such as electronics, opto-electronics, optical coating, solar cell and MEMS.

Simulation of decay processes and radiation transport times in radioactivity measurements

NASA Astrophysics Data System (ADS)

García-Toraño, E.; Peyres, V.; Bé, M.-M.; Dulieu, C.; Lépy, M.-C.; Salvat, F.

2017-04-01

The Fortran subroutine package PENNUC, which simulates random decay pathways of radioactive nuclides, is described. The decay scheme of the active nuclide is obtained from the NUCLEIDE database, whose web application has been complemented with the option of exporting nuclear decay data (possible nuclear transitions, branching ratios, type and energy of emitted particles) in a format that is readable by the simulation subroutines. In the case of beta emitters, the initial energy of the electron or positron is sampled from the theoretical Fermi spectrum. De-excitation of the atomic electron cloud following electron capture and internal conversion is described using transition probabilities from the LLNL Evaluated Atomic Data Library and empirical or calculated energies of released X rays and Auger electrons. The time evolution of radiation showers is determined by considering the lifetimes of nuclear and atomic levels, as well as radiation propagation times. Although PENNUC is designed to operate independently, here it is used in conjunction with the electron-photon transport code PENELOPE, and both together allow the simulation of experiments with radioactive sources in complex material structures consisting of homogeneous bodies limited by quadric surfaces. The reliability of these simulation tools is demonstrated through comparisons of simulated and measured energy spectra from radionuclides with complex multi-gamma spectra, nuclides with metastable levels in their decay pathways, nuclides with two daughters, and beta plus emitters.

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

2015-12-07

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Fortmann-Grote, C.; Bielecki, J.; Jurek, Z.; Santra, R.; Ziaja-Motyka, B.; Mancuso, A. P.

2017-08-01

We employ start-to-end simulations to model coherent diffractive imaging of single biomolecules using x-ray free electron lasers. This technique is expected to yield new structural information about biologically relevant macromolecules thanks to the ability to study the isolated sample in its natural environment as opposed to crystallized or cryogenic samples. The effect of the solvent on the diffraction pattern and interpretability of the data is an open question. We present first results of calculations where the solvent is taken into account explicitly. They were performed with a molecular dynamics scheme for a sample consisting of a protein and a hydration layer of varying thickness. Through R-factor analysis of the simulated diffraction patterns from hydrated samples, we show that the scattering background from realistic hydration layers of up to 3 Å thickness presents no obstacle for the resolution of molecular structures at the sub-nm level.

POSSIBLE EVIDENCE FOR A FISK-TYPE HELIOSPHERIC MAGNETIC FIELD. I. ANALYZING ULYSSES/KET ELECTRON OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sternal, O.; Heber, B.; Kopp, A.

The propagation of energetic charged particles in the heliospheric magnetic field is one of the fundamental problems in heliophysics. In particular, the structure of the heliospheric magnetic field remains an unsolved problem and is discussed as a controversial topic. The first successful analytic approach to the structure of the heliospheric magnetic field was the Parker field. However, the measurements of the Ulysses spacecraft at high latitudes revealed the possible need for refinements of the existing magnetic field model during solar minimum. Among other reasons, this led to the development of the Fisk field. This approach is highly debated and couldmore » not be ruled out with magnetic field measurements so far. A promising method to trace this magnetic field structure is to model the propagation of electrons in the energy range of a few MeV. Employing three-dimensional and time-dependent simulations of the propagation of energetic electrons, this work shows that the influence of a Fisk-type field on the particle transport in the heliosphere leads to characteristic variations of the electron intensities on the timescale of a solar rotation. For the first time it is shown that the Ulysses count rates of 2.5-7 MeV electrons contain the imprint of a Fisk-type heliospheric magnetic field structure. From a comparison of simulation results and the Ulysses count rates, realistic parameters for the Fisk theory are derived. Furthermore, these parameters are used to investigate the modeled relative amplitudes of protons and electrons, including the effects of drifts.« less

Investigating the interaction of x-ray free electron laser radiation with grating structure.

PubMed

Gaudin, Jérôme; Ozkan, Cigdem; Chalupský, Jaromír; Bajt, Saša; Burian, Tomáš; Vyšín, Ludek; Coppola, Nicola; Farahani, Shafagh Dastjani; Chapman, Henry N; Galasso, Germano; Hájková, Vera; Harmand, Marion; Juha, Libor; Jurek, Marek; Loch, Rolf A; Möller, Stefan; Nagasono, Mitsuru; Störmer, Michael; Sinn, Harald; Saksl, Karel; Sobierajski, Ryszard; Schulz, Joachim; Sovak, Pavol; Toleikis, Sven; Tiedtke, Kai; Tschentscher, Thomas; Krzywinski, Jacek

2012-08-01

The interaction of free electron laser pulses with grating structure is investigated using 4.6±0.1 nm radiation at the FLASH facility in Hamburg. For fluences above 63.7±8.7 mJ/cm2, the interaction triggers a damage process starting at the edge of the grating structure as evidenced by optical and atomic force microscopy. Simulations based on solution of the Helmholtz equation demonstrate an enhancement of the electric field intensity distribution at the edge of the grating structure. A procedure is finally deduced to evaluate damage threshold.

The Bravyi-Kitaev transformation for quantum computation of electronic structure

NASA Astrophysics Data System (ADS)

Seeley, Jacob T.; Richard, Martin J.; Love, Peter J.

2012-12-01

Quantum simulation is an important application of future quantum computers with applications in quantum chemistry, condensed matter, and beyond. Quantum simulation of fermionic systems presents a specific challenge. The Jordan-Wigner transformation allows for representation of a fermionic operator by O(n) qubit operations. Here, we develop an alternative method of simulating fermions with qubits, first proposed by Bravyi and Kitaev [Ann. Phys. 298, 210 (2002), 10.1006/aphy.2002.6254; e-print arXiv:quant-ph/0003137v2], that reduces the simulation cost to O(log n) qubit operations for one fermionic operation. We apply this new Bravyi-Kitaev transformation to the task of simulating quantum chemical Hamiltonians, and give a detailed example for the simplest possible case of molecular hydrogen in a minimal basis. We show that the quantum circuit for simulating a single Trotter time step of the Bravyi-Kitaev derived Hamiltonian for H2 requires fewer gate applications than the equivalent circuit derived from the Jordan-Wigner transformation. Since the scaling of the Bravyi-Kitaev method is asymptotically better than the Jordan-Wigner method, this result for molecular hydrogen in a minimal basis demonstrates the superior efficiency of the Bravyi-Kitaev method for all quantum computations of electronic structure.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

DOE PAGES

Fortmann-Grote, Carsten; Buzmakov, Alexey; Jurek, Zoltan; ...

2017-09-01

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. In conclusion, it is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

Probing plasma wakefields using electron bunches generated from a laser wakefield accelerator

NASA Astrophysics Data System (ADS)

Zhang, C. J.; Wan, Y.; Guo, B.; Hua, J. F.; Pai, C.-H.; Li, F.; Zhang, J.; Ma, Y.; Wu, Y. P.; Xu, X. L.; Mori, W. B.; Chu, H.-H.; Wang, J.; Lu, W.; Joshi, C.

2018-04-01

We show experimental results of probing the electric field structure of plasma wakes by using femtosecond relativistic electron bunches generated from a laser wakefield accelerator. Snapshots of laser-driven linear wakes in plasmas with different densities and density gradients are captured. The spatiotemporal evolution of the wake in a plasma density up-ramp is recorded. Two parallel wakes driven by a laser with a main spot and sidelobes are identified in the experiment and reproduced in simulations. The capability of this new method for capturing the electron- and positron-driven wakes is also shown via 3D particle-in-cell simulations.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fortmann-Grote, Carsten; Buzmakov, Alexey; Jurek, Zoltan

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. In conclusion, it is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

Electronic structure and magnetic properties of Pr-Co intermetallics: ab initio FP-LAPW calculations and correlation with experiments

NASA Astrophysics Data System (ADS)

Bakkari, Karim; Fersi, Riadh; Kebir Hlil, El; Bessais, Lotfi; Thabet Mliki, Najeh

2018-03-01

First-principle calculations combining density functional theory and the full-potential linearized augmented plane wave (FP-LAPW) method are performed to investigate the electronic and magnetic structure of Pr2Co7 in its two polymorphic forms, (2:7 H) and (2:7 R), for the first time. This type of calculation was also performed for PrCo5 and PrCo2 intermetallics. We have computed the valence density of states separately for spin-up and spin-down states in order to investigate the electronic band structure. This is governed by the strong contribution of the partial DOS of 3d-Co bands compared to the partial DOS of the 4f-Pr bands. Such a high ferromagnetic state is discussed in terms of the strong spin polarization observed in the total DOS. The magnetic moments carried by the Co and Pr atoms located in several sites for all compounds are computed. These results mainly indicate that cobalt atoms make a dominant contribution to the magnetic moments. The notable difference in the atomic moments of Pr and Co atoms between different structural slabs is explained in terms of the magnetic characteristics of the PrCo2 and PrCo5 compounds and the local chemical environments of the Pr and Co atoms in different structural slabs of Pr2Co7. From spin-polarized calculations we have simulated the 3d and 4f band population to estimate the local magnetic moments. These results are in accordance with the magnetic moments calculated using the FP-LAPW method. In addition, the exchange interactions J ij are calculated and used as input for M(T) simulations. Involving the data obtained from the electronic structure calculations, the appropriate Padé Table is applied to simulate the magnetization M(T) and to estimate the mean-field Curie temperature. We report a fairly good agreement between the ab initio calculation of magnetization and Curie temperature with the experimental data.

Ion irradiation to simulate neutron irradiation in model graphites: Consequences for nuclear graphite

NASA Astrophysics Data System (ADS)

Galy, N.; Toulhoat, N.; Moncoffre, N.; Pipon, Y.; Bérerd, N.; Ammar, M. R.; Simon, P.; Deldicque, D.; Sainsot, P.

2017-10-01

Due to its excellent moderator and reflector qualities, graphite was used in CO2-cooled nuclear reactors such as UNGG (Uranium Naturel-Graphite-Gaz). Neutron irradiation of graphite resulted in the production of 14C which is a key issue radionuclide for the management of the irradiated graphite waste. In order to elucidate the impact of neutron irradiation on 14C behavior, we carried out a systematic investigation of irradiation and its synergistic effects with temperature in Highly Oriented Pyrolitic Graphite (HOPG) model graphite used to simulate the coke grains of nuclear graphite. We used 13C implantation in order to simulate 14C displaced from its original structural site through recoil. The collision of the impinging neutrons with the graphite matrix carbon atoms induces mainly ballistic damage. However, a part of the recoil carbon atom energy is also transferred to the graphite lattice through electronic excitation. The effects of the different irradiation regimes in synergy with temperature were simulated using ion irradiation by varying Sn(nuclear)/Se(electronic) stopping power. Thus, the samples were irradiated with different ions of different energies. The structure modifications were followed by High Resolution Transmission Electron Microscopy (HRTEM) and Raman microspectrometry. The results show that temperature generally counteracts the disordering effects of irradiation but the achieved reordering level strongly depends on the initial structural state of the graphite matrix. Thus, extrapolating to reactor conditions, for an initially highly disordered structure, irradiation at reactor temperatures (200 - 500 °C) should induce almost no change of the initial structure. On the contrary, when the structure is initially less disordered, there should be a "zoning" of the reordering: In "cold" high flux irradiated zones where the ballistic damage is important, the structure should be poorly reordered; In "hot" low flux irradiated zones where the ballistic impact is lower and can therefore be counteracted by temperature, a better reordering of the structure should be achieved. Concerning 14C, except when located close to open pores where it can be removed through radiolytic corrosion, it tends to stabilize in the graphite matrix into sp2 or sp3 structures with variable proportions depending on the irradiation conditions.

Probing Twisted Magnetic Field Using Microwave Observations in an M Class Solar Flare on 11 February, 2014

NASA Astrophysics Data System (ADS)

Sharykin, I. N.; Kuznetsov, A. A.; Myshyakov, I. I.

2018-02-01

This work demonstrates the possibility of magnetic-field topology investigations using microwave polarimetric observations. We study a solar flare of GOES M1.7 class that occurred on 11 February, 2014. This flare revealed a clear signature of spatial inversion of the radio-emission polarization sign. We show that the observed polarization pattern can be explained by nonthermal gyrosynchrotron emission from the twisted magnetic structure. Using observations of the Reuven Ramaty High Energy Solar Spectroscopic Imager, Nobeyama Radio Observatory, Radio Solar Telescope Network, and Solar Dynamics Observatory, we have determined the parameters of nonthermal electrons and thermal plasma and identified the magnetic structure where the flare energy release occurred. To reconstruct the coronal magnetic field, we use nonlinear force-free field (NLFFF) and potential magnetic-field approaches. Radio emission of nonthermal electrons is simulated by the GX Simulator code using the extrapolated magnetic field and the parameters of nonthermal electrons and thermal plasma inferred from the observations; the model radio maps and spectra are compared with observations. We have found that the potential-magnetic-field approach fails to explain the observed circular polarization pattern; on the other hand, the Stokes-V map is successfully explained by assuming nonthermal electrons to be distributed along the twisted magnetic structure determined by the NLFFF extrapolation approach. Thus, we show that the radio-polarization maps can be used for diagnosing the topology of the flare magnetic structures where nonthermal electrons are injected.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Djidel, S.; Bouamar, M.; Khedrouche, D., E-mail: dkhedrouche@yahoo.com

This paper presents a performances study of UWB monopole antenna using half-elliptic radiator conformed on elliptical surface. The proposed antenna, simulated using microwave studio computer CST and High frequency simulator structure HFSS, is designed to operate in frequency interval over 3.1 to 40 GHz. Good return loss and radiation pattern characteristics are obtained in the frequency band of interest. The proposed antenna structure is suitable for ultra-wideband applications, which is, required for many wearable electronics applications.

Correlating structural dynamics and catalytic activity of AgAu nanoparticles with ultrafast spectroscopy and all-atom molecular dynamics simulations.

PubMed

Ferbonink, G F; Rodrigues, T S; Dos Santos, D P; Camargo, P H C; Albuquerque, R Q; Nome, R A

2018-05-29

In this study, we investigated hollow AgAu nanoparticles with the goal of improving our understanding of the composition-dependent catalytic activity of these nanoparticles. AgAu nanoparticles were synthesized via the galvanic replacement method with controlled size and nanoparticle compositions. We studied extinction spectra with UV-Vis spectroscopy and simulations based on Mie theory and the boundary element method, and ultrafast spectroscopy measurements to characterize decay constants and the overall energy transfer dynamics as a function of AgAu composition. Electron-phonon coupling times for each composition were obtained from pump-power dependent pump-probe transients. These spectroscopic studies showed how nanoscale surface segregation, hollow interiors and porosity affect the surface plasmon resonance wavelength and fundamental electron-phonon coupling times. Analysis of the spectroscopic data was used to correlate electron-phonon coupling times to AgAu composition, and thus to surface segregation and catalytic activity. We have performed all-atom molecular dynamics simulations of model hollow AgAu core-shell nanoparticles to characterize nanoparticle stability and equilibrium structures, besides providing atomic level views of nanoparticle surface segregation. Overall, the basic atomistic and electron-lattice dynamics of core-shell AgAu nanoparticles characterized here thus aid the mechanistic understanding and performance optimization of AgAu nanoparticle catalysts.

Kinematical simulation of robotic complex operation for implementing full-scale additive technologies of high-end materials, composites, structures, and buildings

NASA Astrophysics Data System (ADS)

Antsiferov, S. I.; Eltsov, M. Iu; Khakhalev, P. A.

2018-03-01

This paper considers a newly designed electronic digital model of a robotic complex for implementing full-scale additive technologies, funded under a Federal Target Program. The electronic and digital model was used to solve the problem of simulating the movement of a robotic complex using the NX CAD/CAM/CAE system. The virtual mechanism was built and the main assemblies, joints, and drives were identified as part of solving the problem. In addition, the maximum allowed printable area size was identified for the robotic complex, and a simulation of printing a rectangular-shaped article was carried out.

New concept of critical infrastructure strengthening

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gazizov, Talgat R.; Orlov, Pavel E.; Zabolotsky, Alexander M.

2016-06-08

Strengthening of critical infrastructure is considered. Modal reservation of electronics is proposed as a new concept of the strengthening. The concept combines a widely used cold backup and a recently proposed modal filtration. It makes electronics reliable as well as protected against electromagnetic interference, especially the ultra-wide band pulses. New printed circuit board structure is suggested for implementation of the proposed concept. Results of simulation in time and frequency domains are presented for the suggested structures. Considerable attenuation of dangerous excitations shows that the new concept and structure are promising.

Ultra-small rhenium clusters supported on graphene.

PubMed

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J; Mariscal, Marcelo M; Yacaman, Miguel José

2015-03-28

The adsorption of very small rhenium clusters (2-13 atoms) supported on graphene was studied by high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional theory calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones.

Ultra-small rhenium clusters supported on graphene

PubMed Central

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J.; Mariscal, Marcelo M.; Yacaman, Miguel José

2015-01-01

The adsorption of very small rhenium clusters (2 – 13 atoms) supported on graphene was studied with high annular dark field - scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones. PMID:25721176

The Inner Structure of Collisionless Magnetic Reconnection: The Electron-Frame Dissipation Measure and Hall Fields

NASA Technical Reports Server (NTRS)

Zenitani, Seiji; Hesse, Michael; Klimas, Alex; Black, Carrie; Kuznetsova, Masha

2011-01-01

It was recently proposed that the electron-frame dissipation measure, the energy transfer from the electromagnetic field to plasmas in the electron s rest frame, identifies the dissipation region of collisionless magnetic reconnection [Zenitani et al., Phys. Rev. Lett. 106, 195003 (2011)]. The measure is further applied to the electron-scale structures of antiparallel reconnection, by using two-dimensional particle-in-cell simulations. The size of the central dissipation region is controlled by the electron-ion mass ratio, suggesting that electron physics is essential. A narrow electron jet extends along the outflow direction until it reaches an electron shock. The jet region appears to be anti-dissipative. At the shock, electron heating is relevant to a magnetic cavity signature. The results are summarized to a unified picture of the single dissipation region in a Hall magnetic geometry.

The inner structure of collisionless magnetic reconnection: The electron-frame dissipation measure and Hall fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zenitani, Seiji; Hesse, Michael; Klimas, Alex

2011-12-15

It was recently proposed that the electron-frame dissipation measure, the energy transfer from the electromagnetic field to plasmas in the electron's rest frame, identifies the dissipation region of collisionless magnetic reconnection [Zenitani et al., Phys. Rev. Lett. 106, 195003 (2011)]. The measure is further applied to the electron-scale structures of antiparallel reconnection, by using two-dimensional particle-in-cell simulations. The size of the central dissipation region is controlled by the electron-ion mass ratio, suggesting that electron physics is essential. A narrow electron jet extends along the outflow direction until it reaches an electron shock. The jet region appears to be anti-dissipative. Atmore » the shock, electron heating is relevant to a magnetic cavity signature. The results are summarized to a unified picture of the single dissipation region in a Hall magnetic geometry.« less

Periodical plasma structures controlled by external magnetic field

NASA Astrophysics Data System (ADS)

Schweigert, I. V.; Keidar, M.

2017-11-01

The plasma of Hall thruster type in external magnetic field is studied in 2D3V kinetic simulations using PIC MCC method. The periodical structure with maxima of electron and ion densities is formed and becomes more pronounced with increase of magnetic field incidence angle in the plasma. These ridges of electron and ion densities are aligned with the magnetic field vector and shifted relative each other. This leads to formation of two-dimensional double-layers structure in cylindrical plasma chamber. Depending on Larmor radius and Debye length up to nineteen potential steps appear across the oblique magnetic field. The electrical current gathered on the wall is associated with the electron and ion density ridges.

Electronic and structural properties of B i2S e3:Cu

NASA Astrophysics Data System (ADS)

Sobczak, Kamil; Strak, Pawel; Kempisty, Pawel; Wolos, Agnieszka; Hruban, Andrzej; Materna, Andrzej; Borysiuk, Jolanta

2018-04-01

Electronic and structural properties of B i2S e3 and its extension to copper doped B i2S e3:Cu were studied using combined ab initio simulations and transmission electron microscopy based techniques, including electron energy loss spectroscopy, energy filtered transmission electron microscopy, and energy dispersive x-ray spectroscopy. The stability of the mixed phases was investigated for substitutional and intercalation changes of basic B i2S e3 structure. Four systems were compared: B i2S e3 , structures obtaining by Cu intercalation of the van der Waals gap, by substitution of Bi by Cu in quintuple layers, and C u2Se . The structures were identified and their electronic properties were obtained. Transmission electron microscopy measurements of B i2S e3 and the B i2S e3:Cu system identified the first structure as uniform and the second as composite, consisting of a nonuniform lower-Cu-content matrix and randomly distributed high-Cu-concentration precipitates. Critical comparison of the ab initio and experimental data identified the matrix as having a B i2S e3 dominant part with randomly distributed Cu-intercalated regions having 1Cu-B i2S e3 structure. The precipitates were determined to have 3Cu-B i2S e3 structure.

FEAST fundamental framework for electronic structure calculations: Reformulation and solution of the muffin-tin problem

NASA Astrophysics Data System (ADS)

Levin, Alan R.; Zhang, Deyin; Polizzi, Eric

2012-11-01

In a recent article Polizzi (2009) [15], the FEAST algorithm has been presented as a general purpose eigenvalue solver which is ideally suited for addressing the numerical challenges in electronic structure calculations. Here, FEAST is presented beyond the “black-box” solver as a fundamental modeling framework which can naturally address the original numerical complexity of the electronic structure problem as formulated by Slater in 1937 [3]. The non-linear eigenvalue problem arising from the muffin-tin decomposition of the real-space domain is first derived and then reformulated to be solved exactly within the FEAST framework. This new framework is presented as a fundamental and practical solution for performing both accurate and scalable electronic structure calculations, bypassing the various issues of using traditional approaches such as linearization and pseudopotential techniques. A finite element implementation of this FEAST framework along with simulation results for various molecular systems is also presented and discussed.

Geometrical effects on the electron residence time in semiconductor nano-particles.

PubMed

Koochi, Hakimeh; Ebrahimi, Fatemeh

2014-09-07

We have used random walk (RW) numerical simulations to investigate the influence of the geometry on the statistics of the electron residence time τ(r) in a trap-limited diffusion process through semiconductor nano-particles. This is an important parameter in coarse-grained modeling of charge carrier transport in nano-structured semiconductor films. The traps have been distributed randomly on the surface (r(2) model) or through the whole particle (r(3) model) with a specified density. The trap energies have been taken from an exponential distribution and the traps release time is assumed to be a stochastic variable. We have carried out (RW) simulations to study the effect of coordination number, the spatial arrangement of the neighbors and the size of nano-particles on the statistics of τ(r). It has been observed that by increasing the coordination number n, the average value of electron residence time, τ̅(r) rapidly decreases to an asymptotic value. For a fixed coordination number n, the electron's mean residence time does not depend on the neighbors' spatial arrangement. In other words, τ̅(r) is a porosity-dependence, local parameter which generally varies remarkably from site to site, unless we are dealing with highly ordered structures. We have also examined the effect of nano-particle size d on the statistical behavior of τ̅(r). Our simulations indicate that for volume distribution of traps, τ̅(r) scales as d(2). For a surface distribution of traps τ(r) increases almost linearly with d. This leads to the prediction of a linear dependence of the diffusion coefficient D on the particle size d in ordered structures or random structures above the critical concentration which is in accordance with experimental observations.

Emittance study of a 28 GHz electron cyclotron resonance ion source for the Rare Isotope Science Project superconducting linear accelerator.

PubMed

Park, Bum-Sik; Hong, In-Seok; Jang, Ji-Ho; Jin, Hyunchang; Choi, Sukjin; Kim, Yonghwan

2016-02-01

A 28 GHz electron cyclotron resonance (ECR) ion source is being developed for use as an injector for the superconducting linear accelerator of the Rare Isotope Science Project. Beam extraction from the ECR ion source has been simulated using the KOBRA3-INP software. The simulation software can calculate charged particle trajectories in three dimensional complex magnetic field structures, which in this case are formed by the arrangement of five superconducting magnets. In this study, the beam emittance is simulated to understand the effects of plasma potential, mass-to-charge ratio, and spatial distribution. The results of these simulations and their comparison to experimental results are presented in this paper.

Study of multipactor suppression of microwave components using perforated waveguide technology for space applications

NASA Astrophysics Data System (ADS)

Ye, Ming; Li, Yun; He, Yongning; Daneshmand, Mojgan

2017-05-01

With the development of space technology, microwave components with increased power handling capability and reduced weight have been urgently required. In this work, the perforated waveguide technology is proposed to suppress the multipactor effect of high power microwave components. Meanwhile, this novel method has the advantage of reducing components' weight, which makes it to have great potential in space applications. The perforated part of the waveguide components can be seen as an electron absorber (namely, its total electron emission yield is zero) since most of the electrons impacting on this part will go out of the components. Based on thoroughly benchmarked numerical simulation procedures, we simulated an S band and an X band waveguide transformer to conceptually verify this idea. Both electron dynamic simulations and electrical loss simulations demonstrate that the perforation technology can improve the multipactor threshold at least ˜8 dB while maintaining the acceptable insertion loss level compared with its un-perforated components. We also found that the component with larger minimum gap is easier to achieve multipactor suppression. This effect is interpreted by a parallel plate waveguide model. What's more, to improve the multipactor threshold of the X band waveguide transformer with a minimum gap of ˜0.1 mm, we proposed a perforation structure with the slope edge and explained its mechanism. Future study will focus on further optimization of the perforation structure, size, and distribution to maximize the comprehensive performances of microwave components.

Design of spherical electron gun for ultra high frequency, CW power inductive output tube

NASA Astrophysics Data System (ADS)

Kaushik, Meenu; Joshi, L. M.

2016-03-01

Inductive Output Tube (IOT) is an amplifier that usually operates in UHF range. It is an electron tube whose basic structure is similar to conventional vacuum devices. This device is widely used in broadcast applications but is now being explored for scientific applications also specifically, particle accelerators and fusion plasma heating purposes. The paper describes the design approach of a spherical gridded electron gun of a 500 MHz, 100 kW CW power IOT. The electron gun structure has been simulated and optimized for operating voltage and current of 40kV and 3.5 A respectively. The electromagnetic analysis of this spherical electron gun has been carried out in CST and TRAK codes.

Design of spherical electron gun for ultra high frequency, CW power inductive output tube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaushik, Meenu, E-mail: mkceeri@gmail.com; Joshi, L. M., E-mail: lmj1953@gmail.com; Academy of Scientific and Innovative Research

Inductive Output Tube (IOT) is an amplifier that usually operates in UHF range. It is an electron tube whose basic structure is similar to conventional vacuum devices. This device is widely used in broadcast applications but is now being explored for scientific applications also specifically, particle accelerators and fusion plasma heating purposes. The paper describes the design approach of a spherical gridded electron gun of a 500 MHz, 100 kW CW power IOT. The electron gun structure has been simulated and optimized for operating voltage and current of 40kV and 3.5 A respectively. The electromagnetic analysis of this spherical electron gunmore » has been carried out in CST and TRAK codes.« less

A conservative scheme for electromagnetic simulation of magnetized plasmas with kinetic electrons

NASA Astrophysics Data System (ADS)

Bao, J.; Lin, Z.; Lu, Z. X.

2018-02-01

A conservative scheme has been formulated and verified for gyrokinetic particle simulations of electromagnetic waves and instabilities in magnetized plasmas. An electron continuity equation derived from the drift kinetic equation is used to time advance the electron density perturbation by using the perturbed mechanical flow calculated from the parallel vector potential, and the parallel vector potential is solved by using the perturbed canonical flow from the perturbed distribution function. In gyrokinetic particle simulations using this new scheme, the shear Alfvén wave dispersion relation in the shearless slab and continuum damping in the sheared cylinder have been recovered. The new scheme overcomes the stringent requirement in the conventional perturbative simulation method that perpendicular grid size needs to be as small as electron collisionless skin depth even for the long wavelength Alfvén waves. The new scheme also avoids the problem in the conventional method that an unphysically large parallel electric field arises due to the inconsistency between electrostatic potential calculated from the perturbed density and vector potential calculated from the perturbed canonical flow. Finally, the gyrokinetic particle simulations of the Alfvén waves in sheared cylinder have superior numerical properties compared with the fluid simulations, which suffer from numerical difficulties associated with singular mode structures.

Simulations of Large-Area Electron Beam Diodes

NASA Astrophysics Data System (ADS)

Swanekamp, S. B.; Friedman, M.; Ludeking, L.; Smithe, D.; Obenschain, S. P.

1999-11-01

Large area electron beam diodes are typically used to pump the amplifiers of KrF lasers. Simulations of large-area electron beam diodes using the particle-in-cell code MAGIC3D have shown the electron flow in the diode to be unstable. Since this instability can potentially produce a non-uniform current and energy distribution in the hibachi structure and lasing medium it can be detrimental to laser efficiency. These results are similar to simulations performed using the ISIS code.(M.E. Jones and V.A. Thomas, Proceedings of the 8^th) International Conference on High-Power Particle Beams, 665 (1990). We have identified the instability as the so called ``transit-time" instability(C.K. Birdsall and W.B. Bridges, Electrodynamics of Diode Regions), (Academic Press, New York, 1966).^,(T.M. Antonsen, W.H. Miner, E. Ott, and A.T. Drobot, Phys. Fluids 27), 1257 (1984). and have investigated the role of the applied magnetic field and diode geometry. Experiments are underway to characterize the instability on the Nike KrF laser system and will be compared to simulation. Also some possible ways to mitigate the instability will be presented.

Band Gap Tuning in 2D Layered Materials by Angular Rotation.

PubMed

Polanco-Gonzalez, Javier; Carranco-Rodríguez, Jesús Alfredo; Enríquez-Carrejo, José L; Mani-Gonzalez, Pierre G; Domínguez-Esquivel, José Manuel; Ramos, Manuel

2017-02-08

We present a series of computer-assisted high-resolution transmission electron (HRTEM) simulations to determine Moiré patters by induced twisting effects between slabs at rotational angles of 3°, 5°, 8°, and 16°, for molybdenum disulfide, graphene, tungsten disulfide, and tungsten selenide layered materials. In order to investigate the electronic structure, a series of numerical simulations using density functional methods (DFT) methods was completed using Cambridge serial total energy package (CASTEP) with a generalized gradient approximation to determine both the band structure and density of states on honeycomb-like new superlattices. Our results indicated metallic transitions when the rotation approached 8° with respect to each other laminates for most of the two-dimensional systems that were analyzed.

Band Gap Tuning in 2D Layered Materials by Angular Rotation

PubMed Central

Polanco-Gonzalez, Javier; Carranco-Rodríguez, Jesús Alfredo; Enríquez-Carrejo, José L.; Mani-Gonzalez, Pierre G.; Domínguez-Esquivel, José Manuel; Ramos, Manuel

2017-01-01

We present a series of computer-assisted high-resolution transmission electron (HRTEM) simulations to determine Moiré patters by induced twisting effects between slabs at rotational angles of 3°, 5°, 8°, and 16°, for molybdenum disulfide, graphene, tungsten disulfide, and tungsten selenide layered materials. In order to investigate the electronic structure, a series of numerical simulations using density functional methods (DFT) methods was completed using Cambridge serial total energy package (CASTEP) with a generalized gradient approximation to determine both the band structure and density of states on honeycomb-like new superlattices. Our results indicated metallic transitions when the rotation approached 8° with respect to each other laminates for most of the two-dimensional systems that were analyzed. PMID:28772507

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

NASA Astrophysics Data System (ADS)

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

2016-03-01

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starrett, C. E.; Saumon, D.

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Improving the performance of AlGaN-based deep-ultraviolet light-emitting diodes using electron blocking layer with a heart-shaped graded Al composition

NASA Astrophysics Data System (ADS)

Kwon, M. R.; Park, T. H.; Lee, T. H.; Lee, B. R.; Kim, T. G.

2018-04-01

We propose a design for highly efficient AlGaN-based deep-ultraviolet light-emitting diodes (DUV LEDs) using a heart-shaped graded Al composition electron-blocking layer (EBL). This novel structure reduced downward band bending at the interface between the last quantum barrier and the EBL and flattened the electrostatic field in the interlayer between the barriers of the multi-quantum barrier EBL. Consequently, electron leakage was significantly suppressed and hole injection efficiency was found to have improved. The parameter values of simulation were extracted from the experimental data of the reference DUV LEDs. Using the SimuLED, we compared the electrical and optical properties of three structures with different Al compositions in the active region and the EBL. The internal quantum efficiency of the proposed structure was shown to exceed those of the reference DUV LEDs by a factor of 1.9. Additionally, the output power at 20 mA was found to increase by a factor of 2.1.

Electron Thermal Transport due to Magnetic Diffusion in the MST RFP

NASA Astrophysics Data System (ADS)

Reusch, J. A.; Anderson, J. K.; den Hartog, D. J.; Forest, C. B.; Kasten, C. P.; Schnack, D. D.; Stephens, H. D.

2011-10-01

Comparison of measurements made in the MST RFP to the results from extensive nonlinear resistive MHD simulations has provided two key observations. First, trapped particles reduce electron thermal diffusion; inclusion of this effect is required for quantitative agreement of simulation to measurement. Second, the structure and evolution of long-wavelength temperature fluctuations measured in MST shows remarkable qualitative similarity to fluctuations appearing in a finite-pressure simulation. These simulations were run at parameters matching those of 400 kA discharges in MST (S ~ 4 ×106). In a zero β simulation, the measured χe is compared to the thermal diffusion due to parallel losses along diffusing magnetic field lines, χst =v∥Dmag . Agreement is only found if the reduction in χst due to trapped particles is taken into account. In a second simulation, the pressure field was evolved self consistently assuming Ohmic heating and anisotropic thermal conduction. Fluctuations in the simulated temperature are very similar in character and time evolution to temperature fluctuations measured in MST. This includes m = 1 , n = 6 fluctuations that flatten the temperature profile as well as m = 1 , n = 5 fluctuations that generate hot island structures near the core shortly after sawtooth crashes. This work supported by the US DOE and NSF.

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.

PubMed

Caulfield, Thomas R; Devkota, Batsal; Rollins, Geoffrey C

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

Integral equation model for warm and hot dense mixtures.

PubMed

Starrett, C E; Saumon, D; Daligault, J; Hamel, S

2014-09-01

In a previous work [C. E. Starrett and D. Saumon, Phys. Rev. E 87, 013104 (2013)] a model for the calculation of electronic and ionic structures of warm and hot dense matter was described and validated. In that model the electronic structure of one atom in a plasma is determined using a density-functional-theory-based average-atom (AA) model and the ionic structure is determined by coupling the AA model to integral equations governing the fluid structure. That model was for plasmas with one nuclear species only. Here we extend it to treat plasmas with many nuclear species, i.e., mixtures, and apply it to a carbon-hydrogen mixture relevant to inertial confinement fusion experiments. Comparison of the predicted electronic and ionic structures with orbital-free and Kohn-Sham molecular dynamics simulations reveals excellent agreement wherever chemical bonding is not significant.

Fluid aspects of electron streaming instability in electron-ion plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jao, C.-S.; Hau, L.-N.; Department of Physics, National Central University, Jhongli, Taiwan

2014-02-15

Electrons streaming in a background electron and ion plasma may lead to the formation of electrostatic solitary wave (ESW) and hole structure which have been observed in various space plasma environments. Past studies on the formation of ESW are mostly based on the particle simulations due to the necessity of incorporating particle's trapping effects. In this study, the fluid aspects and thermodynamics of streaming instabilities in electron-ion plasmas including bi-streaming and bump-on-tail instabilities are addressed based on the comparison between fluid theory and the results from particle-in-cell simulations. The energy closure adopted in the fluid model is the polytropic lawmore » of d(pρ{sup −γ})/dt=0 with γ being a free parameter. Two unstable modes are identified for the bump-on-tail instability and the growth rates as well as the dispersion relation of the streaming instabilities derived from the linear theory are found to be in good agreement with the particle simulations for both bi-streaming and bump-on-tail instabilities. At the nonlinear saturation, 70% of the electrons are trapped inside the potential well for the drift velocity being 20 times of the thermal velocity and the pρ{sup −γ} value is significantly increased. Effects of ion to electron mass ratio on the linear fluid theory and nonlinear simulations are also examined.« less

Modelling of nanoscale quantum tunnelling structures using algebraic topology method

NASA Astrophysics Data System (ADS)

Sankaran, Krishnaswamy; Sairam, B.

2018-05-01

We have modelled nanoscale quantum tunnelling structures using Algebraic Topology Method (ATM). The accuracy of ATM is compared to the analytical solution derived based on the wave nature of tunnelling electrons. ATM provides a versatile, fast, and simple model to simulate complex structures. We are currently expanding the method for modelling electrodynamic systems.

Metallic hydrogen with a strong electron-phonon interaction at a pressure of 300-500 GPa

NASA Astrophysics Data System (ADS)

Degtyarenko, N. N.; Mazur, E. A.; Grishakov, K. S.

2017-08-01

Atomic metallic hydrogen with a lattice with FDDD symmetry is shown to have a stable phase under hydrostatic compression pressure in the range of 350-500 GPа. The resulting structure has a stable spectrum regarding the collapse of the phonons. Ab-unitio simulation method has been used to calculate the structural, electronic, phononic and other characteristics of the normal metallic phase of the hydrogen at a pressure of 350-500 GPA.

Electron acceleration via magnetic island coalescence

NASA Astrophysics Data System (ADS)

Shinohara, I.; Yumura, T.; Tanaka, K. G.; Fujimoto, M.

2009-06-01

Electron acceleration via fast magnetic island coalescence that happens as quick magnetic reconnection triggering (QMRT) proceeds has been studied. We have carried out a three-dimensional full kinetic simulation of the Harris current sheet with a large enough simulation run for two magnetic islands coalescence. Due to the strong inductive electric field associated with the non-linear evolution of the lower-hybrid-drift instability and the magnetic island coalescence process observed in the non-linear stage of the collisionless tearing mode, electrons are significantly accelerated at around the neutral sheet and the subsequent X-line. The accelerated meandering electrons generated by the non-linear evolution of the lower-hybrid-drift instability are resulted in QMRT, and QMRT leads to fast magnetic island coalescence. As a whole, the reconnection triggering and its transition to large-scale structure work as an effective electron accelerator.

Modeling of projection electron lithography

NASA Astrophysics Data System (ADS)

Mack, Chris A.

2000-07-01

Projection Electron Lithography (PEL) has recently become a leading candidate for the next generation of lithography systems after the successful demonstration of SCAPEL by Lucent Technologies and PREVAIL by IBM. These systems use a scattering membrane mask followed by a lens with limited angular acceptance range to form an image of the mask when illuminated by high energy electrons. This paper presents an initial modeling system for such types of projection electron lithography systems. Monte Carlo modeling of electron scattering within the mask structure creates an effective mask 'diffraction' pattern, to borrow the standard optical terminology. A cutoff of this scattered pattern by the imaging 'lens' provides an electron energy distribution striking the wafer. This distribution is then convolved with a 'point spread function,' the results of a Monte Carlo scattering calculation of a point beam of electrons striking the resist coated substrate and including the effects of beam blur. Resist exposure and development models from standard electron beam lithography simulation are used to simulate the final three-dimensional resist profile.

Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

PubMed

Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

2016-08-17

Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.

Relativistic electron scattering by magnetosonic waves: Effects of discrete wave emission and high wave amplitudes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Artemyev, A. V., E-mail: ante0226@gmail.com; Mourenas, D.; Krasnoselskikh, V. V.

2015-06-15

In this paper, we study relativistic electron scattering by fast magnetosonic waves. We compare results of test particle simulations and the quasi-linear theory for different spectra of waves to investigate how a fine structure of the wave emission can influence electron resonant scattering. We show that for a realistically wide distribution of wave normal angles θ (i.e., when the dispersion δθ≥0.5{sup °}), relativistic electron scattering is similar for a wide wave spectrum and for a spectrum consisting in well-separated ion cyclotron harmonics. Comparisons of test particle simulations with quasi-linear theory show that for δθ>0.5{sup °}, the quasi-linear approximation describes resonantmore » scattering correctly for a large enough plasma frequency. For a very narrow θ distribution (when δθ∼0.05{sup °}), however, the effect of a fine structure in the wave spectrum becomes important. In this case, quasi-linear theory clearly fails in describing accurately electron scattering by fast magnetosonic waves. We also study the effect of high wave amplitudes on relativistic electron scattering. For typical conditions in the earth's radiation belts, the quasi-linear approximation cannot accurately describe electron scattering for waves with averaged amplitudes >300 pT. We discuss various applications of the obtained results for modeling electron dynamics in the radiation belts and in the Earth's magnetotail.« less

Complementary Metal-Oxide-Silicon (CMOS)-Memristor Hybrid Nanoelectronics for Advanced Encryption Standard (AES) Encryption

DTIC Science & Technology

2016-04-01

with Al top electrodes and Cu bottom electrodes. ................... 9 Figure 4. SPICE netlist structure...memory elements play a part in logic gate. 4.4.2 Simulation SPICE Simulation Program for Integrated Circuits Emphasis ( SPICE ) is a general-purpose...analog circuit simulator that was developed at the Electronics Research Laboratory of the University of California, Berkeley [6]. In 1975, SPICE

Electron Source based on Superconducting RF

NASA Astrophysics Data System (ADS)

Xin, Tianmu

High-bunch-charge photoemission electron-sources operating in a Continuous Wave (CW) mode can provide high peak current as well as the high average current which are required for many advanced applications of accelerators facilities, for example, electron coolers for hadron beams, electron-ion colliders, and Free-Electron Lasers (FELs). Superconducting Radio Frequency (SRF) has many advantages over other electron-injector technologies, especially when it is working in CW mode as it offers higher repetition rate. An 112 MHz SRF electron photo-injector (gun) was developed at Brookhaven National Laboratory (BNL) to produce high-brightness and high-bunch-charge bunches for electron cooling experiments. The gun utilizes a Quarter-Wave Resonator (QWR) geometry for a compact structure and improved electron beam dynamics. The detailed RF design of the cavity, fundamental coupler and cathode stalk are presented in this work. A GPU accelerated code was written to improve the speed of simulation of multipacting, an important hurdle the SRF structure has to overcome in various locations. The injector utilizes high Quantum Efficiency (QE) multi-alkali photocathodes (K2CsSb) for generating electrons. The cathode fabrication system and procedure are also included in the thesis. Beam dynamic simulation of the injector was done with the code ASTRA. To find the optimized parameters of the cavities and beam optics, the author wrote a genetic algorithm Python script to search for the best solution in this high-dimensional parameter space. The gun was successfully commissioned and produced world record bunch charge and average current in an SRF photo-injector.

Investigations on the structure of the extracted ion beam from an electron cyclotron resonance ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spaedtke, P.; Lang, R.; Maeder, J.

2012-02-15

Using improved beam diagnostic tools, the structure of an ion beam extracted from an electron cyclotron resonance ion source (ECRIS) becomes visible. Especially viewing targets to display the beam profile and pepper pot devices for emittance measurements turned out to be very useful. On the contrary, diagnostic tools integrating over one space coordinate like wire harps for profile measurements or slit-slit devices, respectively slit-grid devices to measure the emittance might be applicable for beam transport investigations in a quadrupole channel, but are not very meaningful for investigations regarding the given ECRIS symmetry. Here we try to reproduce the experimentally foundmore » structure on the ion beam by simulation. For the simulation, a certain model has to be used to reproduce the experimental results. The model is also described in this paper.« less

Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

DOE PAGES

Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; ...

2016-10-21

Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li + to PC from water, based on electronicmore » structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li +/PF 6 - transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.« less

Structure and Composition of Isolated Core-Shell (In ,Ga )N /GaN Rods Based on Nanofocus X-Ray Diffraction and Scanning Transmission Electron Microscopy

NASA Astrophysics Data System (ADS)

Krause, Thilo; Hanke, Michael; Nicolai, Lars; Cheng, Zongzhe; Niehle, Michael; Trampert, Achim; Kahnt, Maik; Falkenberg, Gerald; Schroer, Christian G.; Hartmann, Jana; Zhou, Hao; Wehmann, Hergo-Heinrich; Waag, Andreas

2017-02-01

Nanofocus x-ray diffraction is used to investigate the structure and local strain field of an isolated (In ,Ga )N /GaN core-shell microrod. Because the high spatial resolution of the x-ray beam is only 80 ×90 nm2, we are able to investigate several distinct volumes on one individual side facet. Here, we find a drastic increase in thickness of the outer GaN shell along the rod height. Additionally, we performed high-angle annular dark-field scanning-transmission-electron-microscopy measurements on several rods from the same sample showing that (In,Ga)N double-quantum-well and GaN barrier thicknesses also increase strongly along the height. Moreover, plastic relaxation is observed in the top part of the rod. Based on the experimentally obtained structural parameters, we simulate the strain-induced deformation using the finite-element method, which serves as the input for subsequent kinematic scattering simulations. The simulations reveal a significant increase of elastic in-plane relaxation along the rod height. However, at a certain height, the occurrence of plastic relaxation yields a decrease of the elastic strain. Because of the experimentally obtained structural input for the finite-element simulations, we can exclude unknown structural influences on the strain distribution, and we are able to translate the elastic relaxation into an indium concentration which increases by a factor of 4 from the bottom to the height where plastic relaxation occurs.

Structural characterization and gas reactions of small metal particles by high-resolution TEM and TED

NASA Technical Reports Server (NTRS)

Heinemann, K.

1985-01-01

The interaction of 100 and 200 keV electron beams with amorphous alumina, titania, and aluminum nitride substrates and nanometer-size palladium particulate deposits was investigated for the two extreme cases of (1) large-area electron-beam flash-heating and (2) small-area high-intensity electron-beam irradiation. The former simulates a short-term heating effect with minimum electron irradiation exposure, the latter simulates high-dosage irradiation with minimum heating effect. All alumina and titania samples responded to the flash-heating treatment with significant recrystallization. However, the size, crystal structure, shape, and orientation of the grains depended on the type and thickness of the films and the thickness of the Pd deposit. High-dosage electron irradiation also readily crystallized the alumina substrate films but did not affect the titania films. The alumina recrystallization products were usually either all in the alpha phase, or they were a mixture of small grains in a number of low-temperature phases including gamma, delta, kappa, beta, theta-alumina. Palladium deposits reacted heavily with the alumina substrates during either treatment, but they were very little effected when supported on titania. Both treatments had the same, less prominent localized crystallization effect on aluminum nitride films.

Computational Evaluation of Amorphous Carbon Coating for Durable Silicon Anodes for Lithium-Ion Batteries

PubMed Central

Hwang, Jeongwoon; Ihm, Jisoon; Lee, Kwang-Ryeol; Kim, Seungchul

2015-01-01

We investigate the structural, mechanical, and electronic properties of graphite-like amorphous carbon coating on bulky silicon to examine whether it can improve the durability of the silicon anodes of lithium-ion batteries using molecular dynamics simulations and ab-initio electronic structure calculations. Structural models of carbon coating are constructed using molecular dynamics simulations of atomic carbon deposition with low incident energies (1–16 eV). As the incident energy decreases, the ratio of sp2 carbons increases, that of sp3 decreases, and the carbon films become more porous. The films prepared with very low incident energy contain lithium-ion conducting channels. Also, those films are electrically conductive to supplement the poor conductivity of silicon and can restore their structure after large deformation to accommodate the volume change during the operations. As a result of this study, we suggest that graphite-like porous carbon coating on silicon will extend the lifetime of the silicon anodes of lithium-ion batteries. PMID:28347087

Computational Evaluation of Amorphous Carbon Coating for Durable Silicon Anodes for Lithium-Ion Batteries.

PubMed

Hwang, Jeongwoon; Ihm, Jisoon; Lee, Kwang-Ryeol; Kim, Seungchul

2015-10-13

We investigate the structural, mechanical, and electronic properties of graphite-like amorphous carbon coating on bulky silicon to examine whether it can improve the durability of the silicon anodes of lithium-ion batteries using molecular dynamics simulations and ab-initio electronic structure calculations. Structural models of carbon coating are constructed using molecular dynamics simulations of atomic carbon deposition with low incident energies (1-16 eV). As the incident energy decreases, the ratio of sp ² carbons increases, that of sp ³ decreases, and the carbon films become more porous. The films prepared with very low incident energy contain lithium-ion conducting channels. Also, those films are electrically conductive to supplement the poor conductivity of silicon and can restore their structure after large deformation to accommodate the volume change during the operations. As a result of this study, we suggest that graphite-like porous carbon coating on silicon will extend the lifetime of the silicon anodes of lithium-ion batteries.

Ion-ion dynamic structure factor, acoustic modes, and equation of state of two-temperature warm dense aluminum

NASA Astrophysics Data System (ADS)

Harbour, L.; Förster, G. D.; Dharma-wardana, M. W. C.; Lewis, Laurent J.

2018-04-01

The ion-ion dynamical structure factor and the equation of state of warm dense aluminum in a two-temperature quasiequilibrium state, with the electron temperature higher than the ion temperature, are investigated using molecular-dynamics simulations based on ion-ion pair potentials constructed from a neutral pseudoatom model. Such pair potentials based on density functional theory are parameter-free and depend directly on the electron temperature and indirectly on the ion temperature, enabling efficient computation of two-temperature properties. Comparison with ab initio simulations and with other average-atom calculations for equilibrium aluminum shows good agreement, justifying a study of quasiequilibrium situations. Analyzing the van Hove function, we find that ion-ion correlations vanish in a time significantly smaller than the electron-ion relaxation time so that dynamical properties have a physical meaning for the quasiequilibrium state. A significant increase in the speed of sound is predicted from the modification of the dispersion relation of the ion acoustic mode as the electron temperature is increased. The two-temperature equation of state including the free energy, internal energy, and pressure is also presented.

Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xin, H.; LaRue, J.; Oberg, H.

2015-04-16

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distributionmore » and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.« less

Electronic and Thermoelectric Properties of Ternary Chalcohalide Semiconductors: First Principles Study

NASA Astrophysics Data System (ADS)

Khan, Wilayat; Hussain, Sajjad; Minar, Jan; Azam, Sikander

2018-02-01

Ternary chalcohalides have been widely utilized for different device applications. The thermoelectric properties of SbSI, SbSeI and SbSBr have been investigated by theoretical simulations, and the findings have been performed using BoltzTraP code, based on semi-classical Boltzmann transport theory. In this study, we simulated the electronic structures using the Englo-Vosko generalized gradient approximation employed in the WIEN2k program. From the electronic band structures, we found a combination of light and heavy bands around the Fermi level in the valence band, which strongly affect the effective masses of the carriers. The entire thermoelectric parameters, like the electrical, the electronic part of the thermal conductivities, the Seebeck coefficient and the power factor have been analysed as functions of temperature and chemical potential. The correlation between the effective masses and the thermoelectric properties is also included in the discussion because the effective mass reveals the mobility of the carriers which in turn affect the thermoelectric properties. The substitution of sulfur reveals high electrical conductivity and a smaller Seebeck coefficient based on effective mass leads to the increase in the power factor.

Electron diffraction study of the sillenites Bi{sub 12}SiO{sub 20}, Bi{sub 25}FeO{sub 39} and Bi{sub 25}InO{sub 39}: Evidence of short-range ordering of oxygen-vacancies in the trivalent sillenites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scurti, Craig A.; Arenas, D. J.; Auvray, Nicolas

We present an electron diffraction study of three sillenites, Bi{sub 12}SiO{sub 20}, Bi{sub 25}FeO{sub 39}, and Bi{sub 25}InO{sub 39} synthesized using the solid-state method. We explore a hypothesis, inspired by optical studies in the literature, that suggests that trivalent sillenites have additional disorder not present in the tetravalent compounds. Electron diffraction patterns of Bi{sub 25}FeO{sub 39} and Bi{sub 25}InO{sub 39} show streaks that confirm deviations from the ideal sillenite structure. Multi-slice simulations of electron-diffraction patterns are presented for different perturbations to the sillenite structure - partial substitution of the M site by Bi{sup 3+}, random and ordered oxygen-vacancies, and amore » frozen-phonon model. Although comparison of experimental data to simulations cannot be conclusive, we consider the streaks as evidence of short-range ordered oxygen-vacancies.« less

Study of Electron-scale Dissipation near the X-line During Magnetic Reconnection in a Laboratory Plasma

NASA Astrophysics Data System (ADS)

Ji, H.; Yoo, J.; Dorfman, S. E.; Jara-Almonte, J.; Yamada, M.; Swanson, C.; Daughton, W. S.; Roytershteyn, V.; Kuwahata, A.; Ii, T.; Inomoto, M.; Ono, Y.; von Stechow, A.; Grulke, O.; Phan, T.; Mozer, F.; Bale, S. D.

2013-12-01

Despite its disruptive influences on the large-scale structures of space and solar plasmas, the crucial topological changes and associated dissipation during magnetic reconnection take place only near an X-line within thin singular layers. In the modern collisionless models where electrons and ions are allowed to move separately, it has been predicted that ions exhaust efficiently through a thicker, ion-scale dissipative layer while mobile electrons can evacuate through a thinner, electron-scale dissipation layer, allowing for efficient release of magnetic energy. While ion dissipation layers have been frequently detected, the existence of election layers near the X-line and the associated dissipation structures and mechanisms are still an open question, and will be a main subject of the coming MMS mission. In this presentation, we will summarize our efforts in the past a few years to study electron-scale dissipation in a well-controlled and well-diagnosed reconnecting current sheet in a laboratory plasma, with close comparisons with the state-of-the-art, 2D and 3D fully kinetic simulations. Key results include: (1) positive identification of electromagnetic waves detected at the current sheet center as long wave-length, lower-hybrid drift instabilities (EM-LHDI), (2) however, there is strong evidence that this EM-LHDI cannot provide the required force to support the reconnection electric field, (3) detection of 3D flux-rope-like magnetic structures during impulsive reconnection events, and (4) electrons are heated through non-classical mechanisms near the X-line with a small but clear temperature anisotropy. These results, unfortunately, do not resolve the outstanding discrepancies on electron layer thickness between best available experiments and fully kinetic simulations. To make further progress, we are continuously pushing in the both experimental and numerical frontiers. Experimentally, we started investigations on EM-LHDI and electron heating as a function of guide field strength and symmetry of reconnection geometry, with new attempts to measure non-thermal electrons and higher frequency fluctuations. Numerically, we started investigations of kinetic simulations at realistic ratios of electron plasma frequency to cyclotron frequency, and also at realistic ratios of ion mass to electron mass. The most updated results of these new projects will be presented with discussions on the relevance to space observations.

Electron heating in the exhaust of magnetic reconnection with negligible guide field

NASA Astrophysics Data System (ADS)

Wang, Shan; Chen, Li-Jen; Bessho, Naoki; Kistler, Lynn M.; Shuster, Jason R.; Guo, Ruilong

2016-03-01

Electron heating in the magnetic reconnection exhaust is investigated with particle-in-cell simulations, space observations, and theoretical analysis. Spatial variations of the electron temperature (Te) and associated velocity distribution functions (VDFs) are examined and understood in terms of particle energization and randomization processes that vary with exhaust locations. Inside the electron diffusion region (EDR), the electron temperature parallel to the magnetic field (Te∥) exhibits a local minimum and the perpendicular temperature (Te⊥) shows a maximum at the current sheet midplane. In the intermediate exhaust downstream from the EDR and far from the magnetic field pileup region, Te⊥/Te∥ is close to unity and Te is approximately uniform, but the VDFs are structured: close to the midplane, VDFs are quasi-isotropic, whereas farther away from the midplane, VDFs exhibit field-aligned beams directed toward the midplane. In the far exhaust, Te generally increases toward the midplane and the pileup region, and the corresponding VDFs show counter-streaming beams. A distinct population with low v∥ and high v⊥ is prominent in the VDFs around the midplane. Test particle results show that the magnetic curvature near the midplane produces pitch angle scattering to generate quasi-isotropic distributions in the intermediate exhaust. In the far exhaust, electrons with initial high v∥ (v⊥) are accelerated mainly through curvature (gradient-B) drift opposite to the electric field, without significant pitch angle scattering. The VDF structures predicted by simulations are observed in magnetotail reconnection measurements, indicating that the energization mechanisms captured in the reported simulations are applicable to magnetotail reconnection with negligible guide field.

Efficient EM Simulation of GCPW Structures Applied to a 200-GHz mHEMT Power Amplifier MMIC

NASA Astrophysics Data System (ADS)

Campos-Roca, Yolanda; Amado-Rey, Belén; Wagner, Sandrine; Leuther, Arnulf; Bangert, Axel; Gómez-Alcalá, Rafael; Tessmann, Axel

2017-05-01

The behaviour of grounded coplanar waveguide (GCPW) structures in the upper millimeter-wave range is analyzed by using full-wave electromagnetic (EM) simulations. A methodological approach to develop reliable and time-efficient simulations is proposed by investigating the impact of different simplifications in the EM modelling and simulation conditions. After experimental validation with measurements on test structures, this approach has been used to model the most critical passive structures involved in the layout of a state-of-the-art 200-GHz power amplifier based on metamorphic high electron mobility transistors (mHEMTs). This millimeter-wave monolithic integrated circuit (MMIC) has demonstrated a measured output power of 8.7 dBm for an input power of 0 dBm at 200 GHz. The measured output power density and power-added efficiency (PAE) are 46.3 mW/mm and 4.5 %, respectively. The peak measured small-signal gain is 12.7 dB (obtained at 196 GHz). A good agreement has been obtained between measurements and simulation results.

Electronic and geometric structure of thin CoO(100) films studied by angle-resolved photoemission spectroscopy and Auger electron diffraction

NASA Astrophysics Data System (ADS)

Heiler, M.; Chassé, A.; Schindler, K.-M.; Hollering, M.; Neddermeyer, H.

2000-05-01

We have prepared ordered thin films of CoO by evaporating cobalt in an O 2 atmosphere on to a heated (500 K) Ag(100) substrate. The geometric and electronic structure of the films was characterized by means of Auger electron diffraction (AED) and angle-resolved photoemission spectroscopy (ARUPS), respectively. The experimental AED results were compared with simulated data, which showed that the film grows in (100) orientation on the Ag(100) substrate. Synchrotron-radiation-induced photoemission investigations were performed in the photon energy range from 25 eV to 67 eV. The dispersion of the transitions was found to be similar to that of previous results on a single-crystal CoO(100) surface. The resonance behaviour of the photoemission lines in the valence-band region was investigated by constant-initial-state (CIS) spectroscopy. The implications of this behaviour for assignment of the photoemission lines to specific electronic transitions is discussed and compared with published theoretical models of the electronic structure.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakanotani, Masaru; Matsukiyo, Shuichi; Hada, Tohru

A shock–shock interaction is investigated by using a one-dimensional full particle-in-cell simulation. The simulation reproduces the collision of two symmetrical high Mach number quasi-perpendicular shocks. The basic structure of the shocks and ion dynamics is similar to that obtained by previous hybrid simulations. The new aspects obtained here are as follows. Electrons are already strongly accelerated before the two shocks collide through multiple reflection. The reflected electrons self-generate waves upstream between the two shocks before they collide. The waves far upstream are generated through the right-hand resonant instability with the anomalous Doppler effect. The waves generated near the shock aremore » due to firehose instability and have much larger amplitudes than those due to the resonant instability. The high-energy electrons are efficiently scattered by the waves so that some of them gain large pitch angles. Those electrons can be easily reflected at the shock of the other side. The accelerated electrons form a power-law energy spectrum. Due to the accelerated electrons, the pressure of upstream electrons increases with time. This appears to cause the deceleration of the approaching shock speed. The accelerated electrons having sufficiently large Larmor radii are further accelerated through the similar mechanism working for ions when the two shocks are colliding.« less

Dielectric barrier structure with hollow electrodes and its recoil effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Shuang; Chen, Qunzhi; Liu, Jiahui

2015-06-15

A dielectric barrier structure with hollow electrodes (HEDBS), in which gas flow oriented parallel to the electric field, was proposed. Results showed that with this structure, air can be effectively ignited, forming atmospheric low temperature plasma, and the proposed HEDBS could achieve much higher electron density (5 × 10{sup 15}/cm{sup 3}). It was also found that the flow condition, including outlet diameter and flow rate, played a key role in the evolution of electron density. Optical emission spectroscopy diagnostic results showed that the concentration of reactive species had the same variation trend as the electron density. The simulated distribution of discharge gasmore » flow indicated that the HEDBS had a strong recoil effect on discharge gas, and could efficiently promote generating electron density as well as reactive species.« less

Design and simulation of a sub-terahertz folded-waveguide extended interaction oscillator

NASA Astrophysics Data System (ADS)

Liu, Wenxin; Zhang, Zhaochuan; Zhao, Chao; Guo, Xin; Liao, Suying

2017-06-01

In this paper, an interesting type of a two-section folded wave-guide (TSFW) slow wave structure (SWS) for the development of sub-Terahertz (sub-THz) extended interaction oscillator (EIO) is proposed. In this sub-THz device, the prebunching electron beam is produced by the TSFW SWS, which results in the enhancement of the output power. To verify this concept, the TSFW for sub-THz EIO is developed, which includes the design, simulation, and some fabrications. A small size of electron optics system (EOS), the TSFW SWS for beam-wave interactions, and the output structure are studied with simulations. Through the codes Egun and Superfish, the EOS is designed and optimized. With a help of CST studio and 3D particle-in-cell (PIC) simulation CHIPIC, the characteristics of beam-wave interaction generated by the TSFW are studied. The results of PIC simulation show that the output power is remarkably enhanced by a factor of 3, which exceeds 200 W at the frequency of 108 GHz. Based on the optimum parameters, the TSFW is manufactured with a high speed numerical mill, and the test transmission characteristic |S21| is 13 dB. At last, the output structure with a pill-box window is optimized, fabricated, integrated, and tested, and the result shows that the voltage standing-wave ratio of the window is about 2.2 at an operating frequency of 108 GHz. This design and simulation can provide an effective method to develop high power THz sources.

Structure and properties of microporous titanosilicate determined by first-principles calculations

NASA Astrophysics Data System (ADS)

Ching, W. Y.; Xu, Yong-Nian; Gu, Zong-Quan

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain.

Metastability of the atomic structures of size-selected gold nanoparticles

NASA Astrophysics Data System (ADS)

Wells, Dawn M.; Rossi, Giulia; Ferrando, Riccardo; Palmer, Richard E.

2015-04-01

All nanostructures are metastable - but some are more metastable than others. Here we employ aberration-corrected electron microscopy and atomistic computer simulations to demonstrate the hierarchy of metastability in deposited, size-selected gold nanoparticles (clusters), an archetypal class of nanomaterials well known for the catalytic activity which only appears on the nanometer-scale. We show that the atomic structures presented by ``magic number'' Au561, Au742 and Au923 clusters are ``locked''. They are in fact determined by the solidification which occurs from the liquid state early in their growth (by assembly from atoms in the gas phase) followed by template growth. It is quite likely that transitions from a locked, metastable configuration to a more stable (but still metastable) structure, as observed here under the electron beam, will occur during catalytic reactions, for example.All nanostructures are metastable - but some are more metastable than others. Here we employ aberration-corrected electron microscopy and atomistic computer simulations to demonstrate the hierarchy of metastability in deposited, size-selected gold nanoparticles (clusters), an archetypal class of nanomaterials well known for the catalytic activity which only appears on the nanometer-scale. We show that the atomic structures presented by ``magic number'' Au561, Au742 and Au923 clusters are ``locked''. They are in fact determined by the solidification which occurs from the liquid state early in their growth (by assembly from atoms in the gas phase) followed by template growth. It is quite likely that transitions from a locked, metastable configuration to a more stable (but still metastable) structure, as observed here under the electron beam, will occur during catalytic reactions, for example. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05811a

Sub-Auroral Polarization Stream (SAPS) Events Under Non-storm Conditions

NASA Astrophysics Data System (ADS)

Sazykin, S. Y.; Coster, A. J.; Huba, J.; Spiro, R. W.; Baker, J. B.; Kunduri, B.; Ruohoniemi, J. M.; Erickson, P. J.; Wolf, R.

2017-12-01

The occurrence of Sub-Auroral Polarization Stream, or SAPS, structures, defined here as latitudinally narrow channels of enhanced westward plasma convection in the evening ionosphere equatorward of the auroral electron precipitation boundary, is most dramatic during geomagnetic storms. However, SAPS-like structures known as Polarization Jets or SAIDs (Sub-Auroral Ion Drift events) are also frequently observed during non-storm conditions, typically during periods of isolated substorm activity or during bursts of enhanced convection associated with southward IMF Bz component. This paper presents results from data analysis and numerical simulations of several SAPS/SAID events observed during non-storm conditions. We use convection velocity measurements from the mid-latitude chain of SuperDARN radars and cross-track drift meter data from DMSP spacecraft to identify SAPS/SAID and to characterize their structure and temporal evolution. DMSP topside ion density data and high-resolution ground-based GPS total electron content (TEC) maps are used to determine the ionospheric and plasmaspheric morphology of SAPS regions. DMSP electron precipitation data are used to determine auroral boundaries. We also present simulation results of the chosen event intervals obtained with the SAMI3-RCM ionosphere-magnetosphere coupled model. Observational results are analyzed to identify systematic differences between non-storm SAPS/SAID and the picture that has emerged based on previous storm time studies. Simulation results are used to provide physical interpretation of these differences.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

PubMed Central

Buzmakov, Alexey; Jurek, Zoltan; Loh, Ne-Te Duane; Samoylova, Liubov; Santra, Robin; Schneidmiller, Evgeny A.; Tschentscher, Thomas; Yakubov, Sergey; Yoon, Chun Hong; Yurkov, Michael V.; Ziaja-Motyka, Beata; Mancuso, Adrian P.

2017-01-01

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs. PMID:28989713

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

NASA Astrophysics Data System (ADS)

Saez, David Adrian; Vöhringer-Martinez, Esteban

2015-10-01

S-Adenosylmethionine (AdoMet) is involved in many biological processes as cofactor in enzymes transferring its sulfonium methyl group to various substrates. Additionally, it is used as drug and nutritional supplement to reduce the pain in osteoarthritis and against depression. Due to the biological relevance of AdoMet it has been part of various computational simulation studies and will also be in the future. However, to our knowledge no rigorous force field parameter development for its simulation in biological systems has been reported. Here, we use electronic structure calculations combined with molecular dynamics simulations in explicit solvent to develop force field parameters compatible with the AMBER99 force field. Additionally, we propose new dynamic Hirshfeld-I atomic charges which are derived from the polarized electron density of AdoMet in aqueous solution to describe its electrostatic interactions in biological systems. The validation of the force field parameters and the atomic charges is performed against experimental interproton NOE distances of AdoMet in aqueous solution and crystal structures of AdoMet in the cavity of three representative proteins.

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

Electron coherent diffraction tomography of a nanocrystal

NASA Astrophysics Data System (ADS)

Dronyak, Roman; Liang, Keng S.; Tsai, Jin-Sheng; Stetsko, Yuri P.; Lee, Ting-Kuo; Chen, Fu-Rong

2010-05-01

Coherent diffractive imaging (CDI) with electron or x-ray sources is a promising technique for investigating the structure of nanoparticles down to the atomic scale. In electron CDI, a two-dimensional reconstruction is demonstrated using highly coherent illumination from a field-emission gun as a source of electrons. In a three-dimensional (3D) electron CDI, we experimentally determine the morphology of a single MgO nanocrystal using the Bragg diffraction geometry. An iterative algorithm is applied to invert the 3D diffraction pattern about a (200) reflection of the nanoparticle measured at an angular range of 1.8°. The results reveal a 3D image of the sample at ˜8 nm resolution, and agree with a simulation. Our work demonstrates an alternative approach to obtain the 3D structure of nanocrystals with an electron microscope.

Electron Debye scale Kelvin-Helmholtz instability: Electrostatic particle-in-cell simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sang-Yun; Lee, Ensang, E-mail: eslee@khu.ac.kr; Kim, Khan-Hyuk

2015-12-15

In this paper, we investigated the electron Debye scale Kelvin-Helmholtz (KH) instability using two-dimensional electrostatic particle-in-cell simulations. We introduced a velocity shear layer with a thickness comparable to the electron Debye length and examined the generation of the KH instability. The KH instability occurs in a similar manner as observed in the KH instabilities in fluid or ion scales producing surface waves and rolled-up vortices. The strength and growth rate of the electron Debye scale KH instability is affected by the structure of the velocity shear layer. The strength depends on the magnitude of the velocity and the growth ratemore » on the velocity gradient of the shear layer. However, the development of the electron Debye scale KH instability is mainly determined by the electric field generated by charge separation. Significant mixing of electrons occurs across the shear layer, and a fraction of electrons can penetrate deeply into the opposite side fairly far from the vortices across the shear layer.« less

Ab Initio Study of Electronic Excitation Effects on SrTiO 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

Interaction of energetic ions or lasers with solids often induces electronic excitations that may modify material properties significantly. In this study, effects of electronic excitations on strontium titanate SrTiO 3 (STO) are investigated based on first-principles calculations. The lattice structure, electronic properties, lattice vibrational frequencies, and dynamical stabilities are studied in detail. The results suggest that electronic excitation induces charge redistribution that is mainly observed in Ti–O bonds. The electronic band gap increases with increasing electronic excitation, as excitation mainly induces depopulation of Ti 3d states. Phonon analysis indicates that there is a large phonon band gap induced by electronicmore » excitation because of the changes in the vibrational properties of Ti and O atoms. In addition, a new peak appears in the phonon density of states with imaginary frequencies, an indication of lattice instability. Further dynamics simulations confirm that STO undergoes transition to an amorphous structure under strong electronic excitations. In conclusion, the optical properties of STO under electronic excitation are consistent with the evolution of atomic and electronic structures, which suggests a possibility to probe the properties of STO in nonequilibrium state using optical measurement.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proven to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

Ab Initio Study of Electronic Excitation Effects on SrTiO 3

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-11-14

Interaction of energetic ions or lasers with solids often induces electronic excitations that may modify material properties significantly. In this study, effects of electronic excitations on strontium titanate SrTiO 3 (STO) are investigated based on first-principles calculations. The lattice structure, electronic properties, lattice vibrational frequencies, and dynamical stabilities are studied in detail. The results suggest that electronic excitation induces charge redistribution that is mainly observed in Ti–O bonds. The electronic band gap increases with increasing electronic excitation, as excitation mainly induces depopulation of Ti 3d states. Phonon analysis indicates that there is a large phonon band gap induced by electronicmore » excitation because of the changes in the vibrational properties of Ti and O atoms. In addition, a new peak appears in the phonon density of states with imaginary frequencies, an indication of lattice instability. Further dynamics simulations confirm that STO undergoes transition to an amorphous structure under strong electronic excitations. In conclusion, the optical properties of STO under electronic excitation are consistent with the evolution of atomic and electronic structures, which suggests a possibility to probe the properties of STO in nonequilibrium state using optical measurement.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

PubMed

Lewis, Nicholas H C; Dong, Hui; Oliver, Thomas A A; Fleming, Graham R

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

Analysis on IGBT and Diode Failures in Distribution Electronic Power Transformers

NASA Astrophysics Data System (ADS)

Wang, Si-cong; Sang, Zi-xia; Yan, Jiong; Du, Zhi; Huang, Jia-qi; Chen, Zhu

2018-02-01

Fault characteristics of power electronic components are of great importance for a power electronic device, and are of extraordinary importance for those applied in power system. The topology structures and control method of Distribution Electronic Power Transformer (D-EPT) are introduced, and an exploration on fault types and fault characteristics for the IGBT and diode failures is presented. The analysis and simulation of different fault types for the fault characteristics lead to the D-EPT fault location scheme.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Yang; Liu, Zhiqiang, E-mail: lzq@semi.ac.cn, E-mail: spring@semi.ac.cn; Yi, Xiaoyan, E-mail: lzq@semi.ac.cn, E-mail: spring@semi.ac.cn

To evaluate electron leakage in InGaN/GaN multiple quantum well (MQW) light emitting diodes (LEDs), analytic models of ballistic and quasi-ballistic transport are developed. With this model, the impact of critical variables effecting electron leakage, including the electron blocking layer (EBL), structure of multiple quantum wells (MQWs), polarization field, and temperature are explored. The simulated results based on this model shed light on previously reported experimental observations and provide basic criteria for suppressing electron leakage, advancing the design of InGaN/GaN LEDs.

“Feathered” fractal surfaces to minimize secondary electron emission for a wide range of incident angles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swanson, Charles; Kaganovich, Igor D.

Complex structures on a material surface can significantly reduce the total secondary electron emission from that surface. The reduction occurs due to the capture of low-energy, true secondary electrons emitted at one point of the structure and intersecting another. We performed Monte Carlo calculations to demonstrate that fractal surfaces can reduce net secondary electron emission produced by the surface as compared to the flat surface. Specifically, we describe one surface, a “feathered” surface, which reduces the secondary electron emission yield more effectively than other previously considered configurations. Specifically, feathers grown onto a surface suppress secondary electron emission from shallow anglesmore » of incidence more effectively than velvet. Here, we find that, for the surface simulated, secondary electron emission yield remains below 20% of its un-suppressed value, even for shallow incident angles, where the velvet-only surface gives reduction factor of only 50%.« less

“Feathered” fractal surfaces to minimize secondary electron emission for a wide range of incident angles

DOE PAGES

Swanson, Charles; Kaganovich, Igor D.

2017-07-24

Complex structures on a material surface can significantly reduce the total secondary electron emission from that surface. The reduction occurs due to the capture of low-energy, true secondary electrons emitted at one point of the structure and intersecting another. We performed Monte Carlo calculations to demonstrate that fractal surfaces can reduce net secondary electron emission produced by the surface as compared to the flat surface. Specifically, we describe one surface, a “feathered” surface, which reduces the secondary electron emission yield more effectively than other previously considered configurations. Specifically, feathers grown onto a surface suppress secondary electron emission from shallow anglesmore » of incidence more effectively than velvet. Here, we find that, for the surface simulated, secondary electron emission yield remains below 20% of its un-suppressed value, even for shallow incident angles, where the velvet-only surface gives reduction factor of only 50%.« less

"Feathered" fractal surfaces to minimize secondary electron emission for a wide range of incident angles

NASA Astrophysics Data System (ADS)

Swanson, Charles; Kaganovich, Igor D.

2017-07-01

Complex structures on a material surface can significantly reduce the total secondary electron emission from that surface. The reduction occurs due to the capture of low-energy, true secondary electrons emitted at one point of the structure and intersecting another. We performed Monte Carlo calculations to demonstrate that fractal surfaces can reduce net secondary electron emission produced by the surface as compared to the flat surface. Specifically, we describe one surface, a "feathered" surface, which reduces the secondary electron emission yield more effectively than other previously considered configurations. Specifically, feathers grown onto a surface suppress secondary electron emission from shallow angles of incidence more effectively than velvet. We find that, for the surface simulated, secondary electron emission yield remains below 20% of its un-suppressed value, even for shallow incident angles, where the velvet-only surface gives reduction factor of only 50%.

Thermal Analysis of AlGaN/GaN High-Electron-Mobility Transistor and Its RF Power Efficiency Optimization with Source-Bridged Field-Plate Structure.

PubMed

Kwak, Hyeon-Tak; Chang, Seung-Bo; Jung, Hyun-Gu; Kim, Hyun-Seok

2018-09-01

In this study, we consider the relationship between the temperature in a two-dimensional electron gas (2-DEG) channel layer and the RF characteristics of an AlGaN/GaN high-electron-mobility transistor by changing the geometrical structure of the field-plate. The final goal is to achieve a high power efficiency by decreasing the channel layer temperature. First, simulations were performed to compare and contrast the experimental data of a conventional T-gate head structure. Then, a source-bridged field-plate (SBFP) structure was used to obtain the lower junction temperature in the 2-DEG channel layer. The peak electric field intensity was reduced, and a decrease in channel temperature resulted in an increase in electron mobility. Furthermore, the gate-to-source capacitance was increased by the SBFP structure. However, under the large current flow condition, the SBFP structure had a lower maximum temperature than the basic T-gate head structure, which improved the device electron mobility. Eventually, an optimum position of the SBFP was used, which led to higher frequency responses and improved the breakdown voltages. Hence, the optimized SBFP structure can be a promising candidate for high-power RF devices.

Periodical plasma structures controlled by external magnetic field

NASA Astrophysics Data System (ADS)

Schweigert, I. V.; Keidar, M.

2017-06-01

The characteristics of two-dimensional periodical structures in a magnetized plasma are studied using kinetic simulations. Ridges (i.e. spikes in electron and ion density) are formed and became more pronounced with an increase of magnetic field incidence angle in the plasma volume in the cylindrical chamber. These ridges are shifted relative to each other, which results in the formation of a two-dimensional double-layer structure. Depending on Larmor radius and Debye length up to 19 potential steps appear across the oblique magnetic field. The electrical current gathered into the channels is associated with the electron and ion density ridges.

FAST TRACK COMMUNICATION: Modelling of streamer propagation in atmospheric-pressure helium plasma jets

NASA Astrophysics Data System (ADS)

Naidis, G. V.

2010-10-01

The results of a two-dimensional numerical simulation of positive streamer propagation in atmospheric-pressure helium jets injected into ambient air are presented. It is shown that depending on the jet width and the initial radial distribution of electron number density streamer structures of two types can be formed: one with maxima of electric field and electron density at the jet axis and another with maxima of these parameters near the boundary between the jet and surrounding air. The latter structure is similar to the observed ring-shaped structures of plasma bullets.

Nanogap structures for molecular nanoelectronics.

PubMed

Motto, Paolo; Dimonte, Alice; Rattalino, Ismael; Demarchi, Danilo; Piccinini, Gianluca; Civera, Pierluigi

2012-02-09

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE PAGES

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

2018-03-22

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

NASA Astrophysics Data System (ADS)

Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

2018-05-01

One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

Particle-in-cell simulations of sheath formation around biased interconnectors in a low-earth-orbit plasma

NASA Technical Reports Server (NTRS)

Thiemann, H.; Schunk, R. W.

1990-01-01

The interaction between satellite solar arrays and the LEO plasma is presently studied with particle-in-cell simulations in which an electrical potential was suddenly applied to the solar cell interconnector. The consequent temporal response was followed for the real O(+)-electron mass ratio in the cases of 100- and 250-V solar cells, various solar cell thicknesses, and solar cells with secondary electron emission. Larger applied potentials and thinner solar cells lead to greater initial polarization surface charges, and therefore longer discharging and shielding times. When secondary electron emission from the cover glass is brought to bear, however, the potential structure is nearly planar, allowing constant interaction between plasma electrons and cover glass; a large fraction of the resulting secondary electrons is collected by the interconnector, constituting an order-of-magnitude increase in collected current.

Performances study of UWB monopole antennas using half-elliptic radiator conformed on elliptical surface

NASA Astrophysics Data System (ADS)

Djidel, S.; Bouamar, M.; Khedrouche, D.

2016-04-01

This paper presents a performances study of UWB monopole antenna using half-elliptic radiator conformed on elliptical surface. The proposed antenna, simulated using microwave studio computer CST and High frequency simulator structure HFSS, is designed to operate in frequency interval over 3.1 to 40 GHz. Good return loss and radiation pattern characteristics are obtained in the frequency band of interest. The proposed antenna structure is suitable for ultra-wideband applications, which is, required for many wearable electronics applications.

Assessment of electron propagator methods for the simulation of vibrationally-resolved valence and core photoionization spectra

PubMed Central

Baiardi, A.; Paoloni, L.; Barone, V.; Zakrzewski, V.G.; Ortiz, J.V.

2017-01-01

The analysis of photoelectron spectra is usually facilitated by quantum mechanical simulations. Due to the recent improvement of experimental techniques, the resolution of experimental spectra is rapidly increasing, and the inclusion of vibrational effects is usually mandatory to obtain a reliable reproduction of the spectra. With the aim of defining a robust computational protocol, a general time-independent formulation to compute different kinds of vibrationally-resolved electronic spectra has been generalized to support also photoelectron spectroscopy. The electronic structure data underlying the simulation are computed using different electron propagator approaches. In addition to the more standard approaches, a new and robust implementation of the second-order self-energy approximation of the electron propagator based on a transition operator reference (TOEP2) is presented. To validate our implementation, a series of molecules has been used as test cases. The result of the simulations shows that, for ultraviolet photoionization spectra, the more accurate non-diagonal approaches are needed to obtain a reliable reproduction of vertical ionization energies, but diagonal approaches are sufficient for energy gradients and pole strengths. For X-ray photoelectron spectroscopy, the TOEP2 approach, besides being more efficient, is also the most accurate in the reproduction of both vertical ionization energies and vibrationally-resolved bandshapes. PMID:28521087

Charge carrier mobility and electronic properties of Al(Op)3: impact of excimer formation

PubMed Central

Friederich, Pascal; Schäfer, Bernhard; Fattori, Valeria; Sun, Xiangnan; Strunk, Timo; Meded, Velimir; Hueso, Luis E; Wenzel, Wolfgang; Ruben, Mario

2015-01-01

Summary We have studied the electronic properties and the charge carrier mobility of the organic semiconductor tris(1-oxo-1H-phenalen-9-olate)aluminium(III) (Al(Op)3) both experimentally and theoretically. We experimentally estimated the HOMO and LUMO energy levels to be −5.93 and −3.26 eV, respectively, which were close to the corresponding calculated values. Al(Op)3 was successfully evaporated onto quartz substrates and was clearly identified in the absorption spectra of both the solution and the thin film. A structured steady state fluorescence emission was detected in solution, whereas a broad, red-shifted emission was observed in the thin film. This indicates the formation of excimers in the solid state, which is crucial for the transport properties. The incorporation of Al(Op)3 into organic thin film transistors (TFTs) was performed in order to measure the charge carrier mobility. The experimental setup detected no electron mobility, while a hole mobility between 0.6 × 10−6 and 2.1 × 10−6 cm2·V−1·s−1 was measured. Theoretical simulations, on the other hand, predicted an electron mobility of 9.5 × 10−6 cm2·V−1·s−1 and a hole mobility of 1.4 × 10−4 cm2·V−1·s−1. The theoretical simulation for the hole mobility predicted an approximately one order of magnitude higher hole mobility than was observed in the experiment, which is considered to be in good agreement. The result for the electron mobility was, on the other hand, unexpected, as both the calculated electron mobility and chemical common sense (based on the capability of extended aromatic structures to efficiently accept and delocalize additional electrons) suggest more robust electron charge transport properties. This discrepancy is explained by the excimer formation, whose inclusion in the multiscale simulation workflow is expected to bring the theoretical simulation and experiment into agreement. PMID:26171287

Study of neoclassical effects on the pedestal structure in ELMy H-mode plasmas

NASA Astrophysics Data System (ADS)

Pankin, A. Y.; Bateman, G.; Kritz, A. H.; Rafiq, T.; Park, G. Y.; Ku, S.; Chang, C. S.; Snyder, P. B.

2009-11-01

The neoclassical effects on the H-mode pedestal structure are investigated in this study. First principles' kinetic simulations of the neoclassical pedestal dynamics are combined with the MHD stability conditions for triggering ELM crashes that limit the pedestal width and height in H-mode plasmas. The neoclassical kinetic XGC0 code [1] is used to produce systematic scans over plasma parameters including plasma current, elongation, and triangularity. As plasma profiles evolve, the MHD stability limits of these profiles are analyzed with the ideal MHD stability ELITE code [2]. The scalings of the pedestal width and height are presented as a function of the scanned plasma parameters. Simulations with the XGC0 code, which include coupled ion-electron dynamics, yield predictions for both ion and electron pedestal profiles. Differences in the electron and ion pedestal scalings are investigated. [1] C.S. Chang et al, Phys. Plasmas 11 (2004) 2649. [2] P.B. Snyder et al, Phys. Plasmas, 9 (2002) 2037.

Investigating fold structures of 2D materials by quantitative transmission electron microscopy.

PubMed

Wang, Zhiwei; Zhang, Zengming; Liu, Wei; Wang, Zhong Lin

2017-04-01

We report an approach developed for deriving 3D structural information of 2D membrane folds based on the recently-established quantitative transmission electron microscopy (TEM) in combination with density functional theory (DFT) calculations. Systematic multislice simulations reveal that the membrane folding leads to sufficiently strong electron scattering which enables a precise determination of bending radius. The image contrast depends also on the folding angles of 2D materials due to the variation of projection potentials, which however exerts much smaller effect compared with the bending radii. DFT calculations show that folded edges are typically characteristic of (fractional) nanotubes with the same curvature retained after energy optimization. Owing to the exclusion of Stobbs factor issue, numerical simulations were directly used in comparison with the experimental measurements on an absolute contrast scale, which results in a successful determination of bending radius of folded monolayer MoS 2 films. The method should be applicable to characterizing all 2D membranes with 3D folding features. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simulation and modeling of whistler mode wave growth through cyclotron resonance with energetic electrons in the magnetosphere

NASA Astrophysics Data System (ADS)

Carlson, Curtis Ray

New models and simulations of wave growth experienced by electromagnetic waves propagating through the magnetosphere in the whistler mode are presented. The main emphasis is to simulate single frequency wave pulses, in the 2 to 6 kHz range, that have been injected into the magnetosphere, near L approximately 4. Simulations using a new transient model reproduce exponential wave growth and saturation coincident with a linearly increasing frequency versus time (up to 60 Hz/s). Unique methods for calculating the phased bunched currents, stimulated radiation, and radiation propagation are based upon test particle trajectories calculated by integrating nonlinear equations of motion generalized to allow the evolution of the frequency and wave number at each point in space. Results show the importance of the transient aspects in the wave growth process. The wave growth established as the wave propagates toward the equator is given a spatially advancing wave phase structure by the geomagnetic inhomogeneity. Through the feedback of this radiation upon other electrons, the conditions are set up which result in the linearly increasing output frequency with time. The transient simulations also show that features like growth rate and total growth are simply related to the various parameters, such as applied wave intensity, energetic electron flux, and energetic electron distribution.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 4-acetylpyridine

NASA Astrophysics Data System (ADS)

Atilgan, A.; Yurdakul, Ş.; Erdogdu, Y.; Güllüoğlu, M. T.

2018-06-01

The spectroscopic (UV-Vis and infrared), structural and some electronic property observations of the 4-acetylpyridine (4-AP) were reported, which are investigated by using some spectral methods and DFT calculations. FT-IR spectra were obtained for 4-AP at room temperature in the region 4000 cm-1- 400 cm-1. In the DFT calculations, the B3LYP functional with 6-311G++G(d,p) basis set was applied to carry out the quantum mechanical calculations. The Fourier Transform Infrared (FT-IR) and FT-Raman spectra were interpreted by using of normal coordinate analysis based on scaled quantum mechanical force field. The present work expands our understanding of the both the vibrational and structural properties as well as some electronic properties of the 4-AP by means of the theoretical and experimental methods.

Fast Plasma Instrument for MMS: Simulation Results

NASA Technical Reports Server (NTRS)

Figueroa-Vinas, Adolfo; Adrian, Mark L.; Lobell, James V.; Simpson, David G.; Barrie, Alex; Winkert, George E.; Yeh, Pen-Shu; Moore, Thomas E.

2008-01-01

Magnetospheric Multiscale (MMS) mission will study small-scale reconnection structures and their rapid motions from closely spaced platforms using instruments capable of high angular, energy, and time resolution measurements. The Dual Electron Spectrometer (DES) of the Fast Plasma Instrument (FPI) for MMS meets these demanding requirements by acquiring the electron velocity distribution functions (VDFs) for the full sky with high-resolution angular measurements every 30 ms. This will provide unprecedented access to electron scale dynamics within the reconnection diffusion region. The DES consists of eight half-top-hat energy analyzers. Each analyzer has a 6 deg. x 11.25 deg. Full-sky coverage is achieved by electrostatically stepping the FOV of each of the eight sensors through four discrete deflection look directions. Data compression and burst memory management will provide approximately 30 minutes of high time resolution data during each orbit of the four MMS spacecraft. Each spacecraft will intelligently downlink the data sequences that contain the greatest amount of temporal structure. Here we present the results of a simulation of the DES analyzer measurements, data compression and decompression, as well as ground-based analysis using as a seed re-processed Cluster/PEACE electron measurements. The Cluster/PEACE electron measurements have been reprocessed through virtual DES analyzers with their proper geometrical, energy, and timing scale factors and re-mapped via interpolation to the DES angular and energy phase-space sampling measurements. The results of the simulated DES measurements are analyzed and the full moments of the simulated VDFs are compared with those obtained from the Cluster/PEACE spectrometer using a standard quadrature moment, a newly implemented spectral spherical harmonic method, and a singular value decomposition method. Our preliminary moment calculations show a remarkable agreement within the uncertainties of the measurements, with the results obtained by the Cluster/PEACE electron spectrometers. The data analyzed was selected because it represented a potential reconnection event as currently published.

Adele Tamboli | NREL

Science.gov Websites

Carlo simulations of disorder in ZnSnN2 and the effects on the electronic structure," Physical Review Materials, 2017 "Effects of Hydrogen on Acceptor Activation in Ternary Nitride Semiconductors

Hybrid platforms of graphane-graphene 2D structures: prototypes for atomically precise nanoelectronics.

PubMed

Mota, F de B; Rivelino, R; Medeiros, P V C; Mascarenhas, A J S; de Castilho, C M C

2014-11-21

First-principles calculations demonstrate that line/ribbon defects, resulting from a controlled dehydrogenation in graphane, lead to the formation of low-dimensional electron-rich tracks in a monolayer. The present simulations point out that hybrid graphane-graphene nanostructures exhibit important elements, greatly required for the fabrication of efficient electronic circuits at the atomic level.

Transient Spectra in TDDFT: Corrections and Correlations

NASA Astrophysics Data System (ADS)

Parkhill, John; Nguyen, Triet

We introduce an atomistic, all-electron, black-box electronic structure code to simulate transient absorption (TA) spectra and apply it to simulate pyrazole and a GFP chromophore derivative. The method is an application of OSCF2, our dissipative extension of time-dependent density functional theory. We compare our simulated spectra directly with recent ultra-fast spectroscopic experiments, showing that they are usefully predicted. We also relate bleaches in the TA signal to Fermi-blocking which would be missed in a simplified model. An important ingredient in the method is the stationary-TDDFT correction scheme recently put forwards by Fischer, Govind, and Cramer which allows us to overcome a limitation of adiabatic TDDFT. We demonstrate that OSCF2 is able to predict both the energies of bleaches and induced absorptions, as well as the decay of the transient spectrum, with only the molecular structure as input. With remaining time we will discuss corrections which resolve the non-resonant behavior of driven TDDFT, and correlated corrections to mean-field dynamics.

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

Gyrokinetic particle simulation of beta-induced Alfven-acoustic eigenmode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, H. S., E-mail: zhang.huasen@gmail.com; Institute of Applied Physics and Computational Mathematics, Beijing 100088; Liu, Y. Q.

2016-04-15

The beta-induced Alfven-acoustic eigenmode (BAAE) in toroidal plasmas is verified and studied by global gyrokinetic particle simulations. When ion temperature is much lower than electron temperature, the existence of the weakly damped BAAE is verified in the simulations using initial perturbation, antenna excitation, and energetic particle excitation, respectively. When the ion temperature is comparable to the electron temperature, the unstable BAAE can be excited by realistic energetic particle density gradient, even though the stable BAAE (in the absence of energetic particles) is heavily damped by the thermal ions. In the simulations with reversed magnetic shear, BAAE frequency sweeping is observedmore » and poloidal mode structure has a triangle shape with a poloidal direction similar to that observed in tokamak experiments. The triangle shape changes the poloidal direction, and no frequency sweeping is found in the simulations with normal magnetic shear.« less

Ab Initio Simulations and Electronic Structure of Lithium-Doped Ionic Liquids: Structure, Transport, and Electrochemical Stability.

PubMed

Haskins, Justin B; Bauschlicher, Charles W; Lawson, John W

2015-11-19

Density functional theory (DFT), density functional theory molecular dynamics (DFT-MD), and classical molecular dynamics using polarizable force fields (PFF-MD) are employed to evaluate the influence of Li(+) on the structure, transport, and electrochemical stability of three potential ionic liquid electrolytes: N-methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([pyr14][TFSI]), N-methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide ([pyr13][FSI]), and 1-ethyl-3-methylimidazolium boron tetrafluoride ([EMIM][BF4]). We characterize the Li(+) solvation shell through DFT computations of [Li(Anion)n]((n-1)-) clusters, DFT-MD simulations of isolated Li(+) in small ionic liquid systems, and PFF-MD simulations with high Li-doping levels in large ionic liquid systems. At low levels of Li-salt doping, highly stable solvation shells having two to three anions are seen in both [pyr14][TFSI] and [pyr13][FSI], whereas solvation shells with four anions dominate in [EMIM][BF4]. At higher levels of doping, we find the formation of complex Li-network structures that increase the frequency of four anion-coordinated solvation shells. A comparison of computational and experimental Raman spectra for a wide range of [Li(Anion)n]((n-1)-) clusters shows that our proposed structures are consistent with experiment. We then compute the ion diffusion coefficients and find measures from small-cell DFT-MD simulations to be the correct order of magnitude, but influenced by small system size and short simulation length. Correcting for these errors with complementary PFF-MD simulations, we find DFT-MD measures to be in close agreement with experiment. Finally, we compute electrochemical windows from DFT computations on isolated ions, interacting cation/anion pairs, and liquid-phase systems with Li-doping. For the molecular-level computations, we generally find the difference between ionization energy and electron affinity from isolated ions and interacting cation/anion pairs to provide upper and lower bounds, respectively, to experiment. In the liquid phase, we find the difference between the lowest unoccupied and highest occupied electronic levels in pure and hybrid functionals to provide lower and upper bounds, respectively, to experiment. Li-doping in the liquid-phase systems results in electrochemical windows little changed from the neat systems.

Simulation of the optical coating deposition

NASA Astrophysics Data System (ADS)

Grigoriev, Fedor; Sulimov, Vladimir; Tikhonravov, Alexander

2018-04-01

A brief review of the mathematical methods of thin-film growth simulation and results of their applications is presented. Both full-atomistic and multi-scale approaches that were used in the studies of thin-film deposition are considered. The results of the structural parameter simulation including density profiles, roughness, porosity, point defect concentration, and others are discussed. The application of the quantum level methods to the simulation of the thin-film electronic and optical properties is considered. Special attention is paid to the simulation of the silicon dioxide thin films.

Numerical simulation of current-free double layers created in a helicon plasma device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Sathyanarayan; Singh, Nagendra

2012-09-15

Two-dimensional simulations reveal that when radially confined source plasma with magnetized electrons and unmagnetized ions expands into diverging magnetic field B, a current-free double layer (CFDL) embedded in a conical density structure forms, as experimentally measured in the Australian helicon plasma device (HPD). The magnetized electrons follow the diverging B while the unmagnetized ions tend to flow directly downstream of the source, resulting in a radial electric field (E{sub Up-Tack }) structure, which couples the ion and electron flows. Ions are transversely (radially) accelerated by E{sub Up-Tack} on the high potential side of the double layer in the CFDL. Themore » accelerated ions are trapped near the conical surface, where E{sub Up-Tack} reverses direction. The potential structure of the CFDL is U-shaped and the plasma density is enhanced on the conical surface. The plasma density is severely depleted downstream of the parallel potential drop ({phi}{sub Double-Vertical-Line Double-Vertical-Line o}) in the CFDL; the density depletion and the potential drop are related by quasi-neutrality condition, including the divergence in the magnetic field and in the plasma flow in the conical structure. The potential and density structures, the CFDL spatial size, its electric field strengths and the electron and ion velocities and energy distributions in the CFDL are found to be in good agreements with those measured in the Australian experiment. The applicability of our results to measured axial potential profiles in magnetic nozzle experiments in HPDs is discussed.« less

Application of a real-space three-dimensional image reconstruction method in the structural analysis of noncrystalline biological macromolecules enveloped by water in coherent x-ray diffraction microscopy.

PubMed

Kodama, Wataru; Nakasako, Masayoshi

2011-08-01

Coherent x-ray diffraction microscopy is a novel technique in the structural analyses of particles that are difficult to crystallize, such as the biological particles composing living cells. As water is indispensable for maintaining particles in functional structures, sufficient hydration of targeted particles is required during sample preparation for diffraction microscopy experiments. However, the water enveloping particles also contributes significantly to the diffraction patterns and reduces the electron-density contrast of the sample particles. In this study, we propose a protocol for the structural analyses of particles in water by applying a three-dimensional reconstruction method in real space for the projection images phase-retrieved from diffraction patterns, together with a developed density modification technique. We examined the feasibility of the protocol through three simulations involving a protein molecule in a vacuum, and enveloped in either a droplet or a cube-shaped water. The simulations were carried out for the diffraction patterns in the reciprocal planes normal to the incident x-ray beam. This assumption and the simulation conditions corresponded to experiments using x-ray wavelengths of shorter than 0.03 Å. The analyses demonstrated that our protocol provided an interpretable electron-density map. Based on the results, we discuss the advantages and limitations of the proposed protocol and its practical application for experimental data. In particular, we examined the influence of Poisson noise in diffraction patterns on the reconstructed three-dimensional electron density in the proposed protocol.

Nonlinear ELM simulations based on a nonideal peeling–ballooning model using the BOUT++ code

DOE PAGES

Xu, X. Q.; Dudson, B. D.; Snyder, P. B.; ...

2011-09-23

A minimum set of equations based on the peeling–ballooning (P–B) model with nonideal physics effects (diamagnetic drift, E × B drift, resistivity and anomalous electron viscosity) is found to simulate pedestal collapse when using the BOUT++ simulation code, developed in part from the original fluid edge code BOUT. Linear simulations of P–B modes find good agreement in growth rate and mode structure with ELITE calculations. The influence of the E × B drift, diamagnetic drift, resistivity, anomalous electron viscosity, ion viscosity and parallel thermal diffusivity on P–B modes is being studied; we find that (1) the diamagnetic drift and Emore » × B drift stabilize the P–B mode in a manner consistent with theoretical expectations; (2) resistivity destabilizes the P–B mode, leading to resistive P–B mode; (3) anomalous electron and parallel ion viscosities destabilize the P–B mode, leading to a viscous P–B mode; (4) perpendicular ion viscosity and parallel thermal diffusivity stabilize the P–B mode. With addition of the anomalous electron viscosity under the assumption that the anomalous kinematic electron viscosity is comparable to the anomalous electron perpendicular thermal diffusivity, or the Prandtl number is close to unity, it is found from nonlinear simulations using a realistic high Lundquist number that the pedestal collapse is limited to the edge region and the ELM size is about 5–10% of the pedestal stored energy. Furthermore, this is consistent with many observations of large ELMs. The estimated island size is consistent with the size of fast pedestal pressure collapse. In the stable α-zones of ideal P–B modes, nonlinear simulations of viscous ballooning modes or current-diffusive ballooning mode (CDBM) for ITER H-mode scenarios are presented.« less

Bright-field electron tomography of individual inorganic fullerene-like structures

NASA Astrophysics Data System (ADS)

Bar Sadan, Maya; Wolf, Sharon G.; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties. Electronic supplementary information (ESI) available: Figs. S1 and S2 and movies S1-S6. See DOI: 10.1039/b9nr00251k

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

PubMed Central

Caulfield, Thomas R.; Devkota, Batsal; Rollins, Geoffrey C.

2011-01-01

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16. PMID:21716650

Simulating Lattice Image of Suspended Graphene Taken by Helium Ion Microscopy

NASA Astrophysics Data System (ADS)

Miyamoto, Yoshiyuki; Zhang, Hong; Rubio, Angel

2013-03-01

Atomic scale image in nano-scale helps us to characterize property of graphene, and performance of high-resolution transmission electron microscopy (HRTEM) is significant, so far. While a tool without pre-treatment of samples is demanded in practice. Helium ion microscopy (HIM), firstly reported by Word et. al. in 2006, was applied for monitoring graphene in device structure (Lumme, et. al., 2009). Motivated by recent HIM explorations, we examined the possibility of taking lattice image of suspended graphene by HIM. The intensity of secondary emitted electron is recorded as a profile of scanned He+-beam in HIM measurement. We mimicked this situation by performing electron-ion dynamics based on the first-principles simulation within the time-dependent density functional theory. He+ ion collision on single graphene sheet at several impact points were simulated and we found that the amount of secondary emitted electron from graphene reflected the valence charge distribution of the graphene sheet. Therefore HIM using atomically thin He-beam should be able to provide the lattice image, and we propose that an experiment generating ultra-thin He+ ion beam (Rezeq et. al., 2006) should be combined with HIM technique. All calculations were performed by using the Earth Simulator.

Fine Structure of Diffuse Scattering Rings in Al-Li-Cu Quasicrystal: A Comparative X-ray and Electron Diffraction Study

NASA Astrophysics Data System (ADS)

Donnadieu, P.; Dénoyer, F.

1996-11-01

A comparative X-ray and electron diffraction study has been performed on Al-Li-Cu icosahedral quasicrystal in order to investigate the diffuse scattering rings revealed by a previous work. Electron diffraction confirms the existence of rings but shows that the rings have a fine structure. The diffuse aspect on the X-ray diffraction patterns is then due to an averaging effect. Recent simulations based on the model of canonical cells related to the icosahedral packing give diffractions patterns in agreement with this fine structure effect. Nous comparons les diagrammes de diffraction des rayon-X et des électrons obtenus sur les mêmes échantillons du quasicristal icosaèdrique Al-Li-Cu. Notre but est d'étudier les anneaux de diffusion diffuse mis en évidence par un travail précédent. Les diagrammes de diffraction électronique confirment la présence des anneaux mais ils montrent aussi que ces anneaux possèdent une structure fine. L'aspect diffus des anneaux révélés par la diffraction des rayons X est dû à un effet de moyenne. Des simulations récentes basées sur la décomposition en cellules canoniques de l'empilement icosaédrique produisent des diagrammes de diffraction en accord avec ces effects de structure fine.

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

DOE PAGES

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; ...

2016-03-30

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtainmore » 14 density maps at ~ 2-nm resolution . Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.« less

Microdosimetry of low-energy electrons.

PubMed

Liamsuwan, Thiansin; Emfietzoglou, Dimitris; Uehara, Shuzo; Nikjoo, Hooshang

2012-12-01

To investigate differences in energy depositions and microdosimetric parameters of low-energy electrons in liquid and gaseous water using Monte Carlo track structure simulations. KURBUC-liq (Kyushu University and Radiobiology Unit Code for liquid water) was used for simulating electron tracks in liquid water. The inelastic scattering cross sections of liquid water were obtained from the dielectric response model of Emfietzoglou et al. (Radiation Research 2005;164:202-211). Frequencies of energy deposited in nanometre-size cylindrical targets per unit absorbed dose and associated lineal energies were calculated for 100-5000 eV monoenergetic electrons and the electron spectrum of carbon K edge X-rays. The results for liquid water were compared with those for water vapour. Regardless of electron energy, there is a limit how much energy electron tracks can deposit in a target. Phase effects on the frequencies of energy depositions are largely visible for the targets with diameters and heights smaller than 30 nm. For the target of 2.3 nm by 2.3 nm (similar to dimension of DNA segments), the calculated frequency- and dose-mean lineal energies for liquid water are up to 40% smaller than those for water vapour. The corresponding difference is less than 12% for the targets with diameters ≥ 30 nm. Condensed-phase effects are non-negligible for microdosimetry of low-energy electrons for targets with sizes smaller than a few tens of nanometres, similar to dimensions of DNA molecular structures and nucleosomes.

Structural and electronic properties of CdSe/ZnS and ZnS/CdSe core/shell nanowires via first principles study

NASA Astrophysics Data System (ADS)

Rehman, Shafiq Ur; Li, H. M.; Ding, Z. J.

2018-05-01

First principles calculations have been performed to predict the structural stability and electronic structures of hydrogen passivated wurtzite CdSe/ZnS and ZnS/CdSe core/shell nanowires (CSNWs) in the [0001] direction. The calculated binding energy shows that ZnS/CdSe CSNWs are more stable than CdSe/ZnS CSNWs and the stability of ZnS/CdSe CSNWs increases with increasing the thickness of ZnS shell. The modulated electronic band gap demonstrates an increase when the size of both CSNWs is reduced, as a result of the quantum confinement effect. The core-to-shell chemical composition of atoms shows that a strong composition effect also exists in these CSNWs, which in turn affects their electronic properties. Our simulated results show that the photoemission spectra of the CSNWs can be significantly improved by tuning the energy gap of CSNWs.

Theoretical Modeling of Electromagnetic Field from Electron Bunches in Periodic Wire Medium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuchurka, S.; Benediktovitch, A.; Galyamin, S. N.

The interaction of relativistic electrons with periodic conducting structures results in radiation via a number of mechanisms. In case of crystals one obtains parametric X-ray radiation, its frequency is determined by the distance between crystallographic planes and the direction of electron beam. If instead of a crystal one considers a periodic structure of metallic wires with the spacing of the order of mm, it is plausible to expect the emission of radiation of a similar nature (“diffraction response”) at THz frequencies. Additionally, a “long-wave” radiation will occur in this case with wavelengths much larger then structure periods. In this contribution,more » we present different theoretical approaches for describing the electromagnetic radiation field from prolonged electron bunch propagated in the lattice of metallic wires. The validity of these analytical descriptions is checked by numerical simulations. We discuss the possible applications of aforementioned structure as sources of coherent THz radiation.« less

Quantum state transfer in double-quantum-well devices

NASA Technical Reports Server (NTRS)

Jakumeit, Jurgen; Tutt, Marcel; Pavlidis, Dimitris

1994-01-01

A Monte Carlo simulation of double-quantum-well (DQW) devices is presented in view of analyzing the quantum state transfer (QST) effect. Different structures, based on the AlGaAs/GaAs system, were simulated at 77 and 300 K and optimized in terms of electron transfer and device speed. The analysis revealed the dominant role of the impurity scattering for the QST. Different approaches were used for the optimization of QST devices and basic physical limitations were found in the electron transfer between the QWs. The maximum transfer of electrons from a high to a low mobility well was at best 20%. Negative differential resistance is hampered by the almost linear rather than threshold dependent relation of electron transfer on electric field. By optimizing the doping profile the operation frequency limit could be extended to 260 GHz.

GPAW - massively parallel electronic structure calculations with Python-based software.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Enkovaara, J.; Romero, N.; Shende, S.

2011-01-01

Electronic structure calculations are a widely used tool in materials science and large consumer of supercomputing resources. Traditionally, the software packages for these kind of simulations have been implemented in compiled languages, where Fortran in its different versions has been the most popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most of the productivity enhancing features together with a good numerical performance. We have used thismore » approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges it is possible to obtain good numerical performance and good parallel scalability with Python based software.« less

Equation of state of dense plasmas with pseudoatom molecular dynamics

DOE PAGES

Starrett, C. E.; Saumon, D.

2016-06-14

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Suppression of the Transit -Time Instability in Large-Area Electron Beam Diodes

NASA Astrophysics Data System (ADS)

Myers, Matthew C.; Friedman, Moshe; Swanekamp, Stephen B.; Chan, Lop-Yung; Ludeking, Larry; Sethian, John D.

2002-12-01

Experiment, theory, and simulation have shown that large-area electron-beam diodes are susceptible to the transit-time instability. The instability modulates the electron beam spatially and temporally, producing a wide spread in electron energy and momentum distributions. The result is gross inefficiency in beam generation and propagation. Simulations indicate that a periodic, slotted cathode structure that is loaded with resistive elements may be used to eliminate the instability. Such a cathode has been fielded on one of the two opposing 60 cm × 200 cm diodes on the NIKE KrF laser at the Naval Research Laboratory. These diodes typically deliver 600 kV, 500 kA, 250 ns electron beams to the laser cell in an external magnetic field of 0.2 T. We conclude that the slotted cathode suppressed the transit-time instability such that the RF power was reduced by a factor of 9 and that electron transmission efficiency into the laser gas was improved by more than 50%.

Footprints of electron correlation in strong-field double ionization of Kr close to the sequential-ionization regime

NASA Astrophysics Data System (ADS)

Li, Xiaokai; Wang, Chuncheng; Yuan, Zongqiang; Ye, Difa; Ma, Pan; Hu, Wenhui; Luo, Sizuo; Fu, Libin; Ding, Dajun

2017-09-01

By combining kinematically complete measurements and a semiclassical Monte Carlo simulation we study the correlated-electron dynamics in the strong-field double ionization of Kr. Interestingly, we find that, as we step into the sequential-ionization regime, there are still signatures of correlation in the two-electron joint momentum spectrum and, more intriguingly, the scaling law of the high-energy tail is completely different from early predictions on the low-Z atom (He). These experimental observations are well reproduced by our generalized semiclassical model adapting a Green-Sellin-Zachor potential. It is revealed that the competition between the screening effect of inner-shell electrons and the Coulomb focusing of nuclei leads to a non-inverse-square central force, which twists the returned electron trajectory at the vicinity of the parent core and thus significantly increases the probability of hard recollisions between two electrons. Our results might have promising applications ranging from accurately retrieving atomic structures to simulating celestial phenomena in the laboratory.

Variational nonadiabatic dynamics in the moving crude adiabatic representation: Further merging of nuclear dynamics and electronic structure

NASA Astrophysics Data System (ADS)

Joubert-Doriol, Loïc; Izmaylov, Artur F.

2018-03-01

A new methodology of simulating nonadiabatic dynamics using frozen-width Gaussian wavepackets within the moving crude adiabatic representation with the on-the-fly evaluation of electronic structure is presented. The main feature of the new approach is the elimination of any global or local model representation of electronic potential energy surfaces; instead, the electron-nuclear interaction is treated explicitly using the Gaussian integration. As a result, the new scheme does not introduce any uncontrolled approximations. The employed variational principle ensures the energy conservation and leaves the number of electronic and nuclear basis functions as the only parameter determining the accuracy. To assess performance of the approach, a model with two electronic and two nuclear spacial degrees of freedom containing conical intersections between potential energy surfaces has been considered. Dynamical features associated with nonadiabatic transitions and nontrivial geometric (or Berry) phases were successfully reproduced within a limited basis expansion.

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

Correlation between structural and opto-electronic characteristics of crystalline Si microhole arrays for photonic light management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sontheimer, Tobias, E-mail: tobias.sontheimer@helmholtz-berlin.de; Schnegg, Alexander; Lips, Klaus

2013-11-07

By employing electron paramagnetic resonance spectroscopy, transmission electron microscopy, and optical measurements, we systematically correlate the structural and optical properties with the deep-level defect characteristics of various tailored periodic Si microhole arrays, which are manufactured in an easily scalable and versatile process on nanoimprinted sol-gel coated glass. While tapered microhole arrays in a structured base layer are characterized by partly nanocrystalline features, poor electronic quality with a defect concentration of 10{sup 17} cm{sup −3} and a high optical sub-band gap absorption, planar polycrystalline Si layers perforated with periodic arrays of tapered microholes are composed of a compact crystalline structure and amore » defect concentration in the low 10{sup 16} cm{sup −3} regime. The low defect concentration is equivalent to the one in planar state-of-the-art solid phase crystallized Si films and correlates with a low optical sub-band gap absorption. By complementing the experimental characterization with 3-dimensional finite element simulations, we provide the basis for a computer-aided approach for the low-cost fabrication of novel high-quality structures on large areas featuring tailored opto-electronic properties.« less

Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations

NASA Astrophysics Data System (ADS)

Ramos-Méndez, José; Schuemann, Jan; Incerti, Sebastien; Paganetti, Harald; Schulte, Reinhard; Faddegon, Bruce

2017-08-01

Flagged uniform particle splitting was implemented with two methods to improve the computational efficiency of Monte Carlo track structure simulations with TOPAS-nBio by enhancing the production of secondary electrons in ionization events. In method 1 the Geant4 kernel was modified. In method 2 Geant4 was not modified. In both methods a unique flag number assigned to each new split electron was inherited by its progeny, permitting reclassification of the split events as if produced by independent histories. Computational efficiency and accuracy were evaluated for simulations of 0.5-20 MeV protons and 1-20 MeV u-1 carbon ions for three endpoints: (1) mean of the ionization cluster size distribution, (2) mean number of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) classified with DBSCAN, and (3) mean number of SSBs and DSBs classified with a geometry-based algorithm. For endpoint (1), simulation efficiency was 3 times lower when splitting electrons generated by direct ionization events of primary particles than when splitting electrons generated by the first ionization events of secondary electrons. The latter technique was selected for further investigation. The following results are for method 2, with relative efficiencies about 4.5 times lower for method 1. For endpoint (1), relative efficiency at 128 split electrons approached maximum, increasing with energy from 47.2  ±  0.2 to 66.9  ±  0.2 for protons, decreasing with energy from 51.3  ±  0.4 to 41.7  ±  0.2 for carbon. For endpoint (2), relative efficiency increased with energy, from 20.7  ±  0.1 to 50.2  ±  0.3 for protons, 15.6  ±  0.1 to 20.2  ±  0.1 for carbon. For endpoint (3) relative efficiency increased with energy, from 31.0  ±  0.2 to 58.2  ±  0.4 for protons, 23.9  ±  0.1 to 26.2  ±  0.2 for carbon. Simulation results with and without splitting agreed within 1% (2 standard deviations) for endpoints (1) and (2), within 2% (1 standard deviation) for endpoint (3). In conclusion, standard particle splitting variance reduction techniques can be successfully implemented in Monte Carlo track structure codes.

Structure and properties of microporous titanosilicate determined by first-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ching, W.Y.; Xu, Y.; Gu, Z.

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain. {copyright} {ital 1996 The American Physicalmore » Society.}« less

Nonlinear Dust Acoustic Waves in a Magnetized Dusty Plasma with Trapped and Superthermal Electrons

NASA Astrophysics Data System (ADS)

Ahmadi, Abrishami S.; Nouri, Kadijani M.

2014-06-01

In this work, the effects of superthermal and trapped electrons on the oblique propagation of nonlinear dust-acoustic waves in a magnetized dusty (complex) plasma are investigated. The dynamic of electrons is simulated by the generalized Lorentzian (κ) distribution function (DF). The dust grains are cold and their dynamics are simulated by hydrodynamic equations. Using the standard reductive perturbation technique (RPT) a nonlinear modified Korteweg-de Vries (mKdV) equation is derived. Two types of solitary waves; fast and slow dust acoustic solitons, exist in this plasma. Calculations reveal that compressive solitary structures are likely to propagate in this plasma where dust grains are negatively (or positively) charged. The properties of dust acoustic solitons (DASs) are also investigated numerically.

Atomistic Simulation and Electronic Structure of Lithium Doped Ionic Liquids: Structure, Transport, and Electrochemical Stability

NASA Technical Reports Server (NTRS)

Haskins, Justin B.; Bauschlicher, Charles W.; Lawson, John W.

2015-01-01

Zero-temperature density functional theory (DFT), density functional theory molecular dynamics (DFT-MD), and classical molecular dynamics using polarizable force fields (PFF-MD) are employed to evaluate the influence of Lithium ion on the structure, transport, and electrochemical stability of three potential ionic liquid electrolytes: N--methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([pyr14][TFSI]), N--methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide ([pyr13][FSI]), and 1-ethyl-3--methylimidazolium boron tetrafluoride ([EMIM][BF4]). We characterize the Lithium ion solvation shell through zero-temperature DFT simulations of [Li(Anion)sub n](exp n-1) -clusters, DFT-MD simulations of isolated lithium ions in small ionic liquid systems, and PFF-MD simulations with high Li-doping levels in large ionic liquid systems. At low levels of Li-salt doping, highly stable solvation shells having 2-3 anions are seen in both [pyr14][TFSI] and [pyr13][FSI], while solvation shells with 4 anions dominate in [EMIM][BF sub 4]. At higher levels of doping, we find the formation of complex Li-network structures that increase the frequency of 4 anion-coordinated solvation shells. A comparison of computational and experimental Raman spectra for a wide range of [Li(Anion) sub n](exp n -1) - clusters shows that our proposed structures are consistent with experiment. We estimate the ion diffusion coefficients and quantify both size and simulation time effects. We find estimates of lithium ion diffusion are a reasonable order of magnitude and can be corrected for simulation time effects. Simulation size, on the other hand, is also important, with diffusion coefficients from long PFF-MD simulations of small cells having 20-40% error compared to large-cell values. Finally, we compute the electrochemical window using differences in electronic energy levels of both isolated cation/anion pairs and small ionic liquid systems with Li-salt doping. The single pair and liquid-phase systems provide similar estimates of electrochemical window, while Li-doping in the liquid-phase systems results in electrochemical windows little changed from the neat systems. Pure and hybrid functionals systematically provide an upper and lower bound, respectively, to the experimental electrochemical window for the systems studied here.

Surface effect investigation on multipactor in microwave components using the EM-PIC method

NASA Astrophysics Data System (ADS)

Li, Yun; Ye, Ming; He, Yong-Ning; Cui, Wan-Zhao; Wang, Dan

2017-11-01

Multipactor poses a great risk to microwave components in space and its accurate controllable suppression is still lacking. To evaluate the secondary electron emission (SEE) of arbitrary surface states on multipactor, metal samples fabricated with ideal smoothness, random roughness, and micro-structures on the surface are investigated through SEE experiments and multipactor simulations. An accurate quantitative relationship between the SEE parameters and the multipactor discharge threshold in practical components has been established through Electromagnetic Particle-In-Cell (EM-PIC) simulation. Simulation results of microwave components, including the impedance transformer and the coaxial filter, exhibit an intuitive correlation between the critical SEE parameters, varied due to different surface states, and multipactor thresholds. It is demonstrated that it is the surface micro-structures with certain depth and morphology that determine the average yield of secondaries, other than the random surface relieves. Both the random surface relieves and micro-structures have a scattering effect on SEE, and the yield is prone to be identical upon different elevation angles of incident electrons. It possesses a great potential in the optimization and improvement of suppression technology without the exhaustion of the technological parameter.

Micro-wrinkling and delamination-induced buckling of stretchable electronic structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oyewole, O. K.; Department of Materials Science and Engineering, Kwara State University, Malete, P.M.B 1530, Ilorin, Kwara State; Yu, D.

This paper presents the results of experimental and theoretical/computational micro-wrinkles and buckling on the surfaces of stretchable poly-dimethylsiloxane (PDMS) coated with nano-scale Gold (Au) layers. The wrinkles and buckles are formed by the unloading of pre-stretched PDMS/Au structure after the evaporation of nano-scale Au layers. They are then characterized using atomic force microscopy and scanning electron microscopy. The critical stresses required for wrinkling and buckling are analyzed using analytical models. The possible interfacial cracking that can occur along with film buckling is also studied using finite element simulations of the interfacial crack growth. The implications of the results are discussedmore » for potential applications of micro-wrinkles and micro-buckles in stretchable electronic structures and biomedical devices.« less

Structural, electronic, magnetic and thermodynamic properties of Ni1-xTixO alloys an ab initio calculation and Monte Carlo study

NASA Astrophysics Data System (ADS)

Klaa, K.; Labidi, S.; Masrour, R.; Jabar, A.; Labidi, M.; Amara, A.; Drici, A.; Hlil, E. K.; Ellouze, M.

2018-06-01

Structural, electronic, magnetic and thermodynamic main features for Ni1-xTixO ternary alloys in rock-salt structure with Ti content in the range ? were studied using the full potential Linearized augmented plane wave (FP-LAPW) method within density functional theory. The exchange-correlation potential was calculated by the generalized gradient approximation. The analysis of the electronic density of states curves allowed the computation of the magnetic moments which are considered to lie along (010) axes. The thermodynamic stability of this alloy was investigated by calculating the excess enthalpy of mixing ? as well as the phase diagram. In addition, the Monte Carlo simulations have been exploited to calculate the transition temperature and magnetic coercive field in the alloy.

Electron and ion distribution functions in magnetopause reconnection

NASA Astrophysics Data System (ADS)

Wang, S.; Chen, L. J.; Bessho, N.; Hesse, M.; Kistler, L. M.; Torbert, R. B.; Mouikis, C.; Pollock, C. J.

2015-12-01

We investigate electron and ion velocity distribution functions in dayside magnetopause reconnection events observed by the Cluster and MMS spacecraft. The goal is to build a spatial map of electron and ion distribution features to enable the indication of the spacecraft location in the reconnection structure, and to understand plasma energization processes. Distribution functions, together with electromagnetic field structures, plasma densities, and bulk velocities, are organized and compared with particle-in-cell simulation results to indicate the proximities to the reconnection X-line. Anisotropic features in the distributions of magnetospheric- and magnetosheath- origin electrons at different locations in the reconnection inflow and exhaust are identified. In particular, parallel electron heating is observed in both the magnetosheath and magnetosphere inflow regions. Possible effects of the guide field strength, waves, and upstream density and temperature asymmetries on the distribution features will be discussed.

Average-atom model for two-temperature states and ionic transport properties of aluminum in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin

2017-03-01

The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.

Excitation of a nonlinear plasma ion wake by intense energy sources with applications to the crunch-in regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahai, Aakash A.

We show the excitation of a nonlinear ion-wake mode by plasma electron modes in the bubble regime driven by intense energy sources, using analytical theory and simulations. The ion wake is shown to be a driven nonlinear ion-acoustic wave in the form of a long-lived cylindrical ion soliton which limits the repetition rate of a plasma-based particle accelerator in the bubble regime. We present the application of this evacuated and radially outwards propagating ion-wake channel with an electron skin-depth scale radius for the “crunch-in” regime of hollow-channel plasma. It is shown that the time-asymmetric focusing force phases in the bubblemore » couple to ion motion significantly differently than in the linear electron mode. The electron compression in the back of the bubble sucks in the ions whereas the space charge within the bubble cavity expels them, driving a cylindrical ion-soliton structure at the bubble radius. Once formed, the soliton is sustained and driven radially outwards by the thermal pressure of the wake energy in electrons. Particle-in-cell simulations are used to study the ion-wake soliton structure, its driven propagation and its use for positron acceleration in the crunch-in regime.« less

Characteristics of gradient-interface-structured ZnCdSSe quantum dots with modified interface and its application to quantum-dot-sensitized solar cells

NASA Astrophysics Data System (ADS)

Jeong, Da-Woon; Kim, Jae-Yup; Seo, Han Wook; Lim, Kyoung-Mook; Ko, Min Jae; Seong, Tae-Yeon; Kim, Bum Sung

2018-01-01

Colloidal quantum dots (QDs) are attractive materials for application in photovoltaics, LEDs, displays, and bio devices owing to their unique properties. In this study, we synthesized gradient-interface-structured ZnCdSSe QDs and modified the interface based on a thermodynamic simulation to investigate its optical and physical properties. In addition, the interface was modified by increasing the molar concentration of Se. QDs at the modified interface were applied to QD-sensitized solar cells, which showed a 25.5% increase in photoelectric conversion efficiency owing to the reduced electron confinement effect. The increase seems to be caused by the excited electrons being relatively easily transferred to the level of TiO2 owing to the reduced electron confinement effect. Consequently, the electron confinement effect was observed to be reduced by increasing the ZnSe (or Zn1-xCdxSe)-rich phase at the interface. This means that, based on the thermodynamic simulation, the interface between the core QDs and the surface of the QDs can be controlled. The improvement of optical and electronic properties by controlling interfaces and surfaces during the synthesis of QDs, as reported in this work, can be useful for many applications beyond solar cells.

Excitation of a nonlinear plasma ion wake by intense energy sources with applications to the crunch-in regime

DOE PAGES

Sahai, Aakash A.

2017-08-23

We show the excitation of a nonlinear ion-wake mode by plasma electron modes in the bubble regime driven by intense energy sources, using analytical theory and simulations. The ion wake is shown to be a driven nonlinear ion-acoustic wave in the form of a long-lived cylindrical ion soliton which limits the repetition rate of a plasma-based particle accelerator in the bubble regime. We present the application of this evacuated and radially outwards propagating ion-wake channel with an electron skin-depth scale radius for the “crunch-in” regime of hollow-channel plasma. It is shown that the time-asymmetric focusing force phases in the bubblemore » couple to ion motion significantly differently than in the linear electron mode. The electron compression in the back of the bubble sucks in the ions whereas the space charge within the bubble cavity expels them, driving a cylindrical ion-soliton structure at the bubble radius. Once formed, the soliton is sustained and driven radially outwards by the thermal pressure of the wake energy in electrons. Particle-in-cell simulations are used to study the ion-wake soliton structure, its driven propagation and its use for positron acceleration in the crunch-in regime.« less

Modeling charge transport in organic photovoltaic materials.

PubMed

Nelson, Jenny; Kwiatkowski, Joe J; Kirkpatrick, James; Frost, Jarvist M

2009-11-17

The performance of an organic photovoltaic cell depends critically on the mobility of charge carriers within the constituent molecular semiconductor materials. However, a complex combination of phenomena that span a range of length and time scales control charge transport in disordered organic semiconductors. As a result, it is difficult to rationalize charge transport properties in terms of material parameters. Until now, efforts to improve charge mobilities in molecular semiconductors have proceeded largely by trial and error rather than through systematic design. However, recent developments have enabled the first predictive simulation studies of charge transport in disordered organic semiconductors. This Account describes a set of computational methods, specifically molecular modeling methods, to simulate molecular packing, quantum chemical calculations of charge transfer rates, and Monte Carlo simulations of charge transport. Using case studies, we show how this combination of methods can reproduce experimental mobilities with few or no fitting parameters. Although currently applied to material systems of high symmetry or well-defined structure, further developments of this approach could address more complex systems such anisotropic or multicomponent solids and conjugated polymers. Even with an approximate treatment of packing disorder, these computational methods simulate experimental mobilities within an order of magnitude at high electric fields. We can both reproduce the relative values of electron and hole mobility in a conjugated small molecule and rationalize those values based on the symmetry of frontier orbitals. Using fully atomistic molecular dynamics simulations of molecular packing, we can quantitatively replicate vertical charge transport along stacks of discotic liquid crystals which vary only in the structure of their side chains. We can reproduce the trends in mobility with molecular weight for self-organizing polymers using a cheap, coarse-grained structural simulation method. Finally, we quantitatively reproduce the field-effect mobility in disordered C60 films. On the basis of these results, we conclude that all of the necessary building blocks are in place for the predictive simulation of charge transport in macromolecular electronic materials and that such methods can be used as a tool toward the future rational design of functional organic electronic materials.

The impact of new Geant4-DNA cross section models on electron track structure simulations in liquid water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kyriakou, I., E-mail: ikyriak@cc.uoi.gr; Šefl, M.; Department of Dosimetry and Application of Ionizing Radiation, Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, 115 19 Prague

The most recent release of the open source and general purpose Geant4 Monte Carlo simulation toolkit (Geant4 10.2 release) contains a new set of physics models in the Geant4-DNA extension for improving the modelling of low-energy electron transport in liquid water (<10 keV). This includes updated electron cross sections for excitation, ionization, and elastic scattering. In the present work, the impact of these developments to track-structure calculations is examined for providing the first comprehensive comparison against the default physics models of Geant4-DNA. Significant differences with the default models are found for the average path length and penetration distance, as well asmore » for dose-point-kernels for electron energies below a few hundred eV. On the other hand, self-irradiation absorbed fractions for tissue-like volumes and low-energy electron sources (including some Auger emitters) reveal rather small differences (up to 15%) between these new and default Geant4-DNA models. The above findings indicate that the impact of the new developments will mainly affect those applications where the spatial pattern of interactions and energy deposition of very-low energy electrons play an important role such as, for example, the modelling of the chemical and biophysical stage of radiation damage to cells.« less

Simulation vs. Reality: A Comparison of In Silico Distance Predictions with DEER and FRET Measurements

PubMed Central

Klose, Daniel; Klare, Johann P.; Grohmann, Dina; Kay, Christopher W. M.; Werner, Finn; Steinhoff, Heinz-Jürgen

2012-01-01

Site specific incorporation of molecular probes such as fluorescent- and nitroxide spin-labels into biomolecules, and subsequent analysis by Förster resonance energy transfer (FRET) and double electron-electron resonance (DEER) can elucidate the distance and distance-changes between the probes. However, the probes have an intrinsic conformational flexibility due to the linker by which they are conjugated to the biomolecule. This property minimizes the influence of the label side chain on the structure of the target molecule, but complicates the direct correlation of the experimental inter-label distances with the macromolecular structure or changes thereof. Simulation methods that account for the conformational flexibility and orientation of the probe(s) can be helpful in overcoming this problem. We performed distance measurements using FRET and DEER and explored different simulation techniques to predict inter-label distances using the Rpo4/7 stalk module of the M. jannaschii RNA polymerase. This is a suitable model system because it is rigid and a high-resolution X-ray structure is available. The conformations of the fluorescent labels and nitroxide spin labels on Rpo4/7 were modeled using in vacuo molecular dynamics simulations (MD) and a stochastic Monte Carlo sampling approach. For the nitroxide probes we also performed MD simulations with explicit water and carried out a rotamer library analysis. Our results show that the Monte Carlo simulations are in better agreement with experiments than the MD simulations and the rotamer library approach results in plausible distance predictions. Because the latter is the least computationally demanding of the methods we have explored, and is readily available to many researchers, it prevails as the method of choice for the interpretation of DEER distance distributions. PMID:22761805

Two-stage bulk electron heating in the diffusion region of anti-parallel symmetric reconnection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Le, Ari Yitzchak; Egedal, Jan; Daughton, William Scott

2016-10-13

Electron bulk energization in the diffusion region during anti-parallel symmetric reconnection entails two stages. First, the inflowing electrons are adiabatically trapped and energized by an ambipolar parallel electric field. Next, the electrons gain energy from the reconnection electric field as they undergo meandering motion. These collisionless mechanisms have been described previously, and they lead to highly structured electron velocity distributions. Furthermore, a simplified control-volume analysis gives estimates for how the net effective heating scales with the upstream plasma conditions in agreement with fully kinetic simulations and spacecraft observations.

Calculation on spectrum of direct DNA damage induced by low-energy electrons including dissociative electron attachment.

PubMed

Liu, Wei; Tan, Zhenyu; Zhang, Liming; Champion, Christophe

2017-03-01

In this work, direct DNA damage induced by low-energy electrons (sub-keV) is simulated using a Monte Carlo method. The characteristics of the present simulation are to consider the new mechanism of DNA damage due to dissociative electron attachment (DEA) and to allow determining damage to specific bases (i.e., adenine, thymine, guanine, or cytosine). The electron track structure in liquid water is generated, based on the dielectric response model for describing electron inelastic scattering and on a free-parameter theoretical model and the NIST database for calculating electron elastic scattering. Ionization cross sections of DNA bases are used to generate base radicals, and available DEA cross sections of DNA components are applied for determining DNA-strand breaks and base damage induced by sub-ionization electrons. The electron elastic scattering from DNA components is simulated using cross sections from different theoretical calculations. The resulting yields of various strand breaks and base damage in cellular environment are given. Especially, the contributions of sub-ionization electrons to various strand breaks and base damage are quantitatively presented, and the correlation between complex clustered DNA damage and the corresponding damaged bases is explored. This work shows that the contribution of sub-ionization electrons to strand breaks is substantial, up to about 40-70%, and this contribution is mainly focused on single-strand break. In addition, the base damage induced by sub-ionization electrons contributes to about 20-40% of the total base damage, and there is an evident correlation between single-strand break and damaged base pair A-T.

Electron bunch structure in energy recovery linac with high-voltage dc photoelectron gun

NASA Astrophysics Data System (ADS)

Saveliev, Y. M.; Jackson, F.; Jones, J. K.; McKenzie, J. W.

2016-09-01

The internal structure of electron bunches generated in an injector line with a dc photoelectron gun is investigated. Experiments were conducted on the ALICE (accelerators and lasers in combined experiments) energy recovery linac at Daresbury Laboratory. At a relatively low dc gun voltage of 230 kV, the bunch normally consisted of two beamlets with different electron energies, as well as transverse and longitudinal characteristics. The beamlets are formed at the head and the tail of the bunch. At a higher gun voltage of 325 kV, the beam substructure is much less pronounced and could be observed only at nonoptimal injector settings. Experiments and computer simulations demonstrated that the bunch structure develops during the initial beam acceleration in the superconducting rf booster cavity and can be alleviated either by increasing the gun voltage to the highest possible level or by controlling the beam acceleration from the gun voltage in the first accelerating structure.

DFT investigations on mechanical stability, electronic structure and magnetism in Co2TaZ (Z = Al, Ga, In) heusler alloys

NASA Astrophysics Data System (ADS)

Khandy, Shakeel Ahmad; Gupta, Dinesh C.

2017-12-01

Ferromagnetic Heusler compounds have vast and imminent applications for novel devices, smart materials thanks to density functional theory (DFT) based simulations, which have scored out a new approach to study these materials. We forecast the structural stability of Co2TaZ alloys on the basis of total energy calculations and mechanical stability criteria. The elastic constants, robust spin-polarized ferromagnetism and electron densities in these half-metallic alloys are also discussed. The observed structural aspects calculated to predict the stability and equilibrium lattice parameters agree well with the experimental results. The elastic parameters like elastic constants, bulk, Young’s and shear moduli, poison’s and Pugh ratios, melting temperatures, etc have been put together to establish their mechanical properties. The elaborated electronic band structures along with indirect band gaps and spin polarization favour the application of these materials in spintronics and memory device technology.

Excited state X-ray absorption spectroscopy: Probing both electronic and structural dynamics

NASA Astrophysics Data System (ADS)

Neville, Simon P.; Averbukh, Vitali; Ruberti, Marco; Yun, Renjie; Patchkovskii, Serguei; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

2016-10-01

We investigate the sensitivity of X-ray absorption spectra, simulated using a general method, to properties of molecular excited states. Recently, Averbukh and co-workers [M. Ruberti et al., J. Chem. Phys. 140, 184107 (2014)] introduced an efficient and accurate L 2 method for the calculation of excited state valence photoionization cross-sections based on the application of Stieltjes imaging to the Lanczos pseudo-spectrum of the algebraic diagrammatic construction (ADC) representation of the electronic Hamiltonian. In this paper, we report an extension of this method to the calculation of excited state core photoionization cross-sections. We demonstrate that, at the ADC(2)x level of theory, ground state X-ray absorption spectra may be accurately reproduced, validating the method. Significantly, the calculated X-ray absorption spectra of the excited states are found to be sensitive to both geometric distortions (structural dynamics) and the electronic character (electronic dynamics) of the initial state, suggesting that core excitation spectroscopies will be useful probes of excited state non-adiabatic dynamics. We anticipate that the method presented here can be combined with ab initio molecular dynamics calculations to simulate the time-resolved X-ray spectroscopy of excited state molecular wavepacket dynamics.

Two-dimensional studies of relativistic electron beam plasma instabilities in an inhomogeneous plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shukla, Chandrasekhar; Das, Amita, E-mail: amita@ipr.res.in; Patel, Kartik

Relativistic electron beam propagation in plasma is fraught with several micro instabilities like two stream, filamentation, etc., in plasma. This results in severe limitation of the electron transport through a plasma medium. Recently, however, there has been an experimental demonstration of improved transport of Mega Ampere of electron currents (generated by the interaction of intense laser with solid target) in a carbon nanotube structured solid target [G. Chatterjee et al., Phys. Rev. Lett. 108, 235005 (2012)]. This then suggests that the inhomogeneous plasma (created by the ionization of carbon nanotube structured target) helps in containing the growth of the beammore » plasma instabilities. This manuscript addresses this issue with the help of a detailed analytical study and 2-D Particle-In-Cell simulations. The study conclusively demonstrates that the growth rate of the dominant instability in the 2-D geometry decreases when the plasma density is chosen to be inhomogeneous, provided the scale length 1/k{sub s} of the inhomogeneous plasma is less than the typical plasma skin depth (c/ω{sub 0}) scale. At such small scale lengths channelization of currents is also observed in simulation.« less

Mabs monograph air blast instrumentation, 1943 - 1993. Measurement techniques and instrumentation. Volume 3. Air blast structural target and gage calibration. Technical report, 17 September 1993-31 May 1994, FLD04

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reisler, R.E.; Keefer, J.H.; Ethridge, N.H.

1995-08-01

Structural response measurement techniques and instrumentation developed by Military Applications of Blast Simulators (MABS) participating countries for field tests over the period 1943 through 1993 are summarized. Electronic and non-electronic devices deployed on multi-ton nuclear and high-explosive events are presented with calibration techniques. The country and the year the gage was introduced are included with the description. References for each are also provided.

Nanoscale High Energetic Materials: A Polymeric Nitrogen Chain N8 Confined inside a Carbon Nanotube

NASA Astrophysics Data System (ADS)

Abou-Rachid, Hakima; Hu, Anguang; Timoshevskii, Vladimir; Song, Yanfeng; Lussier, Louis-Simon

2008-05-01

We present a theoretical study of a new hybrid material, nanostructured polymeric nitrogen, where a polymeric nitrogen chain is encapsulated in a carbon nanotube. The electronic and structural properties of the new system are studied by means of ab initio electronic structure and molecular dynamics calculations. Finite temperature simulations demonstrate the stability of this nitrogen phase at ambient pressure and room temperature using carbon nanotube confinement. This nanostructured confinement may open a new path towards stabilizing polynitrogen or polymeric nitrogen at ambient conditions.

Probing optical excitations in chevron-like armchair graphene nanoribbons.

PubMed

Denk, Richard; Lodi-Rizzini, Alberto; Wang, Shudong; Hohage, Michael; Zeppenfeld, Peter; Cai, Jinming; Fasel, Roman; Ruffieux, Pascal; Berger, Reinhard Franz Josef; Chen, Zongping; Narita, Akimitsu; Feng, Xinliang; Müllen, Klaus; Biagi, Roberto; De Renzi, Valentina; Prezzi, Deborah; Ruini, Alice; Ferretti, Andrea

2017-11-30

The bottom-up fabrication of graphene nanoribbons (GNRs) has opened new opportunities to specifically tune their electronic and optical properties by precisely controlling their atomic structure. Here, we address excitation in GNRs with periodic structural wiggles, the so-called chevron GNRs. Based on reflectance difference and high-resolution electron energy loss spectroscopies together with ab initio simulations, we demonstrate that their excited-state properties are of excitonic nature. The spectral fingerprints corresponding to different reaction stages in their bottom-up fabrication are also unequivocally identified, allowing us to follow the exciton build-up from the starting monomer precursor to the final GNR structure.

Nanogap structures for molecular nanoelectronics

PubMed Central

2012-01-01

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes. PMID:22321736

Ion-acoustic and electron-acoustic type nonlinear waves in dusty plasmas

NASA Astrophysics Data System (ADS)

Volosevich, A.-V.; Meister, C.-V.

2003-04-01

In the present work, two three-dimensional nonlinear theoretical models of electrostatic solitary waves are investigated within the frame of magnetohydrodynamics. Both times, a multi-component plasma is considered, which consists of hot electrons with a rather flexible distribution function, hot ions with Boltzmann-type distribution, and (negatively as well as positively charged) dust. Additionally, cold ion beams are taken into account in the model to study ion-acoustic structures (IAS), and cold electron beams are included into the model to investigate electron-acoustic structures (EAS). The numerical results of the considered theoretical models allow to make the following conclusions: 1) Electrostatic structures with negative potential (of rarefaction type) are formed both in the IAS model and in the EAS model, but structures with negative potential (of compressional type) are formed in the IAS model only. 2) The intervals of various plasma parameters (velocities of ion and electron beams, temperatures, densities of the plasma components, ions' masses), for which the existence of IAS and EAS solitary waves and structures is possible, are calculated. 3) Further, the parameters of the electrostatic structures (wave amplitudes, scales along and perpendicular to the magnetic field, velocities) are estimated. 4) The application of the present numerical simulation for multi-component plasmas to various astrophysical systems under different physical conditions is discussed.

Development of inorganic resists for electron beam lithography: Novel materials and simulations

NASA Astrophysics Data System (ADS)

Jeyakumar, Augustin

Electron beam lithography is gaining widespread utilization as the semiconductor industry progresses towards both advanced optical and non-optical lithographic technologies for high resolution patterning. The current resist technologies are based on organic systems that are imaged most commonly through chain scission, networking, or a chemically amplified polarity change in the material. Alternative resists based on inorganic systems were developed and characterized in this research for high resolution electron beam lithography and their interactions with incident electrons were investigated using Monte Carlo simulations. A novel inorganic resist imaging scheme was developed using metal-organic precursors which decompose to form metal oxides upon electron beam irradiation that can serve as inorganic hard masks for hybrid bilayer inorganic-organic imaging systems and also as directly patternable high resolution metal oxide structures. The electron beam imaging properties of these metal-organic materials were correlated to the precursor structure by studying effects such as interactions between high atomic number species and the incident electrons. Optimal single and multicomponent precursors were designed for utilization as viable inorganic resist materials for sub-50nm patterning in electron beam lithography. The electron beam imaging characteristics of the most widely used inorganic resist material, hydrogen silsesquioxane (HSQ), was also enhanced using a dual processing imaging approach with thermal curing as well as a sensitizer catalyzed imaging approach. The interaction between incident electrons and the high atomic number species contained in these inorganic resists was also studied using Monte Carlo simulations. The resolution attainable using inorganic systems as compared to organic systems can be greater for accelerating voltages greater than 50 keV due to minimized lateral scattering in the high density inorganic systems. The effects of loading nanoparticles in an electron beam resist was also investigated using a newly developed hybrid Monte Carlo approach that accounts for multiple components in a solid film. The resolution of the nanocomposite resist process was found to degrade with increasing nanoparticle loading. Finally, the electron beam patterning of self-assembled monolayers, which were found to primarily utilize backscattered electrons from the high atomic number substrate materials to form images, was also investigated and characterized. It was found that backscattered electrons limit the resolution attainable at low incident electron energies.

Orbiter lessons learned: A guide to future vehicle development

NASA Technical Reports Server (NTRS)

Greenberg, Harry Stan

1993-01-01

Topics addressed are: (1) wind persistence loads methodology; (2) emphasize supportability in design of reusable vehicles; (3) design for robustness; (4) improved aerodynamic environment prediction methods for complex vehicles; (5) automated integration of aerothermal, manufacturing, and structures analysis; (6) continued electronic documentation of structural design and analysis; and (7) landing gear rollout load simulations.

Geometrical effects on the electron residence time in semiconductor nano-particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koochi, Hakimeh; Ebrahimi, Fatemeh, E-mail: f-ebrahimi@birjand.ac.ir; Solar Energy Research Group, University of Birjand, Birjand

2014-09-07

We have used random walk (RW) numerical simulations to investigate the influence of the geometry on the statistics of the electron residence time τ{sub r} in a trap-limited diffusion process through semiconductor nano-particles. This is an important parameter in coarse-grained modeling of charge carrier transport in nano-structured semiconductor films. The traps have been distributed randomly on the surface (r{sup 2} model) or through the whole particle (r{sup 3} model) with a specified density. The trap energies have been taken from an exponential distribution and the traps release time is assumed to be a stochastic variable. We have carried out (RW)more » simulations to study the effect of coordination number, the spatial arrangement of the neighbors and the size of nano-particles on the statistics of τ{sub r}. It has been observed that by increasing the coordination number n, the average value of electron residence time, τ{sup ¯}{sub r} rapidly decreases to an asymptotic value. For a fixed coordination number n, the electron's mean residence time does not depend on the neighbors' spatial arrangement. In other words, τ{sup ¯}{sub r} is a porosity-dependence, local parameter which generally varies remarkably from site to site, unless we are dealing with highly ordered structures. We have also examined the effect of nano-particle size d on the statistical behavior of τ{sup ¯}{sub r}. Our simulations indicate that for volume distribution of traps, τ{sup ¯}{sub r} scales as d{sup 2}. For a surface distribution of traps τ{sup ¯}{sub r} increases almost linearly with d. This leads to the prediction of a linear dependence of the diffusion coefficient D on the particle size d in ordered structures or random structures above the critical concentration which is in accordance with experimental observations.« less

OPTESIM, a Versatile Toolbox for Numerical Simulation of Electron Spin Echo Envelope Modulation (ESEEM) that Features Hybrid Optimization and Statistical Assessment of Parameters

PubMed Central

Sun, Li; Hernandez-Guzman, Jessica; Warncke, Kurt

2009-01-01

Electron spin echo envelope modulation (ESEEM) is a technique of pulsed-electron paramagnetic resonance (EPR) spectroscopy. The analyis of ESEEM data to extract information about the nuclear and electronic structure of a disordered (powder) paramagnetic system requires accurate and efficient numerical simulations. A single coupled nucleus of known nuclear g value (gN) and spin I=1 can have up to eight adjustable parameters in the nuclear part of the spin Hamiltonian. We have developed OPTESIM, an ESEEM simulation toolbox, for automated numerical simulation of powder two- and three-pulse one-dimensional ESEEM for arbitrary number (N) and type (I, gN) of coupled nuclei, and arbitrary mutual orientations of the hyperfine tensor principal axis systems for N>1. OPTESIM is based in the Matlab environment, and includes the following features: (1) a fast algorithm for translation of the spin Hamiltonian into simulated ESEEM, (2) different optimization methods that can be hybridized to achieve an efficient coarse-to-fine grained search of the parameter space and convergence to a global minimum, (3) statistical analysis of the simulation parameters, which allows the identification of simultaneous confidence regions at specific confidence levels. OPTESIM also includes a geometry-preserving spherical averaging algorithm as default for N>1, and global optimization over multiple experimental conditions, such as the dephasing time ( ) for three-pulse ESEEM, and external magnetic field values. Application examples for simulation of 14N coupling (N=1, N=2) in biological and chemical model paramagnets are included. Automated, optimized simulations by using OPTESIM lead to a convergence on dramatically shorter time scales, relative to manual simulations. PMID:19553148

A universal preconditioner for simulating condensed phase materials.

PubMed

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

A universal preconditioner for simulating condensed phase materials

NASA Astrophysics Data System (ADS)

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-01

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

New Relativistic Particle-In-Cell Simulation Studies of Prompt and Early Afterglows from GRBs

NASA Technical Reports Server (NTRS)

Nishikawa, Ken-ichi; Hardee, P.; Mizuno, Y.; Zhang, B.; Medvedev, M.; Hartmann, D.; Fishman, J. F.; Preece, R.

2008-01-01

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., gamma-ray bursts (GRBs), active galactic nuclei (AGNs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations of relativistic electron-ion (electro-positron) jets injected into a stationary medium show that particle acceleration occurs within the downstream jet. In the collisionless relativistic shock particle acceleration is due to plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel (filamentation) instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The 'jitter' radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Short and medium range structures of 80GeSe2–20Ga2Se3 chalcogenide glasses

NASA Astrophysics Data System (ADS)

Petracovschi, Elena; Calvez, Laurent; Cormier, Laurent; Le Coq, David; Du, Jincheng

2018-05-01

The short and medium range structures of 80GeSe2–20Ga2Se3 (or Ge23.5Ga11.8Se64.7) chalcogenide glasses have been studied by combining ab initio molecular dynamics (AIMD) simulations and experimental neutron diffraction studies. The structure factor and total correlation function were calculated from glass structures generated from AIMD simulations and compared with neutron diffraction experiments showing reasonable agreement. The atomic structures of ternary chalcogenide glasses were analyzed in detail, and it was found that gallium atoms are four-fold coordinated by selenium (Se) and form [GaSe4] tetrahedra. Germanium atoms on average also have four-fold coordination, among which Se is 3.5 with the remaining being Ge–Ge homo-nuclear bonds. Ga and Ge tetrahedra link together mainly through corner-sharing and some edge-sharing of Se. No homo-nuclear bonds were observed among Ga atoms or between Ge and Ga. In addition, Se–Se homo-nuclear bonds and Se chains with various lengths were observed. A small fraction of Se atom triclusters that bond to three cations of Ge and Ga were also observed, confirming earlier proposals from 77Se solid state nuclear magnetic resonance studies. Furthermore, the electronic structures of ternary chalcogenide glasses were studied in terms of atomic charge and electronic density of states in order to gain insights into the chemical bonding and electronic properties, as well as to provide an explanation of the observed atomic structures in these ternary chalcogenide glasses.

Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

NASA Astrophysics Data System (ADS)

Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

2017-05-01

Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

Bright-field electron tomography of individual inorganic fullerene-like structures.

PubMed

Bar Sadan, Maya; Wolf, Sharon G; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.

Left-right correlation in coupled F-center defects.

PubMed

Janesko, Benjamin G

2016-08-07

This work explores how left-right correlation, a textbook problem in electronic structure theory, manifests in a textbook example of electrons trapped in crystal defects. I show that adjacent F-center defects in lithium fluoride display symptoms of "strong" left-right correlation, symptoms similar to those seen in stretched H2. Simulations of UV/visible absorption spectra qualitatively fail to reproduce experiment unless left-right correlation is taken into account. This is of interest to both the electronic structure theory and crystal-defect communities. Theorists have a new well-behaved system to test their methods. Crystal-defect groups are cautioned that the approximations that successfully model single F-centers may fail for adjacent F-centers.

Theoretical study on strain induced variations in electronic properties of 2H-MoS{sub 2} bilayer sheets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Liang; Dongare, Avinash M., E-mail: dongare@uconn.edu; Namburu, Raju R.

2014-02-03

The strain dependence of the electronic properties of bilayer sheets of 2H-MoS{sub 2} is studied using ab initio simulations based on density functional theory. An indirect band gap for bilayer MoS{sub 2} is observed for all variations of strain along the basal plane. Several transitions for the indirect band gap are observed for various strains for the bilayer structure. The variation of the band gap and the carrier effective masses for the holes and the electrons for the bilayer MoS{sub 2} structure under conditions of uniaxial strain, biaxial strain, as well as uniaxial stress is investigated.

Characterization of LiBC by phase-contrast scanning transmission electron microscopy.

PubMed

Krumeich, Frank; Wörle, Michael; Reibisch, Philipp; Nesper, Reinhard

2014-08-01

LiBC was used as a model compound for probing the applicability of phase-contrast (PC) imaging in an aberration-corrected scanning transmission electron microscope (STEM) to visualize lithium distributions. In the LiBC structure, boron and carbon are arranged to hetero graphite layers between which lithium is incorporated. The crystal structure is reflected in the PC-STEM images recorded perpendicular to the layers. The experimental images and their defocus dependence match with multi-slice simulations calculated utilizing the reciprocity principle. The observation that a part of the Li positions is not occupied is likely an effect of the intense electron beam triggering Li displacement. Copyright © 2013 Elsevier Ltd. All rights reserved.

Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation.

PubMed

Heck, Alexander; Woiczikowski, P Benjamin; Kubař, Tomáš; Giese, Bernd; Elstner, Marcus; Steinbrecher, Thomas B

2012-02-23

Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist. © 2012 American Chemical Society

Structural properties of thiophenes investigated with simulations of a coarse-grained model

NASA Astrophysics Data System (ADS)

Luettmer-Strathmann, Jutta; Almutairi, Amani

Thiophenes have important applications in organic electronics, energy conversion, and storage. The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. In recent work, we developed a coarse-grained model for alpha-oligothiophenes in the bulk and near gold surfaces. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. In this work, we investigate structural properties of thiophenes with simulations of our coarse-grained model.

Vlasov Simulation Study of Landau Damping Near the Persisting to Arrested Transition

NASA Astrophysics Data System (ADS)

Vinas, A. F.; Klimas, A. J.; Araneda, J. A.

2017-12-01

A 1-D electrostatic filtered Vlasov-Poisson simulation study is discussed. The transition from persisting to arrested Landau damping that is produced by increasing the strength of a sinusoidal perturbation on a background Vlasov-Poisson equilibrium is explored. Emphasis is placed on observed features of the electron phase-space distribution when the perturbation strength is near the transition value. A single ubiquitous waveform is found perturbing the space-averaged phase space distribution at almost any time in all of the simulations; the sole exception is the saturation stage that can occur at the end of the arrested damping scenario. This waveform contains relatively strong, very narrow structures in velocity bracketing ±vres - the velocities at which electrons must move to traverse the dominant field mode wavelength in one of its oscillation periods - and propagating with ±vres respectively. Local streams of electrons are found in these structures crossing the resonant velocities from low speed to high speed during Landau damping and from high speed to low speed during Landau growth. At the arrest time, when the field strength is briefly constant, these streams vanish. It is conjectured that the expected transfer of energy between electrons and field during Landau growth or damping has been visualized for the first time. No evidence is found in the phase-space distribution to support recent well established discoveries of a second order phase transition in the electric field evolution. While trapping is known to play a role for larger perturbation strengths, it is shown that trapping plays no role at any time in any of the simulations near the transition perturbation strength.

Response of radiation belt simulations to different radial diffusion coefficients

NASA Astrophysics Data System (ADS)

Drozdov, A.; Shprits, Y.; Subbotin, D.; Kellerman, A. C.

2013-12-01

Resonant interactions between Ultra Low Frequency (ULF) waves and relativistic electrons may violate the third adiabatic invariant of motion, which produces radial diffusion in the electron radiation belts. This process plays an important role in the formation and structure of the outer electron radiation belt and is important for electron acceleration and losses in that region. Two parameterizations of the resonant wave-particle interaction of electrons with ULF waves in the magnetosphere by Brautigam and Albert [2000] and Ozeke et al. [2012] are evaluated using the Versatile Electron Radiation Belt (VERB) diffusion code to estimate their relative effect on the radiation belt simulation. The period of investigation includes quiet time and storm time geomagnetic activity and is compared to data based on satellite observations. Our calculations take into account wave-particle interactions represented by radial diffusion transport, local acceleration, losses due to pitch-angle diffusion, and mixed diffusion. We show that the results of the 3D diffusion simulations depend on the assumed parametrization of waves. The differences between the simulations and potential missing physical mechanisms are discussed. References Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999JA900344 Ozeke, L. G., I. R. Mann, K. R. Murphy, I. J. Rae, D. K. Milling, S. R. Elkington, A. A. Chan, and H. J. Singer (2012), ULF wave derived radiation belt radial diffusion coefficients, J. Geophys. Res., 117, A04222, doi:10.1029/2011JA017463.

Structural Refinement of Membrane Proteins by Restrained Molecular Dynamics and Solvent Accessibility Data

PubMed Central

Sompornpisut, Pornthep; Roux, Benoît; Perozo, Eduardo

2008-01-01

We present an approach for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (ΠO2) and nickel-ethylenediaminediacetic acid (ΠNiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual “solvent” particles corresponding to O2 and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-label pseudoatoms to the surrounding environment. This approach, “pseudoatom-driven solvent accessibility refinement”, was validated by refolding distorted conformations of the Streptomyces lividans potassium channel (KcsA), corresponding to a range of 2–30 Å root mean-square deviations away from the native structure. Molecular dynamics simulations based on up to 58 electron paramagnetic resonance restraints derived from spin-label mutants were able to converge toward the native structure within 1–3 Å root mean-square deviations with minimal computational cost. The use of energy-based ranking and structure similarity clustering as selection criteria helped in the convergence and identification of correctly folded structures from a large number of simulations. This approach can be applied to a variety of integral membrane protein systems, regardless of oligomeric state, and should be particularly useful in calculating conformational changes from a known reference crystal structure. PMID:18676641

Density-functional study of the structures and properties of holmium-doped silicon clusters HoSi n (n = 3-9) and their anions.

PubMed

Hou, Liyuan; Yang, Jucai; Liu, Yuming

2017-04-01

The structures and properties of Ho-doped Si clusters, including their adiabatic electron affinities (AEAs), simulated photoelectron spectra (PESs), stabilities, magnetic moments, and charge-transfer characteristics, were systematically investigated using four density-functional methods. The results show that the double-hybrid functional (which includes an MP2 correlation component) can accurately predict the ground-state structure and properties of Ho-doped Si clusters. The ground-state structures of HoSi n (n = 3-9) are sextuplet electronic states. The structures of these Ho-doped Si clusters (aside from HoSi 7 ) are substitutional. The ground-state structures of HoSi n - are quintuplet electronic states. Their predicted AEAs are in excellent agreement with the experimental ones. The mean absolute error in the theoretical AEAs of HoSi n (n = 4-9) is only 0.04 eV. The simulated PESs for HoSi n - (n = 5-9) are in good agreement with the experimental PESs. Based on its simulated PES and theoretical AEA, we reassigned the experimental PES of HoSi 4 - and obtained an experimental AEA of 2.2 ± 0.1 eV. The dissociation energies of Ho from HoSi n and HoSi n - (n = 3-9) were evaluated to test the relative stabilities of the clusters. HOMO-LUMO gap analysis indicated that doping the Si clusters with the rare-earth metal atom significantly increases their photochemical reactivity. Natural population analysis showed that the magnetic moments of HoSi n (n = 3-9) and their anions derive mainly from the Ho atom. It was also found that the magnetic moments of Ho in the HoSi n clusters are larger than the magnetic moment of an isolated Ho atom.

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

Determination of the structural phase and octahedral rotation angle in halide perovskites

NASA Astrophysics Data System (ADS)

dos Reis, Roberto; Yang, Hao; Ophus, Colin; Ercius, Peter; Bizarri, Gregory; Perrodin, Didier; Shalapska, Tetiana; Bourret, Edith; Ciston, Jim; Dahmen, Ulrich

2018-02-01

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurement of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). The approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.

Modeling and numerical simulations of growth and morphologies of three dimensional aggregated silver films

NASA Astrophysics Data System (ADS)

Davis, L. J.; Boggess, M.; Kodpuak, E.; Deutsch, M.

2012-11-01

We report on a model for the deposition of three dimensional, aggregated nanocrystalline silver films, and an efficient numerical simulation method developed for visualizing such structures. We compare our results to a model system comprising chemically deposited silver films with morphologies ranging from dilute, uniform distributions of nanoparticles to highly porous aggregated networks. Disordered silver films grown in solution on silica substrates are characterized using digital image analysis of high resolution scanning electron micrographs. While the latter technique provides little volume information, plane-projected (two dimensional) island structure and surface coverage may be reliably determined. Three parameters governing film growth are evaluated using these data and used as inputs for the deposition model, greatly reducing computing requirements while still providing direct access to the complete (bulk) structure of the films throughout the growth process. We also show how valuable three dimensional characteristics of the deposited materials can be extracted using the simulated structures.

A two-dimensional Dirac fermion microscope

NASA Astrophysics Data System (ADS)

Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-06-01

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.

A two-dimensional Dirac fermion microscope

PubMed Central

Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-01-01

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots. PMID:28598421

Global MHD Simulation of the Coronal Mass Ejection on 2011 March 7: from Chromosphere to 1 AU

NASA Astrophysics Data System (ADS)

Jin, M.; Manchester, W.; van der Holst, B.; Oran, R.; Sokolov, I.; Toth, G.; Vourlidas, A.; Liu, Y.; Sun, X.; Gombosi, T. I.

2013-12-01

In this study, we present magnetohydrodynamics simulation results of a fast CME event that occurred on 2011 March 7 by using the newly developed Alfven Wave Solar Model (AWSoM) in Space Weather Modeling Framework (SWMF). The background solar wind is driven by Alfven-wave pressure and heated by Alfven-wave dissipation in which we have incorporated balanced turbulence at the top of the closed field lines. The magnetic field of the inner boundary is specified with a synoptic magnetogram from SDO/HMI. In order to produce the physically correct CME structures and CME-driven shocks, the electron and proton temperatures are separated so that the electron heat conduction is explicitly treated in conjunction with proton shock heating. Also, collisionless heat conduction is implemented for getting the correct electron temperature at 1 AU. We initiate the CME by using the Gibson-Low flux rope model and simulate the CME propagation to 1 AU. A comprehensive validation study is performed using remote as well as in-situ observations from SOHO, STEREOA/B, ACE, and WIND. Our result shows that the new model can reproduce most of the observed features and the arrival time of the CME is correctly estimated, which suggests the forecasting capability of the new model. We also examine the simulated CME-driven shock structures that are important for modeling the associated solar energetic event (SEP) with diffusive shock acceleration.

High-throughput materials discovery and development: breakthroughs and challenges in the mapping of the materials genome

NASA Astrophysics Data System (ADS)

Buongiorno Nardelli, Marco

High-Throughput Quantum-Mechanics computation of materials properties by ab initio methods has become the foundation of an effective approach to materials design, discovery and characterization. This data driven approach to materials science currently presents the most promising path to the development of advanced technological materials that could solve or mitigate important social and economic challenges of the 21st century. In particular, the rapid proliferation of computational data on materials properties presents the possibility to complement and extend materials property databases where the experimental data is lacking and difficult to obtain. Enhanced repositories such as AFLOWLIB open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various properties. The practical realization of these opportunities depends almost exclusively on the the design of efficient algorithms for electronic structure simulations of realistic material systems beyond the limitations of the current standard theories. In this talk, I will review recent progress in theoretical and computational tools, and in particular, discuss the development and validation of novel functionals within Density Functional Theory and of local basis representations for effective ab-initio tight-binding schemes. Marco Buongiorno Nardelli is a pioneer in the development of computational platforms for theory/data/applications integration rooted in his profound and extensive expertise in the design of electronic structure codes and in his vision for sustainable and innovative software development for high-performance materials simulations. His research activities range from the design and discovery of novel materials for 21st century applications in renewable energy, environment, nano-electronics and devices, the development of advanced electronic structure theories and high-throughput techniques in materials genomics and computational materials design, to an active role as community scientific software developer (QUANTUM ESPRESSO, WanT, AFLOWpi)

Carbon phosphide monolayers with superior carrier mobility

NASA Astrophysics Data System (ADS)

Wang, Gaoxue; Pandey, Ravindra; Karna, Shashi P.

2016-04-01

Two dimensional (2D) materials with a finite band gap and high carrier mobility are sought after materials from both fundamental and technological perspectives. In this paper, we present the results based on the particle swarm optimization method and density functional theory which predict three geometrically different phases of the carbon phosphide (CP) monolayer consisting of sp2 hybridized C atoms and sp3 hybridized P atoms in hexagonal networks. Two of the phases, referred to as α-CP and β-CP with puckered or buckled surfaces are semiconducting with highly anisotropic electronic and mechanical properties. More remarkably, they have the lightest electrons and holes among the known 2D semiconductors, yielding superior carrier mobility. The γ-CP has a distorted hexagonal network and exhibits a semi-metallic behavior with Dirac cones. These theoretical findings suggest that the binary CP monolayer is a yet unexplored 2D material holding great promise for applications in high-performance electronics and optoelectronics.Two dimensional (2D) materials with a finite band gap and high carrier mobility are sought after materials from both fundamental and technological perspectives. In this paper, we present the results based on the particle swarm optimization method and density functional theory which predict three geometrically different phases of the carbon phosphide (CP) monolayer consisting of sp2 hybridized C atoms and sp3 hybridized P atoms in hexagonal networks. Two of the phases, referred to as α-CP and β-CP with puckered or buckled surfaces are semiconducting with highly anisotropic electronic and mechanical properties. More remarkably, they have the lightest electrons and holes among the known 2D semiconductors, yielding superior carrier mobility. The γ-CP has a distorted hexagonal network and exhibits a semi-metallic behavior with Dirac cones. These theoretical findings suggest that the binary CP monolayer is a yet unexplored 2D material holding great promise for applications in high-performance electronics and optoelectronics. Electronic supplementary information (ESI) available: Fig. S1 cohesive energy and structure of the CP monolayer with various stoichiometric compositions obtained using CALYPSO, Fig. S2 history of CALYPSO steps and structure of the CP monolayer, Fig. S3 phonon dispersion with DFT-D2 functional, Fig. S4 band structure for β-CP using the DFT-PBE and DFT-D2 functional forms, Fig. S5 strain energy curves, Fig. S6 projected band structure for α-CP, Fig. S7 projected band structure for β-CP, Fig. S8 projected band structure for γ-CP, Fig. S9 band structures obtained with the GGA-PBE and HSE06 functional; Table S1 lattice parameters with the DFT-D2 functional form; Video S1 AIMD simulation of α-CP at 300 K, Video S2 AIMD simulation of β-CP at 300 K, Video S3 AIMD simulation of γ-CP at 300 K. See DOI: 10.1039/c6nr00498a

Radiation from Accelerated Particles in Shocks and Reconnections

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Zhang, B.; Niemiec, J.; Medvedev, M.; Hardee, P.; Mizuno, Y.; Nordlund, A.; Frederiksen, J. T.; Sol, H.; Pohl, M.;

On the structure and dynamics of the hydrated sulfite ion in aqueous solution--an ab initio QMCF MD simulation and large angle X-ray scattering study.

PubMed

Eklund, Lars; Hofer, Thomas S; Pribil, Andreas B; Rode, Bernd M; Persson, Ingmar

2012-05-07

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism has been applied in conjunction to experimental large angle X-ray scattering to study the structure and dynamics of the hydrated sulfite ion in aqueous solution. The results show that there is a considerable effect of the lone electron-pair on sulfur concerning structure and dynamics in comparison with the sulfate ion with higher oxidation number and symmetry of the hydration shell. The S-O bond distance in the hydrated sulfite ion has been determined to 1.53(1) Å by both methods. The hydrogen bonds between the three water molecules bound to each sulfite oxygen are only slightly stronger than those in bulk water. The sulfite ion can therefore be regarded as a weak structure maker. The water exchange rate is somewhat slower for the sulfite ion than for the sulfate ion, τ(0.5) = 3.2 and 2.6 ps, respectively. An even more striking observation in the angular radial distribution (ARD) functions is that the for sulfite ion the water exchange takes place in close vicinity of the lone electron-pair directed at its sides, while in principle no water exchange did take place of the water molecules hydrogen bound to sulfite oxygens during the simulation time. This is also confirmed when detailed pathway analysis is conducted. The simulation showed that the water molecules hydrogen bound to the sulfite oxygens can move inside the hydration shell to the area outside the lone electron-pair and there be exchanged. On the other hand, for the hydrated sulfate ion in aqueous solution one can clearly see from the ARD that the distribution of exchange events is symmetrical around the entire hydration sphere.

Flexible pulse delay control up to picosecond for high-intensity twin electron bunches

DOE PAGES

Zhang, Zhen; Ding, Yuantao; Emma, Paul; ...

2015-09-10

Two closely spaced electron bunches have attracted strong interest due to their applications in two color X-ray free-electron lasers as well as witness bunch acceleration in plasmas and dielectric structures. In this paper, we propose a new scheme of delay system to vary the time delay up to several picoseconds while not affecting the bunch compression. Numerical simulations based on the Linac Coherent Light Source are performed to demonstrate the feasibility of this method.

Polaronic transport in Ag-based quaternary chalcogenides

NASA Astrophysics Data System (ADS)

Wei, Kaya; Khabibullin, Artem R.; Stedman, Troy; Woods, Lilia M.; Nolas, George S.

2017-09-01

Low temperature resistivity measurements on dense polycrystalline quaternary chalcogenides Ag2+xZn1-xSnSe4, with x = 0, 0.1, and 0.3, indicate polaronic type transport which we analyze employing a two-component Holstein model based on itinerant and localized polaron contributions. Electronic structure property calculations via density functional theory simulations on Ag2ZnSnSe4 for both energetically similar kesterite and stannite structure types were also performed in order to compare our results to those of the compositionally similar but well known Cu2ZnSnSe4. This theoretical comparison is crucial in understanding the bonding that results in polaronic type transport for Ag2ZnSnSe4, as well as the structural and electronic properties of both crystal structure types. In addition to possessing this unique electronic transport, the thermal conductivity of Ag2ZnSnSe4 is low and decreases with increasing silver content. This work reveals unique structure-property relationships in materials that continue to be of interest for thermoelectric and photovoltaic applications.

Non-inductive current generation in fusion plasmas with turbulence

NASA Astrophysics Data System (ADS)

Wang, Weixing; Ethier, S.; Startsev, E.; Chen, J.; Hahm, T. S.; Yoo, M. G.

2017-10-01

It is found that plasma turbulence may strongly influence non-inductive current generation. This may have radical impact on various aspects of tokamak physics. Our simulation study employs a global gyrokinetic model coupling self-consistent neoclassical and turbulent dynamics with focus on electron current. Distinct phases in electron current generation are illustrated in the initial value simulation. In the early phase before turbulence develops, the electron bootstrap current is established in a time scale of a few electron collision times, which closely agrees with the neoclassical prediction. The second phase follows when turbulence begins to saturate, during which turbulent fluctuations are found to strongly affect electron current. The profile structure, amplitude and phase space structure of electron current density are all significantly modified relative to the neoclassical bootstrap current by the presence of turbulence. Both electron parallel acceleration and parallel residual stress drive are shown to play important roles in turbulence-induced current generation. The current density profile is modified in a way that correlates with the fluctuation intensity gradient through its effect on k//-symmetry breaking in fluctuation spectrum. Turbulence is shown to deduct (enhance) plasma self-generated current in low (high) collisionality regime, and the reduction of total electron current relative to the neoclassical bootstrap current increases as collisionality decreases. The implication of this result to the fully non-inductive current operation in steady state burning plasma regime should be investigated. Finally, significant non-inductive current is observed in flat pressure region, which is a nonlocal effect and results from turbulence spreading induced current diffusion. Work supported by U.S. DOE Contract DE-AC02-09-CH11466.

Jovian Plasmas Torus Interaction with Europa. Plasma Wake Structure and Effect of Inductive Magnetic Field: 3D Hybrid Kinetic Simulation

NASA Technical Reports Server (NTRS)

Lipatov, A. S.; Cooper, J F.; Paterson, W. R.; Sittler, E. C., Jr.; Hartle, R. E.; Simpson, David G.

2013-01-01

The hybrid kinetic model supports comprehensive simulation of the interaction between different spatial and energetic elements of the Europa moon-magnetosphere system with respect to a variable upstream magnetic field and flux or density distributions of plasma and energetic ions, electrons, and neutral atoms. This capability is critical for improving the interpretation of the existing Europa flyby measurements from the Galileo Orbiter mission, and for planning flyby and orbital measurements (including the surface and atmospheric compositions) for future missions. The simulations are based on recent models of the atmosphere of Europa (Cassidy et al., 2007; Shematovich et al., 2005). In contrast to previous approaches with MHD simulations, the hybrid model allows us to fully take into account the finite gyroradius effect and electron pressure, and to correctly estimate the ion velocity distribution and the fluxes along the magnetic field (assuming an initial Maxwellian velocity distribution for upstream background ions). Photoionization, electron-impact ionization, charge exchange and collisions between the ions and neutrals are also included in our model. We consider the models with Oþ þ and Sþ þ background plasma, and various betas for background ions and electrons, and pickup electrons. The majority of O2 atmosphere is thermal with an extended non-thermal population (Cassidy et al., 2007). In this paper, we discuss two tasks: (1) the plasma wake structure dependence on the parameters of the upstream plasma and Europa's atmosphere (model I, cases (a) and (b) with a homogeneous Jovian magnetosphere field, an inductive magnetic dipole and high oceanic shell conductivity); and (2) estimation of the possible effect of an induced magnetic field arising from oceanic shell conductivity. This effect was estimated based on the difference between the observed and modeled magnetic fields (model II, case (c) with an inhomogeneous Jovian magnetosphere field, an inductive magnetic dipole and low oceanic shell conductivity).

Examining the structural evolution of bicarbonate–water clusters: insights from photoelectron spectroscopy, basin-hopping structural search, and comparison with available IR spectral studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wen, Hui; Hou, Gao-Lei; Liu, Yi-Rong

2016-05-31

Bicarbonate serves a crucial biochemical role in the physiological pH buffering system and also has important atmospheric implications. In the current study, HCO 3 $-$(H 2O) n (n = 0-13) clusters were successfully produced via electrospray ionization of corresponding bulk salt solution, and were characterized by combining negative ion photoelectron spectroscopy and theoretical calculations. The photoelectron spectra reveal that the electron binding energy monotonically increases with the cluster size up to n = 10 and remains largely the same after n > 10. The photo-detaching feature of the solute HCO3$-$itself, which dominates in the small clusters, diminishes with increase ofmore » water coverage. Based on the charge distribution and molecular orbital analyses, the universal high electron binding energy tail that dominates in the larger clusters can be attributed to ionization of water. Thus, the transition of ionization from solute to solvent at the size larger than n=10 has been observed. Extensive theoretical structural search based on the Basin-Hopping unbiased method was carried out, and a plethora of low energy isomers have been obtained for each medium and large size. By comparing the simulated photoelectron spectra and calculated electron binding energies with the experiments, as well as by comparing the simulated infrared spectra with previously reported IR spectra, the probable global minima and the structural evolutionary routes are presented. The nature of bicarbonate-water interactions are mainly electrostatic as implied by the electron localization function (ELF) analysis.« less

Path Integral Monte Carlo Simulations of Warm Dense Matter and Plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Militzer, Burkhard

2018-01-13

New path integral Monte Carlo simulation (PIMC) techniques will be developed and applied to derive the equation of state (EOS) for the regime of warm dense matter and dense plasmas where existing first-principles methods cannot be applied. While standard density functional theory has been used to accurately predict the structure of many solids and liquids up to temperatures on the order of 10,000 K, this method is not applicable at much higher temperature where electronic excitations become important because the number of partially occupied electronic orbitals reaches intractably large numbers and, more importantly, the use of zero-temperature exchange-correlation functionals introducesmore » an uncontrolled approximation. Here we focus on PIMC methods that become more and more efficient with increasing temperatures and still include all electronic correlation effects. In this approach, electronic excitations increase the efficiency rather than reduce it. While it has commonly been assumed such methods can only be applied to elements without core electrons like hydrogen and helium, we recently showed how to extend PIMC to heavier elements by performing the first PIMC simulations of carbon and water plasmas [Driver, Militzer, Phys. Rev. Lett. 108 (2012) 115502]. Here we propose to continue this important development to extend the reach of PIMC simulations to yet heavier elements and also lower temperatures. The goal is to provide a robust first-principles simulation method that can accurately and efficiently study materials with excited electrons at solid-state densities in order to access parts of the phase diagram such the regime of warm dense matter and plasmas where so far only more approximate, semi-analytical methods could be applied.« less

Proton deflectometry of laser-driven relativistic electron jet from thin foil target

NASA Astrophysics Data System (ADS)

Huang, Chengkun; Palaniyappan, S.; Gautier, D. C.; Johnson, R. P.; Shimada, T.; Fernandez, J. C.; Tsung, F. S.; Mori, W. B.

2017-10-01

Near critical density relativistic electron jets from laser solid interaction carry currents approaching the Alfvén-limit and tens of kilo-Tesla magnetic fields. Such jets are often found in kinetic simulations with low areal density targets, but have not been confirmed experimentally. They may be used for X/gamma-ray generation and is also important for the understanding of post-transparency plasma dynamics. With a short-pulse probe beam at the Trident laser facility, we employed proton deflectometry to infer the jet's properties, structure and the long-time dynamics. We develop corresponding GEANT4 simulation model of the proton deflectometry, with input from the kinetic PIC simulations in 2D and quasi-3D geometry, to compare with the experimental radiography images. Detail comparison of the experimental and simulation features in the deflectometry will be discussed. Work supported by the LDRD program at LANL.

Transition in Electron Physics of Magnetic Reconnection in Weakly Collisional Plasma

NASA Astrophysics Data System (ADS)

Le, A.; Roytershteyn, V.; Karimabadi, H.; Daughton, W. S.; Egedal, J.; Forest, C.

2013-12-01

Using self-consistent fully kinetic simulations with a Monte-Carlo treatment of the Coulomb collision operator, we explore the transition between collisional and kinetic regimes of magnetic reconnection in high-Lundquist-number current sheets. Recent research in collisionless reconnection has shown that electron kinetic physics plays a key role in the evolution. Large-scale electron current sheets may form, leading to secondary island formation and turbulent flux rope interactions in 3D. The new collisional simulations demonstrate how increasing collisionality modifies or eliminates these electron structures in the kinetic regimes. Additional basic questions that are addressed include how the reconnection rate and the release of magnetic energy into electrons and ions vary with collisionality. The numerical study provides insight into reconnection in dense regions of the solar corona, the solar wind, and upcoming laboratory experiments at MRX (Princeton) and MPDX (UW-Madison). The implications of these results for studies of turbulence dissipation in weakly collisional plasmas are discussed.

Model for intensity calculation in electron guns

NASA Astrophysics Data System (ADS)

Doyen, O.; De Conto, J. M.; Garnier, J. P.; Lefort, M.; Richard, N.

2007-04-01

The calculation of the current in an electron gun structure is one of the main investigations involved in the electron gun physics understanding. In particular, various simulation codes exist but often present some important discrepancies with experiments. Moreover, those differences cannot be reduced because of the lack of physical information in these codes. We present a simple physical three-dimensional model, valid for all kinds of gun geometries. This model presents a better precision than all the other simulation codes and models encountered and allows the real understanding of the electron gun physics. It is based only on the calculation of the Laplace electric field at the cathode, the use of the classical Child-Langmuir's current density, and a geometrical correction to this law. Finally, the intensity versus voltage characteristic curve can be precisely described with only a few physical parameters. Indeed, we have showed that only the shape of the electric field at the cathode without beam, and a distance of an equivalent infinite planar diode gap, govern mainly the electron gun current generation.

Radiation from Relativistic Jets

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Mizuno, Y.; Hardee, P.; Sol, H.; Medvedev, M.; Zhang, B.; Nordlund, A.; Frederiksen, J. T.; Fishman, G. J.; Preece, R.

2008-01-01

Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., gamma-ray bursts (GRBs), active galactic nuclei (AGNs), and Galactic microquasar systems usually have power-law emission spectra. Recent PIC simulations of relativistic electron-ion (electron-positron) jets injected into a stationary medium show that particle acceleration occurs within the downstream jet. In the presence of relativistic jets, instabilities such as the Buneman instability, other two-streaming instability, and the Weibel (filamentation) instability create collisionless shocks, which are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The 'jitter' radiation from deflected electrons in small-scale magnetic fields has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation, a case of diffusive synchrotron radiation, may be important to understand the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

New aspects of whistler waves driven by an electron beam studied by a 3-D electromagnetic code

NASA Technical Reports Server (NTRS)

Nishikawa, Ken-Ichi; Buneman, Oscar; Neubert, Torsten

1994-01-01

We have restudied electron beam driven whistler waves with a 3-D electromagnetic particle code. The simulation results show electromagnetic whistler wave emissions and electrostatic beam modes like those observed in the Spacelab 2 electron beam experiment. It has been suggested in the past that the spatial bunching of beam electrons associated with the beam mode may directly generate whistler waves. However, the simulation results indicate several inconsistencies with this picture: (1) whistler waves continue to be generated even after the beam mode space charge modulation looses its coherence, (2) the parallel (to the background magnetic field) wavelength of the whistler wave is longer than that of the beam instability, and (3) the parallel phase velocity of the whistler wave is smaller than that of the beam mode. The complex structure of the whistler waves in the vicinity of the beam suggest that the transverse motion (gyration) of the beam and background electrons is also involved in the generation of whistler waves.

Microstructure, electronic structure and optical properties of combustion synthesized Co doped ZnO nanoparticles

NASA Astrophysics Data System (ADS)

Srinatha, N.; Nair, K. G. M.; Angadi, Basavaraj

2015-10-01

We report on the microstructure, electronic structure and optical properties of nanocrystalline Zn1-xCoxO (x=0, 0.01, 0.03, 0.05 and 0.07) particles prepared by solution combustion technique using L-Valine as fuel. The detailed structural and micro-structural studies were carried out by XRD, HRTEM and TEM-SAED respectively, which confirms the formation of single phased, nano-sized particles. The electronic structure was determined through NEXAFS and atomic multiplet calculations/simulations performed for various symmetries and valence states of 'Co' to determine the valance state, symmetry and crystal field splitting. The correlations between the experimental NEXAFS spectra and atomic multiplet simulations, confirms that, 'Co' present is in the 2+ valence state and substituted at the 'Zn' site in tetrahedral symmetry with crystal field splitting, 10Dq =-0.6 eV. The optical properties and 'Co' induced defect formation of as-synthesized materials were examined by using diffuse reflectance and Photoluminescence spectroscopy, respectively. Red-shift of band gap energy (Eg) was observed in Zn1-xCoxO samples due to Co (0.58 Å) substitution at Zn (0.60 Å) site of the host ZnO. Also, in PL spectra, a prominent pre-edge peak corresponds to ultraviolet (UV) emission around 360-370 nm was observed with Co concentration along with near band edge emission (NBE) of the wide band gap ZnO and all samples show emission in the blue region.

PENGEOM-A general-purpose geometry package for Monte Carlo simulation of radiation transport in material systems defined by quadric surfaces

NASA Astrophysics Data System (ADS)

Almansa, Julio; Salvat-Pujol, Francesc; Díaz-Londoño, Gloria; Carnicer, Artur; Lallena, Antonio M.; Salvat, Francesc

2016-02-01

The Fortran subroutine package PENGEOM provides a complete set of tools to handle quadric geometries in Monte Carlo simulations of radiation transport. The material structure where radiation propagates is assumed to consist of homogeneous bodies limited by quadric surfaces. The PENGEOM subroutines (a subset of the PENELOPE code) track particles through the material structure, independently of the details of the physics models adopted to describe the interactions. Although these subroutines are designed for detailed simulations of photon and electron transport, where all individual interactions are simulated sequentially, they can also be used in mixed (class II) schemes for simulating the transport of high-energy charged particles, where the effect of soft interactions is described by the random-hinge method. The definition of the geometry and the details of the tracking algorithm are tailored to optimize simulation speed. The use of fuzzy quadric surfaces minimizes the impact of round-off errors. The provided software includes a Java graphical user interface for editing and debugging the geometry definition file and for visualizing the material structure. Images of the structure are generated by using the tracking subroutines and, hence, they describe the geometry actually passed to the simulation code.

Single-cycle high-intensity electromagnetic pulse generation in the interaction of a plasma wakefield with regular nonlinear structures.

PubMed

Bulanov, S S; Esirkepov, T Zh; Kamenets, F F; Pegoraro, F

2006-03-01

The interaction of regular nonlinear structures (such as subcycle solitons, electron vortices, and wake Langmuir waves) with a strong wake wave in a collisionless plasma can be exploited in order to produce ultrashort electromagnetic pulses. The electromagnetic field of the nonlinear structure is partially reflected by the electron density modulations of the incident wake wave and a single-cycle high-intensity electromagnetic pulse is formed. Due to the Doppler effect the length of this pulse is much shorter than that of the nonlinear structure. This process is illustrated with two-dimensional particle-in-cell simulations. The considered laser-plasma interaction regimes can be achieved in present day experiments and can be used for plasma diagnostics.

The structure and properties of boron carbide ceramics modified by high-current pulsed electron-beam

NASA Astrophysics Data System (ADS)

Ivanov, Yuri; Tolkachev, Oleg; Petyukevich, Maria; Teresov, Anton; Ivanova, Olga; Ikonnikova, Irina; Polisadova, Valentina

2016-01-01

The present work is devoted to numerical simulation of temperature fields and the analysis of structural and strength properties of the samples surface layer of boron carbide ceramics treated by the high-current pulsed electron-beam of the submillisecond duration. The samples made of sintered boron carbide ceramics are used in these investigations. The problem of calculating the temperature field is reduced to solving the thermal conductivity equation. The electron beam density ranges between 8…30 J/cm2, while the pulse durations are 100…200 μs in numerical modelling. The results of modelling the temperature field allowed ascertaining the threshold parameters of the electron beam, such as energy density and pulse duration. The electron beam irradiation is accompanied by the structural modification of the surface layer of boron carbide ceramics either in the single-phase (liquid or solid) or two-phase (solid-liquid) states. The sample surface of boron carbide ceramics is treated under the two-phase state (solid-liquid) conditions of the structural modification. The surface layer is modified by the high-current pulsed electron-beam produced by SOLO installation at the Institute of High Current Electronics of the Siberian Branch of the Russian Academy of Sciences, Tomsk, Russia. The elemental composition and the defect structure of the modified surface layer are analyzed by the optical instrument, scanning electron and transmission electron microscopes. Mechanical properties of the modified layer are determined measuring its hardness and crack resistance. Research results show that the melting and subsequent rapid solidification of the surface layer lead to such phenomena as fragmentation due to a crack network, grain size reduction, formation of the sub-grained structure due to mechanical twinning, and increase of hardness and crack resistance.

3-D RPIC simulations of relativistic jets: Particle acceleration, magnetic field generation, and emission

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.

2006-01-01

Nonthermal radiation observed from astrophysical systems containing (relativistic) jets and shocks, e.g., supernova remnants, active galactic nuclei (AGNs), gamma-ray bursts (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that acceleration occurs within the downstream jet, rather than by the scattering of particles back and forth across the shock as in Fermi acceleration. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the .shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants. We will review recent PIC simulations which show particle acceleration in jets.

A Monte Carlo modeling on charging effect for structures with arbitrary geometries

NASA Astrophysics Data System (ADS)

Li, C.; Mao, S. F.; Zou, Y. B.; Li, Yong Gang; Zhang, P.; Li, H. M.; Ding, Z. J.

2018-04-01

Insulating materials usually suffer charging effects when irradiated by charged particles. In this paper, we present a Monte Carlo study on the charging effect caused by electron beam irradiation for sample structures with any complex geometry. When transporting in an insulating solid, electrons encounter elastic and inelastic scattering events; the Mott cross section and a Lorentz-type dielectric function are respectively employed to describe such scatterings. In addition, the band gap and the electron–long optical phonon interaction are taken into account. The electronic excitation in inelastic scattering causes generation of electron–hole pairs; these negative and positive charges establish an inner electric field, which in turn induces the drift of charges to be trapped by impurities, defects, vacancies etc in the solid, where the distributions of trapping sites are assumed to have uniform density. Under charging conditions, the inner electric field distorts electron trajectories, and the surface electric potential dynamically alters secondary electron emission. We present, in this work, an iterative modeling method for a self-consistent calculation of electric potential; the method has advantages in treating any structure with arbitrary complex geometry, in comparison with the image charge method—which is limited to a quite simple boundary geometry. Our modeling is based on: the combination of the finite triangle mesh method for an arbitrary geometry construction; a self-consistent method for the spatial potential calculation; and a full dynamic description for the motion of deposited charges. Example calculations have been done to simulate secondary electron yield of SiO2 for a semi-infinite solid, the charging for a heterostructure of SiO2 film grown on an Au substrate, and SEM imaging of a SiO2 line structure with rough surfaces and SiO2 nanoparticles with irregular shapes. The simulations have explored interesting interlaced charge layer distribution underneath the nanoparticle surface and the mechanism by which it is produced.

Tetrahedral bonding in amorphous carbon

NASA Astrophysics Data System (ADS)

McKenzie, D. R.

1996-12-01

Electron configurations close to the tetrahedral 0034-4885/59/12/002/img1 hybridization are found in pure amorphous carbon at a concentration which depends on preparation conditions. Tetrahedral bonding at levels of approximately 80% is found in amorphous carbons formed from beams of carbon ions with energies in a `window' between 20 eV and approximately 500 eV. Suitable techniques for its formation include cathodic arc deposition, ion beam deposition and laser ablation. Similar material appears to be formed by pressure treatment of fullerene precursors and by displacement damage in diamond. Highly tetrahedral forms of amorphous carbon (ta-C) show electronic, optical and mechanical properties which approach those of diamond and are quite different from amorphous carbons with low 0034-4885/59/12/002/img1 content. Useful techniques for determining the 0034-4885/59/12/002/img1 content include electron energy loss spectroscopy, electron and neutron diffraction and Raman spectroscopy. Considerable progress has been made in the understanding of this material by simulating its structure in the computer with a range of techniques from empirical potentials to ab initio quantum mechanics. The structure shows departures from an idealized glassy state of diamond which would have a random tetrahedral network structure as used to describe amorphous silicon and germanium. A surprising feature of the structure simulated using ab initio methods is the presence of small rings containing three or four 0034-4885/59/12/002/img1 carbon atoms. The electronic and optical properties are strongly influenced by the residual of 0034-4885/59/12/002/img5 carbon. Applications to electronic devices are at an early stage with the demonstration of photoconductivity and some simple junction devices. Applications as a wear resistant coating are promising, since the theoretically predicted high values of elastic constants, comparable to but less than those of diamond, are achieved experimentally, together with low friction coefficients.

Three-Dimensional Simulations of Electron Beams Focused by Periodic Permanent Magnets

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1999-01-01

A fully three-dimensional (3D) model of an electron beam focused by a periodic permanent magnet (PPM) stack has been developed. First, the simulation code MAFIA was used to model a PPM stack using the magnetostatic solver. The exact geometry of the magnetic focusing structure was modeled; thus, no approximations were made regarding the off-axis fields. The fields from the static solver were loaded into the 3D particle-in-cell (PIC) solver of MAFIA where fully 3D behavior of the beam was simulated in the magnetic focusing field. The PIC solver computes the time-integration of electromagnetic fields simultaneously with the time integration of the equations of motion of charged particles that move under the influence of those fields. Fields caused by those moving charges are also taken into account; thus, effects like space charge and magnetic forces between particles are fully simulated. The electron beam is simulated by a number of macro-particles. These macro-particles represent a given charge Q amounting to that of several million electrons in order to conserve computational time and memory. Particle motion is unrestricted, so particle trajectories can cross paths and move in three dimensions under the influence of 3D electric and magnetic fields. Correspondingly, there is no limit on the initial current density distribution of the electron beam, nor its density distribution at any time during the simulation. Simulation results including beam current density, percent ripple and percent transmission will be presented, and the effects current, magnetic focusing strength and thermal velocities have on beam behavior will be demonstrated using 3D movies showing the evolution of beam characteristics in time and space. Unlike typical beam optics models, this 3D model allows simulation of asymmetric designs such as non- circularly symmetric electrostatic or magnetic focusing as well as the inclusion of input/output couplers.

Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).

PubMed

Terrier, Cyril; Vitorge, Pierre; Gaigeot, Marie-Pierre; Spezia, Riccardo; Vuilleumier, Rodolphe

2010-07-28

Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kant, Deepender, E-mail: dkc@ceeri.ernet.in; Joshi, L. M.; Janyani, Vijay

The klystron is a well-known microwave amplifier which uses kinetic energy of an electron beam for amplification of the RF signal. There are some limitations of conventional single beam klystron such as high operating voltage, low efficiency and bulky size at higher power levels, which are very effectively handled in Multi Beam Klystron (MBK) that uses multiple low purveyance electron beams for RF interaction. Each beam propagates along its individual transit path through a resonant cavity structure. Multi-Beam klystron cavity design is a critical task due to asymmetric cavity structure and can be simulated by 3D code only. The presentmore » paper shall discuss the design of multi beam RF cavities for klystrons operating at 2856 MHz (S-band) and 5 GHz (C-band) respectively. The design approach uses some scaling laws for finding the electron beam parameters of the multi beam device from their single beam counter parts. The scaled beam parameters are then used for finding the design parameters of the multi beam cavities. Design of the desired multi beam cavity can be optimized through iterative simulations in CST Microwave Studio.« less

The linearly scaling 3D fragment method for large scale electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Zhengji; Meza, Juan; Lee, Byounghak

2009-07-28

The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

The Linearly Scaling 3D Fragment Method for Large Scale Electronic Structure Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Zhengji; Meza, Juan; Lee, Byounghak

2009-06-26

The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

Estimating loop length from CryoEM images at medium resolutions.

PubMed

McKnight, Andrew; Si, Dong; Al Nasr, Kamal; Chernikov, Andrey; Chrisochoides, Nikos; He, Jing

2013-01-01

De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5 Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2 Å. The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices.

Mechanisms of interfacial reactivity in near surface and extreme environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Ying; Balaska, Eric; Weare, John

The local water structure surrounding ions in aqueous solutions greatly affects their chemical properties such as reaction rates, ion association, and proton and electron transport. These properties result in the behavior of ions in natural aqueous environments. For example ore transport is facilitated by chloride ion pair formation and the reaction of ions in an interface is strongly dependent on the dehydration of the ion hydration shell. We are developing the use of high-­resolution XAFS observations and 1st principles based MD-­XAFS analysis (spectra simulated using 1st principle methods with no adjustable parameters, AIMD) to interpret the solution properties of stronglymore » interacting aqueous solutes under arbitrary pressure and temperature conditions. In the 1st principle MD-­XAFS method density functional theory (DFT) based MD simulations(Car and Parrinello, 1985) are used to generate a large ensemble of structural snap shots of the hydration region. These are then used to generate scattering intensities. I emphasize three points about this novel approach to analyzing XAFS data. 1st: As illustrated in Figure 1, the level of agreement between the calculated and observed intensities is considerably higher than has been obtained by any XAFS analysis to date (note 2nd shell region, R> 2 Å). 2nd: This result was obtained from a parameter free simulation with no fitting of the interaction potentials to any data. This supports the use of these methods for more difficult environments and more complex solutes (polyions). 3rd: New information about the shell structure (Figure 1) is now available because of this more detailed agreement. We note also that both multiple scattering and second shell features are well represented in the analysis. As far as we know this is the 1st analysis of second shell structure and multiple scattering. Excellent agreement has been obtained for most of the third row metal ions: Ca 2+, Zn 2+, Cu 2+, Ni 2+, Co 2+, Mn 2+, Fe 3+, Cr 3+. Calculations on these systems are demanding because of their open electronic shells, and high ionic charge. Principal Investigator: Professor John Weare (University of California, San Diego) The prediction of the interactions of geochemical fluids with minerals, nanoparticles, and colloids under extreme near surface conditions of temperature (T) and pressure (P) is a grand challenge research need in geosciences (U.S. DOE 2007, Basic Research Needs for Geosciences: Facilitating the 21st Energy Systems.). To evaluate the impact of these processes on energy production and management strategies it is necessary to have a high level of understanding of the interaction between complex natural fluids and mineral formations. This program emphasizes 1st principle parameter free simulations of complex chemical processes in solutions, in the mineral phase, and in the interfaces between these phases The development of new computational tools (with emphasis on oxide materials and reaction dynamics) tailored to treat wide range of conditions and time scales experienced in such geochemical applications is has been developed. Because of the sensitivity of the interaction in these systems to electronic structure and local bonding environments, and of the need to describe bond breaking/formation, our simulations are based on interactions calculated at the electronic structure level (ab-initio molecular dynamics, AIMD). The progress in the computational aspects of program may be summarized in terms of the following themes (objectives); Development of efficient parameter free dynamical simulation technology based on 1st principles force and energy calculations especially adapted for geochemical applications (e.g., mineral, interfaces and aqueous solutions) (continuing program); Calculation of the dynamics of water structure of in the surface-water interface of transition metal oxides and oxihydroxides; and Development of improved (beyond DFT+GGA) electronic structure calculations for minerals and the interface region that more accurately calculate electron correlation, spin density, and localization. The focus of the program is also on the iron oxide and oxihydroxide minerals and Fe 2+(aq)/Fe 3+(cr) oxidation in the mineral solution interface region. These methods included the development of model Hamilitonian methods that can be solved to near convergence for single site models (DMFT) and many-body perturbation methods (MP2, GW); Development of time decomposition methods to extend time scales of molecular dynamics (MD) simulations and support the use of high complexity electronic structure calculations (MP2, CCSD(T)) of forces for use in dynamical simulations where very high chemical accuracy is required (microsolvated reactions in absorbed surface layers); and The development of a new linear scaling finite element solver for eigenvalue problem that supports solution of quantum problems with unusual potential and boundary values. Application progress of the above new simulation technology to problems of geochemical interests includes; The prediction of metal oxide surface structure and the reduction/oxidation of Fe 3+(cr)/Fe 2+ (aq) in metal oxide (hematite, goethite)/solution interfaces. Result: water interacts strongly with the 001 Hematite surface; interaction of water with the 100 goethite is weak; The study of ion solvation and the composition of ion hydration shells under extreme conditions (focus on Fe 3+/2+, Al 3+ and Mg 2+ and their hydroxide speciation). Result: Ion association in water solutions can be calculated from 1st principle methods. Efficient sampling of the free energy requires more development; The continued development of new high resolution analysis of XAFS scattering of disordered systems (particularly Al, Mg) and of XANES calculations for aqueous ions. Result: EXAFS spectra can be calculated to high accuracy with DFT level dynamic simulations; The exploration of electron localization and electron transport in metal oxides (highly correlated materials). Result: Proper description of electron localization requires levels of calculation beyond DFT; and Localization of electrons in DFT type Hamiltonians was studied. Result: For very Dirac high exchange new solutions (New unphysical bifrucations) to the eigenvalue problem are found. The program was highly collaborative involving faculty and students in mathematics, physics and computer science departments as well as coworkers at the Pacific Northwest National Laboratories (PNNL). The students in this program had the opportunity to develop skills in the development of methods, the implementation of method on high performance parallel computers and the application of these methods to problem in geochemical science. Much of the software that was developed was incorporated in the NWchem software package maintained by PNNL.« less

Numerical analysis of azimuthal rotating spokes in a crossed-field discharge plasma

NASA Astrophysics Data System (ADS)

Kawashima, R.; Hara, K.; Komurasaki, K.

2018-03-01

Low-frequency rotating spokes are obtained in a cross-field discharge plasma using two-dimensional numerical simulations. A particle-fluid hybrid model is used to model the plasma flow in a configuration similar to a Hall thruster. It has been reported that the drift-diffusion approximation for an electron fluid results in an ill-conditioned matrix when solving for the potential because of the differences in the electron mobilities across the magnetic field and in the direction of the E × B drift. In this paper, we employ a hyperbolic approach that enables stable calculation, namely, better iterative convergence of the electron fluid model. Our simulation results show a coherent rotating structure propagating in the E × B direction with a phase velocity of 2500 m s‑1, which agrees with experimental data. The phase velocity obtained from the numerical simulations shows good agreement with that predicted by the dispersion relation of the gradient drift instability.

Laser beam coupling with capillary discharge plasma for laser wakefield acceleration applications

NASA Astrophysics Data System (ADS)

Bagdasarov, G. A.; Sasorov, P. V.; Gasilov, V. A.; Boldarev, A. S.; Olkhovskaya, O. G.; Benedetti, C.; Bulanov, S. S.; Gonsalves, A.; Mao, H.-S.; Schroeder, C. B.; van Tilborg, J.; Esarey, E.; Leemans, W. P.; Levato, T.; Margarone, D.; Korn, G.

2017-08-01

One of the most robust methods, demonstrated to date, of accelerating electron beams by laser-plasma sources is the utilization of plasma channels generated by the capillary discharges. Although the spatial structure of the installation is simple in principle, there may be some important effects caused by the open ends of the capillary, by the supplying channels etc., which require a detailed 3D modeling of the processes. In the present work, such simulations are performed using the code MARPLE. First, the process of capillary filling with cold hydrogen before the discharge is fired, through the side supply channels is simulated. Second, the simulation of the capillary discharge is performed with the goal to obtain a time-dependent spatial distribution of the electron density near the open ends of the capillary as well as inside the capillary. Finally, to evaluate the effectiveness of the beam coupling with the channeling plasma wave guide and of the electron acceleration, modeling of the laser-plasma interaction was performed with the code INF&RNO.

Unified analysis of optical absorption spectra of carotenoids based on a stochastic model.

PubMed

Uragami, Chiasa; Saito, Keisuke; Yoshizawa, Masayuki; Molnár, Péter; Hashimoto, Hideki

2018-05-03

The chemical structures of the carotenoid molecules are very simple and one might think that the electronic feature of it is easily predicted. However, it still has so much unknown information except the correlation between the electronic energy state and the length of effective conjugation chain of carotenoids. To investigate the electronic feature of the carotenoids, the most essential method is measuring the optical absorption spectra, but simulating it from the resonance Raman spectra is also the effective way. From this reason, we studied the optical absorption spectra as well as resonance Raman spectra of 15 different kinds of cyclic carotenoid molecules, recorded in tetrahydrofuran (THF) solutions at room temperature. The whole band shapes of the absorption spectra of all these carotenoid molecules were successfully simulated based on a stochastic model using Brownian oscillators. The parameters obtained from the simulation made it possible to discuss the intermolecular interaction between carotenoids and solvent THF molecules quantitatively. Copyright © 2018. Published by Elsevier Inc.

N2 Temperature of Vibration instrument for sounding rocket observation in the lower thermosphere

NASA Astrophysics Data System (ADS)

Kurihara, J.; Iwagami, N.; Oyama, K.-I.

2013-11-01

The N2 Temperature of Vibration (NTV) instrument was developed to study energetics and structure of the lower thermosphere, applying the Electron Beam Fluorescence (EBF) technique to measurements of vibrational temperature, rotational temperature and number density of atmospheric N2. The sounding rocket experiments using this instrument have been conducted four times, including one failure of the electron gun. Aerodynamic effects on the measurement caused by the supersonic motion of the rocket were analyzed quantitatively using three-dimensional simulation of Direct Simulation Monte Carlo (DSMC) method, and the absolute density profile was obtained through the correction of the spin modulation.

Evidence for out-of-equilibrium states in warm dense matter probed by x-ray Thomson scattering.

PubMed

Clérouin, Jean; Robert, Grégory; Arnault, Philippe; Ticknor, Christopher; Kress, Joel D; Collins, Lee A

2015-01-01

A recent and unexpected discrepancy between ab initio simulations and the interpretation of a laser shock experiment on aluminum, probed by x-ray Thomson scattering (XRTS), is addressed. The ion-ion structure factor deduced from the XRTS elastic peak (ion feature) is only compatible with a strongly coupled out-of-equilibrium state. Orbital free molecular dynamics simulations with ions colder than the electrons are employed to interpret the experiment. The relevance of decoupled temperatures for ions and electrons is discussed. The possibility that it mimics a transient, or metastable, out-of-equilibrium state after melting is also suggested.

Institute for Science and Engineering Simulation (ISES)

DTIC Science & Technology

2015-12-18

performance and other functionalities such as electrical , magnetic, optical, thermal, biological, chemical, and so forth. Structural integrity...transmission electron microscopy (HRSTEM) and three-dimensional atom probe (3DAP) tomography , the true atomic scale structure and change in chemical...atom probe tomography (3DAP) techniques, has permitted characterizing and quantifying the multimodal size distribution of different generations of γ

III-Nitride, SiC and Diamond Materials for Electronic Devices. Symposium Held April 8-12 1996, San Francisco, California, U.S.A. Volume 423.

DTIC Science & Technology

1996-12-01

gallium, nitrogen and gallium nitride structures. Thus it can be shown to be transferable and efficient for predictive molecular -dynamic simulations on...potentials and forces for the molecular dynamics simulations are derived by means of a density-functional based nonorthogonal tight-binding (DF-TB) scheme...LDA). Molecular -dynamics simulations for determining the different reconstructions of the SiC surface use the slab method (two-dimensional periodic

Bypassing the Kohn-Sham equations with machine learning.

PubMed

Brockherde, Felix; Vogt, Leslie; Li, Li; Tuckerman, Mark E; Burke, Kieron; Müller, Klaus-Robert

2017-10-11

Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative. The present work overcomes this difficulty by directly learning the density-potential and energy-density maps for test systems and various molecules. We perform the first molecular dynamics simulation with a machine-learned density functional on malonaldehyde and are able to capture the intramolecular proton transfer process. Learning density models now allows the construction of accurate density functionals for realistic molecular systems.Machine learning allows electronic structure calculations to access larger system sizes and, in dynamical simulations, longer time scales. Here, the authors perform such a simulation using a machine-learned density functional that avoids direct solution of the Kohn-Sham equations.

Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble

NASA Astrophysics Data System (ADS)

Zheng, Lixin; Chen, Mohan; Sun, Zhaoru; Ko, Hsin-Yu; Santra, Biswajit; Dhuvad, Pratikkumar; Wu, Xifan

2018-04-01

We perform ab initio molecular dynamics (AIMD) simulation of liquid water in the canonical ensemble at ambient conditions using the strongly constrained and appropriately normed (SCAN) meta-generalized-gradient approximation (GGA) functional approximation and carry out systematic comparisons with the results obtained from the GGA-level Perdew-Burke-Ernzerhof (PBE) functional and Tkatchenko-Scheffler van der Waals (vdW) dispersion correction inclusive PBE functional. We analyze various properties of liquid water including radial distribution functions, oxygen-oxygen-oxygen triplet angular distribution, tetrahedrality, hydrogen bonds, diffusion coefficients, ring statistics, density of states, band gaps, and dipole moments. We find that the SCAN functional is generally more accurate than the other two functionals for liquid water by not only capturing the intermediate-range vdW interactions but also mitigating the overly strong hydrogen bonds prescribed in PBE simulations. We also compare the results of SCAN-based AIMD simulations in the canonical and isothermal-isobaric ensembles. Our results suggest that SCAN provides a reliable description for most structural, electronic, and dynamical properties in liquid water.

HRTEM Analysis of Crystallographic Defects in CdZnTe Single Crystal

NASA Astrophysics Data System (ADS)

Yasar, Bengisu; Ergunt, Yasin; Kabukcuoglu, Merve Pinar; Parlak, Mehmet; Turan, Rasit; Kalay, Yunus Eren

2018-01-01

In recent years, CdZnTe has attracted much attention due to its superior electrical and structural properties for room-temperature operable gamma and x-ray detectors. However, CdZnTe (CZT) material has often suffered from crystallographic defects encountered during the growth and post-growth processes. The identification and structural characterization of these defects is crucial to synthesize defect-free CdZnTe single crystals. In this study, Cd0.95 Zn0.05 Te single crystals were grown using a three-zone vertical Bridgman system. The single crystallinity of the material was ensured by using x-ray diffraction measurements. High-resolution electron microscopy (HRTEM) was used to characterize the nano-scale defects on the CdZnTe matrix. The linear defects oriented along the ⟨211⟩ direction were examined by transmission electron microscopy (TEM) and the corresponding HRTEM image simulations were performed by using a quantitative scanning TEM simulation package.

Body-centered orthorhombic C 16 : A novel topological node-line semimetal

DOE PAGES

Wang, Jian -Tao; Weng, Hongming; Nie, Simin; ...

2016-05-11

We identify by ab initio calculations a novel topological semimetal carbon phase in all-sp 2 bonding networks with a 16-atom body-centered orthorhombic unit cell, termed bco-C 16. Total-energy calculations show that bco-C 16 is comparable to solid fcc-C 60 in energetic stability, and phonon and molecular dynamics simulations confirm its dynamical stability. This all-sp 2 carbon allotrope can be regarded as a three-dimensional modification of graphite, and its simulated x-ray diffraction (XRD) pattern matches well a previously unexplained diffraction peak in measured XRD spectra of detonation and chimney soot, indicating its presence in the specimen. Electronic band structure calculations revealmore » that bco-C 16 is a topological node-line semimetal with a single nodal ring. Lastly, these findings establish a novel carbon phase with intriguing structural and electronic properties of fundamental significance and practical interest.« less

First-principles simulation on thermoelectric propertiesof transition metal dichalcogenide monolayers

NASA Astrophysics Data System (ADS)

Nakamura, Koichi

2018-06-01

Thermoelectric properties of transition metal dichalcogenide (TMDC) monolayer models, such as Seebeck coefficient and lattice heat capacity, were simulated on the basis of first-principles calculations. The calculated Seebeck coefficients are appropriate for the thermoelectric element of all the TMDC monolayer models introduced in this study. In the MoX2/WX2 (X = S, Se, and Te) heterojunction structure, carrier electrons and holes are respectively distributed in the MoX2 and WX2 regions by adopting a common Fermi energy for both electronic structures. In particular, in the X = Te case, the practical carrier concentration with a large Seebeck coefficient can be evaluated without doping. The lattice heat capacities and their temperature dependence tendencies can be classified on the basis of the minimum frequencies of the optical modes. The quotient of the lattice thermal conductivity over the phonon relaxation time gives the temperature-independent specific values according to the kind of TMDC monolayer.

Scaling of Guide-Field Magnetic Reconnection using Anisotropic Fluid Closure

NASA Astrophysics Data System (ADS)

Ohia, O.; Egedal, J.; Lukin, V. S.; Daughton, W.; Le, A.

2012-10-01

Collisionless magnetic reconnection, a process linked to solar flares, coronal mass ejections, and magnetic substorms, has been widely studied through fluid models and fully kinetic simulations. While fluid models often reproduce the fast reconnection rate of fully kinetic simulations, significant differences are observed in the structure of the reconnection regions [1]. However, guide-field fluid simulations implementing new equations of state that accurately account for the anisotropic electron pressure [2] reproduce the detailed reconnection region observed in kinetic simulations [3]. Implementing this two-fluid simulation using the HiFi framework [4], we study the force balance of the electron layers in guide-field reconnection and derive scaling laws for their characteristics.[1ex] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0ex] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0ex] [3] Ohia O, et al., Phys. Rev. Lett. In Press (2012).[0ex] [4] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011)

Effect of hydrostatic pressure on the structural and electronic properties of Cd{sub 0.75}Cr{sub 0.25}S

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rani, Anita; Kaur, Kulwinder; Kumar, Ranjan

In this paper we present the results obtained from first principle calculations of the effect of hydrostatic pressure on the structural and electronic properties of Cd{sub 1-x}Cr{sub x}S diluted magnetic semiconductor in Zinc Blende (B3) phase at x=0.25. High pressure behavior of Cd{sub 1-x}Cr{sub x}S has been investigated between 0 GPa to 100 GPa The calculations have been performed using Density functional theory as implemented in the Spanish Initiative for Electronic Simulations with Thousands of Atoms code using local density approximation as exchange-correlation (XC) potential. Calculated electronic band structures of Cd{sub 1-x}Cr{sub x}S are discussed in terms of contribution ofmore » Cr 3d{sup 5} 4s{sup 1}, Cd 4d{sup 10} 5s{sup 2}, S 3s{sup 2} 3p{sup 4} orbital’s. Study of band structures shows half-metallic ferromagnetic nature of Cd{sub 0.75}Cr{sub 0.25}S with 100% spin polarization. Under application of external pressure, the valence band and conduction band are shifted upward which leads to modification of electronic structure.« less

Filamentation of plasma in the auroral region by an ion-ion instability: A process for the formation of bidimensional potential structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mottez, F.; Chanteur, G.; Roux, A.

1992-07-01

A two-dimensional, explicit, electrostatic particle code is used to investigate the nonlinear behavior of electrostatic ion waves generated by an ion beam flowing through a thermal ion and electron background in a strongly magnetized plasma ({omega}{sub ce} {much gt} {omega}{sub pe} where {omega}{sub ce} and {omega}{sub pe} are the electron gyrofrequency and the plasma frequency). To follow the nonlinear evolution of these ions waves, a long-lasting simulation is run with a large simulation grid: 128 {times} 512{lambda}{sub d}. Beam ions are shown to generate oblique waves. The nonlinear beatings between these oblique waves produce purely transverse waves, which leads tomore » a strong modulation of the density and of the electric potential in a direction transverse to the magnetic field. The transverse scale of these essentially field-aligned filaments is L{sub {perpendicular}} = 10 {rho}{sub i} where {rho}{sub i} is the ion Larmor radius of beam ions. Within these filaments, relatively stable field-aligned density and potential structures develop. The typical size, along the magnetic field, of these structures is L{sub {parallel}} = 10 {lambda}{sub d}, the density is modulated by 30%, and the electric potential is as large as T{sub e} within these structures. Unlike the potential structures that develop in a two-component plasma with downgoing electrons, these structures move upward. These characteristics are in good agreement with the weak double layers recently detected by Viking.« less

The double layers in the plasma sheet boundary layer during magnetic reconnection

NASA Astrophysics Data System (ADS)

Guo, J.; Yu, B.

2014-11-01

We studied the evolutions of double layers which appear after the magnetic reconnection through two-dimensional electromagnetic particle-in-cell simulation. The simulation results show that the double layers are formed in the plasma sheet boundary layer after magnetic reconnection. At first, the double layers which have unipolar structures are formed. And then the double layers turn into bipolar structures, which will couple with another new weak bipolar structure. Thus a new double layer or tripolar structure comes into being. The double layers found in our work are about several ten Debye lengths, which accords with the observation results. It is suggested that the electron beam formed during the magnetic reconnection is responsible for the production of the double layers.

Molecular dynamics simulations give insight into the conformational change, complex formation, and electron transfer pathway for cytochrome P450 reductase

PubMed Central

Sündermann, Axel; Oostenbrink, Chris

2013-01-01

Cytochrome P450 reductase (CYPOR) undergoes a large conformational change to allow for an electron transfer to a redox partner to take place. After an internal electron transfer over its cofactors, it opens up to facilitate the interaction and electron transfer with a cytochrome P450. The open conformation appears difficult to crystallize. Therefore, a model of a human CYPOR in the open conformation was constructed to be able to investigate the stability and conformational change of this protein by means of molecular dynamics simulations. Since the role of the protein is to provide electrons to a redox partner, the interactions with cytochrome P450 2D6 (2D6) were investigated and a possible complex structure is suggested. Additionally, electron pathway calculations with a newly written program were performed to investigate which amino acids relay the electrons from the FMN cofactor of CYPOR to the HEME of 2D6. Several possible interacting amino acids in the complex, as well as a possible electron transfer pathway were identified and open the way for further investigation by site directed mutagenesis studies. PMID:23832577

Excess electrons in methanol clusters: Beyond the one-electron picture

NASA Astrophysics Data System (ADS)

Pohl, Gábor; Mones, Letif; Turi, László

2016-10-01

We performed a series of comparative quantum chemical calculations on various size negatively charged methanol clusters, ("separators=" CH 3 OH ) n - . The clusters are examined in their optimized geometries (n = 2-4), and in geometries taken from mixed quantum-classical molecular dynamics simulations at finite temperature (n = 2-128). These latter structures model potential electron binding sites in methanol clusters and in bulk methanol. In particular, we compute the vertical detachment energy (VDE) of an excess electron from increasing size methanol cluster anions using quantum chemical computations at various levels of theory including a one-electron pseudopotential model, several density functional theory (DFT) based methods, MP2 and coupled-cluster CCSD(T) calculations. The results suggest that at least four methanol molecules are needed to bind an excess electron on a hydrogen bonded methanol chain in a dipole bound state. Larger methanol clusters are able to form stronger interactions with an excess electron. The two simulated excess electron binding motifs in methanol clusters, interior and surface states, correlate well with distinct, experimentally found VDE tendencies with size. Interior states in a solvent cavity are stabilized significantly stronger than electron states on cluster surfaces. Although we find that all the examined quantum chemistry methods more or less overestimate the strength of the experimental excess electron stabilization, MP2, LC-BLYP, and BHandHLYP methods with diffuse basis sets provide a significantly better estimate of the VDE than traditional DFT methods (BLYP, B3LYP, X3LYP, PBE0). A comparison to the better performing many electron methods indicates that the examined one-electron pseudopotential can be reasonably used in simulations for systems of larger size.

Excess electrons in methanol clusters: Beyond the one-electron picture.

PubMed

Pohl, Gábor; Mones, Letif; Turi, László

2016-10-28

We performed a series of comparative quantum chemical calculations on various size negatively charged methanol clusters, CH 3 OH n - . The clusters are examined in their optimized geometries (n = 2-4), and in geometries taken from mixed quantum-classical molecular dynamics simulations at finite temperature (n = 2-128). These latter structures model potential electron binding sites in methanol clusters and in bulk methanol. In particular, we compute the vertical detachment energy (VDE) of an excess electron from increasing size methanol cluster anions using quantum chemical computations at various levels of theory including a one-electron pseudopotential model, several density functional theory (DFT) based methods, MP2 and coupled-cluster CCSD(T) calculations. The results suggest that at least four methanol molecules are needed to bind an excess electron on a hydrogen bonded methanol chain in a dipole bound state. Larger methanol clusters are able to form stronger interactions with an excess electron. The two simulated excess electron binding motifs in methanol clusters, interior and surface states, correlate well with distinct, experimentally found VDE tendencies with size. Interior states in a solvent cavity are stabilized significantly stronger than electron states on cluster surfaces. Although we find that all the examined quantum chemistry methods more or less overestimate the strength of the experimental excess electron stabilization, MP2, LC-BLYP, and BHandHLYP methods with diffuse basis sets provide a significantly better estimate of the VDE than traditional DFT methods (BLYP, B3LYP, X3LYP, PBE0). A comparison to the better performing many electron methods indicates that the examined one-electron pseudopotential can be reasonably used in simulations for systems of larger size.

Efficient generation and transportation of energetic electrons in a carbon nanotube array target

NASA Astrophysics Data System (ADS)

Ji, Yanling; Jiang, Gang; Wu, Weidong; Wang, Chaoyang; Gu, Yuqiu; Tang, Yongjian

2010-01-01

Laser-driven energetic electron propagation in a carbon nanotube-array target is investigated using two-dimensional particle-in-cell simulations. Energetic electrons are efficiently generated when the array is irradiated by a short intense laser pulse. Confined and guided transportation of energetic electrons in the array is achieved by exploiting strong transient electromagnetic fields created at the wall surfaces of nanotubes. The underlying mechanisms are discussed in detail. Our investigation shows that the laser energy can be transferred more effectively to the target electrons in the array than that of in the flat foil due to the hole structures in the array.

Investigation of electronic structures and optical properties of β -Si3N4 doped with IV A elements: A first-principles simulation

NASA Astrophysics Data System (ADS)

Lu, Xuefeng; Gao, Xu; Ren, Junqiang; Li, Cuixia; Guo, Xin; Wei, Yupeng; La, Peiqing

2018-04-01

Based on first-principles simulations with the generalized gradient approximation (GGA) of the Perdew-Burke-Ernzerhof (PBE) functional, we studied the electronic structures and optical properties of hexagonal silicon nitride (β-Si3N4) doped with IV A elements, C, Ge, Sn and Pb. It was found that the Ge-doped system is characterized by a more stable structure with a lower formation energy of 2.584 eV compared with those of the C-, Sn- and Pb-doped systems of 3.877 eV, 5.249 eV and 7.672 eV, respectively. The band gap (EG) of the Pb-doped system was the lowest at 1.6 eV, displaying semiconducting characteristics. Additionally, there was a transition from a direct band gap to an indirect band gap in the C-doped system. Charge difference density analysis showed that the covalent property of the C-N bonds was enhanced by expansion of the electron-free region and the larger Mulliken population values of 0.71 and 0.86. Furthermore, lower absorption and reflectivity peaks at 11.30 eV were observed for the C-doped system, demonstrating its broader potential for application in photoelectric and microelectronic devices.

STEM-EELS analysis of multipole surface plasmon modes in symmetry-broken AuAg nanowire dimers

NASA Astrophysics Data System (ADS)

Schubert, Ina; Sigle, Wilfried; van Aken, Peter A.; Trautmann, Christina; Toimil-Molares, Maria Eugenia

2015-03-01

Surface plasmon coupling in nanowires separated by small gaps generates high field enhancements at the position of the gap and is thus of great interest for sensing applications. It is known that the nanowire dimensions and in particular the symmetry of the structures has strong influence on the plasmonic properties of the dimer structure. Here, we report on multipole surface plasmon coupling in symmetry-broken AuAg nanowire dimers. Our dimers, consisting of two nanowires with different lengths and separated by gaps of only 10 to 30 nm, were synthesized by pulsed electrochemical deposition in ion track-etched polymer templates. Electron energy-loss spectroscopy in scanning transmission electron microscopy allows us to resolve up to nine multipole order surface plasmon modes of these dimers spectrally separated from each other. The spectra evidence plasmon coupling between resonances of different multipole order, resulting in the generation of additional plasmonic modes. Since such complex structures require elaborated synthesis techniques, dimer structures with complex composition, morphology and shape are created. We demonstrate that finite element simulations on pure Au dimers can predict the generated resonances in the fabricated structures. The excellent agreement of our experiment on AuAg dimers with finite integration simulations using CST microwave studio manifests great potential to design complex structures for sensing applications.

A universal preconditioner for simulating condensed phase materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Packwood, David; Ortner, Christoph, E-mail: c.ortner@warwick.ac.uk; Kermode, James, E-mail: j.r.kermode@warwick.ac.uk

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor ofmore » two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.« less

Particle Acceleration in a Statistically Modeled Solar Active-Region Corona

NASA Astrophysics Data System (ADS)

Toutounzi, A.; Vlahos, L.; Isliker, H.; Dimitropoulou, M.; Anastasiadis, A.; Georgoulis, M.

2013-09-01

Elaborating a statistical approach to describe the spatiotemporally intermittent electric field structures formed inside a flaring solar active region, we investigate the efficiency of such structures in accelerating charged particles (electrons). The large-scale magnetic configuration in the solar atmosphere responds to the strong turbulent flows that convey perturbations across the active region by initiating avalanche-type processes. The resulting unstable structures correspond to small-scale dissipation regions hosting strong electric fields. Previous research on particle acceleration in strongly turbulent plasmas provides a general framework for addressing such a problem. This framework combines various electromagnetic field configurations obtained by magnetohydrodynamical (MHD) or cellular automata (CA) simulations, or by employing a statistical description of the field's strength and configuration with test particle simulations. Our objective is to complement previous work done on the subject. As in previous efforts, a set of three probability distribution functions describes our ad-hoc electromagnetic field configurations. In addition, we work on data-driven 3D magnetic field extrapolations. A collisional relativistic test-particle simulation traces each particle's guiding center within these configurations. We also find that an interplay between different electron populations (thermal/non-thermal, ambient/injected) in our simulations may also address, via a re-acceleration mechanism, the so called `number problem'. Using the simulated particle-energy distributions at different heights of the cylinder we test our results against observations, in the framework of the collisional thick target model (CTTM) of solar hard X-ray (HXR) emission. The above work is supported by the Hellenic National Space Weather Research Network (HNSWRN) via the THALIS Programme.

Statistical Exploration of Electronic Structure of Molecules from Quantum Monte-Carlo Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prabhat, Mr; Zubarev, Dmitry; Lester, Jr., William A.

In this report, we present results from analysis of Quantum Monte Carlo (QMC) simulation data with the goal of determining internal structure of a 3N-dimensional phase space of an N-electron molecule. We are interested in mining the simulation data for patterns that might be indicative of the bond rearrangement as molecules change electronic states. We examined simulation output that tracks the positions of two coupled electrons in the singlet and triplet states of an H2 molecule. The electrons trace out a trajectory, which was analyzed with a number of statistical techniques. This project was intended to address the following scientificmore » questions: (1) Do high-dimensional phase spaces characterizing electronic structure of molecules tend to cluster in any natural way? Do we see a change in clustering patterns as we explore different electronic states of the same molecule? (2) Since it is hard to understand the high-dimensional space of trajectories, can we project these trajectories to a lower dimensional subspace to gain a better understanding of patterns? (3) Do trajectories inherently lie in a lower-dimensional manifold? Can we recover that manifold? After extensive statistical analysis, we are now in a better position to respond to these questions. (1) We definitely see clustering patterns, and differences between the H2 and H2tri datasets. These are revealed by the pamk method in a fairly reliable manner and can potentially be used to distinguish bonded and non-bonded systems and get insight into the nature of bonding. (2) Projecting to a lower dimensional subspace ({approx}4-5) using PCA or Kernel PCA reveals interesting patterns in the distribution of scalar values, which can be related to the existing descriptors of electronic structure of molecules. Also, these results can be immediately used to develop robust tools for analysis of noisy data obtained during QMC simulations (3) All dimensionality reduction and estimation techniques that we tried seem to indicate that one needs 4 or 5 components to account for most of the variance in the data, hence this 5D dataset does not necessarily lie on a well-defined, low dimensional manifold. In terms of specific clustering techniques, K-means was generally useful in exploring the dataset. The partition around medoids (pam) technique produced the most definitive results for our data showing distinctive patterns for both a sample of the complete data and time-series. The gap statistic with tibshirani criteria did not provide any distinction across the 2 dataset. The gap statistic w/DandF criteria, Model based clustering and hierarchical modeling simply failed to run on our datasets. Thankfully, the vanilla PCA technique was successful in handling our entire dataset. PCA revealed some interesting patterns for the scalar value distribution. Kernel PCA techniques (vanilladot, RBF, Polynomial) and MDS failed to run on the entire dataset, or even a significant fraction of the dataset, and we resorted to creating an explicit feature map followed by conventional PCA. Clustering using K-means and PAM in the new basis set seems to produce promising results. Understanding the new basis set in the scientific context of the problem is challenging, and we are currently working to further examine and interpret the results.« less

Assessment of pseudo-bilayer structures in the heterogate germanium electron-hole bilayer tunnel field-effect transistor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Padilla, J. L., E-mail: jose.padilladelatorre@epfl.ch; Alper, C.; Ionescu, A. M.

2015-06-29

We investigate the effect of pseudo-bilayer configurations at low operating voltages (≤0.5 V) in the heterogate germanium electron-hole bilayer tunnel field-effect transistor (HG-EHBTFET) compared to the traditional bilayer structures of EHBTFETs arising from semiclassical simulations where the inversion layers for electrons and holes featured very symmetric profiles with similar concentration levels at the ON-state. Pseudo-bilayer layouts are attained by inducing a certain asymmetry between the top and the bottom gates so that even though the hole inversion layer is formed at the bottom of the channel, the top gate voltage remains below the required value to trigger the formation of themore » inversion layer for electrons. Resulting benefits from this setup are improved electrostatic control on the channel, enhanced gate-to-gate efficiency, and higher I{sub ON} levels. Furthermore, pseudo-bilayer configurations alleviate the difficulties derived from confining very high opposite carrier concentrations in very thin structures.« less

Neutral-current weak interactions at an EIC

DOE PAGES

Zhao, Y. X.; Deshpande, A.; Huang, J.; ...

2017-03-21

Here, a simulation study of measurements of neutral current structure functions of the nucleon at the future high-energy and high-luminosity polarized electron-ion collider (EIC) is presented. A new series of γ-Z interference structure functions, F γZ 1, F γZ 3, g γZ 1, g γZ 5 become accessible via parity-violating asymmetries in polarized electron-nucleon deep inelastic scattering (DIS). Within the context of the quark-parton model, they provide a unique and, in some cases, yet-unmeasured combination of unpolarized and polarized parton distribution functions. The uncertainty projections for these structure functions using electron-proton collisions are considered for various EIC beam energy configurations.more » Also presented are uncertainty projections for measurements of the weak mixing angle sin 2θ W using electron-deuteron collisions which cover a much higher Q 2 than that accessible in fixed target measurements. QED and QCD radiative corrections and effects of detector smearing are included with the calculations.« less

Constructing superconductors by graphene Chern-Simons wormholes

NASA Astrophysics Data System (ADS)

Capozziello, Salvatore; Pincak, Richard; Saridakis, Emmanuel N.

2018-03-01

We propose a new model which simulates the motion of free electrons in graphene by the evolution of strings on manifolds. In this model, molecules which constitute sheets of graphene are polygonal point-like structures which build (N + 1) -dimensional manifolds. By breaking the gravitational-analogue symmetry of graphene sheets, we show that two separated child sheets and a Chern-Simons bridge are produced giving rise to a wormhole. In this structure, free electrons are transmitted from one child sheet to the other producing superconductivity. An analogue between "effective gravitons" and "Cooper pairs" is found. In principle, this phenomenology provides the possibility to construct superconductor structures by using the analogue of cosmological models.

Pb chains on reconstructed Si(335) surface

NASA Astrophysics Data System (ADS)

Krawiec, Mariusz

2009-04-01

The structural and electronic properties of Si(335)-Au surface decorated with Pb atoms are studied by means of density-functional theory. The resulting structural model features Pb atoms bonded to neighboring Si and Au surface atoms, forming monoatomic chain located 0.2 nm above the surface. The presence of Pb chain leads to a strong rebonding of Si atoms at the step edge. The fact that Pb atoms occupy positions in the middle of terrace is consistent with scanning tunneling microscopy (STM) data and also confirmed by simulated STM images. The calculated band structure clearly shows one-dimensional metallic character. The calculated electronic bands remain in very good agreement with photoemission data.

Response to 'Comment on 'Three-dimensional numerical investigation of electron transport with rotating spoke in a cylindrical anode layer Hall plasma accelerator''[Phys. Plasmas 20, 014701 (2013)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, D. L.; Qiu, X. M.; Geng, S. F.

The numerical simulation described in our paper [D. L. Tang et al., Phys. Plasmas 19, 073519 (2012)] shows a rotating dense plasma structure, which is the critical characteristic of the rotating spoke. The simulated rotating spoke has a frequency of 12.5 MHz with a rotational speed of {approx}1.0 Multiplication-Sign 10{sup 6} m/s on the surface of the anode. Accompanied by the almost uniform azimuthal ion distribution, the non-axisymmetric electron distribution introduces two azimuthal electric fields with opposite directions. The azimuthal electric fields have the same rotational frequency and speed together with the rotating spoke. The azimuthal electric fields excite themore » axial electron drift upstream and downstream due to the additional E{sub {theta}} x B field and then the axial shear flow is generated. The axial local charge separation induced by the axial shear electron flow may be compensated by the azimuthal electron transport, finally resulting in the azimuthal electric field rotation and electron transport with the rotating spoke.« less

Phase-field model of insulator-to-metal transition in VO2 under an electric field

NASA Astrophysics Data System (ADS)

Shi, Yin; Chen, Long-Qing

2018-05-01

The roles of an electric field and electronic doping in insulator-to-metal transitions are still not well understood. Here we formulated a phase-field model of insulator-to-metal transitions by taking into account both structural and electronic instabilities as well as free electrons and holes in VO2, a strongly correlated transition-metal oxide. Our phase-field simulations demonstrate that in a VO2 slab under a uniform electric field, an abrupt universal resistive transition occurs inside the supercooling region, in sharp contrast to the conventional Landau-Zener smooth electric breakdown. We also show that hole doping may decouple the structural and electronic phase transitions in VO2, leading to a metastable metallic monoclinic phase which could be stabilized through a geometrical confinement and the size effect. This work provides a general mesoscale thermodynamic framework for understanding the influences of electric field, electronic doping, and stress and strain on insulator-to-metal transitions and the corresponding mesoscale domain structure evolution in VO2 and related strongly correlated systems.

Effects of two-step Mg doping in p-GaN on efficiency characteristics of InGaN blue light-emitting diodes without AlGaN electron-blocking layers

NASA Astrophysics Data System (ADS)

Ryu, Han-Youl; Lee, Jong-Moo

2013-05-01

A light-emitting diode (LED) structure containing p-type GaN layers with two-step Mg doping profiles is proposed to achieve high-efficiency performance in InGaN-based blue LEDs without any AlGaN electron-blocking-layer structures. Photoluminescence and electroluminescence (EL) measurement results show that, as the hole concentration in the p-GaN interlayer between active region and the p-GaN layer increases, defect-related nonradiative recombination increases, while the electron current leakage decreases. Under a certain hole-concentration condition in the p-GaN interlayer, the electron leakage and active region degradation are optimized so that high EL efficiency can be achieved. The measured efficiency characteristics are analyzed and interpreted using numerical simulations.

Numerical simulation and analysis of electromagnetic-wave absorption of a plasma slab created by a direct-current discharge with gridded anode

NASA Astrophysics Data System (ADS)

Yuan, Chengxun; Tian, Ruihuan; Eliseev, S. I.; Bekasov, V. S.; Bogdanov, E. A.; Kudryavtsev, A. A.; Zhou, Zhongxiang

2018-03-01

In this paper, we present investigation of a direct-current discharge with a gridded anode from the point of view of using it as a means of creating plasma coating that could efficiently absorb incident electromagnetic (EM) waves. A single discharge cell consists of two parallel plates, one of which (anode) is gridded. Electrons emitted from the cathode surface are accelerated in the short interelectrode gap and are injected into the post-anode space, where they lose acquired energy on ionization and create plasma. Numerical simulations were used to investigate the discharge structure and obtain spatial distributions of plasma density in the post-anode space. The numerical model of the discharge was based on a simple hybrid approach which takes into account non-local ionization by fast electrons streaming from the cathode sheath. Specially formulated transparency boundary conditions allowed performing simulations in 1D. Simulations were carried out in air at pressures of 10 Torr and higher. Analysis of the discharge structure and discharge formation is presented. It is shown that using cathode materials with lower secondary emission coefficients can allow increasing the thickness of plasma slabs for the same discharge current, which can potentially enhance EM wave absorption. Spatial distributions of electron density obtained during simulations were used to calculate attenuation of an incident EM wave propagating perpendicularly to the plasma slab boundary. It is shown that plasma created by means of a DC discharge with a gridded anode can efficiently absorb EM waves in the low frequency range (6-40 GHz). Increasing gas pressure results in a broader range of wave frequencies (up to 500 GHz) where a considerable attenuation is observed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marana, Naiara L.; Albuquerque, Anderson R.; La Porta, Felipe A.

Periodic density functional theory calculations with the B3LYP hybrid functional and all-electron Gaussian basis set were performed to simulate the structural and electronic properties as well as the strain and formation energies of single-walled ZnO nanotubes (SWZnONTs) and Carbon nanotubes (SWCNTs) with different chiralities as functions of their diameters. For all SWZnONTs, the band gap, strain energy, and formation energy converge to ~4.5 eV, 0.0 eV/atom, and 0.40 eV/atom, respectively. This result suggests that the nanotubes are formed more easily from the surface than from the bulk. For SWCNTs, the strain energy is always positive, while the formation energy ismore » negative for armchair and zigzag nanotubes, therefore suggesting that these types of nanotubes can be preferentially formed from the bulk. The electronic properties of SWCNTs depend on the chirality; all armchair nanotubes are metallic, while zigzag and chiral nanotubes can be metallic or semiconducting, depending on the n and m vectors. - Graphical abstract: DFT/B3LYP were performed to simulate the structural and electronic properties as well as the strain and formation energies of SWZnONTs and SWCNTs with different chiralities as functions of their diameters. - Highlights: • The energies of SWZnONTs converge for chirality with diameters up 20 Å. • SWCNTs electronic properties depend on the chirality. • The properties of SWZnONTs are very similar to those of monolayer surface.« less

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Three dimensional Particle-in-Cell (PIC) simulations of the 67P environment

NASA Astrophysics Data System (ADS)

Divin, Andrey; Deca, Jan; Henri, Pierre; Horanyi, Mihaly; Markidis, Stefano; Lapenta, Giovanni; Olshevsky, Vyacheslav; Eriksson, Anders

2017-04-01

ESA's Rosetta orbiter spacecraft escorted comet 67P/Churyumov-Gerasimenko for two years, carrying 21 scientific instruments. Five of those were dedicated to plasma measurements. The mission revealed for the first time, and in unprecedented detail, the fascinating evolution of a comet and its interaction with our Sun as it races along its 6.45yr elliptical orbit around the Sun. Using a self-consistent 3-D fully kinetic electromagnetic particle-in-cell approach, we focus on the global cometary environment and, in particular, on the collisionless electron-kinetic interaction. We include cometary ions and electrons produced by the ionization of the outgassing cometary atmosphere in addition to the solar wind ion and electron plasma flow. We approximate mass-loading of the cold cometary ion and electron populations using a 1/r relation with distance to the comet with a total neutral production rate of Q = 1026 s-1. Our simulation results disentangle for the first time the kinetic ion and electron dynamics of the solar wind interaction with a weakly outgassing comet. The simulated global structure of the solar wind-comet interaction confirms the results reported in hybrid simulations of the induced cometary magnetosphere. Moreover, we show that cometary and solar wind electrons neutralize the solar wind protons and cometary ions, respectively, in the region of influence around the comet, representing to first order a four-fluid behavior. The electron energy distribution close to the comet is shown to be a mix of cometary and solar wind electrons that appear as, respectively, a thermal and a suprathermal components. Analyzing ion and electron energy distribution functions, and comparing with plasma measurements from ESA's Rosetta mission to comet 67P/Churyumov-Gerasimenko, we conclude that a detailed kinetic treatment of the electron dynamics is critical to fully capture the complex physics of mass-loading plasmas.

Formation of Ultrarelativistic Electron Rings from a Laser-Wakefield Accelerator.

PubMed

Pollock, B B; Tsung, F S; Albert, F; Shaw, J L; Clayton, C E; Davidson, A; Lemos, N; Marsh, K A; Pak, A; Ralph, J E; Mori, W B; Joshi, C

2015-07-31

Ultrarelativistic-energy electron ring structures have been observed from laser-wakefield acceleration experiments in the blowout regime. These electron rings had 170-280 MeV energies with 5%-25% energy spread and ∼10  pC of charge and were observed over a range of plasma densities and compositions. Three-dimensional particle-in-cell simulations show that laser intensity enhancement in the wake leads to sheath splitting and the formation of a hollow toroidal pocket in the electron density around the wake behind the first wake period. If the laser propagates over a distance greater than the ideal dephasing length, some of the dephasing electrons in the second period can become trapped within the pocket and form an ultrarelativistic electron ring that propagates in free space over a meter-scale distance upon exiting the plasma. Such a structure acts as a relativistic potential well, which has applications for accelerating positively charged particles such as positrons.

Surface determination through atomically resolved secondary-electron imaging

PubMed Central

Ciston, J.; Brown, H. G.; D'Alfonso, A. J.; Koirala, P.; Ophus, C.; Lin, Y.; Suzuki, Y.; Inada, H.; Zhu, Y.; Allen, L. J.; Marks, L. D.

2015-01-01

Unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we report a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 × 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our work reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO5 units. Dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals. PMID:26082275

Computational modeling of the effect of external electron injection into a direct-current microdischarge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panneer Chelvam, Prem Kumar; Raja, Laxminarayan L.

2015-12-28

Electron emission from the electrode surface plays an important role in determining the structure of a direct-current microdischarge. Here we have developed a computational model of a direct-current microdischarge to study the effect of external electron injection from the cathode surface into the discharge to manipulate its properties. The model provides a self-consistent, multi-species, multi-temperature fluid representation of the plasma. A microdischarge with a metal-insulator-metal configuration is chosen for this study. The effect of external electron injection on the structure and properties of the microdischarge is described. The transient behavior of the microdischarge during the electron injection is examined. Themore » nonlinearities in the dynamics of the plasma result in a large increase of conduction current after active electron injection. For the conditions simulated a switching time of ∼100 ns from a low-current to high-current discharge state is realized.« less

Surface determination through atomically resolved secondary-electron imaging

DOE PAGES

Ciston, J.; Brown, H. G.; D’Alfonso, A. J.; ...

2015-06-17

We report that unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we show a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 x 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our workmore » reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO 5 units. Lastly, dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals.« less

Tunable valley polarization by a gate voltage when an electron tunnels through multiple line defects in graphene.

PubMed

Liu, Zhe; Jiang, Liwei; Zheng, Yisong

2015-02-04

By means of an appropriate wave function connection condition, we study the electronic structure of a line defect superlattice of graphene with the Dirac equation method. We obtain the analytical dispersion relation, which can simulate well the tight-binding numerical result about the band structure of the superlattice. Then, we generalize this theoretical method to study the electronic transmission through a potential barrier where multiple line defects are periodically patterned. We find that there exists a critical incident angle which restricts the electronic transmission through multiple line defects within a specific incident angle range. The critical angle depends sensitively on the potential barrier height, which can be modulated by a gate voltage. As a result, non-trivial transmissions of K and K' valley electrons are restricted, respectively, in two distinct ranges of the incident angle. Our theoretical result demonstrates that a gate voltage can act as a feasible measure to tune the valley polarization when electrons tunnel through multiple line defects.

Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

NASA Astrophysics Data System (ADS)

Blum, Volker

This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

Atomic and electronic structure of exfoliated black phosphorus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok

2015-11-15

Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolutionmore » view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zou, Lianfeng; Li, Jonathan; Zakharov, Dmitri

Using in situ transmission electron microscopy that spatially and temporally resolves the evolution of the atomic structure in the surface and subsurface regions, we Find that the surface segregation of Au atoms in a Cu(Au) solid solution results in the nucleation and growth of a (2 × 1) missing-row reconstructed, half-unit-cell thick L1 2 Cu 3Au(110) surface alloy. Our in situ electron microscopy observations and atomistic simulations demonstrate that the (2 × 1) reconstruction of the Cu 3Au(110) surface alloy remains as a stable surface structure as a result of the favored Cu-Au diatom configuration.

Nanoscale structure of the oil-water interface

DOE PAGES

Fukuto, M.; Ocko, B. M.; Bonthuis, D. J.; ...

2016-12-15

X-ray reflectivity (XR) and atomistic molecular dynamics (MD) simulations, carried out to determine the structure of the oil-water interface, provide new insight into the simplest liquid-liquid interface. For several oils (hexane, dodecane, and hexadecane) the XR shows very good agreement with a monotonic interface-normal electron density profile (EDP) broadened only by capillary waves. Similar agreement is also found for an EDP including a sub-Å thick electron depletion layer separating the oil and the water. As a result, the XR and MD derived depletions are much smaller than reported for the interface between solid-supported hydrophobic monolayers and water.

Probing structure, thermochemistry, electron affinity, and magnetic moment of thulium-doped silicon clusters TmSi n (n = 3-10) and their anions with density functional theory.

PubMed

Huang, Xintao; Yang, Jucai

2017-12-26

The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi n (n = 3-10) and their anions do not participate in bonding. The total magnetic moments of TmSi n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi n and their anions has been calculated to examine relative stability.

DOE Office of Scientific and Technical Information (OSTI.GOV)

dos Reis, Roberto; Yang, Hao; Ophus, Colin

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr 3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr 3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurementmore » of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). Finally, the approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.« less

Left-right correlation in coupled F-center defects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janesko, Benjamin G., E-mail: b.janesko@tcu.edu

This work explores how left-right correlation, a textbook problem in electronic structure theory, manifests in a textbook example of electrons trapped in crystal defects. I show that adjacent F-center defects in lithium fluoride display symptoms of “strong” left-right correlation, symptoms similar to those seen in stretched H{sub 2}. Simulations of UV/visible absorption spectra qualitatively fail to reproduce experiment unless left-right correlation is taken into account. This is of interest to both the electronic structure theory and crystal-defect communities. Theorists have a new well-behaved system to test their methods. Crystal-defect groups are cautioned that the approximations that successfully model single F-centersmore » may fail for adjacent F-centers.« less

Electrostatic odd symmetric eigenmode in inhomogeneous Bernstein-Greene-Kruskal equilibrium

NASA Astrophysics Data System (ADS)

Woo, M.-H.; Dokgo, K.; Yoon, Peter H.; Lee, D.-Y.; Choi, Cheong R.

2018-04-01

A self-consistent electrostatic odd-symmetric eigenmode (OEM) is analytically found in a solitary type Bernstein-Greene-Kruskal (BGK) equilibrium. The frequency of the OEM is order of the electron bounce frequency and it is spatially odd-symmetric with the scale comparable to that of the solitary BGK equilibrium structure. Such an OEM is consistent with the recent observation from particle-in-cell simulation of the solitary wave [Dokgo et al., Phys. Plasmas 23, 092107 (2016)]. The mode can be driven unstable by trapped electrons within the hole structure of the solitary wave. Such a low frequency, pure electron mode, which may possibly interact resonantly with the ion acoustic mode, provides a possible damping mechanism of the BGK equilibrium.

Electronic properties of semiconductor-water interfaces: Predictions from ab-initio molecular dynamics and many-body perturbation theory

NASA Astrophysics Data System (ADS)

Pham, Tuan Anh

2015-03-01

Photoelectrochemical cells offer a promising avenue for hydrogen production from water and sunlight. The efficiency of these devices depends on the electronic structure of the interface between the photoelectrode and liquid water, including the alignment between the semiconductor band edges and the water redox potential. In this talk, we will present the results of first principles calculations of semiconductor-water interfaces that are obtained with a combination of density functional theory (DFT)-based molecular dynamics simulations and many-body perturbation theory (MBPT). First, we will discuss the development of an MBPT approach that is aimed at improving the efficiency and accuracy of existing methodologies while still being applicable to complex heterogeneous interfaces consisting of hundreds of atoms. We will then present studies of the electronic structure of liquid water and aqueous solutions using MBPT, which represent an essential step in establishing a quantitative framework for computing the energy alignment at semiconductor-water interfaces. Finally, using a combination of DFT-based molecular dynamics simulations and MBPT, we will describe the relationship between interfacial structure, electronic properties of semiconductors and their reactivity in aqueous solutions through a number of examples, including functionalized Si surfaces and GaP/InP surfaces in contact with liquid water. T.A.P was supported by the U.S. Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by the Lawrence Fellowship Program.

Conductivity and local structure in LaNiO3

NASA Astrophysics Data System (ADS)

Fowlie, Jennifer; Gibert, Marta; Tieri, Giulio; Gloter, Alexandre; à+/-Iguez, Jorge; Filippetti, Alessio; Catalano, Sara; Gariglio, Stefano; StéPhan, Odile; Triscone, Jean-Marc

In this study we approach the thickness-dependence of the properties of LaNiO3 films along multiple, complementary avenues: sophisticated ab initio calculations, scanning transmission electron microscopy and electronic transport. Specifically, we find an unexpected maximum in conductivity in films of thickness 6 - 10 unit cells (3 nm) for several series of LaNiO3 films. Ab initio transport based on the detailed crystal structure also reveals a maximum in conductivity at the same thickness. In agreement with the structure obtained from scanning transmission electron microscopy (STEM), our simulated structures reveal that the substrate- and surface-induced distortions lead to three types of local structure (heterointerface, interior-layer, surface). Based on this observation, a 3-element parallel conductor model neatly reproduces the trend of conductivity with thickness. This study addresses the question of how structural distortions at the atomic scale evolve in a thin film under the influence of the substrate and the surface. This topic is key to the understanding of the physics of heterostructures and the design of functional oxides.

Surface plasmon induced direct detection of long wavelength photons.

PubMed

Tong, Jinchao; Zhou, Wei; Qu, Yue; Xu, Zhengji; Huang, Zhiming; Zhang, Dao Hua

2017-11-21

Millimeter and terahertz wave photodetectors have long been of great interest due to a wide range of applications, but they still face challenges in detection performance. Here, we propose a new strategy for the direct detection of millimeter and terahertz wave photons based on localized surface-plasmon-polariton (SPP)-induced non-equilibrium electrons in antenna-assisted subwavelength ohmic metal-semiconductor-metal (OMSM) structures. The subwavelength OMSM structure is used to convert the absorbed photons into localized SPPs, which then induce non-equilibrium electrons in the structure, while the antenna increases the number of photons coupled into the OMSM structure. When the structure is biased and illuminated, the unidirectional flow of the SPP-induced non-equilibrium electrons forms a photocurrent. The energy of the detected photons is determined by the structure rather than the band gap of the semiconductor. The detection scheme is confirmed by simulation and experimental results from the devices, made of gold and InSb, and a room temperature noise equivalent power (NEP) of 1.5 × 10 -13 W Hz -1/2 is achieved.

3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xing; Zhang, Lei; Tong, Huimin

2015-05-05

Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

Optimal atomic structure of amorphous silicon obtained from density functional theory calculations

NASA Astrophysics Data System (ADS)

Pedersen, Andreas; Pizzagalli, Laurent; Jónsson, Hannes

2017-06-01

Atomic structure of amorphous silicon consistent with several reported experimental measurements has been obtained from annealing simulations using electron density functional theory calculations and a systematic removal of weakly bound atoms. The excess energy and density with respect to the crystal are well reproduced in addition to radial distribution function, angular distribution functions, and vibrational density of states. No atom in the optimal configuration is locally in a crystalline environment as deduced by ring analysis and common neighbor analysis, but coordination defects are present at a level of 1%-2%. The simulated samples provide structural models of this archetypal disordered covalent material without preconceived notion of the atomic ordering or fitting to experimental data.

Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ionmore » diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.« less

Imaging electronic motions by ultrafast electron diffraction

NASA Astrophysics Data System (ADS)

Shao, Hua-Chieh; Starace, Anthony F.

2017-08-01

Recently ultrafast electron diffraction and microscopy have reached unprecedented temporal resolution, and transient structures with atomic precision have been observed in various reactions. It is anticipated that these extraordinary advances will soon allow direct observation of electronic motions during chemical reactions. We therefore performed a series of theoretical investigations and simulations to investigate the imaging of electronic motions in atoms and molecules by ultrafast electron diffraction. Three prototypical electronic motions were considered for hydrogen atoms. For the case of a breathing mode, the electron density expands and contracts periodically, and we show that the time-resolved scattering intensities reflect such changes of the charge radius. For the case of a wiggling mode, the electron oscillates from one side of the nucleus to the other, and we show that the diffraction images exhibit asymmetric angular distributions. The last case is a hybrid mode that involves both breathing and wiggling motions. Owing to the demonstrated ability of ultrafast electrons to image these motions, we have proposed to image a coherent population transfer in lithium atoms using currently available femtosecond electron pulses. A frequency-swept laser pulse adiabatically drives the valence electron of a lithium atom from the 2s to 2p orbitals, and a time-delayed electron pulse maps such motion. Our simulations show that the diffraction images reflect this motion both in the scattering intensities and the angular distributions.

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Characteristics of pitch angle distributions of relativistic electrons under the interaction with Pc5 waves in the inner magnetosphere

NASA Astrophysics Data System (ADS)

Kamiya, K.; Seki, K.; Saito, S.; Amano, T.; Yoshizumi, M.

2017-12-01

Radial transport of relativistic electrons in the inner magnetosphere has been considered as one of acceleration mechanisms of the outer radiation belt electrons and can be driven by the drift resonance with ULF waves in the Pc5 frequency range. The maximum changes of the electron in the radial distance (L) due to the drift resonance depend on the electron energy, pitch angle, and Pc5 wave structure. Those dependences are expected to form the characteristic pitch angle distributions (PADs) as a function of L and electron energy. In this study, we investigate PADs of relativistic electrons due to the drift resonance with a monochromatic Pc5 wave by using two simulation models of the inner magnetosphere: GEMSIS-Ring Current (RC) and GEMSIS-Radiation Belt (RB) models. The GEMSIS-RB simulations calculate guiding center trajectories of relativistic electrons in electric and magnetic fields obtained from the GEMSIS-RC model, which simulates a monochromatic Pc5 wave propagation in the inner magnetosphere. The results show the characteristic PADs depending on the energy and L, which is explicable with the pitch angle dependence of resonance conditions. At a fixed location, those PADs can change from pancake (90°peaked) to butterfly (two peaks in oblique PAs) distributions as the transport by the monochromatic Pc5 wave progresses. These butterfly distributions are seen in the L range where electrons with lower PAs satisfy the resonance condition. It is also found that the lower PA electron with a fixed magnetic moment can be transported deeper inside because of the PA changes to larger values through the adiabatic transport, which enables them to satisfy the efficient resonance condition in wider L range compared to the 90 degrees PA electrons.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

2014-03-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

The effect of moisture on the structures and properties of lead halide perovskites: a first-principles theoretical investigation.

PubMed

Zhang, Lei; Ju, Ming-Gang; Liang, WanZhen

2016-08-17

With efficiencies exceeding 20% and low production costs, lead halide perovskite solar cells (PSCs) have become potential candidates for future commercial applications. However, there are serious concerns about their long-term stability and environmental friendliness, heavily related to their commercial viability. Herein, we present a theoretical investigation based on the ab initio molecular dynamics (AIMD) simulations and the first-principles density functional theory (DFT) calculations to investigate the effects of sunlight and moisture on the structures and properties of MAPbI3 perovskites. AIMD simulations have been performed to simulate the impact of a few water molecules on the structures of MAPbI3 surfaces terminated in three different ways. The evolution of geometric and electronic structures as well as the absorption spectra has been shown. It is found that the PbI2-terminated surface is the most stable while both the MAI-terminated and PbI2-defective surfaces undergo structural reconstruction, leading to the formation of hydrated compounds in a humid environment. The moisture-induced weakening of photoabsorption is closely related to the formation of hydrated species, and the hydrated crystals MAPbI3·H2O and MA4PbI6·2H2O scarcely absorb the visible light. The electronic excitation in the bare and water-absorbed MAPbI3 nanoparticles tends to weaken Pb-I bonds, especially those around water molecules, and the maximal decrease of photoexcitation-induced bond order can reach up to 20% in the excited state in which the water molecules are involved in the electronic excitation, indicating the accelerated decomposition of perovskites in the presence of sunlight and moisture. This work is valuable for understanding the mechanism of chemical or photochemical instability of MAPbI3 perovskites in the presence of moisture.

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

High Current Density Scandate Cathodes for Future Vacuum Electronics Applications

DTIC Science & Technology

2008-05-30

of Technology HFSS Ansoft Corporation’s High Frequency Structure Simulator TWT Traveling Wave Tube - device for generating high levels of RF power ...cathodes are practical for high power RF sources. Typical thermi- onic cathodes consists of a tungsten matrix impregnated with a mixture of barium oxide...electron beam with the largest possible diameter, consistent with high gain, bandwidth, and efficiency at W- Band . The research concentrated on photonic

Simulation of electron transport in quantum well devices

NASA Technical Reports Server (NTRS)

Miller, D. R.; Gullapalli, K. K.; Reddy, V. R.; Neikirk, D. P.

1992-01-01

Double barrier resonant tunneling diodes (DBRTD) have received much attention as possible terahertz devices. Despite impressive experimental results, the specifics of the device physics (i.e., how the electrons propagate through the structure) are only qualitatively understood. Therefore, better transport models are warranted if this technology is to mature. In this paper, the Lattice Wigner function is used to explain the important transport issues associated with DBRTD device behavior.

Capacitive charge storage at an electrified interface investigated via direct first-principles simulations

NASA Astrophysics Data System (ADS)

Radin, Maxwell D.; Ogitsu, Tadashi; Biener, Juergen; Otani, Minoru; Wood, Brandon C.

2015-03-01

Understanding the impact of interfacial electric fields on electronic structure is crucial to improving the performance of materials in applications based on charged interfaces. Supercapacitors store energy directly in the strong interfacial field between a solid electrode and a liquid electrolyte; however, the complex interplay between the two is often poorly understood, particularly for emerging low-dimensional electrode materials that possess unconventional electronic structure. Typical descriptions tend to neglect the specific electrode-electrolyte interaction, approximating the intrinsic "quantum capacitance" of the electrode in terms of a fixed electronic density of states. Instead, we introduce a more accurate first-principles approach for directly simulating charge storage in model capacitors using the effective screening medium method, which implicitly accounts for the presence of the interfacial electric field. Applying this approach to graphene supercapacitor electrodes, we find that results differ significantly from the predictions of fixed-band models, leading to improved consistency with experimentally reported capacitive behavior. The differences are traced to two key factors: the inhomogeneous distribution of stored charge due to poor electronic screening and interfacial contributions from the specific interaction with the electrolyte. Our results are used to revise the conventional definition of quantum capacitance and to provide general strategies for improving electrochemical charge storage, particularly in graphene and similar low-dimensional materials.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Model-Based Verification and Validation of Spacecraft Avionics

NASA Technical Reports Server (NTRS)

Khan, M. Omair; Sievers, Michael; Standley, Shaun

2012-01-01

Verification and Validation (V&V) at JPL is traditionally performed on flight or flight-like hardware running flight software. For some time, the complexity of avionics has increased exponentially while the time allocated for system integration and associated V&V testing has remained fixed. There is an increasing need to perform comprehensive system level V&V using modeling and simulation, and to use scarce hardware testing time to validate models; the norm for thermal and structural V&V for some time. Our approach extends model-based V&V to electronics and software through functional and structural models implemented in SysML. We develop component models of electronics and software that are validated by comparison with test results from actual equipment. The models are then simulated enabling a more complete set of test cases than possible on flight hardware. SysML simulations provide access and control of internal nodes that may not be available in physical systems. This is particularly helpful in testing fault protection behaviors when injecting faults is either not possible or potentially damaging to the hardware. We can also model both hardware and software behaviors in SysML, which allows us to simulate hardware and software interactions. With an integrated model and simulation capability we can evaluate the hardware and software interactions and identify problems sooner. The primary missing piece is validating SysML model correctness against hardware; this experiment demonstrated such an approach is possible.

Superhydrophobic surfaces: From nature to biomimetic through VOF simulation.

PubMed

Liu, Chunbao; Zhu, Ling; Bu, Weiyang; Liang, Yunhong

2018-04-01

The contact angle, surface structure and chemical compositions of Canna leaves were investigated. According to the surface structure of Canna leaves which observed by Scanning Electron Microscopy(SEM), the CFD (Computational Fluid Dynamics)model was established and the method of volume of fluid (VOF) was used to simulate the process of droplet impacting on the surface and established a smooth surface for comparison to verify that the surface structure was an important factor of the superhydrophobic properties. Based on the study of Canna leaf and VOF simulation of its surface structure, the superhydrophobic samples were processed successfully and showed a good superhydrophobic property with a contact angle of 156 ± 1 degrees. A high-speed camera (5000 frames per second) was used to assess droplet movement and determine the contact time of the samples. The contact time for the sample was 13.1 ms. The results displayed that the artificial superhydrophobic surface is perfect for the performance of superhydrophobic properties. The VOF simulation method was efficient, accurate and low cost before machining artificial superhydrophobic samples. Copyright © 2018 Elsevier Ltd. All rights reserved.

Symplectic modeling of beam loading in electromagnetic cavities

DOE PAGES

Abell, Dan T.; Cook, Nathan M.; Webb, Stephen D.

2017-05-22

Simulating beam loading in radio frequency accelerating structures is critical for understanding higher-order mode effects on beam dynamics, such as beam break-up instability in energy recovery linacs. Full wave simulations of beam loading in radio frequency structures are computationally expensive, and while reduced models can ignore essential physics, it can be difficult to generalize. Here, we present a self-consistent algorithm derived from the least-action principle which can model an arbitrary number of cavity eigenmodes and with a generic beam distribution. It has been implemented in our new Open Library for Investigating Vacuum Electronics (OLIVE).

On simulation of local fluxes in molecular junctions

NASA Astrophysics Data System (ADS)

Cabra, Gabriel; Jensen, Anders; Galperin, Michael

2018-05-01

We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

Elimination of resistive losses in large-area LEDs by new diffusion-driven devices

NASA Astrophysics Data System (ADS)

Kivisaari, Pyry; Kim, Iurii; Suihkonen, Sami; Oksanen, Jani

2017-02-01

High-power operation of conventional GaN-based light-emitting diodes (LEDs) is severely limited by current crowding, which increases the bias voltage of the LED, concentrates light emission close to the p-type contact edge, and aggravates the efficiency droop. Fabricating LEDs on thick n-GaN substrates alleviates current crowding but requires the use of expensive bulk GaN substrates and fairly large n-contacts, which take away a large part of the active region (AR). In this work, we demonstrate through comparative simulations how the recently introduced diffusion-driven charge transport (DDCT) concept can be used to realize lateral heterojunction (LHJ) structures, which eliminate most of the lateral current crowding. Specifically in this work, we analyze how using a single-side graded AR can both facilitate electron and hole diffusion in DDCT and increase the effective AR thickness. Our simulations show that the increased effective AR thickness allows a substantial reduction in the efficiency droop at large currents, and that unlike conventional 2D LEDs, the LHJ structure shows practically no added efficiency loss or differential resistance due to current crowding. Furthermore, as both electrons and holes enter the AR from the same side without any notable potential barriers in the LHJ structure, the LHJ structure shows an additional wall-plug efficiency gain over the conventional structures under comparison. This injection from the same side is expected to be even more interesting in multiple quantum well structures, where carriers typically need to surpass several potential barriers in conventional LEDs before recombining. In addition to simulations, we also demonstrate selective-area growth of a finger structure suitable for operation as an LHJ device with 2µm distance between n- and p-GaN regions.

Numerical simulation of CTE mismatch and thermal-structural stresses in the design of interconnects

NASA Astrophysics Data System (ADS)

Peter, Geoffrey John M.

With the ever-increasing chip complexity, interconnects have to be designed to meet the new challenges. Advances in optical lithography have made chip feature sizes available today at 70 nm dimensions. With advances in Extreme Ultraviolet Lithography, X-ray Lithography, and Ion Projection Lithography it is expected that the line width will further decrease to 20 nm or less. With the decrease in feature size, the number of active devices on the chip increases. With higher levels of circuit integration, the challenge is to dissipate the increased heat flux from the chip surface area. Thermal management considerations include coefficient of thermal expansion (CTE) matching to prevent failure between the chip and the board. This in turn calls for improved system performance and reliability of the electronic structural systems. Experience has shown that in most electronic systems, failures are mostly due to CTE mismatch between the chip, board, and the solder joint (solder interconnect). The resulting high thermal-structural stress and strain due to CTE mismatch produces cracks in the solder joints with eventual failure of the electronic component. In order to reduce the thermal stress between the chip, board, and the solder joint, this dissertation examines the effect of inserting wire bundle (wire interconnect) between the chip and the board. The flexibility of the wires or fibers would reduce the stress at the rigid joints. Numerical simulations of two, and three-dimensional models of the solder and wire interconnects are examined. The numerical simulation is linear in nature and is based on linear isotropic material properties. The effect of different wire material properties is examined. The effect of varying the wire diameter is studied by changing the wire diameter. A major cause of electronic equipment failure is due to fatigue failure caused by thermal cycling, and vibrations. A two-dimensional modal and harmonic analysis was simulated for the wire interconnect and the solder interconnect. The numerical model simulated using ANSYS program was validated with the numerical/experimental results of other published researchers. In addition the results were cross-checked by IDEAS program. A prototype non-working wire interconnect is proposed to emphasize practical application. The numerical analysis, in this dissertation is based on a U.S. Patent granted to G. Peter(42).

Mixed Network Former Effect on Structure, Physical Properties, and Bioactivity of 45S5 Bioactive Glasses: An Integrated Experimental and Molecular Dynamics Simulation Study.

PubMed

Lu, Xiaonan; Deng, Lu; Huntley, Caitlin; Ren, Mengguo; Kuo, Po-Hsuen; Thomas, Ty; Chen, Jonathan; Du, Jincheng

2018-03-08

Boron-containing bioactive glasses display a strong potential in various biomedical applications lately due to their controllable dissolution rates. In this paper, we prepared a series of B 2 O 3 /SiO 2 -substituded 45S5 bioactive glasses and performed in vitro biomineralization tests with both simulated body fluid and K 2 HPO 4 solutions to evaluate the bioactivities of these glasses as a function of boron oxide to silica substitution. The samples were examined with scanning electron microscopy, X-ray diffraction, and Fourier transform infrared spectrometry after immersing them in the two solutions (simulated body fluid and K 2 HPO 4 ) up to 3 weeks. It was found that introduction of boron oxide delayed the formation of hydroxyapatite, but all the glasses were shown to be bioactive. Molecular dynamics (MD) simulations were used to complement the experimental efforts to understand the structural changes due to boron oxide to silica substitution by using newly developed partial charge composition-dependent potentials. Local structures around the glass network formers, medium-range structural information, network connectivity, and self-diffusion coefficients of ions were elucidated from MD simulation. Relationships between boron content and glass properties such as structure, density, glass transition temperature, and in vitro bioactivity were discussed in light of both experimental and simulation results.

Mechanical properties and electronic structure of edge-doped graphene nanoribbons with F, O, and Cl atoms.

PubMed

Piriz, Sebastián; Fernández-Werner, Luciana; Pardo, Helena; Jasen, Paula; Faccio, Ricardo; Mombrú, Álvaro W

2017-08-16

In this study, we present the structural, electronic, and mechanical properties of edge-doped zigzag graphene nanoribbons (ZGNRs) doped with fluorine, oxygen, and chlorine atoms. To the best of our knowledge, to date, no experimental results concerning the mechanical properties of graphene-derived nanoribbons have been reported in the literature. Simulations indicate that Cl- and F-doped ZGNRs present an equivalent 2-dimensional Young's modulus E 2D , which seems to be higher than those of graphene and H-doped ZGNRs. This is a consequence of the electronic structure of the system, particularly originating from strong interactions between the dopant atoms localized at the edges. The interaction between dopant atoms located at the edges is higher for Cl and lower for F and O atoms. This is the origin of the observed trend, in which E > E > E for all the analyzed ZGNRs.

Thermoelectric band engineering: The role of carrier scattering

NASA Astrophysics Data System (ADS)

Witkoske, Evan; Wang, Xufeng; Lundstrom, Mark; Askarpour, Vahid; Maassen, Jesse

2017-11-01

Complex electronic band structures, with multiple valleys or bands at the same or similar energies, can be beneficial for thermoelectric performance, but the advantages can be offset by inter-valley and inter-band scattering. In this paper, we demonstrate how first-principles band structures coupled with recently developed techniques for rigorous simulation of electron-phonon scattering provide the capabilities to realistically assess the benefits and trade-offs associated with these materials. We illustrate the approach using n-type silicon as a model material and show that intervalley scattering is strong. This example shows that the convergence of valleys and bands can improve thermoelectric performance, but the magnitude of the improvement depends sensitively on the relative strengths of intra- and inter-valley electron scattering. Because anisotropy of the band structure also plays an important role, a measure of the benefit of band anisotropy in the presence of strong intervalley scattering is presented.

A plasma source driven predator-prey like mechanism as a potential cause of spiraling intermittencies in linear plasma devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reiser, D.; Ohno, N.; Tanaka, H.

2014-03-15

Three-dimensional global drift fluid simulations are carried out to analyze coherent plasma structures appearing in the NAGDIS-II linear device (nagoya divertor plasma Simulator-II). The numerical simulations reproduce several features of the intermittent spiraling structures observed, for instance, statistical properties, rotation frequency, and the frequency of plasma expulsion. The detailed inspection of the three-dimensional plasma dynamics allows to identify the key mechanism behind the formation of these intermittent events. The resistive coupling between electron pressure and parallel electric field in the plasma source region gives rise to a quasilinear predator-prey like dynamics where the axisymmetric mode represents the prey and themore » spiraling structure with low azimuthal mode number represents the predator. This interpretation is confirmed by a reduced one-dimensional quasilinear model derived on the basis of the findings in the full three-dimensional simulations. The dominant dynamics reveals certain similarities to the classical Lotka-Volterra cycle.« less

Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles.

PubMed

Feliciano, Gustavo T; da Silva, Antonio J R; Reguera, Gemma; Artacho, Emilio

2012-08-02

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Application of Koopmans' theorem for density functional theory to full valence-band photoemission spectroscopy modeling.

PubMed

Li, Tsung-Lung; Lu, Wen-Cai

2015-10-05

In this work, Koopmans' theorem for Kohn-Sham density functional theory (KS-DFT) is applied to the photoemission spectra (PES) modeling over the entire valence-band. To examine the validity of this application, a PES modeling scheme is developed to facilitate a full valence-band comparison of theoretical PES spectra with experiments. The PES model incorporates the variations of electron ionization cross-sections over atomic orbitals and a linear dispersion of spectral broadening widths. KS-DFT simulations of pristine rubrene (5,6,11,12-tetraphenyltetracene) and potassium-rubrene complex are performed, and the simulation results are used as the input to the PES models. Two conclusions are reached. First, decompositions of the theoretical total spectra show that the dissociated electron of the potassium mainly remains on the backbone and has little effect on the electronic structures of phenyl side groups. This and other electronic-structure results deduced from the spectral decompositions have been qualitatively obtained with the anionic approximation to potassium-rubrene complexes. The qualitative validity of the anionic approximation is thus verified. Second, comparison of the theoretical PES with the experiments shows that the full-scale simulations combined with the PES modeling methods greatly enhance the agreement on spectral shapes over the anionic approximation. This agreement of the theoretical PES spectra with the experiments over the full valence-band can be regarded, to some extent, as a collective validation of the application of Koopmans' theorem for KS-DFT to valence-band PES, at least, for this hydrocarbon and its alkali-adsorbed complex. Copyright © 2015 Elsevier B.V. All rights reserved.

Implementation of an Electronic Objective Structured Clinical Exam for Assessing Practical Skills in Pre-Professional Physiotherapy and Occupational Therapy Programs: Examiner and Course Coordinator Perspectives

ERIC Educational Resources Information Center

Snodgrass, Suzanne J.; Ashby, Samantha E.; Rivett, Darren A.; Russell, Trevor

2014-01-01

Assessment of practical clinical skills is essential in the health fields. Objective Structured Clinical Exams (OSCEs), where examiners assess students performing clinical procedures on simulated patients (actors), are central to the evaluation of practical skills. However, traditional OSCEs require considerable time-investment to administer, and…

IMACS 󈨟: Proceedings of the IMACS World Congress on Computation and Applied Mathematics (13th) Held in Dublin, Ireland on July 22-26, 1991. Volume 4. Modelling and Simulation for Electrical, Electronic and Semiconductor Devices, Computation for Management Systems, Applications of Modelling and Simulation, Environmental Systems Simulation, Software Forum, Poster Sessions

DTIC Science & Technology

1991-07-01

synchronous machine case study . IEEE T rons. on For the ease nd -nq -2, four time scales trust be used And the A.C, Vol. 36. nul 3, March 1989. damnper... studied . A spot welded(Csse 3) * ss s i* r 0. or a line welded( Case 4) reinforcement plate is attached on the colliding surface of box beams arnd their...phased armature, is given on Figure 1. analytical field calculation in the machine magnetic structure. Il - MAGNETIC STRUCTURE MODELLING: In the case

Extended interaction oversized coaxial relativistic klystron amplifier with gigawatt-level output at Ka band

NASA Astrophysics Data System (ADS)

Li, Shifeng; Duan, Zhaoyun; Huang, Hua; Liu, Zhenbang; He, Hu; Wang, Fei; Wang, Zhanliang; Gong, Yubin

2018-04-01

In this paper, an extended interaction oversized coaxial relativistic klystron amplifier (EIOC-RKA) with Gigawatt-level output at Ka band is proposed. We introduce the oversized coaxial and multi-gap resonant cavities to increase the power capacity and investigate a non-uniform extended interaction output cavity to improve the electronic efficiency of the EIOC-RKA. We develop a high order mode gap in the input and output cavities to easily design and fabricate the input and output couplers. Meanwhile, we design the EIOC-RKA by using the particle-in-cell simulation. In the simulations, we use an electron beam with a current of 6 kA and a voltage of 525 kV, which is focused by a low focusing magnetic flux intensity of 0.5 T. The simulation results demonstrate that the saturated output power is 1.17 GW, the electronic efficiency is 37.1%, and the saturated gain is 57 dB at 30 GHz. The self-oscillation is suppressed by adopting the absorbing materials. The proposed EIOC-RKA has plenty of advantages such as large power capacity, high electronic efficiency, low focusing magnetic, high gain, and simple structure.

Self-Consistent Monte Carlo Study of the Coulomb Interaction under Nano-Scale Device Structures

NASA Astrophysics Data System (ADS)

Sano, Nobuyuki

2011-03-01

It has been pointed that the Coulomb interaction between the electrons is expected to be of crucial importance to predict reliable device characteristics. In particular, the device performance is greatly degraded due to the plasmon excitation represented by dynamical potential fluctuations in high-doped source and drain regions by the channel electrons. We employ the self-consistent 3D Monte Carlo (MC) simulations, which could reproduce both the correct mobility under various electron concentrations and the collective plasma waves, to study the physical impact of dynamical potential fluctuations on device performance under the Double-gate MOSFETs. The average force experienced by an electron due to the Coulomb interaction inside the device is evaluated by performing the self-consistent MC simulations and the fixed-potential MC simulations without the Coulomb interaction. Also, the band-tailing associated with the local potential fluctuations in high-doped source region is quantitatively evaluated and it is found that the band-tailing becomes strongly dependent of position in real space even inside the uniform source region. This work was partially supported by Grants-in-Aid for Scientific Research B (No. 2160160) from the Ministry of Education, Culture, Sports, Science and Technology in Japan.

Investigations of Turbulent Transport Channels in Gyrokinetic Simulations

NASA Astrophysics Data System (ADS)

Dimits, A. M.; Candy, J.; Guttenfelder, W.; Holland, C.; Howard, N.; Nevins, W. M.; Wang, E.

2014-10-01

Magnetic-field stochasticity arises due to microtearing perturbations, which can be driven linearly or nonlinearly (in cases where they are linearly stable), even at very modest values of the plasma beta. The resulting magnetic-flutter contribution may or may not be a significant component of the overall electron (particle and thermal) transport. Investigations of the effect of ExB flow shear on electron-drift magnetic-flutter diffusion coefficient Dedr (r ,v||) using perturbed magnetic fields from simulations, using the GYRO code, of ITG turbulence show a significant effect for electrons with parallel velocities v|| surprisingly far from the resonant velocity. We further examine changes in the radial dependence of this diffusion coefficient vs. v|| and which resonant magnetic-field perturbations are important to the values and radial structure of Dedr. The resulting electron transport fluxes are compared with the simulation results. Improvements over in treating the ambipolar field in the relationship between the magnetic (or drift) diffusion coefficients and the transport have been made in these comparisons. Prepared for US DOE by LLNL under Contract DE-AC52-07NA27344, by GA under Contract DE-FG03-95ER54309, and by PPPL under Contract DE-AC02-09CH11466.

On the generation of double layers from ion- and electron-acoustic instabilities

DOE PAGES

Fu, Xiangrong; Cowee, Misa M.; Gary, Stephen Peter; ...

2016-03-17

A plasma double layer (DL) is a nonlinear electrostatic structure that carries a uni-polar electric field parallel to the background magnetic field due to local charge separation. Past studies showed that DLs observed in space plasmas are mostly associated with the ion acoustic instability. Recent Van Allen Probes observations of parallel electric fields traveling much faster than the ion acoustic speed have motivated a computational study to test the hypothesis that a new type of DLs – electron acoustic DLs – generated from the electron acoustic instability are responsible for these electric fields. Nonlinear particle-in-cell simulations yield negative results, i.e.more » the hypothetical electron acoustic DLs cannot be formed in a way similar to ion acoustic DLs. We find that linear theory analysis and the simulations show that the frequencies of electron acoustic waves are too high for ions to respond and maintain charge separation required by DLs. However, our results do show that local density perturbations in a two-electron-component plasma can result in unipolar-like electric fields that propagate at the electron thermal speed, suggesting another potential explanation for the observations.« less

Modeling and Simulation of III-Nitride-Based Solar Cells using NextnanoRTM

NASA Astrophysics Data System (ADS)

Refaei, Malak

Nextnano3 software is a well-known package for simulating semiconductor band-structures at the nanoscale and predicting the general electronic structure. In this work, it is further demonstrated as a viable tool for the simulation of III-nitride solar cells. In order to prove this feasibility, the generally accepted solar cell simulation package, PC1D, was chosen for comparison. To critique the results from both PC1D and Nextnano3, the fundamental drift-diffusion equations were used to calculate the performance of a simple p-n homojunction solar cell device analytically. Silicon was picked as the material for this comparison between the outputs of the two simulators as well as the results of the drift-diffusion equations because it is a well-known material in both software tools. After substantiating the capabilities of Nextnano3 for the simulation solar cells, an InGaN single-junction solar cell was simulated. The effects of various indium compositions and device structures on the performance of this InGaN p-n homojunction solar cell was then investigated using Nextnano 3 as a simulation tool. For single-junction devices with varying bandgap, an In0.6Ga0.4N device with a bandgap of 1.44 eV was found to be the optimum. The results of this research demonstrate that the Nextnano3 software can be used to usefully simulate solar cells in general, and III-nitride solar cells specifically, for future study of nanoscale structured devices.

Au-induced deep groove nanowire structure on the Ge(001) surface: DFT calculations

NASA Astrophysics Data System (ADS)

Tsay, Shiow-Fon

2016-09-01

The atomic geometry, stability, and electronic properties of self-organized Au induced nanowires on the Ge(001) surface are investigated based on the density-functional theory in GGA and the stoichiometry of Au. A giant Ge zigzag chain structure is suggested for 0.75 ML Au coverage, which displays c(8 × 2) deep groove zigzag nanowire structure simulated STM images. The top layer Ge and Au atomic disorder introduces the chevron units into the zigzag nanowire structure STM image as per the experimental observations. The zigzag Ge nanowire exhibits a semi-metallic characteristic, and the electric transport occurs in between the Ge zigzag nanowire and the subsurface. The system exhibits obvious electronic correlations among the Ge nanowire, the nano-facet Au trimers and the deeper layer Ge atoms, that play an important role in the electronic structure. At surface Brillouin zone boundaries, an anisotropic two-dimensional upward parabolic surface-state band is consistent with the ARPES spectra reported by Nakatsuji et al. [Phys. Rev. B 80, 081406(R) (2009); Phys. Rev. B 84, 115411 (2011)]; this electronic structure is different from the quasi-one-dimensional energy trough reported by Schäfer et al. [Phys. Rev. Lett. 101, 236802 (2008); Phys. Rev. B 83, 121411(R) (2011)].

Determination of the structural phase and octahedral rotation angle in halide perovskites

DOE PAGES

dos Reis, Roberto; Yang, Hao; Ophus, Colin; ...

2018-02-12

A key to the unique combination of electronic and optical properties in halide perovskite materials lies in their rich structural complexity. However, their radiation sensitive nature limits nanoscale structural characterization requiring dose efficient microscopic techniques in order to determine their structures precisely. In this work, we determine the space-group and directly image the Br halide sites of CsPbBr 3, a promising material for optoelectronic applications. Based on the symmetry of high-order Laue zone reflections of convergent-beam electron diffraction, we identify the tetragonal (I4/mcm) structural phase of CsPbBr 3 at cryogenic temperature. Electron ptychography provides a highly sensitive phase contrast measurementmore » of the halide positions under low electron-dose conditions, enabling imaging of the elongated Br sites originating from the out-of-phase octahedral rotation viewed along the [001] direction of I4/mcm persisting at room temperature. The measurement of these features and comparison with simulations yield an octahedral rotation angle of 6.5°(±1.5°). Finally, the approach demonstrated here opens up opportunities for understanding the atomic scale structural phenomena applying advanced characterization tools on a wide range of radiation sensitive halide-based all-inorganic and hybrid organic-inorganic perovskites.« less

New insights into photodissociation dynamics of cyclobutanone from the AIMS dynamic simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Lihong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn

2016-04-14

In this work, the combined electronic structure calculations and non-adiabatic dynamics simulations were performed for understanding mechanistic photodissociation of cyclobutanone at ∼248 nm. Besides the stationary and intersection structures reported before, two new conical intersections between the ground (S{sub 0}) and the first excited singlet (S{sub 1}) states were determined in the present study, which were confirmed to be the new S{sub 1} → S{sub 0} funnels by the ab initio multiple spawning dynamic simulation, giving rise to products in the S{sub 0} state selectively. The time evolution of the S{sub 1} electronic population was fitted with the pure exponentialmore » formulae, from which the S{sub 1} lifetime was estimated to be 484.0 fs. The time constant for the S{sub 1} α-cleavage is calculated to be 176.6 fs, which is based on the present dynamics simulation. As a result of the ultrafast S{sub 1} processes, the statistical distribution of the excess energies is prevented in the S{sub 1} state. The S{sub 1} dynamic effect (the nonergodic behavior) was predicted to be an important factor that is responsible for the wavelength dependence of the branching ratio of photodissociation products, which will be discussed in detail.« less

Extremely high frequency RF effects on electronics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loubriel, Guillermo Manuel; Vigliano, David; Coleman, Phillip Dale

The objective of this work was to understand the fundamental physics of extremely high frequency RF effects on electronics. To accomplish this objective, we produced models, conducted simulations, and performed measurements to identify the mechanisms of effects as frequency increases into the millimeter-wave regime. Our purpose was to answer the questions, 'What are the tradeoffs between coupling, transmission losses, and device responses as frequency increases?', and, 'How high in frequency do effects on electronic systems continue to occur?' Using full wave electromagnetics codes and a transmission-line/circuit code, we investigated how extremely high-frequency RF propagates on wires and printed circuit boardmore » traces. We investigated both field-to-wire coupling and direct illumination of printed circuit boards to determine the significant mechanisms for inducing currents at device terminals. We measured coupling to wires and attenuation along wires for comparison to the simulations, looking at plane-wave coupling as it launches modes onto single and multiconductor structures. We simulated the response of discrete and integrated circuit semiconductor devices to those high-frequency currents and voltages, using SGFramework, the open-source General-purpose Semiconductor Simulator (gss), and Sandia's Charon semiconductor device physics codes. This report documents our findings.« less

Core heat convection in NSTX-U via modification of electron orbits by high frequency Alfvén eigenmodes

NASA Astrophysics Data System (ADS)

Crocker, N. A.; Tritz, K.; White, R. B.; Fredrickson, E. D.; Gorelenkov, N. N.; NSTX-U Team

2015-11-01

New simulation results demonstrate that high frequency compressional (CAE) and global (GAE) Alfvén eigenmodes cause radial convection of electrons, with implications for particle and energy confinement, as well as electric field formation in NSTX-U. Simulations of electron orbits in the presence of multiple experimentally determined CAEs and GAEs, using the gyro-center code ORBIT, have revealed substantial convective transport, in addition to the expected diffusion via orbit stochastization. These results advance understanding of anomalous core energy transport expected in high performance, beam-heated NSTX-U plasmas. The simulations make use of experimentally determined density perturbation (δn) amplitudes and mode structures obtained by inverting measurements from 16 a channel reflectometer array using a synthetic diagnostic. Combined with experimentally determined mode polarizations (i.e. CAE or GAE), the δn are used to estimate the ExB displacements for use in ORBIT. Preliminary comparison of the simulation results with transport modeling by TRANSP indicate that the convection is currently underestimated. Supported by US DOE Contracts DE-SC0011810, DE-FG02-99ER54527 & DE-AC02-09CH11466.

Time-dependent first-principles study of angle-resolved secondary electron emission from atomic sheets

NASA Astrophysics Data System (ADS)

Ueda, Yoshihiro; Suzuki, Yasumitsu; Watanabe, Kazuyuki

2018-02-01

Angle-resolved secondary electron emission (ARSEE) spectra were analyzed for two-dimensional atomic sheets using a time-dependent first-principles simulation of electron scattering. We demonstrate that the calculated ARSEE spectra capture the unoccupied band structure of the atomic sheets. The excitation dynamics that lead to SEE have also been revealed by the time-dependent Kohn-Sham decomposition scheme. In the present study, the mechanism for the experimentally observed ARSEE from atomic sheets is elucidated with respect to both energetics and the dynamical aspects of SEE.

Model for Generation of Neutrons in a Compact Diode with Laser-Plasma Anode and Suppression of Electron Conduction Using a Permanent Cylindrical Magnet

NASA Astrophysics Data System (ADS)

Shikanov, A. E.; Vovchenko, E. D.; Kozlovskii, K. I.; Rashchikov, V. I.; Shatokhin, V. L.

2018-04-01

A model for acceleration of deuterons and generation of neutrons in a compact laser-plasma diode with electron isolation using magnetic field generated by a hollow cylindrical permanent magnet is presented. Experimental and computer-simulated neutron yields are compared for the diode structure under study. An accelerating neutron tube with a relatively high neutron generation efficiency can be constructed using suppression of electron conduction with the aid of a magnet placed in the vacuum volume.

The effectiveness of training with an emergency department simulator on medical student performance in a simulated disaster.

PubMed

Franc-Law, Jeffrey Michael; Ingrassia, Pier Luigi; Ragazzoni, Luca; Della Corte, Francesco

2010-01-01

Training in practical aspects of disaster medicine is often impossible, and simulation may offer an educational opportunity superior to traditional didactic methods. We sought to determine whether exposure to an electronic simulation tool would improve the ability of medical students to manage a simulated disaster. We stratified 22 students by year of education and randomly assigned 50% from each category to form the intervention group, with the remaining 50% forming the control group. Both groups received the same didactic training sessions. The intervention group received additional disaster medicine training on a patient simulator (disastermed.ca), and the control group spent equal time on the simulator in a nondisaster setting. We compared markers of patient flow during a simulated disaster, including mean differences in time and number of patients to reach triage, bed assignment, patient assessment and disposition. In addition, we compared triage accuracy and scores on a structured command-and-control instrument. We collected data on the students' evaluations of the course for secondary purposes. Participants in the intervention group triaged their patients more quickly than participants in the control group (mean difference 43 s, 99.5% confidence interval [CI] 12 to 75 s). The score of performance indicators on a standardized scale was also significantly higher in the intervention group (18/18) when compared with the control group (8/18) (p < 0.001). All students indicated that they preferred the simulation-based curriculum to a lecture-based curriculum. When asked to rate the exercise overall, both groups gave a median score of 8 on a 10-point modified Likert scale. Participation in an electronic disaster simulation using the disastermed.ca software package appears to increase the speed at which medical students triage simulated patients and increase their score on a structured command-and-control performance indicator instrument. Participants indicated that the simulation-based curriculum in disaster medicine is preferable to a lecture-based curriculum. Overall student satisfaction with the simulation-based curriculum was high.

Multiscale Processes in Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Surjalal Sharma, A.; Jain, Neeraj

The characteristic scales of the plasma processes in magnetic reconnection range from the elec-tron skin-depth to the magnetohydrodynamic (MHD) scale, and cross-scale coupling among them play a key role. Modeling these processes requires different physical models, viz. kinetic, electron-magnetohydrodynamics (EMHD), Hall-MHD, and MHD. The shortest scale processes are at the electron scale and these are modeled using an EMHD code, which provides many features of the multiscale behavior. In simulations using initial conditions consisting of pertur-bations with many scale sizes the reconnection takes place at many sites and the plasma flows from these interact with each other. This leads to thin current sheets with length less than 10 electron skin depths. The plasma flows also generate current sheets with multiple peaks, as observed by Cluster. The quadrupole structure of the magnetic field during reconnection starts on the electron scale and the interaction of inflow to the secondary sites and outflow from the dominant site generates a nested structure. In the outflow regions, the interaction of the electron outflows generated at the neighboring sites lead to the development of electron vortices. A signature of the nested structure of the Hall field is seen in Cluster observations, and more details of these features are expected from MMS.

Physics Computing '92: Proceedings of the 4th International Conference

NASA Astrophysics Data System (ADS)

de Groot, Robert A.; Nadrchal, Jaroslav

1993-04-01

The Table of Contents for the book is as follows: * Preface * INVITED PAPERS * Ab Initio Theoretical Approaches to the Structural, Electronic and Vibrational Properties of Small Clusters and Fullerenes: The State of the Art * Neural Multigrid Methods for Gauge Theories and Other Disordered Systems * Multicanonical Monte Carlo Simulations * On the Use of the Symbolic Language Maple in Physics and Chemistry: Several Examples * Nonequilibrium Phase Transitions in Catalysis and Population Models * Computer Algebra, Symmetry Analysis and Integrability of Nonlinear Evolution Equations * The Path-Integral Quantum Simulation of Hydrogen in Metals * Digital Optical Computing: A New Approach of Systolic Arrays Based on Coherence Modulation of Light and Integrated Optics Technology * Molecular Dynamics Simulations of Granular Materials * Numerical Implementation of a K.A.M. Algorithm * Quasi-Monte Carlo, Quasi-Random Numbers and Quasi-Error Estimates * What Can We Learn from QMC Simulations * Physics of Fluctuating Membranes * Plato, Apollonius, and Klein: Playing with Spheres * Steady States in Nonequilibrium Lattice Systems * CONVODE: A REDUCE Package for Differential Equations * Chaos in Coupled Rotators * Symplectic Numerical Methods for Hamiltonian Problems * Computer Simulations of Surfactant Self Assembly * High-dimensional and Very Large Cellular Automata for Immunological Shape Space * A Review of the Lattice Boltzmann Method * Electronic Structure of Solids in the Self-interaction Corrected Local-spin-density Approximation * Dedicated Computers for Lattice Gauge Theory Simulations * Physics Education: A Survey of Problems and Possible Solutions * Parallel Computing and Electronic-Structure Theory * High Precision Simulation Techniques for Lattice Field Theory * CONTRIBUTED PAPERS * Case Study of Microscale Hydrodynamics Using Molecular Dynamics and Lattice Gas Methods * Computer Modelling of the Structural and Electronic Properties of the Supported Metal Catalysis * Ordered Particle Simulations for Serial and MIMD Parallel Computers * "NOLP" -- Program Package for Laser Plasma Nonlinear Optics * Algorithms to Solve Nonlinear Least Square Problems * Distribution of Hydrogen Atoms in Pd-H Computed by Molecular Dynamics * A Ray Tracing of Optical System for Protein Crystallography Beamline at Storage Ring-SIBERIA-2 * Vibrational Properties of a Pseudobinary Linear Chain with Correlated Substitutional Disorder * Application of the Software Package Mathematica in Generalized Master Equation Method * Linelist: An Interactive Program for Analysing Beam-foil Spectra * GROMACS: A Parallel Computer for Molecular Dynamics Simulations * GROMACS Method of Virial Calculation Using a Single Sum * The Interactive Program for the Solution of the Laplace Equation with the Elimination of Singularities for Boundary Functions * Random-Number Generators: Testing Procedures and Comparison of RNG Algorithms * Micro-TOPIC: A Tokamak Plasma Impurities Code * Rotational Molecular Scattering Calculations * Orthonormal Polynomial Method for Calibrating of Cryogenic Temperature Sensors * Frame-based System Representing Basis of Physics * The Role of Massively Data-parallel Computers in Large Scale Molecular Dynamics Simulations * Short-range Molecular Dynamics on a Network of Processors and Workstations * An Algorithm for Higher-order Perturbation Theory in Radiative Transfer Computations * Hydrostochastics: The Master Equation Formulation of Fluid Dynamics * HPP Lattice Gas on Transputers and Networked Workstations * Study on the Hysteresis Cycle Simulation Using Modeling with Different Functions on Intervals * Refined Pruning Techniques for Feed-forward Neural Networks * Random Walk Simulation of the Motion of Transient Charges in Photoconductors * The Optical Hysteresis in Hydrogenated Amorphous Silicon * Diffusion Monte Carlo Analysis of Modern Interatomic Potentials for He * A Parallel Strategy for Molecular Dynamics Simulations of Polar Liquids on Transputer Arrays * Distribution of Ions Reflected on Rough Surfaces * The Study of Step Density Distribution During Molecular Beam Epitaxy Growth: Monte Carlo Computer Simulation * Towards a Formal Approach to the Construction of Large-scale Scientific Applications Software * Correlated Random Walk and Discrete Modelling of Propagation through Inhomogeneous Media * Teaching Plasma Physics Simulation * A Theoretical Determination of the Au-Ni Phase Diagram * Boson and Fermion Kinetics in One-dimensional Lattices * Computational Physics Course on the Technical University * Symbolic Computations in Simulation Code Development and Femtosecond-pulse Laser-plasma Interaction Studies * Computer Algebra and Integrated Computing Systems in Education of Physical Sciences * Coordinated System of Programs for Undergraduate Physics Instruction * Program Package MIRIAM and Atomic Physics of Extreme Systems * High Energy Physics Simulation on the T_Node * The Chapman-Kolmogorov Equation as Representation of Huygens' Principle and the Monolithic Self-consistent Numerical Modelling of Lasers * Authoring System for Simulation Developments * Molecular Dynamics Study of Ion Charge Effects in the Structure of Ionic Crystals * A Computational Physics Introductory Course * Computer Calculation of Substrate Temperature Field in MBE System * Multimagnetical Simulation of the Ising Model in Two and Three Dimensions * Failure of the CTRW Treatment of the Quasicoherent Excitation Transfer * Implementation of a Parallel Conjugate Gradient Method for Simulation of Elastic Light Scattering * Algorithms for Study of Thin Film Growth * Algorithms and Programs for Physics Teaching in Romanian Technical Universities * Multicanonical Simulation of 1st order Transitions: Interface Tension of the 2D 7-State Potts Model * Two Numerical Methods for the Calculation of Periodic Orbits in Hamiltonian Systems * Chaotic Behavior in a Probabilistic Cellular Automata? * Wave Optics Computing by a Networked-based Vector Wave Automaton * Tensor Manipulation Package in REDUCE * Propagation of Electromagnetic Pulses in Stratified Media * The Simple Molecular Dynamics Model for the Study of Thermalization of the Hot Nucleon Gas * Electron Spin Polarization in PdCo Alloys Calculated by KKR-CPA-LSD Method * Simulation Studies of Microscopic Droplet Spreading * A Vectorizable Algorithm for the Multicolor Successive Overrelaxation Method * Tetragonality of the CuAu I Lattice and Its Relation to Electronic Specific Heat and Spin Susceptibility * Computer Simulation of the Formation of Metallic Aggregates Produced by Chemical Reactions in Aqueous Solution * Scaling in Growth Models with Diffusion: A Monte Carlo Study * The Nucleus as the Mesoscopic System * Neural Network Computation as Dynamic System Simulation * First-principles Theory of Surface Segregation in Binary Alloys * Data Smooth Approximation Algorithm for Estimating the Temperature Dependence of the Ice Nucleation Rate * Genetic Algorithms in Optical Design * Application of 2D-FFT in the Study of Molecular Exchange Processes by NMR * Advanced Mobility Model for Electron Transport in P-Si Inversion Layers * Computer Simulation for Film Surfaces and its Fractal Dimension * Parallel Computation Techniques and the Structure of Catalyst Surfaces * Educational SW to Teach Digital Electronics and the Corresponding Text Book * Primitive Trinomials (Mod 2) Whose Degree is a Mersenne Exponent * Stochastic Modelisation and Parallel Computing * Remarks on the Hybrid Monte Carlo Algorithm for the ∫4 Model * An Experimental Computer Assisted Workbench for Physics Teaching * A Fully Implicit Code to Model Tokamak Plasma Edge Transport * EXPFIT: An Interactive Program for Automatic Beam-foil Decay Curve Analysis * Mapping Technique for Solving General, 1-D Hamiltonian Systems * Freeway Traffic, Cellular Automata, and Some (Self-Organizing) Criticality * Photonuclear Yield Analysis by Dynamic Programming * Incremental Representation of the Simply Connected Planar Curves * Self-convergence in Monte Carlo Methods * Adaptive Mesh Technique for Shock Wave Propagation * Simulation of Supersonic Coronal Streams and Their Interaction with the Solar Wind * The Nature of Chaos in Two Systems of Ordinary Nonlinear Differential Equations * Considerations of a Window-shopper * Interpretation of Data Obtained by RTP 4-Channel Pulsed Radar Reflectometer Using a Multi Layer Perceptron * Statistics of Lattice Bosons for Finite Systems * Fractal Based Image Compression with Affine Transformations * Algorithmic Studies on Simulation Codes for Heavy-ion Reactions * An Energy-Wise Computer Simulation of DNA-Ion-Water Interactions Explains the Abnormal Structure of Poly[d(A)]:Poly[d(T)] * Computer Simulation Study of Kosterlitz-Thouless-Like Transitions * Problem-oriented Software Package GUN-EBT for Computer Simulation of Beam Formation and Transport in Technological Electron-Optical Systems * Parallelization of a Boundary Value Solver and its Application in Nonlinear Dynamics * The Symbolic Classification of Real Four-dimensional Lie Algebras * Short, Singular Pulses Generation by a Dye Laser at Two Wavelengths Simultaneously * Quantum Monte Carlo Simulations of the Apex-Oxygen-Model * Approximation Procedures for the Axial Symmetric Static Einstein-Maxwell-Higgs Theory * Crystallization on a Sphere: Parallel Simulation on a Transputer Network * FAMULUS: A Software Product (also) for Physics Education * MathCAD vs. FAMULUS -- A Brief Comparison * First-principles Dynamics Used to Study Dissociative Chemisorption * A Computer Controlled System for Crystal Growth from Melt * A Time Resolved Spectroscopic Method for Short Pulsed Particle Emission * Green's Function Computation in Radiative Transfer Theory * Random Search Optimization Technique for One-criteria and Multi-criteria Problems * Hartley Transform Applications to Thermal Drift Elimination in Scanning Tunneling Microscopy * Algorithms of Measuring, Processing and Interpretation of Experimental Data Obtained with Scanning Tunneling Microscope * Time-dependent Atom-surface Interactions * Local and Global Minima on Molecular Potential Energy Surfaces: An Example of N3 Radical * Computation of Bifurcation Surfaces * Symbolic Computations in Quantum Mechanics: Energies in Next-to-solvable Systems * A Tool for RTP Reactor and Lamp Field Design * Modelling of Particle Spectra for the Analysis of Solid State Surface * List of Participants

NASCAP user's manual, 1978

NASA Technical Reports Server (NTRS)

Cassidy, J. J., III

1978-01-01

NASCAP simulates the charging process for a complex object in either tenuous plasma (geosynchronous orbit) or ground test (electron gun source) environment. Program control words, the structure of user input files, and various user options available are described in this computer programmer's user manual.

Global response of the ionosphere to atmospheric tides forced from below: Comparison between COSMIC measurements and simulations by atmosphere-ionosphere coupled model GAIA

NASA Astrophysics Data System (ADS)

Pancheva, D.; Miyoshi, Y.; Mukhtarov, P.; Jin, H.; Shinagawa, H.; Fujiwara, H.

2012-07-01

This paper for the first time presents a detailed comparison between simulated and observed global electron density responses to different atmospheric tides forced from below. The recently developed Earth's whole atmospheric model from the troposphere to the ionosphere, called GAIA, has been used for the simulation of the electron density tidal responses. They have been compared with the extracted from the COSMIC electron density data tidal responses for the period of time October 2007 to March 2009. Particular attention has been paid to the nonmigrating DE3/DE2 and migrating DW1, SW2 and TW3 electron density responses. The GAIA model reproduced quite well the COSMIC DE3/DE2 responses. Both simulations and observations revealed three altitude regions of enhanced electron density responses: (1) an upper level response, above 300 km height, apparently shaped mainly by the “fountain effect” (2) a response located near altitudes of ˜200-270 km, and (3) a lower thermospheric response situated near 120-150 km height. A possible mechanism is suggested for explaining the two lower level responses. For the first time the GAIA model simulations supported the observational evidence found in the COSMIC measurements that the ionospheric WN4 (WN3) longitude structure is not generated only by the DE3 (DE2) tide as it has been often assumed. As regards the comparison of the migrating DW1, SW2 and TW3 responses the obtained results clearly demonstrate that the GAIA model reproduce very well of the SW2 and TW3 COSMIC electron density responses. The only main discrepancy is seen in the migrating DW1 response; the observation does not support the splitting of the simulated response at both sides of the equator. This is due mainly to the difference between the SABER and GAIA SW2 tide in the lower thermosphere as it turned out that the DW1 electron density response strongly depends on the mean features of the lower thermospheric SW2 tide.

Effect of simulated microgravitation on phytohormones and cell structure of tropical orchids

NASA Astrophysics Data System (ADS)

Cherevchenko, T.; Zaimenko, N.; Majko, T.; Sytnjanskaja, N.

When studing the effect of two month clinostating on the phytohormonal system of orchids with different types of shoot system branching and different shoot morphology, it was determined that, as a result of simulated microgravitation, endogenous growth regulators changed less in the species with sympodial branching than in species with monopodial branching and without pseudobulbs. Stimulators prevail in the balance of growth regulators in species of the first type and inhibitors in species of the second type. Besides this, comparative analysis of structural organization of juvenile leaf surface tissue of tested orchids was carried out. Variability of size, number and structure of stomatal organization were found according to species belonging to each branching type after clinostating. Electronic microscope studies show some structural peculiarities of epidermal and mesophilous cells.

Theoretical study of the ionospheric plasma cave in the equatorial ionization anomaly region

NASA Astrophysics Data System (ADS)

Chen, Yu-Tsung; Lin, C. H.; Chen, C. H.; Liu, J. Y.; Huba, J. D.; Chang, L. C.; Liu, H.-L.; Lin, J. T.; Rajesh, P. K.

2014-12-01

This paper investigates the physical mechanism of an unusual equatorial electron density structure, plasma cave, located underneath the equatorial ionization anomaly by using theoretical simulations. The simulation results provide important new understanding of the dynamics of the equatorial ionosphere. It has been suggested previously that unusual E>⇀×B>⇀ drifts might be responsible for the observed plasma cave structure, but model simulations in this paper suggest that the more likely cause is latitudinal meridional neutral wind variations. The neutral winds are featured by two divergent wind regions at off-equator latitudes and a convergent wind region around the magnetic equator, resulting in plasma divergences and convergence, respectively, to form the plasma caves structure. The tidal-decomposition analysis further suggests that the cave related meridional neutral winds and the intensity of plasma cave are highly associated with the migrating terdiurnal tidal component of the neutral winds.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Simulation of femtosecond two-dimensional electronic spectra of conical intersections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krčmář, Jindřich; Gelin, Maxim F.; Domcke, Wolfgang

2015-08-21

We have simulated femtosecond two-dimensional (2D) electronic spectra for an excited-state conical intersection using the wave-function version of the equation-of-motion phase-matching approach. We show that 2D spectra at fixed values of the waiting time provide information on the structure of the vibronic eigenstates of the conical intersection, while the evolution of the spectra with the waiting time reveals predominantly ground-state wave-packet dynamics. The results show that 2D spectra of conical intersection systems differ significantly from those obtained for chromophores with well separated excited-state potential-energy surfaces. The spectral signatures which can be attributed to conical intersections are discussed.

Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.

2015-09-01

In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expandmore » the number of potential types of graphene electronic devices.« less

Non-spectroscopic composition measurements of SrTiO 3-La 0.7Sr 0.3MnO 3 multilayers using scanning convergent beam electron diffraction

DOE PAGES

Ophus, Colin; Ercius, Peter; Huijben, Mark; ...

2017-02-08

The local atomic structure of a crystalline sample aligned along a zone axis can be probed with a focused electron probe, which produces a convergent beam electron diffraction pattern. The introduction of high speed direct electron detectors has allowed for experiments that can record a full diffraction pattern image at thousands of probe positions on a sample. By incoherently summing these patterns over crystalline unit cells, we demonstrate in this paper that in addition to crystal structure and thickness, we can also estimate the local composition of a perovskite superlattice sample. This is achieved by matching the summed patterns tomore » a library of simulated diffraction patterns. Finally, this technique allows for atomic-scale chemical measurements without requiring a spectrometer or hardware aberration correction.« less

Fine structure of microwave spike bursts and associated cross-field energy transport

NASA Technical Reports Server (NTRS)

Winglee, R. M.; Dulk, G. A.; Pritchett, P. L.

1988-01-01

The characteristics of the maser emission from a driven system where energetic electrons continue to flow through the source region is investigated using electronic particle simulations. It is shown that, under appropriate conditions, the maser can efficiently radiate a significant portion of the energy of the fast electrons in a very short time. The radiation is emitted in pulses even though the flow of electrons through the system is at a constant rate. The mission of these pulses is proposed as the source of the fine structure. Under other conditions the dominant maser emission changes from fundamental x-mode to either fundamental z-mode or to electrostatic upper hybrid or Bernstein modes. The bulk of the emission from the maser instability cannot propagate across field lines in this regime, and hence strong local plasma heating is expected, with little energy transport across the magnetic field lines.

Early time evolution of negative ion clouds and electron density depletions produced during electron attachment chemical release experiments

NASA Technical Reports Server (NTRS)

Scales, W. A.; Bernhardt, P. A.; Ganguli, G.

1994-01-01

Two-dimensional electrostatic particle-in-cell simulations are used to study the early time evolution of electron depletions and negative ion clouds produced during electron attachment chemical releases in the ionosphere. The simulation model considers the evolution in the plane perpendicular to the magnetic field and a three-species plasma that contains electrons, positive ions, and also heavy negative ions that result as a by-product of the electron attachment reaction. The early time evolution (less than the negative ion cyclotron period) of the system shows that a negative charge surplus initially develops outside of the depletion boundary as the heavy negative ions move across the boundary. The electrons are initially restricted from moving into the depletion due to the magnetic field. An inhomogenous electric field develops across the boundary layer due to this charge separation. A highly sheared electron flow velocity develops in the depletion boundary due to E x B and Delta-N x B drifts that result from electron density gradients and this inhomogenous electric field. Structure eventually develops in the depletion boundary layer due to low-frequency electrostatic waves that have growth times shorter than the negative ion cyclotron period. It is proposed that these waves are most likely produced by the electron-ion hybrid instability that results from sufficiently large shears in the electron flow velocity.

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Reproducing the observed energy-dependent structure of Earth's electron radiation belts during storm recovery with an event-specific diffusion model

DOE PAGES

Ripoll, J. -F.; Reeves, Geoffrey D.; Cunningham, Gregory Scott; ...

2016-06-11

Here, we present dynamic simulations of energy-dependent losses in the radiation belt “slot region” and the formation of the two-belt structure for the quiet days after the 1 March storm. The simulations combine radial diffusion with a realistic scattering model, based data-driven spatially and temporally resolved whistler-mode hiss wave observations from the Van Allen Probes satellites. The simulations reproduce Van Allen Probes observations for all energies and L shells (2–6) including (a) the strong energy dependence to the radiation belt dynamics (b) an energy-dependent outer boundary to the inner zone that extends to higher L shells at lower energies andmore » (c) an “S-shaped” energy-dependent inner boundary to the outer zone that results from the competition between diffusive radial transport and losses. We find that the characteristic energy-dependent structure of the radiation belts and slot region is dynamic and can be formed gradually in ~15 days, although the “S shape” can also be reproduced by assuming equilibrium conditions. The highest-energy electrons (E > 300 keV) of the inner region of the outer belt (L ~ 4–5) also constantly decay, demonstrating that hiss wave scattering affects the outer belt during times of extended plasmasphere. Through these simulations, we explain the full structure in energy and L shell of the belts and the slot formation by hiss scattering during storm recovery. We show the power and complexity of looking dynamically at the effects over all energies and L shells and the need for using data-driven and event-specific conditions.« less