Atomically precise lateral modulation of a two-dimensional electron liquid in anatase TiO 2 thin films

DOE PAGES

Wang, Zhiming; Zhong, Z.; Walker, S. McKeown; ...

2017-03-10

Engineering the electronic band structure of two-dimensional electron liquids (2DELs) confined at the surface or interface of transition metal oxides is key to unlocking their full potential. Here we describe a new approach to tailoring the electronic structure of an oxide surface 2DEL demonstrating the lateral modulation of electronic states with atomic scale precision on an unprecedented length scale comparable to the Fermi wavelength. To this end, we use pulsed laser deposition to grow anatase TiO 2 films terminated by a (1 x 4) in-plane surface reconstruction. Employing photo-stimulated chemical surface doping we induce 2DELs with tunable carrier densities thatmore » are confined within a few TiO 2 layers below the surface. Subsequent in situ angle resolved photoemission experiments demonstrate that the (1 x 4) surface reconstruction provides a periodic lateral perturbation of the electron liquid. Furthermore, this causes strong backfolding of the electronic bands, opening of unidirectional gaps and a saddle point singularity in the density of states near the chemical potential.« less

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

Electronic structure studies of a clock-reconstructed Al/Pd(1 0 0) surface alloy

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Tainter, Craig J.

We have employed solid-state Fenske-Hall band structure calculations to examine the electronic structure of Al/Pd(1 0 0), a surface alloy that undergoes a reconstruction, or rearrangement, of the atoms in the top few surface layers. Surface alloys are materials that consist primarily of a single elemental metal, but which have a bimetallic surface composition that is only a few atomic layers in thickness. The results of this study indicate that reconstruction into a clock configuration simultaneously optimizes the intralayer bonding within the surface plane and the bonding between the first and second atomic layers. These results also allow us to examine the fundamental relationship between the electronic and physical structures of this reconstructed surface alloy.

Electronic structure studies of adsorbate-induced surface reconstructions: oxygen on Rh(1 0 0)

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2004-03-01

Solid-state Fenske-Hall band structure calculations have been used to study the electronic structure and bonding that occur on an "asymmetric" clock reconstructed Rh(1 0 0) surface with a half-monolayer of O atom adsorbates. The displacement of the top-layer Rh atoms on reconstructed O/Rh(1 0 0) is similar to that observed when a half-monolayer of C or N atoms adsorb onto clean Ni(1 0 0). Unlike the five-coordinate C or N adsorbates that adsorb into effectively coplanar sites on the Ni(1 0 0) surface, however, O atoms sit well above the Rh surface plane and occupy three-coordinate adsorption sites. The results of these calculations show that the asymmetric clock reconstruction of O/Rh(1 0 0) increases the negative charge localized on the highly electronegative O atoms and strengthens the O-Rh bonding relative to an unreconstructed surface. This suggests that, in contrast to the C(N)/Ni(1 0 0) clock, which appears to be driven primarily by the restoration of metal-metal bonding, the asymmetric O/Rh(1 0 0) clock reconstruction is driven by the optimization of the O atom bonding environment. Comparisons of the O/Rh(1 0 0) and C(N, O)/Ni(1 0 0) surfaces further indicate that the electronegativity and electron count of the adsorbed species, as well as the electron count and physical size of the metal, all play a role in determining the preferred atomic geometries of these adsorbate-covered transition metal surfaces.

Simulation of Heterogeneous Atom Probe Tip Shapes Evolution during Field Evaporation Using a Level Set Method and Different Evaporation Models

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

Xu, Zhijie; Li, Dongsheng; Xu, Wei

2015-04-01

In atom probe tomography (APT), accurate reconstruction of the spatial positions of field evaporated ions from measured detector patterns depends upon a correct understanding of the dynamic tip shape evolution and evaporation laws of component atoms. Artifacts in APT reconstructions of heterogeneous materials can be attributed to the assumption of homogeneous evaporation of all the elements in the material in addition to the assumption of a steady state hemispherical dynamic tip shape evolution. A level set method based specimen shape evolution model is developed in this study to simulate the evaporation of synthetic layered-structured APT tips. The simulation results ofmore » the shape evolution by the level set model qualitatively agree with the finite element method and the literature data using the finite difference method. The asymmetric evolving shape predicted by the level set model demonstrates the complex evaporation behavior of heterogeneous tip and the interface curvature can potentially lead to the artifacts in the APT reconstruction of such materials. Compared with other APT simulation methods, the new method provides smoother interface representation with the aid of the intrinsic sub-grid accuracy. Two evaporation models (linear and exponential evaporation laws) are implemented in the level set simulations and the effect of evaporation laws on the tip shape evolution is also presented.« less

First-principles study of structure, electronic properties and stability of tungsten adsorption on TiC(111) surface with disordered vacancies

NASA Astrophysics Data System (ADS)

Ilyasov, Victor V.; Pham, Khang D.; Zhdanova, Tatiana P.; Phuc, Huynh V.; Hieu, Nguyen N.; Nguyen, Chuong V.

2017-12-01

In this paper, we systematically investigate the atomic structure, electronic and thermodynamic properties of adsorbed W atoms on the polar Ti-terminated TixCy (111) surface with different configurations of adsorptions using first principle calculations. The bond length, adsorption energy, and formation energy for different reconstructions of the atomic structure of the W/TixCy (111) systems were established. The effect of the tungsten coverage on the electronic structure and the adsorption mechanism of tungsten atom on the TixCy (111) are also investigated. We also suggest the possible mechanisms of W nucleation on the TixCy (111) surface. The effective charges on W atoms and nearest-neighbor atoms in the examined reconstructions were identified. Additionally, we have established the charge transfer from titanium atom to tungsten and carbon atoms which determine by the reconstruction of the local atomic and electronic structures. Our calculations showed that the charge transfer correlates with the electronegativity of tungsten and nearest-neighbor atoms. We also determined the effective charge per atom of titanium, carbon atoms, and neighboring adsorbed tungsten atom in different binding configurations. We found that, with reduction of the lattice symmetry associated with titanium and carbon vacancies, the adsorption energy increases by 1.2 times in the binding site A of W/TixCy systems.

Method and apparatus for atomic imaging

DOEpatents

Saldin, Dilano K.; de Andres Rodriquez, Pedro L.

1993-01-01

A method and apparatus for three dimensional imaging of the atomic environment of disordered adsorbate atoms are disclosed. The method includes detecting and measuring the intensity of a diffuse low energy electron diffraction pattern formed by directing a beam of low energy electrons against the surface of a crystal. Data corresponding to reconstructed amplitudes of a wave form is generated by operating on the intensity data. The data corresponding to the reconstructed amplitudes is capable of being displayed as a three dimensional image of an adsorbate atom. The apparatus includes a source of a beam of low energy electrons and a detector for detecting the intensity distribution of a DLEED pattern formed at the detector when the beam of low energy electrons is directed onto the surface of a crystal. A device responsive to the intensity distribution generates a signal corresponding to the distribution which represents a reconstructed amplitude of a wave form and is capable of being converted into a three dimensional image of the atomic environment of an adsorbate atom on the crystal surface.

Giant photovoltaic effects driven by residual polar field within unit-cell-scale LaAlO3 films on SrTiO3

PubMed Central

Liang, Haixing; Cheng, Long; Zhai, Xiaofang; Pan, Nan; Guo, Hongli; Zhao, Jin; Zhang, Hui; Li, Lin; Zhang, Xiaoqiang; Wang, Xiaoping; Zeng, Changgan; Zhang, Zhenyu; Hou, J. G.

2013-01-01

For polar/nonpolar heterostructures, Maxwell's theory dictates that the electric potential in the polar components will increase divergently with the film thickness. For LaAlO3/SrTiO3, a conceptually intriguing route, termed charge reconstruction, has been proposed to avert such “polar catastrophe”. The existence of a polar potential in LaAlO3 is a prerequisite for the validity of the charge reconstruction picture, yet to date, its direct measurement remains a major challenge. Here we establish unambiguously the existence of the residual polar potential in ultrathin LaAlO3 films on SrTiO3, using a novel photovoltaic device design as an effective probe. The measured lower bound of the residual polar potential is 1.0 V. Such a direct observation of the giant residual polar potential within the unit-cell-scale LaAlO3 films amounts to a definitive experimental evidence for the charge reconstruction picture, and also points to new technological significance of oxide heterostructures in photovoltaic and sensing devices with atomic-scale control. PMID:23756918

Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Wolf, Sharon G; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef; Urban, Knut

2008-03-01

We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomic-scale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2-3 A. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subångström resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm3, preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scale at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.

Surface reconstruction of InAs (001) depending on the pressure and temperature examined by density functional thermodynamics.

PubMed

Yeu, In Won; Park, Jaehong; Han, Gyuseung; Hwang, Cheol Seong; Choi, Jung-Hae

2017-09-06

A detailed understanding of the atomic configuration of the compound semiconductor surface, especially after reconstruction, is very important for the device fabrication and performance. While there have been numerous experimental studies using the scanning probe techniques, further theoretical studies on surface reconstruction are necessary to promote the clear understanding of the origins and development of such subtle surface structures. In this work, therefore, a pressure-temperature surface reconstruction diagram was constructed for the model case of the InAs (001) surface considering both the vibrational entropy and configurational entropy based on the density functional theory. Notably, the equilibrium fraction of various reconstructions was determined as a function of the pressure and temperature, not as a function of the chemical potential, which largely facilitated the direct comparison with the experiments. By taking into account the entropy effects, the coexistence of the multiple reconstructions and the fractional change of each reconstruction by the thermodynamic condition were predicted and were in agreement with the previous experimental observations. This work provides the community with a useful framework for such type of theoretical studies.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

PubMed Central

Nguyen, Bao Linh; Pettitt, B. Montgomery

2015-01-01

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations. PMID:26388706

Electronic structure and surface properties of MgB2(0001) upon oxygen adsorption

NASA Astrophysics Data System (ADS)

Kim, Chang-Eun; Ray, Keith G.; Bahr, David F.; Lordi, Vincenzo

2018-05-01

We use density-functional theory to investigate the bulk and surface properties of MgB2. The unique bonding structure of MgB2 is investigated by Bader's atoms-in-molecules, charge density difference, and occupancy projected band structure analyses. Oxygen adsorption on the charge-depleted surfaces of MgB2 is studied by a surface potential energy mapping method, reporting a complete map including low-symmetry binding sites. The B-terminated MgB2(0001) demonstrates reconstruction of the graphenelike B layer, and the reconstructed geometry exposes a threefold site of the subsurface Mg, making it accessible from the surface. Detailed reconstruction mechanisms are studied by simulated annealing method based on ab initio molecular dynamics and nudged elastic band calculations. The surface clustering of B atoms significantly modifies the B 2 p states to occupy low energy valence states. The present paper emphasizes that a thorough understanding of the surface phase may explain an apparent inconsistency in the experimental surface characterization of MgB2. Furthermore, these results suggest that the surface passivation can be an important technical challenge when it comes to development of a superconducting device using MgB2.

Surface modification of nano-silica on the ligament advanced reinforcement system for accelerated bone formation: primary human osteoblasts testing in vitro and animal testing in vivo

NASA Astrophysics Data System (ADS)

Li, Mengmeng; Wang, Shiwen; Jiang, Jia; Sun, Jiashu; Li, Yuzhuo; Huang, Deyong; Long, Yun-Ze; Zheng, Wenfu; Chen, Shiyi; Jiang, Xingyu

2015-04-01

The Ligament Advanced Reinforcement System (LARS) has been considered as a promising graft for ligament reconstruction. To improve its biocompatibility and effectiveness on new bone formation, we modified the surface of a polyethylene terephthalate (PET) ligament with nanoscale silica using atom transfer radical polymerization (ATRP) and silica polymerization. The modified ligament is tested by both in vitro and in vivo experiments. Human osteoblast testing in vitro exhibits an ~21% higher value in cell viability for silica-modified grafts compared with original grafts. Animal testing in vivo shows that there is new formed bone in the case of a nanoscale silica-coated ligament. These results demonstrate that our approach for nanoscale silica surface modification on LARS could be potentially applied for ligament reconstruction.The Ligament Advanced Reinforcement System (LARS) has been considered as a promising graft for ligament reconstruction. To improve its biocompatibility and effectiveness on new bone formation, we modified the surface of a polyethylene terephthalate (PET) ligament with nanoscale silica using atom transfer radical polymerization (ATRP) and silica polymerization. The modified ligament is tested by both in vitro and in vivo experiments. Human osteoblast testing in vitro exhibits an ~21% higher value in cell viability for silica-modified grafts compared with original grafts. Animal testing in vivo shows that there is new formed bone in the case of a nanoscale silica-coated ligament. These results demonstrate that our approach for nanoscale silica surface modification on LARS could be potentially applied for ligament reconstruction. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01439e

Reconstructing Solvent Density of Myoglobin Unit Cell from Proximal Radial Distribution Functions of Amino Acids

NASA Astrophysics Data System (ADS)

Galbraith, Madeline; Lynch, Gc; Pettitt, Bm

Understanding the solvent density around a protein crystal structure is an important step for refining accurate crystal structures for use in dynamics simulations or in free energy calculations. The free energy of solvation has typically been approximated using an implicit continuum solvent model or an all atom MD simulation, with a trade-off between accuracy and computation time. For proteins, using precomputed proximal radial distribution functions (pRDFs) of the solvent to reconstruct solvent density on a grid is much faster than all atom MD simulations and more accurate than using implicit solvent models. MD simulations were run for the 20 common amino acids and pRDFs were calculated for several atom type data sets with and without hydrogens, using atom types representative of amino acid side chain atoms. Preliminary results from reconstructions suggest using a data set with 15 heavy atoms and 3 hydrogen yields results with the lowest error without a tradeoff on time. The results of using precomputed pRDFs to reconstruct the solvent density of water for the myoglobin (pdb ID 2mgk) unit cell quantifies the accuracy of the method in comparison with the crystallographic data. Funding Acknowledgement: This research was funded by the CPRIT Summer Undergraduate Program in Computational Cancer Biology, training Grant award RP 140113 from the Cancer Prevention & Research Institute of Texas (CPRIT).

Simulation of angular-resolved RABBITT measurements in noble-gas atoms

NASA Astrophysics Data System (ADS)

Bray, Alexander W.; Naseem, Faiza; Kheifets, Anatoli S.

2018-06-01

We simulate angular-resolved RABBITT (reconstruction of attosecond beating by interference of two-photon transitions) measurements on valence shells of noble-gas atoms (Ne, Ar, Kr, and Xe). Our nonperturbative numerical simulation is based on solution of the time-dependent Schrödinger equation (TDSE) for a target atom driven by an ionizing XUV and dressing IR fields. From these simulations we extract the angular-dependent magnitude and phase of the RABBITT oscillations and deduce the corresponding angular anisotropy β parameter and Wigner time delay τW for the single XUV photon absorption that initiates the RABBITT process. Said β and τW parameters are compared with calculations in the random-phase approximation with exchange (RPAE), which includes intershell correlation. This comparison is used to test various effective potentials employed in the one-electron TDSE. In lighter atoms (Ne and Ar), several effective potentials are found to provide accurate simulations of RABBITT measurements for a wide range of photon energies up to 100 eV above the valence-shell threshold. In heavier atoms (Kr and Xe), the onset of strong correlation with the d shell restricts the validity of the single active electron approximation to several tens of eV above the valence-shell threshold.

Atom probe trajectory mapping using experimental tip shape measurements.

PubMed

Haley, D; Petersen, T; Ringer, S P; Smith, G D W

2011-11-01

Atom probe tomography is an accurate analytical and imaging technique which can reconstruct the complex structure and composition of a specimen in three dimensions. Despite providing locally high spatial resolution, atom probe tomography suffers from global distortions due to a complex projection function between the specimen and detector which is different for each experiment and can change during a single run. To aid characterization of this projection function, this work demonstrates a method for the reverse projection of ions from an arbitrary projection surface in 3D space back to an atom probe tomography specimen surface. Experimental data from transmission electron microscopy tilt tomography are combined with point cloud surface reconstruction algorithms and finite element modelling to generate a mapping back to the original tip surface in a physically and experimentally motivated manner. As a case study, aluminium tips are imaged using transmission electron microscopy before and after atom probe tomography, and the specimen profiles used as input in surface reconstruction methods. This reconstruction method is a general procedure that can be used to generate mappings between a selected surface and a known tip shape using numerical solutions to the electrostatic equation, with quantitative solutions to the projection problem readily achievable in tens of minutes on a contemporary workstation. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Application of composite dictionary multi-atom matching in gear fault diagnosis.

PubMed

Cui, Lingli; Kang, Chenhui; Wang, Huaqing; Chen, Peng

2011-01-01

The sparse decomposition based on matching pursuit is an adaptive sparse expression method for signals. This paper proposes an idea concerning a composite dictionary multi-atom matching decomposition and reconstruction algorithm, and the introduction of threshold de-noising in the reconstruction algorithm. Based on the structural characteristics of gear fault signals, a composite dictionary combining the impulse time-frequency dictionary and the Fourier dictionary was constituted, and a genetic algorithm was applied to search for the best matching atom. The analysis results of gear fault simulation signals indicated the effectiveness of the hard threshold, and the impulse or harmonic characteristic components could be separately extracted. Meanwhile, the robustness of the composite dictionary multi-atom matching algorithm at different noise levels was investigated. Aiming at the effects of data lengths on the calculation efficiency of the algorithm, an improved segmented decomposition and reconstruction algorithm was proposed, and the calculation efficiency of the decomposition algorithm was significantly enhanced. In addition it is shown that the multi-atom matching algorithm was superior to the single-atom matching algorithm in both calculation efficiency and algorithm robustness. Finally, the above algorithm was applied to gear fault engineering signals, and achieved good results.

Holographic Reconstruction of Photoelectron Diffraction and Its Circular Dichroism for Local Structure Probing

NASA Astrophysics Data System (ADS)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

The local atomic structure around a specific element atom can be recorded as a photoelectron diffraction pattern. Forward focusing peaks and diffraction rings around them indicate the directions and distances from the photoelectron emitting atom to the surrounding atoms. The state-of-the-art holography reconstruction algorithm enables us to image the local atomic arrangement around the excited atom in a real space. By using circularly polarized light as an excitation source, the angular momentum transfer from the light to the photoelectron induces parallax shifts in these diffraction patterns. As a result, stereographic images of atomic arrangements are obtained. These diffraction patterns can be used as atomic-site-resolved probes for local electronic structure investigation in combination with spectroscopy techniques. Direct three-dimensional atomic structure visualization and site-specific electronic property analysis methods are reviewed. Furthermore, circular dichroism was also found in valence photoelectron and Auger electron diffraction patterns. The investigation of these new phenomena provides hints for the development of new techniques for local structure probing.

Single-layer TiO x reconstructions on SrTiO 3 (111): (√7 × √7)R19.1°, (√13 × √13)R13.9°, and related structures

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

Andersen, Tassie K.; Wang, Shuqiu; Castell, Martin R.

The atomic structures of two reconstructions, (√7 × √7)R19.1° and (√13 × √13)R13.9°, on the SrTiO 3 (111) surface were determined using a combination of density functional theory and scanning tunneling microscopy data and simulations. The combination of these methods allows for potential surface structures to be generated and verified in the absence of diffraction data, providing another tool for solving surface reconstructions. These reconstructions belong to the same stoichiometric, nSrTiO 3 • mTiO 2, structural family made up of an interconnected, single layer of edge-sharing TiO 6 and TiO 5[] octahedra. This family is found to include the previously-solvedmore » (2 × 2)a reconstruction as its smallest unit-cell sized member and serves as a tool for better understanding and predicting the structure of other reconstructions of arbitrary surface unit-cell size on SrTiO 3 (111). This reconstruction family and the calculations of surface energies for different hypothesis structures also shed light on the structure of Schottky defects observed on these reconstructed SrTO 3 (111) surfaces.« less

On the retrieval of crystallographic information from atom probe microscopy data via signal mapping from the detector coordinate space.

PubMed

Wallace, Nathan D; Ceguerra, Anna V; Breen, Andrew J; Ringer, Simon P

2018-06-01

Atom probe tomography is a powerful microscopy technique capable of reconstructing the 3D position and chemical identity of millions of atoms within engineering materials, at the atomic level. Crystallographic information contained within the data is particularly valuable for the purposes of reconstruction calibration and grain boundary analysis. Typically, analysing this data is a manual, time-consuming and error prone process. In many cases, the crystallographic signal is so weak that it is difficult to detect at all. In this study, a new automated signal processing methodology is demonstrated. We use the affine properties of the detector coordinate space, or the 'detector stack', as the basis for our calculations. The methodological framework and the visualisation tools are shown to be superior to the standard method of crystallographic pole visualisation directly from field evaporation images and there is no requirement for iterations between a full real-space initial tomographic reconstruction and the detector stack. The mapping approaches are demonstrated for aluminium, tungsten, magnesium and molybdenum. Implications for reconstruction calibration, accuracy of crystallographic measurements, reliability and repeatability are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Holographic method for site-resolved detection of a 2D array of ultracold atoms

NASA Astrophysics Data System (ADS)

Hoffmann, Daniel Kai; Deissler, Benjamin; Limmer, Wolfgang; Hecker Denschlag, Johannes

2016-08-01

We propose a novel approach to site-resolved detection of a 2D gas of ultracold atoms in an optical lattice. A near-resonant laser beam is coherently scattered by the atomic array, and after passing a lens its interference pattern is holographically recorded by superimposing it with a reference laser beam on a CCD chip. Fourier transformation of the recorded intensity pattern reconstructs the atomic distribution in the lattice with single-site resolution. The holographic detection method requires only about two hundred scattered photons per atom in order to achieve a high reconstruction fidelity of 99.9 %. Therefore, additional cooling during detection might not be necessary even for light atomic elements such as lithium. Furthermore, first investigations suggest that small aberrations of the lens can be post-corrected in imaging processing.

Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction

NASA Astrophysics Data System (ADS)

Miao, Jianwei; Hodgson, Keith O.; Ishikawa, Tetsuya; Larabell, Carolyn A.; Legros, Mark A.; Nishino, Yoshinori

2003-01-01

We report the first experimental recording, to our knowledge, of the diffraction pattern from intact Escherichia coli bacteria using coherent x-rays with a wavelength of 2 Å. By using the oversampling phasing method, a real space image at a resolution of 30 nm was directly reconstructed from the diffraction pattern. An R factor used for characterizing the quality of the reconstruction was in the range of 5%, which demonstrated the reliability of the reconstruction process. The distribution of proteins inside the bacteria labeled with manganese oxide has been identified and this distribution confirmed by fluorescence microscopy images. Compared with lens-based microscopy, this diffraction-based imaging approach can examine thicker samples, such as whole cultured cells, in three dimensions with resolution limited only by radiation damage. Looking forward, the successful recording and reconstruction of diffraction patterns from biological samples reported here represent an important step toward the potential of imaging single biomolecules at near-atomic resolution by combining single-particle diffraction with x-ray free electron lasers.

Giant (12 ×12 ) and (4 ×8 ) reconstructions of the 6 H -SiC(0001) surface obtained by progressive enrichment in Si atoms

NASA Astrophysics Data System (ADS)

Martrou, David; Leoni, Thomas; Chaumeton, Florian; Castanié, Fabien; Gauthier, Sébastien; Bouju, Xavier

2018-02-01

Silicon carbide (SiC) is nowadays a major material for applications in high power electronics, quantum optics, or nitride semiconductors growth. Mastering the surface of SiC substrate is crucial to obtain reproducible results. Previous studies on the 6 H -SiC(0001) surface have determined several reconstructions, including the (√{3 }×√{3 }) -R 30∘ and the (3 ×3 ) . Here, we introduce a process of progressive Si enrichment that leads to the formation of two reconstructions, the giant (12 ×12 ) and the (4 ×8 ) . From electron diffraction and tunneling microscopy completed by molecular dynamics simulations, we build models introducing a type of Si adatom bridging two Si surface atoms. Using these Si bridges, we also propose a structure for two other reconstructions, the (2 √{3 }×2 √{3 }) -R 30∘ and the (2 √{3 }×2 √{13 } ). We show that five reconstructions follow each other with Si coverage ranging from 1 and 1.444 monolayer. This result opens the way to greatly improve the control of 6 H -SiC(0001) at the atomic scale.

Interstitial copper defect induced reconstruction of a new ;CuO4; quadrilateral in CaCu3Ti4O12: A first-principles study

NASA Astrophysics Data System (ADS)

Xiao, Haibo; Xu, Linfang; Wang, Ruilong; Yang, Changping

2017-09-01

The geometric structure, electronic structure and formation energy of CaCu3Ti4O12 (CCTO) with interstitial copper atom have been studied using the density-functional method within the GGA approximation. Result of structural optimization shows that the interstitial Cu-atom (Cu7) prefers to occupy a special location which is symmetrical with an intrinsic copper atom (Cu13) deviated from the normal site. The mulliken analysis indicates the loss of electrons from interstitial atom (Cu7) and Cu13 are only half more of the losing in other copper atom, which reveals a characteristics of covalent bonding between Cu7/Cu13 and surrounding oxygen atoms respectively. Meanwhile, it is found from electron density difference (EDD) and orbital analysis that the introduction of interstitial Cu atom causes prominent structural reconstruction of a new ;CuO4; quadrilateral. Moreover, the new ;CuO4; planar leads to a corresponding electronic reconstruction in the hybridization between Cu7/Cu13 3d and O 2p at the vicinity of fermi surface, for which a new conductive filament channel comes into being. Besides, the formation energies of the interstitial defects in various charge states are corrected with the value of 2.18, -4.17 and -9.46 eV for charge of 0, 1+ and 2+, respectively.

Dynamic probe of ZnTe(110) surface by scanning tunneling microscopy

PubMed Central

Kanazawa, Ken; Yoshida, Shoji; Shigekawa, Hidemi; Kuroda, Shinji

2015-01-01

The reconstructed surface structure of the II–VI semiconductor ZnTe (110), which is a promising material in the research field of semiconductor spintronics, was studied by scanning tunneling microscopy/spectroscopy (STM/STS). First, the surface states formed by reconstruction by the charge transfer of dangling bond electrons from cationic Zn to anionic Te atoms, which are similar to those of IV and III–V semiconductors, were confirmed in real space. Secondly, oscillation in tunneling current between binary states, which is considered to reflect a conformational change in the topmost Zn–Te structure between the reconstructed and bulk-like ideal structures, was directly observed by STM. Third, using the technique of charge injection, a surface atomic structure was successfully fabricated, suggesting the possibility of atomic-scale manipulation of this widely applicable surface of ZnTe. PMID:27877752

High-resolution structure of viruses from random diffraction snapshots

PubMed Central

Hosseinizadeh, A.; Schwander, P.; Dashti, A.; Fung, R.; D'Souza, R. M.; Ourmazd, A.

2014-01-01

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the three-dimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution. We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects. PMID:24914154

High-resolution structure of viruses from random diffraction snapshots.

PubMed

Hosseinizadeh, A; Schwander, P; Dashti, A; Fung, R; D'Souza, R M; Ourmazd, A

2014-07-17

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the three-dimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution. We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects.

X-ray fluorescence holography studies for a Cu3Au crystal

NASA Astrophysics Data System (ADS)

Dąbrowski, K. M.; Dul, D. T.; Jaworska-Gołąb, T.; Rysz, J.; Korecki, P.

2015-12-01

In this work we show that performing a numerical correction for beam attenuation and indirect excitation allows one to fully restore element sensitivity in the three-dimensional reconstruction of the atomic structure. This is exemplified by a comparison of atomic images reconstructed from holograms measured for ordered and disordered phases of a Cu3Au crystal that clearly show sensitivity to changes in occupancy of the atomic sites. Moreover, the numerical correction, which is based on quantitative methods of X-ray fluorescence spectroscopy, was extended to take into account the influence of a disturbed overlayer in the sample.

Quantum chemistry study on the open end of single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Hou, Shimin; Shen, Ziyong; Zhao, Xingyu; Xue, Zengquan

2003-05-01

Geometrical and electronic structures of open-ended single-walled carbon nanotubes (SWCNTs) are calculated using density functional theory (DFT) with hybrid functional (B3LYP) approximation. Due to different distances between carbon atoms along the edge, reconstruction occurs at the open end of the (4,4) armchair SWCNT, i.e., triple bonds are formed in the carbon atom pairs at the mouth; however, for the (6,0) zigzag SWCNT, electrons in dangling bonds still remain at 'no-bonding' states. The ionization potential (IP) of both (4,4) and (6,0) SWCNTs is increased by their negative intrinsic dipole moments, and localized electronic states existed at both of their open ends.

Observation of electromagnetically induced Talbot effect in an atomic system

NASA Astrophysics Data System (ADS)

Zhang, Zhaoyang; Liu, Xing; Zhang, Dan; Sheng, Jiteng; Zhang, Yiqi; Zhang, Yanpeng; Xiao, Min

2018-01-01

The electromagnetically induced Talbot effect (EITE) resulting from the repeated self-reconstruction of a spatially intensity-modulated probe field is experimentally demonstrated in a three-level atomic configuration. The probe beam is launched into an optically induced lattice (established by the interference of two coupling fields) inside a rubidium vapor cell and is diffracted by the electromagnetically induced grating that was formed. The diffraction pattern repeats itself at the planes of integer multiple Talbot lengths. In addition, a fractional EITE is also investigated. The experimental observations agree well with the theoretical predictions. This investigation may potentially pave the way for studying the nonlinear and quantum dynamical features that have been predicted for established periodic optical systems.

The effect orientation of features in reconstructed atom probe data on the resolution and measured composition of T1 plates in an A2198 aluminium alloy.

PubMed

Mullin, Maria A; Araullo-Peters, Vicente J; Gault, Baptiste; Cairney, Julie M

2015-12-01

Artefacts in atom probe tomography can impact the compositional analysis of microstructure in atom probe studies. To determine the integrity of information obtained, it is essential to understand how the positioning of features influences compositional analysis. By investigating the influence of feature orientation within atom probe data on measured composition in microstructural features within an AA2198 Al alloy, this study shows differences in the composition of T1 (Al2CuLi) plates that indicates imperfections in atom probe reconstructions. The data fits a model of an exponentially-modified Gaussian that scales with the difference in evaporation field between solutes and matrix. This information provides a guide for obtaining the most accurate information possible. Copyright © 2015 Elsevier B.V. All rights reserved.

Protein-protein interaction specificity is captured by contact preferences and interface composition.

PubMed

Nadalin, Francesca; Carbone, Alessandra

2018-02-01

Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. alessandra.carbone@lip6.fr. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Si Nanoribbons on Ag(110) Studied by Grazing-Incidence X-Ray Diffraction, Scanning Tunneling Microscopy, and Density-Functional Theory: Evidence of a Pentamer Chain Structure.

PubMed

Prévot, Geoffroy; Hogan, Conor; Leoni, Thomas; Bernard, Romain; Moyen, Eric; Masson, Laurence

2016-12-30

We report a combined grazing incidence x-ray diffraction (GIXD), scanning tunneling microscopy (STM), and density-functional theory (DFT) study which clearly elucidates the atomic structure of the Si nanoribbons grown on the missing-row reconstructed Ag(110) surface. Our study allows us to discriminate between the theoretical models published in the literature, including the most stable atomic configurations and those based on a missing-row reconstructed Ag(110) surface. GIXD measurements unambiguously validate the pentamer model grown on the reconstructed surface, obtained from DFT. This pentamer atomistic model accurately matches the high-resolution STM images of the Si nanoribbons adsorbed on Ag(110). Our study closes the long-debated atomic structure of the Si nanoribbons grown on Ag(110) and definitively excludes a honeycomb structure similar to that of freestanding silicene.

Low energy electron diffraction and low energy electron microscopy microspot I/V analysis of the (4 x 4)O structure on Ag(111): surface oxide or reconstruction?

PubMed

Reichelt, R; Günther, S; Wintterlin, J; Moritz, W; Aballe, L; Mentes, T O

2007-10-07

A low energy electron diffraction (LEED) I/V analysis was performed of the (4 x 4) oxygen structure on Ag(111). Two data sets were used, one recorded with a conventional LEED system and a second with a low energy electron microscope (LEEM). The data sets agree well with each other, demonstrating that I/V structure analyses can be performed with the same quality with LEEM as with conventional LEED. The structure obtained confirms the recently proposed model that involves a reconstruction of the Ag(111) surface. Previous models based on a thin layer of Ag(2)O that had been accepted for more than 30 years are disproved. The reconstruction model contains two units of six triangularly arranged Ag atoms and a stacking fault in one half of the unit cell. The six O atoms per unit cell occupy sites in the trenches between the Ag(6) triangles. Small lateral displacements of the Ag atoms lift the mirror symmetry of the structure, leading to two nonequivalent groups of O atoms. The atoms of both groups are located approximately 0.5 Angstrom below the top Ag layer, on fourfold positions with respect to the top layer Ag atoms. Ag-O distances between 2.05 and 2.3 Angstrom are found. The oxygen atoms exhibit large static or dynamic displacements of up to 0.3 Angstrom at 300 K.

Atomically Visualizing Elemental Segregation-Induced Surface Alloying and Restructuring

DOE PAGES

Zou, Lianfeng; Li, Jonathan; Zakharov, Dmitri; ...

2017-12-01

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.

Chlorine adsorption on the InAs (001) surface

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

Bakulin, A. V.; Eremeev, S. V.; Tereshchenko, O. E.

2011-01-15

Chlorine adsorption on the In-stabilized InAs(001) surface with {zeta}-(4 Multiplication-Sign 2) and {beta}3 Prime -(4 Multiplication-Sign 2) reconstructions and on the Ga-stabilized GaAs (001)-{zeta}-(4 Multiplication-Sign 2) surface has been studied within the electron density functional theory. The equilibrium structural parameters of these reconstructions, surface atom positions, bond lengths in dimers, and their changes upon chlorine adsorption are determined. The electronic characteristics of the clean surface and the surface with adsorbed chlorine are calculated. It is shown that the most energetically favorable positions for chlorine adsorption are top positions over dimerized indium or gallium atoms. The mechanism of chlorine binding withmore » In(Ga)-stabilized surface is explained. The interaction of chlorine atoms with dimerized surface atoms weakens surface atom bonds and controls the initial stage of surface etching.« less

Detailed low-energy electron diffraction analysis of the (4×4) surface structure of C60 on Cu(111): Seven-atom-vacancy reconstruction

NASA Astrophysics Data System (ADS)

Xu, Geng; Shi, Xing-Qiang; Zhang, R. Q.; Pai, Woei Wu; Jeng, H. T.; Van Hove, M. A.

2012-08-01

A detailed and exhaustive structural analysis by low-energy electron diffraction (LEED) is reported for the C60-induced reconstruction of Cu(111), in the system Cu(111) + (4 × 4)-C60. A wide LEED energy range allows enhanced sensitivity to the crucial C60-metal interface that is buried below the 7-Å-thick molecular layer. The analysis clearly favors a seven-Cu-atom vacancy model (with Pendry R-factor Rp = 0.376) over a one-Cu-atom vacancy model (Rp = 0.608) and over nonreconstructed models (Rp = 0.671 for atop site and Rp = 0.536 for hcp site). The seven-Cu-atom vacancy forms a (4 × 4) lattice of bowl-like holes. In each hole, a C60 molecule can nestle by forming strong bonds (shorter than 2.30 Å) between 15 C atoms of the molecule and 12 Cu atoms of the outermost and second Cu layers.

Locating structures and evolution pathways of reconstructed rutile TiO2(011) using genetic algorithm aided density functional theory calculations.

PubMed

Ding, Pan; Gong, Xue-Qing

2016-05-01

Titanium dioxide (TiO2) is an important metal oxide that has been used in many different applications. TiO2 has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO2 by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO2 structures that obey (2 × 1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process.

Quantum control and quantum tomography on neutral atom qudits

NASA Astrophysics Data System (ADS)

Sosa Martinez, Hector

Neutral atom systems are an appealing platform for the development and testing of quantum control and measurement techniques. This dissertation presents experimental investigations of control and measurement tools using as a testbed the 16-dimensional hyperfine manifold associated with the electronic ground state of cesium atoms. On the control side, we present an experimental realization of a protocol to implement robust unitary transformations in the presence of static and dynamic perturbations. We also present an experimental realization of inhomogeneous quantum control. Specifically, we demonstrate our ability to perform two different unitary transformations on atoms that see different light shifts from an optical addressing field. On the measurement side, we present experimental realizations of quantum state and process tomography. The state tomography project encompasses a comprehensive evaluation of several measurement strategies and state estimation algorithms. Our experimental results show that in the presence of experimental imperfections, there is a clear tradeoff between accuracy, efficiency and robustness in the reconstruction. The process tomography project involves an experimental demonstration of efficient reconstruction by using a set of intelligent probe states. Experimental results show that we are able to reconstruct unitary maps in Hilbert spaces with dimension ranging from d=4 to d=16. To the best of our knowledge, this is the first time that a unitary process in d=16 is successfully reconstructed in the laboratory.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Photoelectron Holographic Atomic Arrangement Imaging of Cleaved Bimetal-intercalated Graphite Superconductor Surface

PubMed Central

Matsui, Fumihiko; Eguchi, Ritsuko; Nishiyama, Saki; Izumi, Masanari; Uesugi, Eri; Goto, Hidenori; Matsushita, Tomohiro; Sugita, Kenji; Daimon, Hiroshi; Hamamoto, Yuji; Hamada, Ikutaro; Morikawa, Yoshitada; Kubozono, Yoshihiro

2016-01-01

From the C 1s and K 2p photoelectron holograms, we directly reconstructed atomic images of the cleaved surface of a bimetal-intercalated graphite superconductor, (Ca, K)C8, which differed substantially from the expected bulk crystal structure based on x-ray diffraction (XRD) measurements. Graphene atomic images were collected in the in-plane cross sections of the layers 3.3 Å and 5.7 Å above the photoelectron emitter C atom and the stacking structures were determined as AB- and AA-type, respectively. The intercalant metal atom layer was found between two AA-stacked graphenes. The K atomic image revealing 2 × 2 periodicity, occupying every second centre site of C hexagonal columns, was reconstructed, and the Ca 2p peak intensity in the photoelectron spectra of (Ca, K)C8 from the cleaved surface was less than a few hundredths of the K 2p peak intensity. These observations indicated that cleavage preferentially occurs at the KC8 layers containing no Ca atoms. PMID:27811975

Atomic scale morphology, growth behaviour and electronic properties of semipolar {101[overline]3} GaN surfaces.

PubMed

Kioseoglou, J; Kalesaki, E; Lymperakis, L; Karakostas, Th; Komninou, Ph

2013-01-30

First-principles calculations relating to the atomic structure and electronic properties of {101[overline]3} GaN surfaces reveal significant differentiations between the two polarity orientations. The (101[overline]3) surface exhibits a remarkable morphological stability, stabilizing a metallic structure (Ga adlayer) over the entire range of the Ga chemical potential. In contrast, the semiconducting, cleaved surface is favoured on (101[overline]3[overline]) under extremely and moderately N-rich conditions, a Ga bilayer is stabilized under corresponding Ga-rich conditions and various transitions between metallic reconstructions take place in intermediate growth stoichiometries. Efficient growth schemes for smooth, two-dimensional GaN layers and the isolation of {101[overline]3} material from parasitic orientations are identified.

Trilateration-based reconstruction of ortho-positronium decays into three photons with the J-PET detector

NASA Astrophysics Data System (ADS)

Gajos, A.; Kamińska, D.; Czerwiński, E.; Alfs, D.; Bednarski, T.; Białas, P.; Głowacz, B.; Gorgol, M.; Jasińska, B.; Kapłon, Ł.; Korcyl, G.; Kowalski, P.; Kozik, T.; Krzemień, W.; Kubicz, E.; Mohammed, M.; Niedźwiecki, Sz.; Pałka, M.; Pawlik-Niedźwiecka, M.; Raczyński, L.; Rudy, Z.; Rundel, O.; Sharma, N. G.; Silarski, M.; Słomski, A.; Strzelecki, A.; Wieczorek, A.; Wiślicki, W.; Zgardzińska, B.; Zieliński, M.; Moskal, P.

2016-05-01

This work reports on a new reconstruction algorithm allowing us to reconstruct the decays of ortho-positronium atoms into three photons using the places and times of photons recorded in the detector. The method is based on trilateration and allows for a simultaneous reconstruction of both location and time of the decay. Results of resolution tests of the new reconstruction in the J-PET detector based on Monte Carlo simulations are presented, which yield a spatial resolution at the level of 2 cm (FWHM) for X and Y and at the level of 1 cm (FWHM) for Z available with the present resolution of J-PET after application of a kinematic fit. Prospects of employment of this method for studying angular correlations of photons in decays of polarized ortho-positronia for the needs of tests of CP and CPT discrete symmetries are also discussed. The new reconstruction method allows for discrimination of background from random three-photon coincidences as well as for application of a novel method for determination of the linear polarization of ortho-positronium atoms, which is also introduced in this work.

Surface effects on mean inner potentials studied using density functional theory.

PubMed

Pennington, Robert S; Boothroyd, Chris B; Dunin-Borkowski, Rafal E

2015-12-01

Quantitative materials characterization using electron holography frequently requires knowledge of the mean inner potential, but reported experimental mean inner potential measurements can vary widely. Using density functional theory, we have simulated the mean inner potential for materials with a range of different surface conditions and geometries. We use both "thin-film" and "nanowire" specimen geometries. We consider clean bulk-terminated surfaces with different facets and surface reconstructions using atom positions from both structural optimization and experimental data and we also consider surfaces both with and without adsorbates. We find that the mean inner potential is surface-dependent, with the strongest dependency on surface adsorbates. We discuss the outlook and perspective for future mean inner potential measurements. Copyright © 2015 Elsevier B.V. All rights reserved.

The Au modified Ge(1 1 0) surface

NASA Astrophysics Data System (ADS)

Zhang, L.; Kabanov, N. S.; Bampoulis, P.; Saletsky, A. M.; Zandvliet, H. J. W.; Klavsyuk, A. L.

2018-05-01

The pristine Ge(1 1 0) surface is composed of Ge pentagons, which are arranged in relatively large (16 × 2) and c(8 × 10) unit cells. The deposition of sub-monolayer amounts of Au and mild annealing results into de-reconstructed Ge(1 1 0) regions completely free of Ge pentagons and regions composed of nanowires that are aligned along the high symmetry [ 1 1 bar 0 ] direction of the Ge(1 1 0) surface. The de-reconstructed Ge(1 1 0) regions consist of atomic rows that are aligned along the [ 1 1 bar 0 ] direction. A substantial fraction of these substrate rows are straight and resemble the atom rows of the unreconstructed, i.e. bulk terminated, Ge(1 1 0) surface, whereas the other substrate rows have a meandering appearance. These meandering atom rows are comprised of two types of atoms, one type that appears dim, whereas the other type appears bright in filled-state scanning tunneling microscopy images. Using density functional theory calculations, we have tested more than 20 different atomic models for the meandering atom rows. The density functional theory calculations reveal that it is energetically favorable for the deposited Au atoms to exchange position with Ge atoms in the first layer. Based on these findings we conclude that the bright atoms are Ge atoms, whereas the dim atoms are Au atoms.

Ferromagnetism regulated by edged cutting and optical identification in monolayer PtSe2 nanoribbons

NASA Astrophysics Data System (ADS)

Meng, Ming; Zhang, QiZhen; Wang, Lifen; Shan, Yun; Du, Yuandong; Qin, Nan; Liu, Lizhe

2018-06-01

Regulation of ferromagnetism and electronic structure in PtSe2 nanostructures has attracted much attention because of its potential in spintronics. The magnetic and optical properties of PtSe2 nanoribbons with different edge reconstruction and external deformations are calculated by density function theory. In 1 T phase PtSe2 nanoribbons, the ferromagnetism induced by spin polarization of exposed Pt or Se atoms is decreased with the reducing nanoribbon width. For smaller nanoribbon, the magnetism can be regulated by external strain more easily. However, the magnetism cannot occur in 1 H phase PtSe2 nanoribbon. The absorption spectra are suggested to identify the nanoribbon structural changes in detail. Our results suggest the use of edge reconstruction and strain engineering in spintronics applications.

Nonpolar Solvation Free Energy from Proximal Distribution Functions

PubMed Central

Ou, Shu-Ching; Drake, Justin A.; Pettitt, B. Montgomery

2017-01-01

Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute–solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute–solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute–solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ~ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems. PMID:27992228

Measuring the dynamic polarizability of tungsten atom via electrical wire explosion in vacuum

NASA Astrophysics Data System (ADS)

Shi, Huantong; Zou, Xiaobing; Wang, Xinxin

2018-02-01

Electrical explosion of wire provides a practical approach to the experimental measurement of dynamic polarizability of metal atoms with high melting and boiling temperatures. With the help of insulation coating, a section of tungsten wire was transformed to the plasma state while the near electrode region was partially vaporized, which enabled us to locate the "neutral-region" (consisting of gaseous atoms) in the Mach-Zehnder interferogram. In this paper, the polarizability of the tungsten atom at 532 nm was reconstructed based on a technique previously used for the same purpose, and the basic preconditions of the measurement were verified in detail, including the existence of the neutral region, conservation of linear density of tungsten during wire expansion, and neglect of the vaporized insulation coating. The typical imaging time varied from 80 ns to as late as 200 ns and the reconstructed polarizability of the tungsten atom was 16 ± 1 Å3, which showed good statistical consistency and was also in good agreement with the previous results.

First-principles study of atomic and electronic structures of 60° perfect and 30°/90° partial glide dislocations in CdTe

DOE PAGES

Kweon, Kyoung E.; Aberg, Daniel; Lordi, Vincenzo

2016-05-16

The atomic and electronic structures of 60° glide perfect and 30°/90° glide partial dislocations in CdTe are studied using combined semi-empirical and density functional theory calculations. The calculations predict that the dislocation cores tend to undergo significant reconstructions along the dislocation lines from the singly-periodic (SP) structures, yielding either doubly-periodic (DP) ordering by forming a dimer or quadruply-periodic (QP) ordering by alternating a dimer and a missing dimer. Charge modulation along the dislocation line, accompanied by the QP reconstruction for the Cd-/Te-core 60° perfect and 30° partials or the DP reconstruction for the Cd-core 90° partial, results in semiconducting character,more » as opposed to the metallic character of the SP dislocation cores. Dislocation-induced defect states for the 60° Cd-/Te-core are located relatively close to the band edges, whereas the defect states lie in the middle of the band gap for the 30° Cd-/Te-core partial dislocations. In addition to the intracore charge modulation within each QP core, the possibility of intercore charge transfer between two different dislocation cores when they are paired together in the same system is discussed. As a result, the analysis of the electronic structures reveals the potential role of the dislocations on charge transport in CdTe, particularly in terms of charge trapping and recombination.« less

The Effects of Surface Reconstruction and Electron-Positron Correlation on the Annihilation Characteristics of Positrons Trapped at Semiconductor Surfaces

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Jung, E.; Weiss, A. H.

2009-03-01

Experimental positron annihilation induced Auger electron spectroscopy (PAES) data from Ge(100) and Ge(111) surfaces display several strong Auger peaks corresponding to M4,5N1N2,3, M2,3M4,5M4,5, M2,3M4,5V, and M1M4,5M4,5 Auger transitions. The integrated peak intensities of Auger transitions have been used to obtain experimental annihilation probabilities for the Ge 3d and 3p core electrons. The experimental data were analyzed by performing theoretical studies of the effects of surface reconstructions and electron-positron correlations on image potential induced surface states and annihilation characteristics of positrons trapped at the reconstructed Ge(100) and Ge(111) surfaces. Calculations of positron surface states and annihilation characteristics have been performed for Ge(100) surface with (2×1), (2×2), and (4×2) reconstructions, and for Ge(111) surface with c(2×8) reconstruction. Estimates of the positron binding energy and annihilation characteristics reveal their sensitivity to the specific atomic structure of the topmost layers of the semiconductor and to the approximations used to describe electron-positron correlations. The results of these theoretical studies are compared with the ones obtained for the reconstructed Si(100)-(2×1) and Si(111)-(7×7) surfaces.

Electronic structure studies of Ni( 1 0 0 ) surface reconstructions resulting from carbon, nitrogen, or oxygen atom adsorption

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2003-01-01

Solid-state Fenske-Hall band structure calculations have been used to study the different surface structures which result from adsorption of a half monolayer of C, N, or O atoms on the Ni(1 0 0) surface. C or N atoms sit nearly coplanar with the surface Ni atoms and induce the "clock" reconstruction of the surface. In contrast, adsorbed O atoms sit slightly above the Ni(1 0 0) surface plane and have little effect on the overall surface structure. The local environments of the C, N, and O atoms on these surfaces are similar to their environments in a series of late transition metal carbonyl clusters, suggesting that some of the same electronic factors may play a role in favoring the different structures. Results of the calculations indicate that when adsorbates occupy coplanar sites on Ni(1 0 0), much of the Ni-Ni bonding within the surface layer and between the surface- and second-layers is disrupted. On the C- and N-covered surfaces the disruption is more than compensated for by the formation of strong adsorbate-Ni bonds and by new Ni-Ni surface bonds resulting from the clock reconstruction. When O is forced into a coplanar site, however, both the higher electron count and increased electronegativity of the O atoms lead to severe disruption of the surface bonding and weak Ni-O bonds. When O atoms sit above the surface, they form more polar Ni-O bonds, contribute less electron density to the Ni surface bands, and cause less disruption to Ni-Ni surface bonds. These results suggest that, similar to the organometallic clusters, the site preferences of C, N, and O atoms are directly related to their electron count, and in turn to the relative occupation of both Ni-Ni and X-Ni (X=C, N, O) antibonding bands.

Atomic and electronic structure of the CdTe(111)B–(2√3 × 4) orthogonal surface

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

Bekenev, V. L., E-mail: bekenev@ipms.kiev.ua; Zubkova, S. M.

2017-01-15

The atomic and electronic structure of four variants of Te-terminated CdTe(111)B–(2√3 × 4) orthogonal polar surface (ideal, relaxed, reconstructed, and reconstructed with subsequent relaxation) are calculated ab initio for the first time. The surface is modeled by a film composed of 12 atomic layers with a vacuum gap of ~16 Å in the layered superlattice approximation. To close Cd dangling bonds on the opposite side of the film, 24 fictitious hydrogen atoms with a charge of 1.5 electrons each are added. Ab initio calculations are performed using the Quantum Espresso program based on density functional theory. It is demonstrated thatmore » relaxation leads to splitting of the four upper layers. The band energy structures and total and layer-by-layer densities of electronic states for the four surface variants are calculated and analyzed.« less

Direct observation for atomically flat and ordered vertical {111} side-surfaces on three-dimensionally figured Si(110) substrate using scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Yang, Haoyu; Hattori, Azusa N.; Ohata, Akinori; Takemoto, Shohei; Hattori, Ken; Daimon, Hiroshi; Tanaka, Hidekazu

2017-11-01

A three-dimensional Si{111} vertical side-surface structure on a Si(110) wafer was fabricated by reactive ion etching (RIE) followed by wet-etching and flash-annealing treatments. The side-surface was studied with scanning tunneling microscopy (STM) in atomic scale for the first time, in addition to atomic force microscopy (AFM), scanning electron microscopy (SEM), and low-energy electron diffraction (LEED). AFM and SEM showed flat and smooth vertical side-surfaces without scallops, and STM proved the realization of an atomically-flat 7 × 7-reconstructed structure, under optimized RIE and wet-etching conditions. STM also showed that a step-bunching occurred on the produced {111} side-surface corresponding to a reversely taped side-surface with a tilt angle of a few degrees, but did not show disordered structures. Characteristic LEED patterns from both side- and top-reconstructed surfaces were also demonstrated.

Local-feature analysis for automated coarse-graining of bulk-polymer molecular dynamics simulations.

PubMed

Xue, Y; Ludovice, P J; Grover, M A

2012-12-01

A method for automated coarse-graining of bulk polymers is presented, using the data-mining tool of local feature analysis. Most existing methods for polymer coarse-graining define superatoms based on their covalent bonding topology along the polymer backbone, but here superatoms are defined based only on their correlated motions, as observed in molecular dynamics simulations. Correlated atomic motions are identified in the simulation data using local feature analysis, between atoms in the same or in different polymer chains. Groups of highly correlated atoms constitute the superatoms in the coarse-graining scheme, and the positions of their seed coordinates are then projected forward in time. Based on only the seed positions, local feature analysis enables the full reconstruction of all atomic positions. This reconstruction suggests an iterative scheme to reduce the computation of the simulations to initialize another short molecular dynamic simulation, identify new superatoms, and again project forward in time.

Charge-Induced (1 x 3) Reconstruction of Au(110): Mechanistic Insights from Potentiodynamic Scanning Tunneling Microscopy in Alkali Iodide Electrolytes

DTIC Science & Technology

1994-02-01

In potassium iodide electrolyte, the usual "three-missing-row" (1 x 3) structure is seen to be generated by single gold atomic-row segments shifting...observed, involving the intermediate local formation of "one-missing-row" (I x 3) domains by removal of one-third of the top layer gold rows onto nearby...structure is achieved by aggregation of the displaced monoatomic row segments. The mechanistic value of following atomic-level reconstruction processes by

Retrieval of the atomic displacements in the crystal from the coherent X-ray diffraction pattern.

PubMed

Minkevich, A A; Köhl, M; Escoubas, S; Thomas, O; Baumbach, T

2014-07-01

The retrieval of spatially resolved atomic displacements is investigated via the phases of the direct(real)-space image reconstructed from the strained crystal's coherent X-ray diffraction pattern. It is demonstrated that limiting the spatial variation of the first- and second-order spatial displacement derivatives improves convergence of the iterative phase-retrieval algorithm for displacements reconstructions to the true solution. This approach is exploited to retrieve the displacement in a periodic array of silicon lines isolated by silicon dioxide filled trenches.

Studies of carbon incorporation on the diamond [100] surface during chemical vapor deposition using density functional theory.

PubMed

Cheesman, Andrew; Harvey, Jeremy N; Ashfold, Michael N R

2008-11-13

Accurate potential energy surface calculations are presented for many of the key steps involved in diamond chemical vapor deposition on the [100] surface (in its 2 x 1 reconstructed and hydrogenated form). The growing diamond surface was described by using a large (approximately 1500 atoms) cluster model, with the key atoms involved in chemical steps being described by using a quantum mechanical (QM, density functional theory, DFT) method and the bulk of the atoms being described by molecular mechanics (MM). The resulting hybrid QM/MM calculations are more systematic and/or at a higher level of theory than previous work on this growth process. The dominant process for carbon addition, in the form of methyl radicals, is predicted to be addition to a surface radical site, opening of the adjacent C-C dimer bond, insertion, and ultimate ring closure. Other steps such as insertion across the trough between rows of dimer bonds or addition to a neighboring dimer leading to formation of a reconstruction on the next layer may also contribute. Etching of carbon can also occur; the most likely mechanism involves loss of a two-carbon moiety in the form of ethene. The present higher-level calculations confirm that migration of inserted carbon along both dimer rows and chains should be relatively facile, with barriers of approximately 150 kJ mol (-1) when starting from suitable diradical species, and that this step should play an important role in establishing growth of smooth surfaces.

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

DOE PAGES

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-10-25

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy.

PubMed

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-01-01

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic , using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic .

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

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

Pryor, Alan; Ophus, Colin; Miao, Jianwei

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

Two-dimensional membrane as elastic shell with proof on the folds revealed by three-dimensional atomic mapping

NASA Astrophysics Data System (ADS)

Zhao, Jiong; Deng, Qingming; Ly, Thuc Hue; Han, Gang Hee; Sandeep, Gorantla; Rümmeli, Mark H.

2015-11-01

The great application potential for two-dimensional (2D) membranes (MoS2, WSe2, graphene and so on) aroused much effort to understand their fundamental mechanical properties. The out-of-plane bending rigidity is the key factor that controls the membrane morphology under external fields. Herein we provide an easy method to reconstruct the 3D structures of the folded edges of these 2D membranes on the atomic scale, using high-resolution (S)TEM images. After quantitative comparison with continuum mechanics shell model, it is verified that the bending behaviour of the studied 2D materials can be well explained by the linear elastic shell model. And the bending rigidities can thus be derived by fitting with our experimental results. Recall almost only theoretical approaches can access the bending properties of these 2D membranes before, now a new experimental method to measure the bending rigidity of such flexible and atomic thick 2D membranes is proposed.

Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic Resolution Electron Microscopy and Field Evaporation Simulation

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

Devaraj, Arun; Colby, Robert J.; Vurpillot, F.

2014-03-26

Metal-dielectric composite materials, specifically metal nanoparticles supported on or embedded in metal oxides, are widely used in catalysis. The accurate optimization of such nanostructures warrants the need for detailed three-dimensional characterization. Atom probe tomography is uniquely capable of generating sub-nanometer structural and compositional data with part-per-million mass sensitivity, but there are reconstruction artifacts for composites containing materials with strongly differing fields of evaporation, as for oxide-supported metal nanoparticles. By correlating atom probe tomography with scanning transmission electron microscopy for Au nanoparticles embedded in an MgO support, deviations from an ideal topography during evaporation are demonstrated directly, and correlated with compositionalmore » errors in the reconstructed data. Finite element simulations of the field evaporation process confirm that protruding Au nanoparticles will evolve on the tip surface, and that evaporation field variations lead to an inaccurate assessment of the local composition, effectively lowering the spatial resolution of the final reconstructed dataset. Cross-correlating the experimental data with simulations results in a more detailed understanding of local evaporation aberrations during APT analysis of metal-oxide composites, paving the way towards a more accurate three-dimensional characterization of this technologically important class of materials.« less

Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

PubMed

Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

2013-04-01

When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

Surface modification of nano-silica on the ligament advanced reinforcement system for accelerated bone formation: primary human osteoblasts testing in vitro and animal testing in vivo.

PubMed

Li, Mengmeng; Wang, Shiwen; Jiang, Jia; Sun, Jiashu; Li, Yuzhuo; Huang, Deyong; Long, Yun-Ze; Zheng, Wenfu; Chen, Shiyi; Jiang, Xingyu

2015-05-07

The Ligament Advanced Reinforcement System (LARS) has been considered as a promising graft for ligament reconstruction. To improve its biocompatibility and effectiveness on new bone formation, we modified the surface of a polyethylene terephthalate (PET) ligament with nanoscale silica using atom transfer radical polymerization (ATRP) and silica polymerization. The modified ligament is tested by both in vitro and in vivo experiments. Human osteoblast testing in vitro exhibits an ∼21% higher value in cell viability for silica-modified grafts compared with original grafts. Animal testing in vivo shows that there is new formed bone in the case of a nanoscale silica-coated ligament. These results demonstrate that our approach for nanoscale silica surface modification on LARS could be potentially applied for ligament reconstruction.

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

DOE PAGES

Preciat Gonzalez, German A.; El Assal, Lemmer R. P.; Noronha, Alberto; ...

2017-06-14

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, manymore » algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.« less

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

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

Preciat Gonzalez, German A.; El Assal, Lemmer R. P.; Noronha, Alberto

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, manymore » algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.« less

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

PubMed

Preciat Gonzalez, German A; El Assal, Lemmer R P; Noronha, Alberto; Thiele, Ines; Haraldsdóttir, Hulda S; Fleming, Ronan M T

2017-06-14

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, many algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.

Correlating Atom Probe Crystallographic Measurements with Transmission Kikuchi Diffraction Data.

PubMed

Breen, Andrew J; Babinsky, Katharina; Day, Alec C; Eder, K; Oakman, Connor J; Trimby, Patrick W; Primig, Sophie; Cairney, Julie M; Ringer, Simon P

2017-04-01

Correlative microscopy approaches offer synergistic solutions to many research problems. One such combination, that has been studied in limited detail, is the use of atom probe tomography (APT) and transmission Kikuchi diffraction (TKD) on the same tip specimen. By combining these two powerful microscopy techniques, the microstructure of important engineering alloys can be studied in greater detail. For the first time, the accuracy of crystallographic measurements made using APT will be independently verified using TKD. Experimental data from two atom probe tips, one a nanocrystalline Al-0.5Ag alloy specimen collected on a straight flight-path atom probe and the other a high purity Mo specimen collected on a reflectron-fitted instrument, will be compared. We find that the average minimum misorientation angle, calculated from calibrated atom probe reconstructions with two different pole combinations, deviate 0.7° and 1.4°, respectively, from the TKD results. The type of atom probe and experimental conditions appear to have some impact on this accuracy and the reconstruction and measurement procedures are likely to contribute further to degradation in angular resolution. The challenges and implications of this correlative approach will also be discussed.

Detection of isolated protein-bound metal ions by single-particle cryo-STEM.

PubMed

Elad, Nadav; Bellapadrona, Giuliano; Houben, Lothar; Sagi, Irit; Elbaum, Michael

2017-10-17

Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography.

Detection of isolated protein-bound metal ions by single-particle cryo-STEM

PubMed Central

Elad, Nadav; Bellapadrona, Giuliano; Houben, Lothar; Sagi, Irit; Elbaum, Michael

2017-01-01

Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography. PMID:28973937

Preparation of atomically flat rutile TiO 2(001) surfaces for oxide film growth

DOE PAGES

Wang, Yang; Lee, Shinbuhm; Vilmercati, P.; ...

2016-01-01

The availability of low-index rutile TiO 2 single crystal substrates with atomically flat surfaces is essential for enabling epitaxialgrowth of rutile transition metal oxide films. The high surface energy of the rutile (001) surface often leads to surface faceting, which precludes the sputter and annealing treatment commonly used for the preparation of clean and atomically flat TiO 2(110) substrate surfaces. In this work, we reveal that stable and atomically flat rutile TiO 2(001) surfaces can be prepared with an atomically ordered reconstructedsurface already during a furnace annealing treatment in air. We tentatively ascribe this result to the decrease in surfacemore » energy associated with the surface reconstruction, which removes the driving force for faceting. Despite the narrow temperature window where this morphology can initially be formed, we demonstrate that it persists in homoepitaxialgrowth of TiO 2(001) thin films. The stabilization of surface reconstructions that prevent faceting of high-surface-energy crystal faces may offer a promising avenue towards the realization of a wider range of high quality epitaxial transition metal oxide heterostructures.« 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.

The Effects of Surface Reconstruction and Electron-Positron Correlation on the Annihilation Characteristics of Positrons Trapped at Semiconductor Surfaces

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

Fazleev, N. G.; Department of Physics, Kazan State University, Kazan 420008; Jung, E.

2009-03-10

Experimental positron annihilation induced Auger electron spectroscopy (PAES) data from Ge(100) and Ge(111) surfaces display several strong Auger peaks corresponding to M{sub 4,5}N{sub 1}N{sub 2,3}, M{sub 2,3}M{sub 4,5}M{sub 4,5}, M{sub 2,3}M{sub 4,5}V, and M{sub 1}M{sub 4,5}M{sub 4,5} Auger transitions. The integrated peak intensities of Auger transitions have been used to obtain experimental annihilation probabilities for the Ge 3d and 3p core electrons. The experimental data were analyzed by performing theoretical studies of the effects of surface reconstructions and electron-positron correlations on image potential induced surface states and annihilation characteristics of positrons trapped at the reconstructed Ge(100) and Ge(111) surfaces. Calculationsmore » of positron surface states and annihilation characteristics have been performed for Ge(100) surface with (2x1), (2x2), and (4x2) reconstructions, and for Ge(111) surface with c(2x8) reconstruction. Estimates of the positron binding energy and annihilation characteristics reveal their sensitivity to the specific atomic structure of the topmost layers of the semiconductor and to the approximations used to describe electron-positron correlations. The results of these theoretical studies are compared with the ones obtained for the reconstructed Si(100)-(2x1) and Si(111)-(7x7) surfaces.« less

Electronic-Reconstruction-Enhanced Tunneling Conductance at Terrace Edges of Ultrathin Oxide Films.

PubMed

Wang, Lingfei; Kim, Rokyeon; Kim, Yoonkoo; Kim, Choong H; Hwang, Sangwoon; Cho, Myung Rae; Shin, Yeong Jae; Das, Saikat; Kim, Jeong Rae; Kalinin, Sergei V; Kim, Miyoung; Yang, Sang Mo; Noh, Tae Won

2017-11-01

Quantum mechanical tunneling of electrons across ultrathin insulating oxide barriers has been studied extensively for decades due to its great potential in electronic-device applications. In the few-nanometers-thick epitaxial oxide films, atomic-scale structural imperfections, such as the ubiquitously existed one-unit-cell-high terrace edges, can dramatically affect the tunneling probability and device performance. However, the underlying physics has not been investigated adequately. Here, taking ultrathin BaTiO 3 films as a model system, an intrinsic tunneling-conductance enhancement is reported near the terrace edges. Scanning-probe-microscopy results demonstrate the existence of highly conductive regions (tens of nanometers wide) near the terrace edges. First-principles calculations suggest that the terrace-edge geometry can trigger an electronic reconstruction, which reduces the effective tunneling barrier width locally. Furthermore, such tunneling-conductance enhancement can be discovered in other transition metal oxides and controlled by surface-termination engineering. The controllable electronic reconstruction can facilitate the implementation of oxide electronic devices and discovery of exotic low-dimensional quantum phases. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Emergence of Metallic Properties at LiFePO4 Surfaces and LiFePO4/Li2S Interfaces: An Ab Initio Study.

PubMed

Timoshevskii, Vladimir; Feng, Zimin; Bevan, Kirk H; Zaghib, Karim

2015-08-26

The atomic and electronic structures of the LiFePO4 (LFP) surface, both bare and reconstructed upon possible oxygenation, are theoretically studied by ab initio methods. On the basis of total energy calculations, the atomic structure of the oxygenated surface is proposed, and the effect of surface reconstruction on the electronic properties of the surface is clarified. While bare LFP(010) surface is insulating, adsorption of oxygen leads to the emergence of semimetallic behavior by inducing the conducting states in the band gap of the system. The physical origin of these conducting states is investigated. We further demonstrate that deposition of Li2S layers on top of oxygenated LFP(010) surface leads to the formation of additional conducting hole states in the first layer of Li2S surface because of the charge transfer from sulfur p-states to the gap states of LFP surface. This demonstrates that oxygenated LFP surface not only provides conducting layers itself, but also induces conducting channels in the top layer of Li2S. These results help to achieve further understanding of potential role of LFP particles in improving the performance of Li-S batteries through emergent interface conductivity.

Theoretical Studies of the Structure and the Dynamics on Clean and Chemisorbed Metal Surfaces

NASA Astrophysics Data System (ADS)

Yang, Liqiu

Molecular dynamics (MD) and lattice dynamics (LD) techniques are employed to investigate several phenomena related to the structure and vibrations at metal surfaces. The MD simulations are performed with the many-body interaction potentials obtained using the Embedded-Atom Method (EAM). As specific examples, we present the results for Ag(100) at 300 K and Cu(100) at 150 K, 300 K, and 600 K. The calculated frequencies and polarizations of all surface modes and resonances at the high-symmetry points in the two-dimensional Brillouin zone are in good agreement with available data, as well as, existing lattice dynamics results with force constants obtained from first-principles calculations. Our calculated surface relaxation is also in reasonable agreement with the data. We also test a much simpler lattice dynamics model with nearest neighbor central force interactions, and conclude that it can reproduce the main features of the phonon modes, but only when adjustable surface parameters are used. Additionally, the temperature dependent studies of the phonon line-widths and the mean-square displacement (MSD) of surface atoms are indicative of enhanced surface anharmonicity. On several chemisorbed metal surfaces, for which force constants are not available from first-principles calculations or the EAM, we perform lattice dynamics studies of phonon dispersion curves using simple force-constant models. These studies provide reliable mean-square displacement of surface atoms and can distinguish between possible reconstruction patterns, the results being insensitive to the exact values of the surface parameters. On c(2 times 2)S-Ni(100), it is found that the parallel component of the mean-square displacement for sulfur is around 50% larger than the vertical component, but for the mean-square displacement of oxygen atoms in the system c(2 times 2)O-Ni(100), the opposite is the case. As regards surface reconstruction, for both p(2 times 1)O-Ag(110) and p(2 times 1)O-Ni(110) surfaces, it is concluded that a substrate missing-row type reconstruction is induced by the adsorbates, but the local symmetry is C_{2v} with oxygen atoms at the long-bridge sites for the former and C_{s} with (110) being the only symmetry axis for the latter. In the above theoretical analysis, close contacts are made to many available experimental results such as surface phonon dispersion curves, interlayer relaxations, and Debye -Waller factors and adsorbate-substrate bond lengths.

Dynamic polarizability of tungsten atoms reconstructed from fast electrical explosion of fine wires in vacuum

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

Sarkisov, G. S.; Rosenthal, S. E.; Struve, K. W.

For nanosecond electrical explosion of fine metal wires in vacuum generates calibrated, radially expanded gas cylinders of metal atoms are surrounded by low-density fast expanding plasma corona. Here, a novel integrated-phase technique, based on laser interferometry, provides the dynamic dipole polarizability of metal atoms. This data was previously unavailable for tungsten atoms. Furthermore, an extremely high melting temperature and significant pre-melt electronic emission make these measurements particularly complicated for this refractory metal.

Dynamic polarizability of tungsten atoms reconstructed from fast electrical explosion of fine wires in vacuum

DOE PAGES

Sarkisov, G. S.; Rosenthal, S. E.; Struve, K. W.

2016-10-12

For nanosecond electrical explosion of fine metal wires in vacuum generates calibrated, radially expanded gas cylinders of metal atoms are surrounded by low-density fast expanding plasma corona. Here, a novel integrated-phase technique, based on laser interferometry, provides the dynamic dipole polarizability of metal atoms. This data was previously unavailable for tungsten atoms. Furthermore, an extremely high melting temperature and significant pre-melt electronic emission make these measurements particularly complicated for this refractory metal.

SU-E-I-43: Photoelectric Cross Section Revisited

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

Haga, A; Nakagawa, K; Kotoku, J

2015-06-15

Purpose: The importance of the precision in photoelectric cross-section value increases for recent developed technology such as dual energy computed tomography, in which some reconstruction algorithms require the energy dependence of the photo-absorption in each material composition of human being. In this study, we revisited the photoelectric cross-section calculation by self-consistent relativistic Hartree-Fock (HF) atomic model and compared with that widely distributed as “XCOM database” in National Institute of Standards and Technology, which was evaluated with localdensity approximation for electron-exchange (Fock)z potential. Methods: The photoelectric cross section can be calculated with the electron wave functions in initial atomic state (boundmore » electron) and final continuum state (photoelectron). These electron states were constructed based on the selfconsistent HF calculation, where the repulsive Coulomb potential from the electron charge distribution (Hartree term) and the electron exchange potential with full electromagnetic interaction (Fock term) were included for the electron-electron interaction. The photoelectric cross sections were evaluated for He (Z=2), Be (Z=4), C (Z=6), O (Z=8), and Ne (Z=10) in energy range of 10keV to 1MeV. The Result was compared with XCOM database. Results: The difference of the photoelectric cross section between the present calculation and XCOM database was 8% at a maximum (in 10keV for Be). The agreement tends to be better as the atomic number increases. The contribution from each atomic shell has a considerable discrepancy with XCOM database except for K-shell. However, because the photoelectric cross section arising from K-shell is dominant, the net photoelectric cross section was almost insensitive to the different handling in Fock potential. Conclusion: The photoelectric cross-section program has been developed based on the fully self-consistent relativistic HF atomic model. Due to small effect on the Fock potential for K-shell electrons, the difference from XCOM database was limited: 1% to 8% for low-Z elements in 10keV-1MeV energy ranges. This work was partly supported by the JSPS Core-to-Core Program (No. 23003)« less

Communication: Determining the structure of the N{sub 2}Ar van der Waals complex with laser-based channel-selected Coulomb explosion

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

Wu, Chengyin, E-mail: cywu@pku.edu.cn; Liu, Yunquan; Gong, Qihuang

2014-04-14

We experimentally reconstructed the structure of the N{sub 2}Ar van der Waals complex with the technique of laser-based channel-selected Coulomb explosion imaging. The internuclear distance between the N{sub 2} center of mass and the Ar atom, i.e., the length of the van der Waals bond, was determined to be 3.88 Å from the two-body explosion channels. The angle between the van der Waals bond and the N{sub 2} principal axis was determined to be 90° from the three-body explosion channels. The reconstructed structure was contrasted with our high level ab initio calculations. The agreement demonstrated the potential application of laser-basedmore » Coulomb explosion in imaging transient molecular structure, particularly for floppy van der Waals complexes, whose structures remain difficult to be determined by conventional spectroscopic methods.« less

Multienergy CT acquisition and reconstruction with a stepped tube potential scan

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

Shen, Le; Xing, Yuxiang, E-mail: xingyx@mail.tsinghua.edu.cn

Purpose: Based on an energy-dependent property of matter, one may obtain a pseudomonochromatic attenuation map, a material composition image, an electron-density distribution, and an atomic number image using a dual- or multienergy computed tomography (CT) scan. Dual- and multienergy CT scans broaden the potential of x-ray CT imaging. The development of such systems is very useful in both medical and industrial investigations. In this paper, the authors propose a new dual- and multienergy CT system design (segmental multienergy CT, SegMECT) using an innovative scanning scheme that is conveniently implemented on a conventional single-energy CT system. The two-step-energy dual-energy CT canmore » be regarded as a special case of SegMECT. A special reconstruction method is proposed to support SegMECT. Methods: In their SegMECT, a circular trajectory in a CT scan is angularly divided into several arcs. The x-ray source is set to a different tube voltage for each arc of the trajectory. Thus, the authors only need to make a few step changes to the x-ray energy during the scan to complete a multienergy data acquisition. With such a data set, the image reconstruction might suffer from severe limited-angle artifacts if using conventional reconstruction methods. To solve the problem, they present a new prior-image-based reconstruction technique using a total variance norm of a quotient image constraint. On the one hand, the prior extracts structural information from all of the projection data. On the other hand, the effect from a possibly imprecise intensity level of the prior can be mitigated by minimizing the total variance of a quotient image. Results: The authors present a new scheme for a SegMECT configuration and establish a reconstruction method for such a system. Both numerical simulation and a practical phantom experiment are conducted to validate the proposed reconstruction method and the effectiveness of the system design. The results demonstrate that the proposed SegMECT can provide both attenuation images and material decomposition images of reasonable image quality. Compared to existing methods, the new system configuration demonstrates advantages in simplicity of implementation, system cost, and dose control. Conclusions: This proposed SegMECT imaging approach has great potential for practical applications. It can be readily realized on a conventional CT system.« less

Reconstructive dosimetry for cutaneous radiation syndrome

PubMed Central

Lima, C.M.A.; Lima, A.R.; Degenhardt, Ä.L.; Valverde, N.J.; Da Silva, F.C.A.

2015-01-01

According to the International Atomic Energy Agency (IAEA), a relatively significant number of radiological accidents have occurred in recent years mainly because of the practices referred to as potentially high-risk activities, such as radiotherapy, large irradiators and industrial radiography, especially in gammagraphy assays. In some instances, severe injuries have occurred in exposed persons due to high radiation doses. In industrial radiography, 80 cases involving a total of 120 radiation workers, 110 members of the public including 12 deaths have been recorded up to 2014. Radiological accidents in industrial practices in Brazil have mainly resulted in development of cutaneous radiation syndrome (CRS) in hands and fingers. Brazilian data include 5 serious cases related to industrial gammagraphy, affecting 7 radiation workers and 19 members of the public; however, none of them were fatal. Some methods of reconstructive dosimetry have been used to estimate the radiation dose to assist in prescribing medical treatment. The type and development of cutaneous manifestations in the exposed areas of a person is the first achievable gross dose estimation. This review article presents the state-of-the-art reconstructive dosimetry methods enabling estimation of local radiation doses and provides guidelines for medical handling of the exposed individuals. The review also presents the Chilean and Brazilian radiological accident cases to highlight the importance of reconstructive dosimetry. PMID:26445332

Reconstruction dynamics of recorded holograms in photochromic glass.

PubMed

Mihailescu, Mona; Pavel, Eugen; Nicolae, Vasile B

2011-06-20

We have investigated the dynamics of the record-erase process of holograms in photochromic glass using continuum Nd:YVO₄ laser radiation (λ=532 nm). A bidimensional microgrid pattern was formed and visualized in photochromic glass, and its diffraction efficiency decay versus time (during reconstruction step) gave us information (D, Δn) about the diffusion process inside the material. The recording and reconstruction processes were carried out in an off-axis setup, and the images of the reconstructed object were recorded by a CCD camera. Measurements realized on reconstructed object images using holograms recorded at a different incident power laser have shown a two-stage process involved in silver atom kinetics.

Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions.

PubMed

Gomes, Antonio L C; de Rezende, Júlia R; Pereira de Araújo, Antônio F; Shakhnovich, Eugene I

2007-02-01

We perform a statistical analysis of atomic distributions as a function of the distance R from the molecular geometrical center in a nonredundant set of compact globular proteins. The number of atoms increases quadratically for small R, indicating a constant average density inside the core, reaches a maximum at a size-dependent distance R(max), and falls rapidly for larger R. The empirical curves turn out to be consistent with the volume increase of spherical concentric solid shells and a Fermi-Dirac distribution in which the distance R plays the role of an effective atomic energy epsilon(R) = R. The effective chemical potential mu governing the distribution increases with the number of residues, reflecting the size of the protein globule, while the temperature parameter beta decreases. Interestingly, betamu is not as strongly dependent on protein size and appears to be tuned to maintain approximately half of the atoms in the high density interior and the other half in the exterior region of rapidly decreasing density. A normalized size-independent distribution was obtained for the atomic probability as a function of the reduced distance, r = R/R(g), where R(g) is the radius of gyration. The global normalized Fermi distribution, F(r), can be reasonably decomposed in Fermi-like subdistributions for different atomic types tau, F(tau)(r), with Sigma(tau)F(tau)(r) = F(r), which depend on two additional parameters mu(tau) and h(tau). The chemical potential mu(tau) affects a scaling prefactor and depends on the overall frequency of the corresponding atomic type, while the maximum position of the subdistribution is determined by h(tau), which appears in a type-dependent atomic effective energy, epsilon(tau)(r) = h(tau)r, and is strongly correlated to available hydrophobicity scales. Better adjustments are obtained when the effective energy is not assumed to be necessarily linear, or epsilon(tau)*(r) = h(tau)*r(alpha,), in which case a correlation with hydrophobicity scales is found for the product alpha(tau)h(tau)*. These results indicate that compact globular proteins are consistent with a thermodynamic system governed by hydrophobic-like energy functions, with reduced distances from the geometrical center, reflecting atomic burials, and provide a conceptual framework for the eventual prediction from sequence of a few parameters from which whole atomic probability distributions and potentials of mean force can be reconstructed. Copyright 2006 Wiley-Liss, Inc.

Direct visualization of quasi-ordered oxygen chain structures on Au(110)-(1 × 2)

NASA Astrophysics Data System (ADS)

Hiebel, F.; Montemore, M. M.; Kaxiras, E.; Friend, C. M.

2016-08-01

The Au(110) surface offers unique advantages for atomically-resolved model studies of catalytic oxidation processes on gold. We investigate the adsorption of oxygen on Au(110) using a combination of scanning tunneling microscopy (STM) and density functional theory (DFT) methods. We identify the typical (empty-states) STM contrast resulting from adsorbed oxygen as atomic-sized dark features of electronic origin. DFT-based image simulations confirm that chemisorbed oxygen is generally detected indirectly, from the binding-induced electronic structure modification of gold. STM images show that adsorption occurs without affecting the general structure of the pristine Au(110) missing-row reconstruction. The tendency to form one-dimensional structures is observed already at low coverage (< 0.05 ML), with oxygen adsorbing on alternate sides of the reconstruction ridges. Consistently, calculations yield preferred adsorption on the (111) facets of the reconstruction, on a 3-fold coordination site, with increased stability when adsorbed in chains. Gold atoms with two oxygen neighbors exhibit enhanced electronic hybridization with the O states. Finally, the species observed are reactive to CO oxidation at 200 K and desorption of CO2 leaves a clean and ordered gold surface.

"Verbal Atom Cracking": Burke and a Rhetoric of Reading.

ERIC Educational Resources Information Center

Enos, Theresa

"Verbal atom cracking," according to Kenneth Burke, entails a process where the reader reconstructs what the writer has constructed--a necessary process before the reader can begin deconstructing. Foregrounding opposites, rather than looking for apposites, may not be the best way to approach discourse that covers especially esoteric…

Stabilization of Au Monatomic-High Islands on the (2 ×2 )-Nad Reconstructed Surface of Wurtzite AlN(0001)

NASA Astrophysics Data System (ADS)

Eydoux, Benoit; Baris, Bulent; Khoussa, Hassan; Guillermet, Olivier; Gauthier, Sébastien; Bouju, Xavier; Martrou, David

2017-10-01

Noncontact atomic force microscopy images show that gold grows on the (2 ×2 )-Nad reconstructed polar (0001) surface of AlN insulating films, in the form of large monatomic islands. High-resolution images and in situ reflection high-energy electron diffraction spectra reveal two moiré patterns from which an atomic model can be built. Density functional theory calculations confirm this model and give insight into the mechanisms that lead to the stabilization of the monolayer. Gold adsorption is accompanied, first, by a global vertical charge transfer from the AlN substrate that fulfills the electrostatic stability criterion for a polar material, and second, by lateral charge transfers that are driven by the local chemical properties of the (2 ×2 )-Nad reconstruction. These results present alternative strategies to grow metal electrodes onto nitride compounds with a better controlled interface, a crucial issue for applications.

Joint Remote State Preparation of a Single-Atom Qubit State via a GHZ Entangled State

NASA Astrophysics Data System (ADS)

Xiao, Xiao-Qi; Yao, Fengwei; Lin, Xiaochen; Gong, Lihua

2018-04-01

We proposed a physical protocol for the joint remote preparation of a single-atom qubit state via a three-atom entangled GHZ-type state previously shared by the two senders and one receiver. Only rotation operations of single-atom, which can be achieved though the resonant interaction between the two-level atom and the classical field, are required in the scheme. It shows that the splitting way of the classical information of the secret qubit not only determines the success of reconstruction of the secret qubit, but also influences the operations of the senders.

Atomic Resolution of Calcium and Oxygen Sublattices of Calcite in Ambient Conditions by Atomic Force Microscopy Using qPlus Sensors with Sapphire Tips.

PubMed

Wastl, Daniel S; Judmann, Michael; Weymouth, Alfred J; Giessibl, Franz J

2015-01-01

Characterization and imaging at the atomic scale with atomic force microscopy in biocompatible environments is an ongoing challenge. We demonstrate atomically resolved imaging of the calcite (101̅4) surface plane using stiff quartz cantilevers ("qPlus sensors", stiffness k = 1280 N/m) equipped with sapphire tips in ambient conditions without any surface preparation. With 10 atoms in one surface unit cell, calcite has a highly complex surface structure comprising three different chemical elements (Ca, C, and O). We obtain true atomic resolution of calcite in air at relative humidity ranging from 20% to 40%, imaging atomic steps and single atomic defects. We observe a great durability of sapphire tips with their Mohs hardness of 9, only one step below diamond. Depending on the state of the sapphire tip, we resolve either the calcium or the oxygen sublattice. We determine the tip termination by comparing the experimental images with simulations and discuss the possibility of chemical tip identification in air. The main challenges for imaging arise from the presence of water layers, which form on almost all surfaces and have the potential to dissolve the crystal surface. Frequency shift versus distance spectra show the presence of at least three ordered hydration layers. The measured height of the first hydration layer corresponds well to X-ray diffraction data and molecular dynamic simulations, namely, ∼220 pm. For the following hydration layers we measure ∼380 pm for the second and third layer, ending up in a total hydration layer thickness of at least 1 nm. Understanding the influence of water layers and their structure is important for surface segregation, surface reactions including reconstructions, healing of defects, and corrosion.

An analytical model accounting for tip shape evolution during atom probe analysis of heterogeneous materials.

PubMed

Rolland, N; Larson, D J; Geiser, B P; Duguay, S; Vurpillot, F; Blavette, D

2015-12-01

An analytical model describing the field evaporation dynamics of a tip made of a thin layer deposited on a substrate is presented in this paper. The difference in evaporation field between the materials is taken into account in this approach in which the tip shape is modeled at a mesoscopic scale. It was found that the non-existence of sharp edge on the surface is a sufficient condition to derive the morphological evolution during successive evaporation of the layers. This modeling gives an instantaneous and smooth analytical representation of the surface that shows good agreement with finite difference simulations results, and a specific regime of evaporation was highlighted when the substrate is a low evaporation field phase. In addition, the model makes it possible to calculate theoretically the tip analyzed volume, potentially opening up new horizons for atom probe tomographic reconstruction. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantum storage of orbital angular momentum entanglement in an atomic ensemble.

PubMed

Ding, Dong-Sheng; Zhang, Wei; Zhou, Zhi-Yuan; Shi, Shuai; Xiang, Guo-Yong; Wang, Xi-Shi; Jiang, Yun-Kun; Shi, Bao-Sen; Guo, Guang-Can

2015-02-06

Constructing a quantum memory for a photonic entanglement is vital for realizing quantum communication and network. Because of the inherent infinite dimension of orbital angular momentum (OAM), the photon's OAM has the potential for encoding a photon in a high-dimensional space, enabling the realization of high channel capacity communication. Photons entangled in orthogonal polarizations or optical paths had been stored in a different system, but there have been no reports on the storage of a photon pair entangled in OAM space. Here, we report the first experimental realization of storing an entangled OAM state through the Raman protocol in a cold atomic ensemble. We reconstruct the density matrix of an OAM entangled state with a fidelity of 90.3%±0.8% and obtain the Clauser-Horne-Shimony-Holt inequality parameter S of 2.41±0.06 after a programed storage time. All results clearly show the preservation of entanglement during the storage.

In situ mechanical characterization of the cell nucleus by atomic force microscopy.

PubMed

Liu, Haijiao; Wen, Jun; Xiao, Yun; Liu, Jun; Hopyan, Sevan; Radisic, Milica; Simmons, Craig A; Sun, Yu

2014-04-22

The study of nuclear mechanical properties can provide insights into nuclear dynamics and its role in cellular mechanotransduction. While several methods have been developed to characterize nuclear mechanical properties, direct intracellular probing of the nucleus in situ is challenging. Here, a modified AFM (atomic force microscopy) needle penetration technique is demonstrated to mechanically characterize cell nuclei in situ. Cytoplasmic and nuclear stiffness were determined based on two different segments on the AFM indentation curves and were correlated with simultaneous confocal Z-stack microscopy reconstructions. On the basis of direct intracellular measurement, we show that the isolated nuclei from fibroblast-like cells exhibited significantly lower Young's moduli than intact nuclei in situ. We also show that there is in situ nucleus softening in the highly metastatic bladder cancer cell line T24 when compared to its less metastatic counterpart RT4. This technique has potential to become a reliable quantitative measurement tool for intracellular mechanics studies.

Do general physics textbooks discuss scientists’ ideas about atomic structure? A case in Korea

NASA Astrophysics Data System (ADS)

Niaz, Mansoor; Kwon, Sangwoon; Kim, Nahyun; Lee, Gyoungho

2013-01-01

Research in science education has recognized the importance of teaching atomic structure within a history and philosophy of science perspective. The objective of this study is to evaluate general physics textbooks published in Korea based on the eight criteria developed in previous research. The result of this study shows that Korean general physics textbooks often lack detail about the history and philosophy of science. This result is quite similar to those published for the USA. Furthermore, chemistry textbooks published in the USA, Turkey and Venezuela are quite similar to the physics textbooks. This is a cause for concern as textbooks present theories as facts and ignore the historical reconstructions based on the development of scientific theories that frequently involve controversies and conflicts among scientists. The inclusion of historical reconstructions of ideas about atomic structure can provide students with a better appreciation of the dynamics of scientific progress.

Y-90 SPECT ML image reconstruction with a new model for tissue-dependent bremsstrahlung production using CT information: a proof-of-concept study

NASA Astrophysics Data System (ADS)

Lim, Hongki; Fessler, Jeffrey A.; Wilderman, Scott J.; Brooks, Allen F.; Dewaraja, Yuni K.

2018-06-01

While the yield of positrons used in Y-90 PET is independent of tissue media, Y-90 SPECT imaging is complicated by the tissue dependence of bremsstrahlung photon generation. The probability of bremsstrahlung production is proportional to the square of the atomic number of the medium. Hence, the same amount of activity in different tissue regions of the body will produce different numbers of bremsstrahlung photons. Existing reconstruction methods disregard this tissue-dependency, potentially impacting both qualitative and quantitative imaging of heterogeneous regions of the body such as bone with marrow cavities. In this proof-of-concept study, we propose a new maximum-likelihood method that incorporates bremsstrahlung generation probabilities into the system matrix, enabling images of the desired Y-90 distribution to be reconstructed instead of the ‘bremsstrahlung distribution’ that is obtained with existing methods. The tissue-dependent probabilities are generated by Monte Carlo simulation while bone volume fractions for each SPECT voxel are obtained from co-registered CT. First, we demonstrate the tissue dependency in a SPECT/CT imaging experiment with Y-90 in bone equivalent solution and water. Visually, the proposed reconstruction approach better matched the true image and the Y-90 PET image than the standard bremsstrahlung reconstruction approach. An XCAT phantom simulation including bone and marrow regions also demonstrated better agreement with the true image using the proposed reconstruction method. Quantitatively, compared with the standard reconstruction, the new method improved estimation of the liquid bone:water activity concentration ratio by 40% in the SPECT measurement and the cortical bone:marrow activity concentration ratio by 58% in the XCAT simulation.

Three Dimensional Imaging of Cold Atoms in a Magneto Optical Trap with a Light Field Microscope

DTIC Science & Technology

2017-09-14

dimensional (3D) volume of the atoms is reconstructed using a modeled point spread function (PSF), taking into consideration the low magnification (1.25...axis fluorescence image. Optical axis separation between two atom clouds is measured to a 100µm accuracy in a 3mm deep volume , with a 16µm in-focus...79 vi Page 4.5 Phase Term Effects on the 3D Volume

75 FR 28626 - Subcommittee on Procedures Review, Advisory Board on Radiation and Worker Health (ABRWH...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-21

...''), OTIB-0051 (``Effect of Threshold Energy and Angular Response of NTA Film on Missed Neutron Dose at the... Reconstruction During Residual Radioactivity Periods at Atomic Weapons Employer Facilities''), and TBD 6000 (``Site Profile for Atomic Weapons Employers that Worked Uranium and Thorium Metals''); and a continuation...

Tensor-based Dictionary Learning for Dynamic Tomographic Reconstruction

PubMed Central

Tan, Shengqi; Zhang, Yanbo; Wang, Ge; Mou, Xuanqin; Cao, Guohua; Wu, Zhifang; Yu, Hengyong

2015-01-01

In dynamic computed tomography (CT) reconstruction, the data acquisition speed limits the spatio-temporal resolution. Recently, compressed sensing theory has been instrumental in improving CT reconstruction from far few-view projections. In this paper, we present an adaptive method to train a tensor-based spatio-temporal dictionary for sparse representation of an image sequence during the reconstruction process. The correlations among atoms and across phases are considered to capture the characteristics of an object. The reconstruction problem is solved by the alternating direction method of multipliers. To recover fine or sharp structures such as edges, the nonlocal total variation is incorporated into the algorithmic framework. Preclinical examples including a sheep lung perfusion study and a dynamic mouse cardiac imaging demonstrate that the proposed approach outperforms the vectorized dictionary-based CT reconstruction in the case of few-view reconstruction. PMID:25779991

Composition and structure of surfaces by time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Ahn, Jeongheon

1997-10-01

Time-of-flight scattering and recoiling spectrometry (TOF-SARS) was applied to characterize surface structures in order to understand the chemical and physical phenomena on various surfaces. The combination of TOF-SARS, LEED, and classical ion trajectory simulations has allowed characterization of the elemental composition in the outermost atomic layers, surface symmetry, and possible reconstruction or relaxation. The composition and structure of the CdS\\{0001\\}-(1 x 1) and CdS\\{000bar1\\}-(1 x 1) surfaces were investigated. The termination layer of each surface was determined by grazing incidence TOF-SARS. Both (1 x 1) surfaces are bulk-terminated without any reconstruction or relaxation detected by TOF-SARS. Each surface has two domains which are rotated by 60sp° from each other and there exist steps on both surfaces. The CdS\\{0001\\}-(1 x 1) surface is stabilized by O and H covering half a monolayer which are structurally ordered on the surface, while the O and H on the CdS\\{000bar1\\}-(1 x 1) stabilize the surface without ordering. The study of GaN\\{000bar1\\}-(1 x 1) shows the bulk-termination of the surface with no detectable reconstruction or relaxation. The surface is terminated in a N layer with Ga in the 2sp{nd}-layer. H atoms are bound to the outermost N atoms with a coverage of ˜3/4 monolayer and protrude outward from the surface. The surface termination, composition and structure of the Alsb2Osb3 (sapphire) were examined. The surface relaxation was studied quantitatively using classical ion trajectory simulations along with TOF-SARS. The surface undergoes 1sp{st}{-}2sp{nd}-layer relaxation as large as 0.5 A from the bulk value resulting in near coplanarity of Al and O atoms. The reconstruction of the Ni\\{100\\}-(2 x 2)-C surface was studied by TOF-SARS. The surface contained 80% of the (2 x 2)p4g phase and 20% of the unreconstructed (2 x 2) phase. The displacement of Ni atoms was determined by comparing the experimental and simulated results.

Magneto-electronic properties of graphene nanoribbons with various edge structures passivated by phosphorus and hydrogen atoms.

PubMed

Yu, Z L; Wang, D; Zhu, Z; Zhang, Z H

2015-10-07

The electronic and magnetic structures of graphene nanoribbons (GNRs) with various edge structures passivated by P atoms are investigated systematically, and compared with H passivation as well. GNRs with the entire reconstructed Klein edge or armchair edge are found to be nonmagnetic regardless of P or H passivation. However, if the edge of GNRs is a mixture of zigzag edge and reconstructed Klein edge, they are nonmagnetic for H passivation but significantly magnetic for P passivation, which could be attributed to the "charge transfer doping" effect. And the corresponding magnetic device shows a noticeable negative differential resistance phenomenon and an excellent spin filtering effect under AP configuration, which originate from the special energy band structure. The GNRs with zigzag edge, reconstructed Klein edge, or mixed edge shapes are all metals in the nonmagnetic state regardless of the H or P atoms involved. The relationship between the energy gap and the width in armchair-edged GNRs by P passivation with a dimer structure also satisfies the 3p periodicity, but different in detail from the case of H passivation. The calculated edge formation energy indicates that P-passivated GNRs are energetically more favorable, suggesting that they can stably exist in the experiment.

WE-G-18A-04: 3D Dictionary Learning Based Statistical Iterative Reconstruction for Low-Dose Cone Beam CT Imaging

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

Bai, T; UT Southwestern Medical Center, Dallas, TX; Yan, H

2014-06-15

Purpose: To develop a 3D dictionary learning based statistical reconstruction algorithm on graphic processing units (GPU), to improve the quality of low-dose cone beam CT (CBCT) imaging with high efficiency. Methods: A 3D dictionary containing 256 small volumes (atoms) of 3x3x3 voxels was trained from a high quality volume image. During reconstruction, we utilized a Cholesky decomposition based orthogonal matching pursuit algorithm to find a sparse representation on this dictionary basis of each patch in the reconstructed image, in order to regularize the image quality. To accelerate the time-consuming sparse coding in the 3D case, we implemented our algorithm inmore » a parallel fashion by taking advantage of the tremendous computational power of GPU. Evaluations are performed based on a head-neck patient case. FDK reconstruction with full dataset of 364 projections is used as the reference. We compared the proposed 3D dictionary learning based method with a tight frame (TF) based one using a subset data of 121 projections. The image qualities under different resolutions in z-direction, with or without statistical weighting are also studied. Results: Compared to the TF-based CBCT reconstruction, our experiments indicated that 3D dictionary learning based CBCT reconstruction is able to recover finer structures, to remove more streaking artifacts, and is less susceptible to blocky artifacts. It is also observed that statistical reconstruction approach is sensitive to inconsistency between the forward and backward projection operations in parallel computing. Using high a spatial resolution along z direction helps improving the algorithm robustness. Conclusion: 3D dictionary learning based CBCT reconstruction algorithm is able to sense the structural information while suppressing noise, and hence to achieve high quality reconstruction. The GPU realization of the whole algorithm offers a significant efficiency enhancement, making this algorithm more feasible for potential clinical application. A high zresolution is preferred to stabilize statistical iterative reconstruction. This work was supported in part by NIH(1R01CA154747-01), NSFC((No. 61172163), Research Fund for the Doctoral Program of Higher Education of China (No. 20110201110011), China Scholarship Council.« less

Detection of subsurface core-level shifts in Si 2p core-level photoemission from Si(111)-(1x1):As

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

Paggel, J.J.; Hasselblatt, M.; Horn, K.

1997-04-01

The (7 x 7) reconstruction of the Si(111) surface arises from a lowering energy through the reduction of the number of dangling bonds. This reconstruction can be removed by the adsorption of atoms such as hydrogen which saturate the dangling bonds, or by the incorporation of atoms, such as arsenic which, because of the additional electron it possesses, can form three bonds and a nonreactive lone pair orbital from the remaining two electrons. Core and valence level photoemission and ion scattering data have shown that the As atoms replace the top silicon atoms. Previous core level spectra were interpreted inmore » terms of a bulk and a single surface doublet. The authors present results demonstrate that the core level spectrum contains two more lines. The authors assign these to subsurface silicon layers which also experience changes in the charge distribution when a silicon atom is replaced by an arsenic atom. Subsurface core level shifts are not unexpected since the modifications of the electronic structure and/or of photohole screening are likely to decay into the bulk and not just to affect the top-most substrate atoms. The detection of subsurface components suggests that the adsorption of arsenic leads to charge flow also in the second double layer of the Si(111) surface. In view of the difference in atomic radius between As and Si, it was suggested that the (1 x 1): As surface is strained. The presence of charge rearrangement up to the second double layer implies that the atomic coordinates also exhibit deviations from their ideal Si(111) counterparts, which might be detected through a LEED I/V or photoelectron diffraction analysis.« less

Modeling and Control of State-Affine Probabilistic Systems for Atomic-Scale Dynamics

DTIC Science & Technology

2007-06-01

Analysis for Nonlinear Systems. New York: Spring -Verlag, 1987. [5] M. Itoh, "Atomic-scale homoepitaxial growth simulations of reconstructed III-V surfaces...Ridge, NJ; 1995. -- SSC function of the Node 182 [2] M. K. Weldon , K. T. Queeney, J. Eng Jr., K. Raghavachari, and Y. J. Chabal, "The surface science

Towards the low-dose characterization of beam sensitive nanostructures via implementation of sparse image acquisition in scanning transmission electron microscopy

NASA Astrophysics Data System (ADS)

Hwang, Sunghwan; Han, Chang Wan; Venkatakrishnan, Singanallur V.; Bouman, Charles A.; Ortalan, Volkan

2017-04-01

Scanning transmission electron microscopy (STEM) has been successfully utilized to investigate atomic structure and chemistry of materials with atomic resolution. However, STEM’s focused electron probe with a high current density causes the electron beam damages including radiolysis and knock-on damage when the focused probe is exposed onto the electron-beam sensitive materials. Therefore, it is highly desirable to decrease the electron dose used in STEM for the investigation of biological/organic molecules, soft materials and nanomaterials in general. With the recent emergence of novel sparse signal processing theories, such as compressive sensing and model-based iterative reconstruction, possibilities of operating STEM under a sparse acquisition scheme to reduce the electron dose have been opened up. In this paper, we report our recent approach to implement a sparse acquisition in STEM mode executed by a random sparse-scan and a signal processing algorithm called model-based iterative reconstruction (MBIR). In this method, a small portion, such as 5% of randomly chosen unit sampling areas (i.e. electron probe positions), which corresponds to pixels of a STEM image, within the region of interest (ROI) of the specimen are scanned with an electron probe to obtain a sparse image. Sparse images are then reconstructed using the MBIR inpainting algorithm to produce an image of the specimen at the original resolution that is consistent with an image obtained using conventional scanning methods. Experimental results for down to 5% sampling show consistency with the full STEM image acquired by the conventional scanning method. Although, practical limitations of the conventional STEM instruments, such as internal delays of the STEM control electronics and the continuous electron gun emission, currently hinder to achieve the full potential of the sparse acquisition STEM in realizing the low dose imaging condition required for the investigation of beam-sensitive materials, the results obtained in our experiments demonstrate the sparse acquisition STEM imaging is potentially capable of reducing the electron dose by at least 20 times expanding the frontiers of our characterization capabilities for investigation of biological/organic molecules, polymers, soft materials and nanostructures in general.

Theoretical aspects of studies of oxide and semiconductor surfaces using low energy positrons

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Maddox, W. B.; Weiss, A. H.

2011-01-01

This paper presents the results of a theoretical study of positron surface and bulk states and annihilation characteristics of surface trapped positrons at the oxidized Cu(100) single crystal and at both As- and Ga-rich reconstructed GaAs(100) surfaces. The variations in atomic structure and chemical composition of the topmost layers of the surfaces associated with oxidation and reconstructions and the charge redistribution at the surfaces are found to affect localization and spatial extent of the positron surface-state wave functions. The computed positron binding energy, work function, and annihilation characteristics reveal their sensitivity to charge transfer effects, atomic structure and chemical composition of the topmost layers of the surfaces. Theoretical positron annihilation probabilities with relevant core electrons computed for the oxidized Cu(100) surface and the As- and Ga-rich reconstructed GaAs(100) surfaces are compared with experimental ones estimated from the positron annihilation induced Auger peak intensities measured from these surfaces.

Period-doubling reconstructions of semiconductor partial dislocations

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

Park, Ji -Sang; Huang, Bing; Wei, Su -Huai

2015-09-18

Atomic-scale understanding and control of dislocation cores is of great technological importance, because they act as recombination centers for charge carriers in optoelectronic devices. Using hybrid density-functional calculations, we present period-doubling reconstructions of a 90 degrees partial dislocation in GaAs, for which the periodicity of like-atom dimers along the dislocation line varies from one to two, to four dimers. The electronic properties of a dislocation change drastically with each period doubling. The dimers in the single-period dislocation are able to interact, to form a dispersive one-dimensional band with deep-gap states. However, the inter-dimer interaction for the double-period dislocation becomes significantlymore » reduced; hence, it is free of mid-gap states. The Ga core undergoes a further period-doubling transition to a quadruple-period reconstruction induced by the formation of small hole polarons. In conclusion, the competition between these dislocation phases suggests a new passivation strategy via population manipulation of the detrimental single-period phase.« less

Direct Observation of Charge Transfer at a MgO(111) Surface

NASA Astrophysics Data System (ADS)

Subramanian, A.; Marks, L. D.; Warschkow, O.; Ellis, D. E.

2004-01-01

Transmission electron diffraction (TED) combined with direct methods have been used to study the √(3)×√(3)R30° reconstruction on the polar (111) surface of MgO and refine the valence charge distribution. The surface is nonstoichiometric and is terminated by a single magnesium atom. A charge-compensating electron hole is localized in the next oxygen layer and there is a nominal charge transfer from the oxygen atoms to the top magnesium atom. The partial charges that we obtain for the surface atoms are in reasonable agreement with empirical bond-valence estimations.

Entropic Comparison of Atomic-Resolution Electron Tomography of Crystals and Amorphous Materials.

PubMed

Collins, S M; Leary, R K; Midgley, P A; Tovey, R; Benning, M; Schönlieb, C-B; Rez, P; Treacy, M M J

2017-10-20

Electron tomography bears promise for widespread determination of the three-dimensional arrangement of atoms in solids. However, it remains unclear whether methods successful for crystals are optimal for amorphous solids. Here, we explore the relative difficulty encountered in atomic-resolution tomography of crystalline and amorphous nanoparticles. We define an informational entropy to reveal the inherent importance of low-entropy zone-axis projections in the reconstruction of crystals. In turn, we propose considerations for optimal sampling for tomography of ordered and disordered materials.

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

DOE PAGES

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

2017-01-16

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order ofmore » $$1{{k}_{\\text{B}}}T$$ . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.« less

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

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

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order ofmore » $$1{{k}_{\\text{B}}}T$$ . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.« less

A phantom-based JAFROC observer study of two CT reconstruction methods: the search for optimisation of lesion detection and effective dose

NASA Astrophysics Data System (ADS)

Thompson, John D.; Chakraborty, Dev P.; Szczepura, Katy; Vamvakas, Ioannis; Tootell, Andrew; Manning, David J.; Hogg, Peter

2015-03-01

Purpose: To investigate the dose saving potential of iterative reconstruction (IR) in a computed tomography (CT) examination of the thorax. Materials and Methods: An anthropomorphic chest phantom containing various configurations of simulated lesions (5, 8, 10 and 12mm; +100, -630 and -800 Hounsfield Units, HU) was imaged on a modern CT system over a tube current range (20, 40, 60 and 80mA). Images were reconstructed with (IR) and filtered back projection (FBP). An ATOM 701D (CIRS, Norfolk, VA) dosimetry phantom was used to measure organ dose. Effective dose was calculated. Eleven observers (15.11+/-8.75 years of experience) completed a free response study, localizing lesions in 544 single CT image slices. A modified jackknife alternative free-response receiver operating characteristic (JAFROC) analysis was completed to look for a significant effect of two factors: reconstruction method and tube current. Alpha was set at 0.05 to control the Type I error in this study. Results: For modified JAFROC analysis of reconstruction method there was no statistically significant difference in lesion detection performance between FBP and IR when figures-of-merit were averaged over tube current (F(1,10)=0.08, p = 0.789). For tube current analysis, significant differences were revealed between multiple pairs of tube current settings (F(3,10) = 16.96, p<0.001) when averaged over image reconstruction method. Conclusion: The free-response study suggests that lesion detection can be optimized at 40mA in this phantom model, a measured effective dose of 0.97mSv. In high-contrast regions the diagnostic value of IR, compared to FBP, is less clear.

Image reconstruction of muon tomographic data using a density-based clustering method

NASA Astrophysics Data System (ADS)

Perry, Kimberly B.

Muons are subatomic particles capable of reaching the Earth's surface before decaying. When these particles collide with an object that has a high atomic number (Z), their path of travel changes substantially. Tracking muon movement through shielded containers can indicate what types of materials lie inside. This thesis proposes using a density-based clustering algorithm called OPTICS to perform image reconstructions using muon tomographic data. The results show that this method is capable of detecting high-Z materials quickly, and can also produce detailed reconstructions with large amounts of data.

Atomically resolved structural determination of graphene and its point defects via extrapolation assisted phase retrieval

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

Latychevskaia, Tatiana; Fink, Hans-Werner

Previously reported crystalline structures obtained by an iterative phase retrieval reconstruction of their diffraction patterns seem to be free from displaying any irregularities or defects in the lattice, which appears to be unrealistic. We demonstrate here that the structure of a nanocrystal including its atomic defects can unambiguously be recovered from its diffraction pattern alone by applying a direct phase retrieval procedure not relying on prior information of the object shape. Individual point defects in the atomic lattice are clearly apparent. Conventional phase retrieval routines assume isotropic scattering. We show that when dealing with electrons, the quantitatively correct transmission functionmore » of the sample cannot be retrieved due to anisotropic, strong forward scattering specific to electrons. We summarize the conditions for this phase retrieval method and show that the diffraction pattern can be extrapolated beyond the original record to even reveal formerly not visible Bragg peaks. Such extrapolated wave field pattern leads to enhanced spatial resolution in the reconstruction.« less

Automatic software correction of residual aberrations in reconstructed HRTEM exit waves of crystalline samples

DOE PAGES

Ophus, Colin; Rasool, Haider I.; Linck, Martin; ...

2016-11-30

We develop an automatic and objective method to measure and correct residual aberrations in atomic-resolution HRTEM complex exit waves for crystalline samples aligned along a low-index zone axis. Our method uses the approximate rotational point symmetry of a column of atoms or single atom to iteratively calculate a best-fit numerical phase plate for this symmetry condition, and does not require information about the sample thickness or precise structure. We apply our method to two experimental focal series reconstructions, imaging a β-Si 3N 4 wedge with O and N doping, and a single-layer graphene grain boundary. We use peak and latticemore » fitting to evaluate the precision of the corrected exit waves. We also apply our method to the exit wave of a Si wedge retrieved by off-axis electron holography. In all cases, the software correction of the residual aberration function improves the accuracy of the measured exit waves.« less

Temperature effects on the atomic structure and kinetics in single crystal electrochemistry

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

Gründer, Yvonne; Markovic, Nenad M.; Thompson, Paul

2015-01-01

The influence of temperature on the atomic structure at the electrochemical interface has been studied using in-situ surface x-ray scattering (SXS) during the formation of metal monolayers on a Au(111) electrode. For the surface reconstruction of Au(111), higher temperatures increase the mobility of surface atoms in the unreconstructed phase which then determines the surface ordering during the formation of the reconstruction. For the underpotential deposition (UPD) systems, the surface diffusion of the depositing metal adatoms is significantly reduced at low temperatures which results in the frustration of ordered structures in the case of Cu UPD, occurring on a Br-modified surface,more » and in the formation of a disordered Ag monolayer during Ag UPD. The results indicate that temperature changes affect the mass transport and diffusion of metal adatoms on the electrode surface. This demonstrates the importance of including temperature as a variable in studying surface structure and reactions at the electrochemical interface.« less

Automatic software correction of residual aberrations in reconstructed HRTEM exit waves of crystalline samples

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

Ophus, Colin; Rasool, Haider I.; Linck, Martin

We develop an automatic and objective method to measure and correct residual aberrations in atomic-resolution HRTEM complex exit waves for crystalline samples aligned along a low-index zone axis. Our method uses the approximate rotational point symmetry of a column of atoms or single atom to iteratively calculate a best-fit numerical phase plate for this symmetry condition, and does not require information about the sample thickness or precise structure. We apply our method to two experimental focal series reconstructions, imaging a β-Si 3N 4 wedge with O and N doping, and a single-layer graphene grain boundary. We use peak and latticemore » fitting to evaluate the precision of the corrected exit waves. We also apply our method to the exit wave of a Si wedge retrieved by off-axis electron holography. In all cases, the software correction of the residual aberration function improves the accuracy of the measured exit waves.« less

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.

Ghost imaging with atoms

NASA Astrophysics Data System (ADS)

Khakimov, R. I.; Henson, B. M.; Shin, D. K.; Hodgman, S. S.; Dall, R. G.; Baldwin, K. G. H.; Truscott, A. G.

2016-12-01

Ghost imaging is a counter-intuitive phenomenon—first realized in quantum optics—that enables the image of a two-dimensional object (mask) to be reconstructed using the spatio-temporal properties of a beam of particles with which it never interacts. Typically, two beams of correlated photons are used: one passes through the mask to a single-pixel (bucket) detector while the spatial profile of the other is measured by a high-resolution (multi-pixel) detector. The second beam never interacts with the mask. Neither detector can reconstruct the mask independently, but temporal cross-correlation between the two beams can be used to recover a ‘ghost’ image. Here we report the realization of ghost imaging using massive particles instead of photons. In our experiment, the two beams are formed by correlated pairs of ultracold, metastable helium atoms, which originate from s-wave scattering of two colliding Bose-Einstein condensates. We use higher-order Kapitza-Dirac scattering to generate a large number of correlated atom pairs, enabling the creation of a clear ghost image with submillimetre resolution. Future extensions of our technique could lead to the realization of ghost interference, and enable tests of Einstein-Podolsky-Rosen entanglement and Bell’s inequalities with atoms.

Adsorbate-induced reconstruction in the phase 1 × 2-3H/Rh(110)

NASA Astrophysics Data System (ADS)

Michl, M.; Nichtl-Pecher, W.; Oed, W.; Landskron, H.; Heinz, K.; Müller, K.

1989-10-01

The 1 × 2-3H superstructure of hydrogen on Rh(110) at coverage θ = {3}/{2} is analysed by low energy electron diffraction at 90 K. The spectra of eight beams are recorded with a computer-controlled TV measurement technique which yields low noise data even for weak superstructure spots by multiple averaging. Comparison to full dynamical calculations shows that a kinematic treatment of the hydrogen layer diffraction coupled to the full dynamical diffraction of the substrate is a very good approximation. Spectra computed in this way are compared with experimental data by R-factor evaluation. The three non-equivalent hydrogen atoms are found to adsorb in quasi-three-fold coordinated adsorption sites with slightly different local configurations and with H-Rh bond lengths between 1.87 and 1.93 Å to the first-layer rhodium atoms. Interaction between the adatoms seems to weaken the bonding to the adjacent atom in the second layer, so that H-Rh bond lengths larger than 2.17 Å result. A slight reconstruction of the substrate is necessary to bring superstructure spot intensities near the experimentally observed level. Rhodium atoms bonded to two hydrogen atoms are moved out of the surface by 0.03 ± 0.02 Å relative to Rh atoms bonded to only a single H atom. The relaxation of the first Rh layer spacing is determined to be {d 12}/{d 0} = -3.8 ± 1% and {d 22}/{d 0} = 0 ± 1% . The best fit Pendry R-factor is 0.33.

Theory and Application of Auger and Photoelectron Diffraction and Holography

NASA Astrophysics Data System (ADS)

Chen, Xiang

This dissertation addresses the theories and applications of three important surface analysis techniques: Auger electron diffraction (AED), x-ray photoelectron diffraction (XPD), and Auger and photoelectron holography. A full multiple-scattering scheme for the calculations of XPD, AED, and Kikuchi electron diffraction pattern from a surface cluster is described. It is used to simulate 64 eV M_{2,3}VV and 913 eV L_3VV AED patterns from Cu(001) surfaces, in order to test assertions in the literature that they are explicable by a classical "blocking" and channeling model. We find that this contention is not valid, and that only a quantum mechanical multiple-scattering calculation is able to simulate these patterns well. The same multiple scattering simulation scheme is also used to investigate the anomalous phenomena of peak shifts off the forward-scattering directions in photo -electron diffraction patterns of Mg KLL (1180 eV) and O 1s (955 eV) from MgO(001) surfaces. These shifts are explained by calculations assuming a short electron mean free path. Similar simulations of XPD from a CoSi_2(111) surface for Co-3p and Si-2p normal emission agree well with experimental diffraction patterns. A filtering process aimed at eliminating the self -interference effect in photoelectron holography is developed. A better reconstructed image from Si-2p XPD from a Si(001) (2 times 1) surface is seen at atomic resolution. A reconstruction algorithm which corrects for the anisotropic emitter waves as well as the anisotropic atomic scattering factors is used for holographic reconstruction from a Co-3p XPD pattern from a CoSi_2 surface. This new algorithm considerably improves the reconstructed image. Finally, a new reconstruction algorithm called "atomic position recovery by iterative optimization of reconstructed intensities" (APRIORI), which takes account of the self-interference terms omitted by the other holographic algorithms, is developed. Tests on a Ni-C-O chain and Si(111)(sqrt{3} times sqrt{3})B surface suggest that this new method may overcome the twin image problem in the traditional holographic methods, reduce the artifacts in real space, and even separately identify the chemical species of the scatterers.

Highly Scalable Matching Pursuit Signal Decomposition Algorithm

NASA Technical Reports Server (NTRS)

Christensen, Daniel; Das, Santanu; Srivastava, Ashok N.

2009-01-01

Matching Pursuit Decomposition (MPD) is a powerful iterative algorithm for signal decomposition and feature extraction. MPD decomposes any signal into linear combinations of its dictionary elements or atoms . A best fit atom from an arbitrarily defined dictionary is determined through cross-correlation. The selected atom is subtracted from the signal and this procedure is repeated on the residual in the subsequent iterations until a stopping criterion is met. The reconstructed signal reveals the waveform structure of the original signal. However, a sufficiently large dictionary is required for an accurate reconstruction; this in return increases the computational burden of the algorithm, thus limiting its applicability and level of adoption. The purpose of this research is to improve the scalability and performance of the classical MPD algorithm. Correlation thresholds were defined to prune insignificant atoms from the dictionary. The Coarse-Fine Grids and Multiple Atom Extraction techniques were proposed to decrease the computational burden of the algorithm. The Coarse-Fine Grids method enabled the approximation and refinement of the parameters for the best fit atom. The ability to extract multiple atoms within a single iteration enhanced the effectiveness and efficiency of each iteration. These improvements were implemented to produce an improved Matching Pursuit Decomposition algorithm entitled MPD++. Disparate signal decomposition applications may require a particular emphasis of accuracy or computational efficiency. The prominence of the key signal features required for the proper signal classification dictates the level of accuracy necessary in the decomposition. The MPD++ algorithm may be easily adapted to accommodate the imposed requirements. Certain feature extraction applications may require rapid signal decomposition. The full potential of MPD++ may be utilized to produce incredible performance gains while extracting only slightly less energy than the standard algorithm. When the utmost accuracy must be achieved, the modified algorithm extracts atoms more conservatively but still exhibits computational gains over classical MPD. The MPD++ algorithm was demonstrated using an over-complete dictionary on real life data. Computational times were reduced by factors of 1.9 and 44 for the emphases of accuracy and performance, respectively. The modified algorithm extracted similar amounts of energy compared to classical MPD. The degree of the improvement in computational time depends on the complexity of the data, the initialization parameters, and the breadth of the dictionary. The results of the research confirm that the three modifications successfully improved the scalability and computational efficiency of the MPD algorithm. Correlation Thresholding decreased the time complexity by reducing the dictionary size. Multiple Atom Extraction also reduced the time complexity by decreasing the number of iterations required for a stopping criterion to be reached. The Course-Fine Grids technique enabled complicated atoms with numerous variable parameters to be effectively represented in the dictionary. Due to the nature of the three proposed modifications, they are capable of being stacked and have cumulative effects on the reduction of the time complexity.

Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling.

PubMed

Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki

2016-01-07

Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene.

Building alternate protein structures using the elastic network model.

PubMed

Yang, Qingyi; Sharp, Kim A

2009-02-15

We describe a method for efficiently generating ensembles of alternate, all-atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low-frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more force parameters to characterize the interaction between the consecutive carbon alphas and those within the same secondary structure domain. The relative stiffness of the three parameters is parameterized to reproduce B-factors, while maintaining good bonded geometry. After parameterization, violations of experimental Calpha-Calpha distances and Calpha-Calpha-Calpha pseudo angles along the backbone are reduced to less than 1%. Simultaneously, the average B-factor correlation coefficient improves to R = 0.77. Two applications illustrate the potential of the approach. (1) 102,051 protein backbones spanning a conformational space of 15 A root mean square deviation were generated from 148 nonredundant proteins in the PDB database, and all-atom models with minimal bonded and nonbonded violations were produced from this ensemble of backbone structures using the SCWRL side chain building program. (2) Improved backbone templates for homology modeling. Fifteen query sequences were each modeled on two targets. For each of the 30 target frameworks, dozens of improved templates could be produced In all cases, improved full atom homology models resulted, of which 50% could be identified blind using the D-Fire statistical potential. (c) 2008 Wiley-Liss, Inc.

Aggregation in organic light emitting diodes

NASA Astrophysics Data System (ADS)

Meyer, Abigail

Organic light emitting diode (OLED) technology has great potential for becoming a solid state lighting source. However, there are inefficiencies in OLED devices that need to be understood. Since these inefficiencies occur on a nanometer scale there is a need for structural data on this length scale in three dimensions which has been unattainable until now. Local Electron Atom Probe (LEAP), a specific implementation of Atom Probe Tomography (APT), is used in this work to acquire morphology data in three dimensions on a nanometer scale with much better chemical resolution than is previously seen. Before analyzing LEAP data, simulations were used to investigate how detector efficiency, sample size and cluster size affect data analysis which is done using radial distribution functions (RDFs). Data is reconstructed using the LEAP software which provides mass and position data. Two samples were then analyzed, 3% DCM2 in C60 and 2% DCM2 in Alq3. Analysis of both samples indicated little to no clustering was present in this system.

Photochemical Escape of Atomic Carbon from Mars

NASA Astrophysics Data System (ADS)

Fox, J. L.; Hac, A. B.

2009-12-01

Determining the escape rate of C over time is necessary to reconstructing the time-dependent history of volatiles on Mars. We report initial results from a one-dimensional spherical Monte Carlo calculation of photochemical escape fluxes and rates of atomic carbon from the Martian atmosphere. This model has recently been used to estimate the photochemical escape flux of O from Mars. We include as sources photodissociation of CO, dissociative recombination of CO+, photoelectron-impact dissociation of CO, photodissociative ionization and photoelectron impact dissociative ionization. Dissociative recombination of CO2+ has been suggested as a source of C (in the channel that produces C + O2) but later studies have found that the yield of this channel is negligible. We test the potential importance of this reaction by comparing the final results produced by including it and excluding it. Finally we compare the range of the escape rate to that of C in ions that have been modeled or measured by ASPERA instruments on MEX and Phobos.

AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

PubMed

Lounnas, V; Vriend, G

2012-02-27

Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The AsteriX Web server is freely available at http://swift.cmbi.ru.nl/bitmapb/.

Electrostatic Interactions in Aminoglycoside-RNA Complexes

PubMed Central

Kulik, Marta; Goral, Anna M.; Jasiński, Maciej; Dominiak, Paulina M.; Trylska, Joanna

2015-01-01

Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity. PMID:25650932

20 CFR 30.318 - Can the FAB consider objections to HHS's reconstruction of a radiation dose or to the guidelines...

Code of Federal Regulations, 2010 CFR

2010-04-01

... reconstruction of a radiation dose or to the guidelines OWCP uses to determine if a claimed cancer was at least... if a claimed cancer was at least as likely as not related to employment? (a) If the claimant objects... if a claimed cancer was at least as likely as not related to employment at a DOE facility, an atomic...

20 CFR 30.318 - Can the FAB consider objections to HHS's reconstruction of a radiation dose or to the guidelines...

Code of Federal Regulations, 2011 CFR

2011-04-01

... reconstruction of a radiation dose or to the guidelines OWCP uses to determine if a claimed cancer was at least... if a claimed cancer was at least as likely as not related to employment? (a) If the claimant objects... if a claimed cancer was at least as likely as not related to employment at a DOE facility, an atomic...

20 CFR 30.318 - Can the FAB consider objections to HHS's reconstruction of a radiation dose or to the guidelines...

Code of Federal Regulations, 2014 CFR

2014-04-01

... reconstruction of a radiation dose or to the guidelines OWCP uses to determine if a claimed cancer was at least... if a claimed cancer was at least as likely as not related to employment? (a) If the claimant objects... if a claimed cancer was at least as likely as not related to employment at a DOE facility, an atomic...

20 CFR 30.318 - Can the FAB consider objections to HHS's reconstruction of a radiation dose or to the guidelines...

Code of Federal Regulations, 2012 CFR

2012-04-01

... reconstruction of a radiation dose or to the guidelines OWCP uses to determine if a claimed cancer was at least... if a claimed cancer was at least as likely as not related to employment? (a) If the claimant objects... if a claimed cancer was at least as likely as not related to employment at a DOE facility, an atomic...

20 CFR 30.318 - Can the FAB consider objections to HHS's reconstruction of a radiation dose or to the guidelines...

Code of Federal Regulations, 2013 CFR

2013-04-01

... reconstruction of a radiation dose or to the guidelines OWCP uses to determine if a claimed cancer was at least... if a claimed cancer was at least as likely as not related to employment? (a) If the claimant objects... if a claimed cancer was at least as likely as not related to employment at a DOE facility, an atomic...

A scanning tunnelling microscopy study of C and N adsorption phases on the vicinal Ni(100) surfaces Ni(810) and Ni(911)

NASA Astrophysics Data System (ADS)

Driver, S. M.; Toomes, R. L.; Woodruff, D. P.

2016-04-01

The influence of N and C chemisorption on the morphology and local structure of nominal Ni(810) and Ni(911) surfaces, both vicinal to (100) but with [001] and [ 01 1 bar ] step directions, respectively, has been investigated using scanning tunnelling microscopy (STM) and low energy electron diffraction. Ni(911) undergoes substantial step bunching in the presence of both adsorbates, with the (911)/N surface showing (411) facets, whereas for Ni(810), multiple steps 2-4 layers high are more typical. STM atomic-scale images show the (2 × 2)pg 'clock' reconstruction on the (100) terraces of the (810) surfaces with both C and N, although a second c(2 × 2) structure, most readily reconciled with a 'rumpling' reconstruction, is also seen on Ni(810)/N. On Ni(911), the clock reconstruction is not seen on the (100) terraces with either adsorbate, and these images are typified by protrusions on a (1 × 1) mesh. This absence of clock reconstruction is attributed to the different constraints imposed on the lateral movements of the surface Ni atoms adjacent to the up-step edge of the terraces with a [ 01 1 bar ] step direction.

Influence of AlN(0001) Surface Reconstructions on the Wettability of an Al/AlN System: A First-Principle Study.

PubMed

Cao, Junhua; Liu, Yang; Ning, Xiao-Shan

2018-05-11

A successful application of a hot dip coating process that coats aluminum (Al) on aluminum nitride (AlN) ceramics, revealed that Al had a perfect wettability to the ceramics under specific circumstances, which was different from previous reports. In order to elucidate the mechanism that controlled the supernormal wetting phenomenon during the dip coating, a first-principle calculation of an Al(111)/AlN(0001) interface, based on the density functional theory (DFT), was employed. The wettability of the Al melt on the AlN(0001) surface, as well as the effect that the surface reconstruction of AlN and the oxygen adsorption had on Al for the adhesion and the wettability of the Al/AlN system, were studied. The results revealed that a LCM (laterally contracted monolayer) reconstruction could improve the adhesion and wettability of the system. Oxygen adsorption on the free surface of Al decreased the contact angle, because the adsorption reduced of the surface tension of Al. A prefect wetting was obtained only after some of the oxygen atoms adsorbed on the free surface of Al. The supernormal wetting phenomenon came from the surface reconstruction of the AlN and the adsorption of oxygen atoms on the Al melt surface.

GEANT4 simulation of a scintillating-fibre tracker for the cosmic-ray muon tomography of legacy nuclear waste containers

NASA Astrophysics Data System (ADS)

Clarkson, A.; Hamilton, D. J.; Hoek, M.; Ireland, D. G.; Johnstone, J. R.; Kaiser, R.; Keri, T.; Lumsden, S.; Mahon, D. F.; McKinnon, B.; Murray, M.; Nutbeam-Tuffs, S.; Shearer, C.; Staines, C.; Yang, G.; Zimmerman, C.

2014-05-01

Cosmic-ray muons are highly penetrative charged particles that are observed at the sea level with a flux of approximately one per square centimetre per minute. They interact with matter primarily through Coulomb scattering, which is exploited in the field of muon tomography to image shielded objects in a wide range of applications. In this paper, simulation studies are presented that assess the feasibility of a scintillating-fibre tracker system for use in the identification and characterisation of nuclear materials stored within industrial legacy waste containers. A system consisting of a pair of tracking modules above and a pair below the volume to be assayed is simulated within the GEANT4 framework using a range of potential fibre pitches and module separations. Each module comprises two orthogonal planes of fibres that allow the reconstruction of the initial and Coulomb-scattered muon trajectories. A likelihood-based image reconstruction algorithm has been developed that allows the container content to be determined with respect to the scattering density λ, a parameter which is related to the atomic number Z of the scattering material. Images reconstructed from this simulation are presented for a range of anticipated scenarios that highlight the expected image resolution and the potential of this system for the identification of high-Z materials within a shielded, concrete-filled container. First results from a constructed prototype system are presented in comparison with those from a detailed simulation. Excellent agreement between experimental data and simulation is observed showing clear discrimination between the different materials assayed throughout.

Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome

NASA Astrophysics Data System (ADS)

Chwastyk, Mateusz; Poma Bernaola, Adolfo; Cieplak, Marek

2015-07-01

We propose to improve and simplify protein refinement procedures through consideration of which pairs of amino acid residues should form native contacts. We first consider 11 330 proteins from the CATH database to determine statistical distributions of contacts associated with a given type of amino acid. The distributions are set across the distances between the α-C atoms that are in contact. Based on this data, we determine typical radii of effective spheres that can be placed on the α-C atoms in order to reconstruct the distribution of the contact lengths. This is done by checking for overlaps with enlarged van der Waals spheres associated with heavy atoms on other amino acids. The resulting contacts can be used to identify non-native contacts that may arise during the time evolution of structure-based models. Here, the radii are used to guide reconstruction of nine missing side chains in a type I cohesin domain with the Protein Data Bank code 1AOH. We first identify the likely missing contacts and then sculpt the corresponding side chains by standard refinement tools to achieve consistency with the expected contact map. One ambiguity in refinement is resolved by determining all-atom conformational energies.

Increasing circular synthetic aperture sonar resolution via adapted wave atoms deconvolution.

PubMed

Pailhas, Yan; Petillot, Yvan; Mulgrew, Bernard

2017-04-01

Circular Synthetic Aperture Sonar (CSAS) processing computes coherently Synthetic Aperture Sonar (SAS) data acquired along a circular trajectory. This approach has a number of advantages, in particular it maximises the aperture length of a SAS system, producing very high resolution sonar images. CSAS image reconstruction using back-projection algorithms, however, introduces a dissymmetry in the impulse response, as the imaged point moves away from the centre of the acquisition circle. This paper proposes a sampling scheme for the CSAS image reconstruction which allows every point, within the full field of view of the system, to be considered as the centre of a virtual CSAS acquisition scheme. As a direct consequence of using the proposed resampling scheme, the point spread function (PSF) is uniform for the full CSAS image. Closed form solutions for the CSAS PSF are derived analytically, both in the image and the Fourier domain. The thorough knowledge of the PSF leads naturally to the proposed adapted atom waves basis for CSAS image decomposition. The atom wave deconvolution is successfully applied to simulated data, increasing the image resolution by reducing the PSF energy leakage.

Plenoptic Imaging of a Three Dimensional Cold Atom Cloud

NASA Astrophysics Data System (ADS)

Lott, Gordon

2017-04-01

A plenoptic imaging system is capable of sampling the rays of light in a volume, both spatially and angularly, providing information about the three dimensional (3D) volume being imaged. The extraction of the 3D structure of a cold atom cloud is demonstrated, using a single plenoptic camera and a single image. The reconstruction is tested against a reference image and the results discussed along with the capabilities and limitations of the imaging system. This capability is useful when the 3D distribution of the atoms is desired, such as determining the shape of an atom trap, particularly when there is limited optical access. Gratefully acknowledge support from AFRL.

Effects of the local structure dependence of evaporation fields on field evaporation behavior

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

Yao, Lan; Marquis, Emmanuelle A., E-mail: emarq@umich.edu; Withrow, Travis

2015-12-14

Accurate three dimensional reconstructions of atomic positions and full quantification of the information contained in atom probe microscopy data rely on understanding the physical processes taking place during field evaporation of atoms from needle-shaped specimens. However, the modeling framework for atom probe microscopy has only limited quantitative justification. Building on the continuum field models previously developed, we introduce a more physical approach with the selection of evaporation events based on density functional theory calculations. This model reproduces key features observed experimentally in terms of sequence of evaporation, evaporation maps, and depth resolution, and provides insights into the physical limit formore » spatial resolution.« less

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

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

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

3D reconstruction of the magnetic vector potential using model based iterative reconstruction.

PubMed

Prabhat, K C; Aditya Mohan, K; Phatak, Charudatta; Bouman, Charles; De Graef, Marc

2017-11-01

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. A comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach. Copyright © 2017 Elsevier B.V. All rights reserved.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

DOE PAGES

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta; ...

2017-07-03

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

Entanglement of 3000 atoms by detecting one photon

NASA Astrophysics Data System (ADS)

Vuletic, Vladan

2016-05-01

Quantum-mechanically correlated (entangled) states of many particles are of interest in quantum information, quantum computing and quantum metrology. In particular, entangled states of many particles can be used to overcome limits on measurements performed with ensembles of independent atoms (standard quantum limit). Metrologically useful entangled states of large atomic ensembles (spin squeezed states) have been experimentally realized. These states display Gaussian spin distribution functions with a non-negative Wigner quasiprobability distribution function. We report the generation of entanglement in a large atomic ensemble via an interaction with a very weak laser pulse; remarkably, the detection of a single photon prepares several thousand atoms in an entangled state. We reconstruct a negative-valued Wigner function, and verify an entanglement depth (the minimum number of mutually entangled atoms) that comprises 90% of the atomic ensemble containing 3100 atoms. Further technical improvement should allow the generation of more complex Schrödinger cat states, and of states the overcome the standard quantum limit.

Silicon and Germanium (111) Surface Reconstruction

NASA Astrophysics Data System (ADS)

Hao, You Gong

Silicon (111) surface (7 x 7) reconstruction has been a long standing puzzle. For the last twenty years, various models were put forward to explain this reconstruction, but so far the problem still remains unsolved. Recent ion scattering and channeling (ISC), scanning tunneling microscopy (STM) and transmission electron diffraction (TED) experiments reveal some new results about the surface which greatly help investigators to establish better models. This work proposes a silicon (111) surface reconstruction mechanism, the raising and lowering mechanism which leads to benzene -like ring and flower (raised atom) building units. Based on these building units a (7 x 7) model is proposed, which is capable of explaining the STM and ISC experiment and several others. Furthermore the building units of the model can be used naturally to account for the germanium (111) surface c(2 x 8) reconstruction and other observed structures including (2 x 2), (5 x 5) and (7 x 7) for germanium as well as the (/3 x /3)R30 and (/19 x /19)R23.5 impurity induced structures for silicon, and the higher temperature disordered (1 x 1) structure for silicon. The model is closely related to the silicon (111) surface (2 x 1) reconstruction pi-bonded chain model, which is the most successful model for the reconstruction now. This provides an explanation for the rather low conversion temperature (560K) of the (2 x 1) to the (7 x 7). The model seems to meet some problems in the explanation of the TED result, which is explained very well by the dimer, adatom and stacking fault (DAS) model proposed by Takayanagi. In order to explain the TED result, a variation of the atomic scattering factor is proposed. Comparing the benzene-like ring model with the DAS model, the former needs more work to explain the TED result and the later has to find a way to explain the silicon (111) surface (1 x 1) disorder experiment.

Light-induced charge separation across bio-inorganic interface.

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

Dimitrijevic, N. M.; Rajh, T.; De La Garza, L.

Rational design of hybrid biomolecule - nanoparticulate semiconductor conjugates enables coupling of functionality of biomolecules with the capability of semiconductors for solar energy capture, that can have potential application in energy conversion, sensing and catalysis. The particular challenge is to obtain efficient charge separation analogous to the natural photosynthesis process. The synthesis of axially anisotropic TiO{sub 2} nano-objects such as tubes, rods and bricks, as well as spherical and faceted nanoparticles has been developed in our laboratory. Depending on their size and shape, these nanostructures exhibit different domains of crystallinity, surface areas and aspect ratios. Moreover, in order to accommodatemore » for high curvature in nanoscale regime, the surfaces of TiO{sub 2} nano-objects reconstructs resulting in changes in the coordination of surface Ti atoms from octahedral (D{sub 2d}) to square pyramidal structures (C{sub 4v}). The formation of these coordinatively unsaturated Ti atoms, thus depends strongly on the size and shape of nanocrystallites and affects trapping and reactivity of photogenerated charges. We have exploited these coordinatively unsaturated Ti atoms to coupe electron-donating (such as dopamine) and electron-accepting (pyrroloquinoline quinone) conductive linkers that allow wiring of biomolecules and proteins resulting in enhanced charge separation which increases the yield of ensuing chemical transformations.« less

Positron Annihilation Induced Auger Electron Spectroscopic Studies Of Reconstructed Semiconductor Surfaces

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Reed, J. A.; Starnes, S. G.; Weiss, A. H.

2011-06-01

The positron annihilation induced Auger spectrum from GaAs(100) displays six As and three Ga Auger peaks below 110 eV corresponding to M4,5VV, M2M4V, M2,3M4,5M4,5 Auger transitions for As and M2,3M4,5M4,5 Auger transitions for Ga. The integrated Auger peak intensities have been used to obtain experimental annihilation probabilities of surface trapped positrons with As 3p and 3d and Ga 3p core level electrons. PAES data is analyzed by performing calculations of positron surface and bulk states and annihilation characteristics of surface trapped positrons with relevant Ga and As core level electrons for both Ga- and As-rich (100) surfaces of GaAs, ideally terminated, non-reconstructed and with (2×8), (2×4), and (4×4) reconstructions. The orientation-dependent variations of the atomic and electron densities associated with reconstructions are found to affect localization of the positron wave function at the surface. Computed positron binding energy, work function, and annihilation characteristics demonstrate their sensitivity both to chemical composition and atomic structure of the topmost layers of the surface. Theoretical annihilation probabilities of surface trapped positrons with As 3d, 3p, and Ga 3p core level electrons are compared with the ones estimated from the measured Auger peak intensities.

Atomic electron tomography: 3D structures without crystals

DOE PAGES

Miao, Jianwei; Ercius, Peter; Billinge, S. J. L.

2016-09-23

Crystallography has been fundamental to the development of many fields of science over the last century. However, much of our modern science and technology relies on materials with defects and disorders, and their three-dimensional (3D) atomic structures are not accessible to crystallography. One method capable of addressing this major challenge is atomic electron tomography. By combining advanced electron microscopes and detectors with powerful data analysis and tomographic reconstruction algorithms, it is now possible to determine the 3D atomic structure of crystal defects such as grain boundaries, stacking faults, dislocations, and point defects, as well as to precisely localize the 3Dmore » coordinates of individual atoms in materials without assuming crystallinity. In this work, we review the recent advances and the interdisciplinary science enabled by this methodology. We also outline further research needed for atomic electron tomography to address long-standing unresolved problems in the physical sciences.« less

The 2.3-Angstrom Structure of Porcine Circovirus 2

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

Khayat, Reza; Brunn, Nicholas; Speir, Jeffrey A.

Porcine circovirus 2 (PCV2) is a T = 1 nonenveloped icosahedral virus that has had severe impact on the swine industry. Here we report the crystal structure of an N-terminally truncated PCV2 virus-like particle at 2.3-{angstrom} resolution, and the cryo-electron microscopy (cryo-EM) image reconstruction of a full-length PCV2 virus-like particle at 9.6-{angstrom} resolution. This is the first atomic structure of a circovirus. The crystal structure revealed that the capsid protein fold is a canonical viral jelly roll. The loops connecting the strands of the jelly roll define the limited features of the surface. Sulfate ions interacting with the surface andmore » electrostatic potential calculations strongly suggest a heparan sulfate binding site that allows PCV2 to gain entry into the cell. The crystal structure also allowed previously determined epitopes of the capsid to be visualized. The cryo-EM image reconstruction showed that the location of the N terminus, absent in the crystal structure, is inside the capsid. As the N terminus was previously shown to be antigenic, it may externalize through viral 'breathing'.« less

High Precision Seawater Sr/Ca Measurements in the Florida Keys by Inductively Coupled Plasma Atomic Emission Spectrometry: Analytical Method and Implications for Coral Paleothermometry

NASA Astrophysics Data System (ADS)

Khare, A.; Kilbourne, K. H.; Schijf, J.

2017-12-01

Standard methods of reconstructing past sea surface temperatures (SSTs) with coral skeletal Sr/Ca ratios assume the seawater Sr/Ca ratio is constant. However, there is little data to support this assumption, in part because analytical techniques capable of determining seawater Sr/Ca with sufficient accuracy and precision are expensive and time consuming. We demonstrate a method to measure seawater Sr/Ca using inductively coupled plasma atomic emission spectrometry where we employ an intensity ratio calibration routine that reduces the self- matrix effects of calcium and cancels out the matrix effects that are common to both calcium and strontium. A seawater standard solution cross-calibrated with multiple instruments is used to correct for long-term instrument drift and any remnant matrix effects. The resulting method produces accurate seawater Sr/Ca determinations rapidly, inexpensively, and with a precision better than 0.2%. This method will make it easier for coral paleoclimatologists to quantify potentially problematic fluctuations in seawater Sr/Ca at their study locations. We apply our method to test for variability in surface seawater Sr/Ca along the Florida Keys Reef Tract. We are collecting winter and summer samples for two years in a grid with eleven nearshore to offshore transects across the reef, as well as continuous samples collected by osmotic pumps at four locations adjacent to our grid. Our initial analysis of the grid samples indicates a trend of decreasing Sr/Ca values offshore potentially due to a decreasing groundwater influence. The values differ by as much as 0.05 mmol/mol which could lead to an error of 1°C in mean SST reconstructions. Future work involves continued sampling in the Florida Keys to test for seasonal and interannual variability in seawater Sr/Ca, as well as collecting data from small reefs in the Virgin Islands to test the stability of seawater Sr/Ca under different geologic, hydrologic and hydrographic environments.

Modern Possibilities for Calculating Some Properties of Molecules and Crystals from the Experimental Electron Density

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

Stash, A.I.; Tsirelson, V.G.

2005-03-01

Methods for calculating some properties of molecules and crystals from the electron density reconstructed from a precise X-ray diffraction experiment using the multipole model are considered. These properties include, on the one hand, the characteristics of the electron density and the inner-crystal electrostatic field and, on the other hand, the local electronic energies (kinetic, potential, total), the exchange energy density, the electron-pair localization function, the localized-orbital locator, the effective crystal potential, and others. It is shown that the integration of these characteristics over pseudoatomic volumes bounded by the surfaces of the zero flux of the electron density gradient makes itmore » possible to characterize directly from an experiment the properties of molecules and crystals in terms of the atomic contributions. The computer program WinXPRO2004, realizing these possibilities, is briefly described.« less

Landau free energy for a bcc-hcp reconstructive phase transformation

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

Sanati, Mahdi; Saxena, A.; Lookman, T.

We study the bcc-hcp phase transition in Ti and Zr with the use of first-principles calculations. We have determined the complete energy surface from the bcc to hcp structure. The results are used to find an appropriate Landau free energy density for describing this transformation. The proposed Landau free energy density has two relevant order parameters: shear and shuffle. Through first-principles calculations, we show that the bcc structure is unstable with respect to the shuffle of atoms (TA{sub 1} N-point phonon) rather than the shear. Therefore, we reduce the two order parameter Landau free energy to an effective one ordermore » parameter (shuffle) potential, which is a reasonable approximation. In general, the effective Landau free energy is a triple-well potential. From the phonon dispersion data and the change in entropy at the transition temperature we find the free energy coefficients for Ti and Zr.« less

Reconstruction of the two-dimensional gravitational potential of galaxy clusters from X-ray and Sunyaev-Zel'dovich measurements

NASA Astrophysics Data System (ADS)

Tchernin, C.; Bartelmann, M.; Huber, K.; Dekel, A.; Hurier, G.; Majer, C. L.; Meyer, S.; Zinger, E.; Eckert, D.; Meneghetti, M.; Merten, J.

2018-06-01

Context. The mass of galaxy clusters is not a direct observable, nonetheless it is commonly used to probe cosmological models. Based on the combination of all main cluster observables, that is, the X-ray emission, the thermal Sunyaev-Zel'dovich (SZ) signal, the velocity dispersion of the cluster galaxies, and gravitational lensing, the gravitational potential of galaxy clusters can be jointly reconstructed. Aims: We derive the two main ingredients required for this joint reconstruction: the potentials individually reconstructed from the observables and their covariance matrices, which act as a weight in the joint reconstruction. We show here the method to derive these quantities. The result of the joint reconstruction applied to a real cluster will be discussed in a forthcoming paper. Methods: We apply the Richardson-Lucy deprojection algorithm to data on a two-dimensional (2D) grid. We first test the 2D deprojection algorithm on a β-profile. Assuming hydrostatic equilibrium, we further reconstruct the gravitational potential of a simulated galaxy cluster based on synthetic SZ and X-ray data. We then reconstruct the projected gravitational potential of the massive and dynamically active cluster Abell 2142, based on the X-ray observations collected with XMM-Newton and the SZ observations from the Planck satellite. Finally, we compute the covariance matrix of the projected reconstructed potential of the cluster Abell 2142 based on the X-ray measurements collected with XMM-Newton. Results: The gravitational potentials of the simulated cluster recovered from synthetic X-ray and SZ data are consistent, even though the potential reconstructed from X-rays shows larger deviations from the true potential. Regarding Abell 2142, the projected gravitational cluster potentials recovered from SZ and X-ray data reproduce well the projected potential inferred from gravitational-lensing observations. We also observe that the covariance matrix of the potential for Abell 2142 reconstructed from XMM-Newton data sensitively depends on the resolution of the deprojected grid and on the smoothing scale used in the deprojection. Conclusions: We show that the Richardson-Lucy deprojection method can be effectively applied on a grid and that the projected potential is well recovered from real and simulated data based on X-ray and SZ signal. The comparison between the reconstructed potentials from the different observables provides additional information on the validity of the assumptions as function of the projected radius.

A new method for mapping the three-dimensional atomic distribution within nanoparticles by atom probe tomography (APT).

PubMed

Kim, Se-Ho; Kang, Phil Woong; Park, O Ok; Seol, Jae-Bok; Ahn, Jae-Pyoung; Lee, Ji Yeong; Choi, Pyuck-Pa

2018-07-01

We present a new method of preparing needle-shaped specimens for atom probe tomography from freestanding Pd and C-supported Pt nanoparticles. The method consists of two steps, namely electrophoresis of nanoparticles on a flat Cu substrate followed by electrodeposition of a Ni film acting as an embedding matrix for the nanoparticles. Atom probe specimen preparation can be subsequently carried out by means of focused-ion-beam milling. Using this approach, we have been able to perform correlative atom probe tomography and transmission electron microscopy analyses on both nanoparticle systems. Reliable mass spectra and three-dimensional atom maps could be obtained for Pd nanoparticle specimens. In contrast, atom probe samples prepared from C-supported Pt nanoparticles showed uneven field evaporation and hence artifacts in the reconstructed atom maps. Our developed method is a viable means of mapping the three-dimensional atomic distribution within nanoparticles and is expected to contribute to an improved understanding of the structure-composition-property relationships of various nanoparticle systems. Copyright © 2018 Elsevier B.V. All rights reserved.

Electron holography—basics and applications

NASA Astrophysics Data System (ADS)

Lichte, Hannes; Lehmann, Michael

2008-01-01

Despite the huge progress achieved recently by means of the corrector for aberrations, allowing now a true atomic resolution of 0.1 nm, hence making it an unrivalled tool for nanoscience, transmission electron microscopy (TEM) suffers from a severe drawback: in a conventional electron micrograph only a poor phase contrast can be achieved, i.e. phase structures are virtually invisible. Therefore, conventional TEM is nearly blind for electric and magnetic fields, which are pure phase objects. Since such fields provoked by the atomic structure, e.g. of semiconductors and ferroelectrics, largely determine the solid state properties, hence the importance for high technology applications, substantial object information is missing. Electron holography in TEM offers the solution: by superposition with a coherent reference wave, a hologram is recorded, from which the image wave can be completely reconstructed by amplitude and phase. Now the object is displayed quantitatively in two separate images: one representing the amplitude, the other the phase. From the phase image, electric and magnetic fields can be determined quantitatively in the range from micrometre down to atomic dimensions by all wave optical methods that one can think of, both in real space and in Fourier space. Electron holography is pure wave optics. Therefore, we discuss the basics of coherence and interference, the implementation into a TEM, the path of rays for recording holograms as well as the limits in lateral and signal resolution. We outline the methods of reconstructing the wave by numerical image processing and procedures for extracting the object properties of interest. Furthermore, we present a broad spectrum of applications both at mesoscopic and atomic dimensions. This paper gives an overview of the state of the art pointing at the needs for further development. It is also meant as encouragement for those who refrain from holography, thinking that it can only be performed by specialists in highly specialized laboratories. In fact, a modern TEM built for atomic resolution and equipped with a field emitter or a Schottky emitter, well aligned by a skilled operator, can deliver good holograms. Running commercially available image processing software and mathematics programs on a laptop-computer is sufficient for reconstruction of the amplitude and phase images and extracting desirable object information.

Mapping power-law rheology of living cells using multi-frequency force modulation atomic force microscopy

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

Takahashi, Ryosuke; Okajima, Takaharu, E-mail: okajima@ist.hokudai.ac.jp

We present multi-frequency force modulation atomic force microscopy (AFM) for mapping the complex shear modulus G* of living cells as a function of frequency over the range of 50–500 Hz in the same measurement time as the single-frequency force modulation measurement. The AFM technique enables us to reconstruct image maps of rheological parameters, which exhibit a frequency-dependent power-law behavior with respect to G{sup *}. These quantitative rheological measurements reveal a large spatial variation in G* in this frequency range for single cells. Moreover, we find that the reconstructed images of the power-law rheological parameters are much different from those obtained inmore » force-curve or single-frequency force modulation measurements. This indicates that the former provide information about intracellular mechanical structures of the cells that are usually not resolved with the conventional force measurement methods.« less

CG2AA: backmapping protein coarse-grained structures.

PubMed

Lombardi, Leandro E; Martí, Marcelo A; Capece, Luciana

2016-04-15

Coarse grain (CG) models allow long-scale simulations with a much lower computational cost than that of all-atom simulations. However, the absence of atomistic detail impedes the analysis of specific atomic interactions that are determinant in most interesting biomolecular processes. In order to study these phenomena, it is necessary to reconstruct the atomistic structure from the CG representation. This structure can be analyzed by itself or be used as an onset for atomistic molecular dynamics simulations. In this work, we present a computer program that accurately reconstructs the atomistic structure from a CG model for proteins, using a simple geometrical algorithm. The software is free and available online at http://www.ic.fcen.uba.ar/cg2aa/cg2aa.py Supplementary data are available at Bioinformatics online. lula@qi.fcen.uba.ar. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

Kweon, Kyoung E.; Aberg, Daniel; Lordi, Vincenzo

The atomic and electronic structures of 60° glide perfect and 30°/90° glide partial dislocations in CdTe are studied using combined semi-empirical and density functional theory calculations. The calculations predict that the dislocation cores tend to undergo significant reconstructions along the dislocation lines from the singly-periodic (SP) structures, yielding either doubly-periodic (DP) ordering by forming a dimer or quadruply-periodic (QP) ordering by alternating a dimer and a missing dimer. Charge modulation along the dislocation line, accompanied by the QP reconstruction for the Cd-/Te-core 60° perfect and 30° partials or the DP reconstruction for the Cd-core 90° partial, results in semiconducting character,more » as opposed to the metallic character of the SP dislocation cores. Dislocation-induced defect states for the 60° Cd-/Te-core are located relatively close to the band edges, whereas the defect states lie in the middle of the band gap for the 30° Cd-/Te-core partial dislocations. In addition to the intracore charge modulation within each QP core, the possibility of intercore charge transfer between two different dislocation cores when they are paired together in the same system is discussed. As a result, the analysis of the electronic structures reveals the potential role of the dislocations on charge transport in CdTe, particularly in terms of charge trapping and recombination.« less

Surface imaging microscope

NASA Astrophysics Data System (ADS)

Rogala, Eric W.; Bankman, Isaac N.

2008-04-01

The three-dimensional shapes of microscopic objects are becoming increasingly important for battlespace CBRNE sensing. Potential applications of microscopic 3D shape observations include characterization of biological weapon particles and manufacturing of micromechanical components. Aerosol signatures of stand-off lidar systems, using elastic backscatter or polarization, are dictated by the aerosol particle shapes and sizes that must be well characterized in the lab. A low-cost, fast instrument for 3D surface shape microscopy will be a valuable point sensor for biological particle sensing applications. Both the cost and imaging durations of traditional techniques such as confocal microscopes, atomic force microscopes, and electron scanning microscopes are too high. We investigated the feasibility of a low-cost, fast interferometric technique for imaging the 3D surface shape of microscopic objects at frame rates limited only by the camera in the system. The system operates at two laser wavelengths producing two fringe images collected simultaneously by a digital camera, and a specialized algorithm we developed reconstructs the surface map of the microscopic object. The current implementation assembled to test the concept and develop the new 3D reconstruction algorithm has 0.25 micron resolution in the x and y directions, and about 0.1 micron accuracy in the z direction, as tested on a microscopic glass test object manufactured with etching techniques. We describe the interferometric instrument, present the reconstruction algorithm, and discuss further development.

Surface reconstruction switching induced by tensile stress of DB steps: From Ba/Si(0 0 1)- 2 × 3 to Ba/Si(0 0 1)-4° off- 3 × 2

NASA Astrophysics Data System (ADS)

Kim, Hidong; Lkhagvasuren, Altaibaatar; Zhang, Rui; Seo, Jae M.

2018-05-01

The alkaline-earth metal adsorption on Si(0 0 1) has attracted much interest for finding a proper template in the growth of high- κ and crystalline films. Up to now on the flat Si(0 0 1) surface with double domains and single-layer steps, the adsorbed Ba atoms are known to induce the 2 × 3 structure through removing two Si dimers and adding a Ba atom per unit cell in each domain. In the present investigation, the Si(0 0 1)-4° off surface with DB steps and single domains has been employed as a substrate and the reconstruction at the initial stage of Ba adsorption has been investigated by scanning tunneling microscopy and synchrotron photoemission spectroscopy. On this vicinal and single domain terrace, a novel 3 × 2 structure rotated by 90° from the 2 × 3 structure has been found. Such a 3 × 2 structure turns out to be formed by adding a Ba atom and a Si dimer per unit cell. This results from the fact that the adsorbed Ba2+ ions with a larger ionic radius relieve tensile stress on the original Si dimers exerted by the rebonded atoms at the DB step.

Hydrogen adsorption site on the Ni?110?-p(1 × 2)-H surface from time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Bu, H.; Roux, C. D.; Rabalais, J. W.

The adsorption site of hydrogen on the Ni{110}-p(1 × 2)-H surface resulting from saturation exposure to H 2 at ˜ 310-350 K has been investigated by time-of-flight scattering and recoiling spectrometry (TOF-SARS). The recoiled neutral plus ion hydrogen atom flux resulting from 2-5 keV Ar + or Ne + pulsed ion beams incident on the surface was monitored as a function of crystal azimuthal angle and beam incidence angle. From classical trajectory calculations and shadowing and blocking analyses, it is concluded that hydrogen atoms are localized at the pseudo-three-fold sites on the (1 × 2) missing-row (MR) reconstructed Ni{110} surface; the (1 × 2) MR reconstruction is induced by hydrogen adsorption shown elsewhere [Surf. Sci. 259 (1991) 253]. Only the pseudo-three-fold site is consistent with all of the experimental data. The coordinates of the hydrogen adsorption site with respect to the nickel lattice were determined. The lateral distance of hydrogen from the 1st-layer Ni <1 overline10> rows is 1.56 ± 0.12 Å and the vertical distance above the substrate is 0.21 ± 0.12 Å, providing NiH bond lengths of 2.0 Å to the two-layer Ni atoms and 1.5 Å to the 2nd-layer Ni atom.

Passivation effect of Cl, F and H atoms on CuIn0.75Ga0.25Se2 (1 1 2) surface

NASA Astrophysics Data System (ADS)

Qi, Rong-fei; Wang, Zhao-hui; Tang, Fu-ling; Agbonkina, Itohan C.; Xue, Hong-tao; Si, Feng-juan; Ma, Sheng-ling; Wang, Xiao-ka

2018-06-01

Using the first-principles calculations within the density functional-theory (DFT) framework, we theoretically investigated the surface reconstruction, surface states near the Fermi level and their passivation on CuIn0.75Ga0.25Se2 (1 1 2) (CIGS) surface by chlorine, fluorine and hydrogen. Surface reconstruction appears on CIG-terminated CIGS (1 1 2) surface and it is a self-passivation. For the locations of Cl, F and H atoms adsorbing on Se-terminated CIGS (1 1 2) surface, four high symmetry adsorption sites: top sites, bridge sites, hexagonal close-packed (hcp) sites and faced centered cubic (fcc) sites were studied respectively. With the coverage of 0.5 monolayer (ML), Cl, F and H adatoms energetically occupy the top sites on the CIGS (112) surface. The corresponding adsorption energies were -2.20 eV, -3.29 eV, -2.60 eV, respectively. The bond length and electronic properties were analyzed. We found that the surface state density near the Fermi level was markedly diminished for 0.5 ML Cl, F and H adsorption on Se-terminated CIGS (1 1 2) surface at top sites. It was also found that H can more efficiently passivate the surface state density than Cl and F atoms, and the effect of adsorption of Cl atoms is better than that of F.

Thermodynamic Behavior of Nano-sized Gold Clusters on the (001) Surface

NASA Technical Reports Server (NTRS)

Paik, Sun M.; Yoo, Sung M.; Namkung, Min; Wincheski, Russell A.; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

We have studied thermal expansion of the surface layers of the hexagonally reconstructed Au (001) surface using a classical Molecular Dynamics (MD) simulation technique with an Embedded Atomic Method (EAM) type many-body potential. We find that the top-most hexagonal layer contracts as temperature increases, whereas the second layer expands or contracts depending on the system size. The magnitude of expansion coefficient of the top layer is much larger than that of the other layers. The calculated thermal expansion coefficients of the top-most layer are about -4.93 x 10(exp -5)Angstroms/Kelvin for the (262 x 227)Angstrom cluster and -3.05 x 10(exp -5)Angstroms/Kelvin for (101 x 87)Angstrom cluster. The Fast Fourier Transform (FFT) image of the atomic density shows that there exists a rotated domain of the top-most hexagonal cluster with rotation angle close to 1 degree at temperature T less than 1000Kelvin. As the temperature increases this domain undergoes a surface orientational phase transition. These predictions are in good agreement with previous phenomenological theories and experimental studies.

Role of Defects on Regioselectivity of Nano Pristine Graphene.

PubMed

Kudur Jayaprakash, Gururaj; Casillas, Norberto; Astudillo-Sánchez, Pablo D; Flores-Moreno, Roberto

2016-11-17

Here analytical Fukui functions based on density functional theory are applied to investigate the redox reactivity of pristine and defected graphene lattices. A carbon H-terminated graphene structure (with 96 carbon atoms) and a graphene defected surface with Stone-Wales rearrangement and double vacancy defects are used as models. Pristine sp 2 -hybridized, hexagonal arranged carbon atoms exhibit a symmetric reactivity. In contrast, common carbon atoms at reconstructed polygons in Stone-Wales and double vacancy graphene display large reactivity variations. The improved reactivity and the regioselectivity at defected graphene is correlated to structural changes that caused carbon-carbon bond length variations at defected zones.

Predicting supramolecular self-assembly on reconstructed metal surfaces

NASA Astrophysics Data System (ADS)

Roussel, Thomas J.; Barrena, Esther; Ocal, Carmen; Faraudo, Jordi

2014-06-01

The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern.The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern. GA image adapted from refs: (a) Phys. Chem. Chem. Phys., 2001, 3, 3399-3404, with permission from the PCCP Owner Societies, and (b) J. Phys. Chem. C, 2008, 112 (18), 7168-7172, reprinted with permission from the American Chemical Society, copyright © 2008.

Joint denoising and distortion correction of atomic scale scanning transmission electron microscopy images

NASA Astrophysics Data System (ADS)

Berkels, Benjamin; Wirth, Benedikt

2017-09-01

Nowadays, modern electron microscopes deliver images at atomic scale. The precise atomic structure encodes information about material properties. Thus, an important ingredient in the image analysis is to locate the centers of the atoms shown in micrographs as precisely as possible. Here, we consider scanning transmission electron microscopy (STEM), which acquires data in a rastering pattern, pixel by pixel. Due to this rastering combined with the magnification to atomic scale, movements of the specimen even at the nanometer scale lead to random image distortions that make precise atom localization difficult. Given a series of STEM images, we derive a Bayesian method that jointly estimates the distortion in each image and reconstructs the underlying atomic grid of the material by fitting the atom bumps with suitable bump functions. The resulting highly non-convex minimization problems are solved numerically with a trust region approach. Existence of minimizers and the model behavior for faster and faster rastering are investigated using variational techniques. The performance of the method is finally evaluated on both synthetic and real experimental data.

Image simulation and surface reconstruction of undercut features in atomic force microscopy

NASA Astrophysics Data System (ADS)

Qian, Xiaoping; Villarrubia, John; Tian, Fenglei; Dixson, Ronald

2007-03-01

CD-AFMs (critical dimension atomic force microscopes) are instruments with servo-control of the tip in more than one direction. With appropriately "boot-shaped" or flared tips, such instruments can image vertical or even undercut features. As with any AFM, the image is a dilation of the sample shape with the tip shape. Accurate extraction of the CD requires a correction for the tip effect. Analytical methods to correct images for the tip shape have been available for some time for the traditional (vertical feedback only) AFMs, but were until recently unavailable for instruments with multi-dimensional feedback. Dahlen et al. [J. Vac. Sci. Technol. B23, pp. 2297-2303, (2005)] recently introduced a swept-volume approach, implemented for 2-dimensional (2D) feedback. It permits image simulation and sample reconstruction, techniques previously developed for the traditional instruments, to be extended for the newer tools. We have introduced [X. Qian and J. S. Villarrubia, Ultramicroscopy, in press] an alternative dexel-based method, that does the same in either 2D or 3D. This paper describes the application of this method to sample shapes of interest in semiconductor manufacturing. When the tip shape is known (e.g., by prior measurement using a tip characterizer) a 3D sample surface may be reconstructed from its 3D image. Basing the CD measurement upon such a reconstruction is shown here to remove some measurement artifacts that are not removed (or are incompletely removed) by the existing measurement procedures.

Positron probes of the Ge(1 0 0) surface: The effects of surface reconstructions and electron positron correlations on positron trapping and annihilation characteristics

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Jung, E.; Weiss, A. H.

2007-08-01

Positron annihilation induced Auger electron spectroscopy (PAES) has been applied to study the Ge(1 0 0) surface. The high-resolution PAES spectrum from the Ge(1 0 0) surface displays several strong Auger peaks corresponding to M4,5N1N2,3, M2,3M4,5M4,5, M2,3M4,5V and M1M4,5M4,5 Auger transitions. The integrated peak intensities of Auger transitions are used to obtain experimental annihilation probabilities for the Ge 3d and 3p core level electrons. These experimental results are analyzed by performing calculations of positron surface states and annihilation characteristics of surface trapped positrons with relevant Ge core-level electrons for the non-reconstructed and reconstructed Ge(1 0 0)-p(2 × 1), Ge(1 0 0)-p(2 × 2) and Ge(1 0 0)-c(4 × 2) surfaces. It is found that the positron surface state wave function extends into the Ge lattice in the regions where atoms are displaced from their ideal terminated positions due to reconstructions. Estimates of the positron binding energy and the positron annihilation characteristics reveal their sensitivity to the specific atomic structure of the topmost layers of Ge(1 0 0). A comparison with PAES data reveals an agreement with theoretical core annihilation probabilities for the Auger transitions considered.

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

Miao, Jianwei; Ercius, Peter; Billinge, S. J. L.

Crystallography has been fundamental to the development of many fields of science over the last century. However, much of our modern science and technology relies on materials with defects and disorders, and their three-dimensional (3D) atomic structures are not accessible to crystallography. One method capable of addressing this major challenge is atomic electron tomography. By combining advanced electron microscopes and detectors with powerful data analysis and tomographic reconstruction algorithms, it is now possible to determine the 3D atomic structure of crystal defects such as grain boundaries, stacking faults, dislocations, and point defects, as well as to precisely localize the 3Dmore » coordinates of individual atoms in materials without assuming crystallinity. In this work, we review the recent advances and the interdisciplinary science enabled by this methodology. We also outline further research needed for atomic electron tomography to address long-standing unresolved problems in the physical sciences.« less

Real-Space Formation and Dissipation Dynamics of Hexagonal Reconstruction on Au(100) in Aqueous Media as Explored by Potentiodynamic Scanning Tunneling Microscopy

DTIC Science & Technology

1993-04-01

the clusters appear to form monoatomic layers on the (i x 1) substrate. This assertion, derived from the apparent z-corrugation in the STH images, is...top-layer lattice and thereby displacing one of the nearest-neighbor atoms. A related , although more concerted, atomic motion can also provide a viable...microscopic rate-limiting step(s) for this process are not necessarily related straightforwardly to the free- energy difference for the overall macroscopic

Reconstruction of Laser-Induced Surface Topography from Electron Backscatter Diffraction Patterns.

PubMed

Callahan, Patrick G; Echlin, McLean P; Pollock, Tresa M; De Graef, Marc

2017-08-01

We demonstrate that the surface topography of a sample can be reconstructed from electron backscatter diffraction (EBSD) patterns collected with a commercial EBSD system. This technique combines the location of the maximum background intensity with a correction from Monte Carlo simulations to determine the local surface normals at each point in an EBSD scan. A surface height map is then reconstructed from the local surface normals. In this study, a Ni sample was machined with a femtosecond laser, which causes the formation of a laser-induced periodic surface structure (LIPSS). The topography of the LIPSS was analyzed using atomic force microscopy (AFM) and reconstructions from EBSD patterns collected at 5 and 20 kV. The LIPSS consisted of a combination of low frequency waviness due to curtaining and high frequency ridges. The morphology of the reconstructed low frequency waviness and high frequency ridges matched the AFM data. The reconstruction technique does not require any modification to existing EBSD systems and so can be particularly useful for measuring topography and its evolution during in situ experiments.

Correlation between surface reconstruction and polytypism in InAs nanowire selective area epitaxy

NASA Astrophysics Data System (ADS)

Liu, Ziyang; Merckling, Clement; Rooyackers, Rita; Richard, Olivier; Bender, Hugo; Mols, Yves; Vila, María; Rubio-Zuazo, Juan; Castro, Germán R.; Collaert, Nadine; Thean, Aaron; Vandervorst, Wilfried; Heyns, Marc

2017-12-01

The mechanism of widely observed intermixing of wurtzite and zinc-blende crystal structures in InAs nanowire (NW) grown by selective area epitaxy (SAE) is studied. We demonstrate that the crystal structure in InAs NW grown by SAE can be controlled using basic growth parameters, and wurtzitelike InAs NWs are achieved. We link the polytypic InAs NWs SAE to the reconstruction of the growth front (111)B surface. Surface reconstruction study of InAs (111) substrate and the following homoepitaxy experiment suggest that (111) planar defect nucleation is related to the (1 × 1) reconstruction of InAs (111)B surface. In order to reveal it more clearly, a model is presented to correlate growth temperature and arsenic partial pressure with InAs NW crystal structure. This model considers the transition between (1 × 1) and (2 × 2) surface reconstructions in the frame of adatom atoms adsorption/desorption, and the polytypism is thus linked to reconstruction quantitatively. The experimental data fit well with the model, which highly suggests that surface reconstruction plays an important role in the polytypism phenomenon in InAs NWs SAE.

Impact of local electrostatic field rearrangement on field ionization

NASA Astrophysics Data System (ADS)

Katnagallu, Shyam; Dagan, Michal; Parviainen, Stefan; Nematollahi, Ali; Grabowski, Blazej; Bagot, Paul A. J.; Rolland, Nicolas; Neugebauer, Jörg; Raabe, Dierk; Vurpillot, François; Moody, Michael P.; Gault, Baptiste

2018-03-01

Field ion microscopy allows for direct imaging of surfaces with true atomic resolution. The high charge density distribution on the surface generates an intense electric field that can induce ionization of gas atoms. We investigate the dynamic nature of the charge and the consequent electrostatic field redistribution following the departure of atoms initially constituting the surface in the form of an ion, a process known as field evaporation. We report on a new algorithm for image processing and tracking of individual atoms on the specimen surface enabling quantitative assessment of shifts in the imaged atomic positions. By combining experimental investigations with molecular dynamics simulations, which include the full electric charge, we confirm that change is directly associated with the rearrangement of the electrostatic field that modifies the imaging gas ionization zone. We derive important considerations for future developments of data reconstruction in 3D field ion microscopy, in particular for precise quantification of lattice strains and characterization of crystalline defects at the atomic scale.

Accelerating atomic structure search with cluster regularization

NASA Astrophysics Data System (ADS)

Sørensen, K. H.; Jørgensen, M. S.; Bruix, A.; Hammer, B.

2018-06-01

We present a method for accelerating the global structure optimization of atomic compounds. The method is demonstrated to speed up the finding of the anatase TiO2(001)-(1 × 4) surface reconstruction within a density functional tight-binding theory framework using an evolutionary algorithm. As a key element of the method, we use unsupervised machine learning techniques to categorize atoms present in a diverse set of partially disordered surface structures into clusters of atoms having similar local atomic environments. Analysis of more than 1000 different structures shows that the total energy of the structures correlates with the summed distances of the atomic environments to their respective cluster centers in feature space, where the sum runs over all atoms in each structure. Our method is formulated as a gradient based minimization of this summed cluster distance for a given structure and alternates with a standard gradient based energy minimization. While the latter minimization ensures local relaxation within a given energy basin, the former enables escapes from meta-stable basins and hence increases the overall performance of the global optimization.

Energetics of edge oxidization of graphene nanoribbons

NASA Astrophysics Data System (ADS)

Yasuma, Airi; Yamanaka, Ayaka; Okada, Susumu

2018-06-01

On the basis of the density functional theory, we studied the geometries and energetics of O atoms adsorbed on graphene edges for simulating the initial stage of the edge oxidization of graphene. Our calculations showed that oxygen atoms are preferentially adsorbed onto the graphene edges with the zigzag portion, resulting in a large adsorption energy of about 5 eV. On the other hand, the edges with armchair shape are rarely oxidized, or the oxidization causes substantial structural reconstructions, because of the stable covalent bond at the armchair edge with the triple bond nature. Furthermore, the energetics sensitively depends on the edge angles owing to the inhomogeneity of the charge density at the edge atomic sites.

Resolving the morphology of niobium carbonitride nano-precipitates in steel using atom probe tomography.

PubMed

Breen, Andrew J; Xie, Kelvin Y; Moody, Michael P; Gault, Baptiste; Yen, Hung-Wei; Wong, Christopher C; Cairney, Julie M; Ringer, Simon P

2014-08-01

Atom probe is a powerful technique for studying the composition of nano-precipitates, but their morphology within the reconstructed data is distorted due to the so-called local magnification effect. A new technique has been developed to mitigate this limitation by characterizing the distribution of the surrounding matrix atoms, rather than those contained within the nano-precipitates themselves. A comprehensive chemical analysis enables further information on size and chemistry to be obtained. The method enables new insight into the morphology and chemistry of niobium carbonitride nano-precipitates within ferrite for a series of Nb-microalloyed ultra-thin cast strip steels. The results are supported by complementary high-resolution transmission electron microscopy.

Impact of Dynamic Specimen Shape Evolution on the Atom Probe Tomography Results of Doped Epitaxial Oxide Multilayers: Comparison of Experiment and Simulation

DOE PAGES

Madaan, Nitesh; Bao, Jie; Nandasiri, Manjula I.; ...

2015-08-31

The experimental atom probe tomography results from two different specimen orientations (top-down and side-ways) of a high oxygen ion conducting Samaria-doped-ceria/Scandia-stabilized-zirconia multilayer thin film solid oxide fuel cell electrolyte was correlated with level-set method based field evaporation simulations for the same specimen orientations. This experiment-theory correlation explains the dynamic specimen shape evolution and ion trajectory aberrations that can induce density artifacts in final reconstruction leading to inaccurate estimation of interfacial intermixing. This study highlights the need and importance of correlating experimental results with field evaporation simulations when using atom probe tomography for studying oxide heterostructure interfaces.

Electronic and mechanical properties of graphene-germanium interfaces grown by chemical vapor deposition

DOE PAGES

Kiraly, Brian T.; Jacobberger, Robert M.; Mannix, Andrew J.; ...

2015-10-27

Epitaxially oriented wafer-scale graphene grown directly on semiconducting Ge substrates is of high interest for both fundamental science and electronic device applications. To date, however, this material system remains relatively unexplored structurally and electronically, particularly at the atomic scale. To further understand the nature of the interface between graphene and Ge, we utilize ultrahigh vacuum scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) along with Raman and X-ray photoelectron spectroscopy to probe interfacial atomic structure and chemistry. STS reveals significant differences in electronic interactions between graphene and Ge(110)/Ge(111), which is consistent with a model of stronger interaction on Ge(110)more » leading to epitaxial growth. Raman spectra indicate that the graphene is considerably strained after growth, with more point-to-point variation on Ge(111). Furthermore, this native strain influences the atomic structure of the interface by inducing metastable and previously unobserved Ge surface reconstructions following annealing. These nonequilibrium reconstructions cover >90% of the surface and, in turn, modify both the electronic and mechanical properties of the graphene overlayer. Finally, graphene on Ge(001) represents the extreme strain case, where graphene drives the reorganization of the Ge surface into [107] facets. From this study, it is clear that the interaction between graphene and the underlying Ge is not only dependent on the substrate crystallographic orientation, but is also tunable and strongly related to the atomic reconfiguration of the graphene–Ge interface.« less

Atomic Mechanism of Hybridization-Dependent Surface Reconstruction with Tailored Functionality in Hexagonal Multiferroics.

PubMed

Deng, Shiqing; Cheng, Shaobo; Xu, Changsong; Ge, Binghui; Sun, Xuefeng; Yu, Rong; Duan, Wenhui; Zhu, Jing

2017-08-16

The broken symmetry along with anomalous defect structures and charging conditions at multiferroics surface can alter both crystal structures and electronic configurations, bringing in emergent physical properties. Extraordinary surface states are induced into original mutually coupled order parameters in such strongly correlated oxides, which flourish in diverse properties but remain less explored. Here, we report the peculiar surface ferroelectric states and reconfigurable functionalities driven by the relaxation of surface and consequent changes in O 2p and Y 4d orbital (p-d) hybridization within a representative hexagonal multiferroics, YMnO 3 . An unprecedented surface reconstruction is achieved by tailored p-d hybridization coupling with in-plane oxygen vacancies, which is atomically revealed on the basis of the advantages of state-of-the-art aberration-corrected (scanning) transmission electron microscopy. Further ab initio density functional theory calculations verify the key roles of in-plane oxygen vacancies in modulating polarization properties and electronic structure, which should be regarded as the atomic multiferroic element. This surface configuration is found to induce tunable functionalities, such as surface ferromagnetism and conductivity. Meanwhile, the controversial origin of improper ferroelectricity that is unexpectedly free from critical size has also been atomically unraveled. Our findings provide new insights into the design and implementation of surface chemistry devices by simply controlling the oxygen stoichiometry, greatly advance our understandings of surface science in strongly correlated oxides, and enable exciting innovations and new technological functionality paradigms.

Structure and Formation Mechanism of Black TiO 2 Nanoparticles

DOE PAGES

Tian, Mengkun; Mahjouri-Samani, Masoud; Eres, Gyula; ...

2015-10-27

The remarkable properties of black TiO 2 are due to its disordered surface shell surrounding a crystalline core. However, the chemical composition and the atomic and electronic structure of the disordered shell and its relationship to the core remain poorly understood. Using advanced transmission electron microscopy methods, we show that the outermost layer of black TiO 2 nanoparticles consists of a disordered Ti 2O 3 shell. The measurements show a transition region that connects the disordered Ti 2O 3 shell to the perfect rutile core consisting first of four to five monolayers of defective rutile, containing clearly visible Ti interstitialmore » atoms, followed by an ordered reconstruction layer of Ti interstitial atoms. Our data suggest that this reconstructed layer presents a template on which the disordered Ti 2O 3 layers form by interstitial diffusion of Ti ions. In contrast to recent reports that attribute TiO 2 band-gap narrowing to the synergistic action of oxygen vacancies and surface disorder of nonspecific origin, our results point to Ti 2O 3, which is a narrow-band-gap semiconductor. In conclusion, as a stoichiometric compound of the lower oxidation state Ti 3+ it is expected to be a more robust atomic structure than oxygen-deficient TiO 2 for preserving and stabilizing Ti 3+ surface species that are the key to the enhanced photocatalytic activity of black TiO 2.« less

Topographic profiling and refractive-index analysis by use of differential interference contrast with bright-field intensity and atomic force imaging.

PubMed

Axelrod, Noel; Radko, Anna; Lewis, Aaron; Ben-Yosef, Nissim

2004-04-10

A methodology is described for phase restoration of an object function from differential interference contrast (DIC) images. The methodology involves collecting a set of DIC images in the same plane with different bias retardation between the two illuminating light components produced by a Wollaston prism. These images, together with one conventional bright-field image, allows for reduction of the phase deconvolution restoration problem from a highly complex nonlinear mathematical formulation to a set of linear equations that can be applied to resolve the phase for images with a relatively large number of pixels. Additionally, under certain conditions, an on-line atomic force imaging system that does not interfere with the standard DIC illumination modes resolves uncertainties in large topographical variations that generally lead to a basic problem in DIC imaging, i.e., phase unwrapping. Furthermore, the availability of confocal detection allows for a three-dimensional reconstruction with high accuracy of the refractive-index measurement of the object that is to be imaged. This has been applied to reconstruction of the refractive index of an arrayed waveguide in a region in which a defect in the sample is present. The results of this paper highlight the synergism of far-field microscopies integrated with scanned probe microscopies and restoration algorithms for phase reconstruction.

Abstract ID: 176 Geant4 implementation of inter-atomic interference effect in small-angle coherent X-ray scattering for materials of medical interest.

PubMed

Paternò, Gianfranco; Cardarelli, Paolo; Contillo, Adriano; Gambaccini, Mauro; Taibi, Angelo

2018-01-01

Advanced applications of digital mammography such as dual-energy and tomosynthesis require multiple exposures and thus deliver higher dose compared to standard mammograms. A straightforward manner to reduce patient dose without affecting image quality would be removal of the anti-scatter grid, provided that the involved reconstruction algorithms are able to take the scatter figure into account [1]. Monte Carlo simulations are very well suited for the calculation of X-ray scatter distribution and can be used to integrate such information within the reconstruction software. Geant4 is an open source C++ particle tracking code widely used in several physical fields, including medical physics [2,3]. However, the coherent scattering cross section used by the standard Geant4 code does not take into account the influence of molecular interference. According to the independent atomic scattering approximation (the so-called free-atom model), coherent radiation is indistinguishable from primary radiation because its angular distribution is peaked in the forward direction. Since interference effects occur between x-rays scattered by neighbouring atoms in matter, it was shown experimentally that the scatter distribution is affected by the molecular structure of the target, even in amorphous materials. The most important consequence is that the coherent scatter distribution is not peaked in the forward direction, and the position of the maximum is strongly material-dependent [4]. In this contribution, we present the implementation of a method to take into account inter-atomic interference in small-angle coherent scattering in Geant4, including a dedicated data set of suitable molecular form factor values for several materials of clinical interest. Furthermore, we present scatter images of simple geometric phantoms in which the Rayleigh contribution is rigorously evaluated. Copyright © 2017.

Sensor-Based Vibration Signal Feature Extraction Using an Improved Composite Dictionary Matching Pursuit Algorithm

PubMed Central

Cui, Lingli; Wu, Na; Wang, Wenjing; Kang, Chenhui

2014-01-01

This paper presents a new method for a composite dictionary matching pursuit algorithm, which is applied to vibration sensor signal feature extraction and fault diagnosis of a gearbox. Three advantages are highlighted in the new method. First, the composite dictionary in the algorithm has been changed from multi-atom matching to single-atom matching. Compared to non-composite dictionary single-atom matching, the original composite dictionary multi-atom matching pursuit (CD-MaMP) algorithm can achieve noise reduction in the reconstruction stage, but it cannot dramatically reduce the computational cost and improve the efficiency in the decomposition stage. Therefore, the optimized composite dictionary single-atom matching algorithm (CD-SaMP) is proposed. Second, the termination condition of iteration based on the attenuation coefficient is put forward to improve the sparsity and efficiency of the algorithm, which adjusts the parameters of the termination condition constantly in the process of decomposition to avoid noise. Third, composite dictionaries are enriched with the modulation dictionary, which is one of the important structural characteristics of gear fault signals. Meanwhile, the termination condition of iteration settings, sub-feature dictionary selections and operation efficiency between CD-MaMP and CD-SaMP are discussed, aiming at gear simulation vibration signals with noise. The simulation sensor-based vibration signal results show that the termination condition of iteration based on the attenuation coefficient enhances decomposition sparsity greatly and achieves a good effect of noise reduction. Furthermore, the modulation dictionary achieves a better matching effect compared to the Fourier dictionary, and CD-SaMP has a great advantage of sparsity and efficiency compared with the CD-MaMP. The sensor-based vibration signals measured from practical engineering gearbox analyses have further shown that the CD-SaMP decomposition and reconstruction algorithm is feasible and effective. PMID:25207870

Sensor-based vibration signal feature extraction using an improved composite dictionary matching pursuit algorithm.

PubMed

Cui, Lingli; Wu, Na; Wang, Wenjing; Kang, Chenhui

2014-09-09

This paper presents a new method for a composite dictionary matching pursuit algorithm, which is applied to vibration sensor signal feature extraction and fault diagnosis of a gearbox. Three advantages are highlighted in the new method. First, the composite dictionary in the algorithm has been changed from multi-atom matching to single-atom matching. Compared to non-composite dictionary single-atom matching, the original composite dictionary multi-atom matching pursuit (CD-MaMP) algorithm can achieve noise reduction in the reconstruction stage, but it cannot dramatically reduce the computational cost and improve the efficiency in the decomposition stage. Therefore, the optimized composite dictionary single-atom matching algorithm (CD-SaMP) is proposed. Second, the termination condition of iteration based on the attenuation coefficient is put forward to improve the sparsity and efficiency of the algorithm, which adjusts the parameters of the termination condition constantly in the process of decomposition to avoid noise. Third, composite dictionaries are enriched with the modulation dictionary, which is one of the important structural characteristics of gear fault signals. Meanwhile, the termination condition of iteration settings, sub-feature dictionary selections and operation efficiency between CD-MaMP and CD-SaMP are discussed, aiming at gear simulation vibration signals with noise. The simulation sensor-based vibration signal results show that the termination condition of iteration based on the attenuation coefficient enhances decomposition sparsity greatly and achieves a good effect of noise reduction. Furthermore, the modulation dictionary achieves a better matching effect compared to the Fourier dictionary, and CD-SaMP has a great advantage of sparsity and efficiency compared with the CD-MaMP. The sensor-based vibration signals measured from practical engineering gearbox analyses have further shown that the CD-SaMP decomposition and reconstruction algorithm is feasible and effective.

Te Monolayer-Driven Spontaneous van der Waals Epitaxy of Two-dimensional Pnictogen Chalcogenide Film on Sapphire.

PubMed

Hwang, Jae-Yeol; Kim, Young-Min; Lee, Kyu Hyoung; Ohta, Hiromichi; Kim, Sung Wng

2017-10-11

Demands on high-quality layer structured two-dimensional (2D) thin films such as pnictogen chalcogenides and transition metal dichalcogenides are growing due to the findings of exotic physical properties and potentials for device applications. However, the difficulties in controlling epitaxial growth and the unclear understanding of van der Waals epitaxy (vdWE) for a 2D chalcogenide film on a three-dimensional (3D) substrate have been major obstacles for the further advances of 2D materials. Here, we exploit the spontaneous vdWE of a high-quality 2D chalcogenide (Bi 0.5 Sb 1.5 Te 3 ) film by the chalcogen-driven surface reconstruction of a conventional 3D sapphire substrate. It is verified that the in situ formation of a pseudomorphic Te atomic monolayer on the surface of sapphire, which results in a dangling bond-free surface, allows the spontaneous vdWE of 2D chalcogenide film. Since this route uses the natural surface reconstruction of sapphire with chalcogen under vacuum condition, it can be scalable and easily utilized for the developments of various 2D chalcogenide vdWE films through conventional thin-film fabrication technologies.

Progress in electron- and ion-interferometry

NASA Astrophysics Data System (ADS)

Hasselbach, Franz

2010-01-01

In the 1970s the prominent goal was to overcome the limitations of electron microscopy caused by aberrations of electron lenses by the development of electron holography. In the meantime this problem has been solved, not only in the roundabout way of holography, but directly by correcting the aberrations of the lenses. Nevertheless, many quantitative electron microscopical measurement methods—e.g. mapping and visualization of electric and magnetic fields—were developed within the context of holography and have become fields of their own. In this review we focus on less popular electron interferometric experiments which complement the field of electron holography. The paper is organized as follows. After a short sketch of the development of electron biprism interferometry after its invention in 1954, recent advances in technology are discussed that made electron biprism interferometry an indispensable tool for solving fundamental and applied questions in physics: the development and preparation of conventional and single-atom field electron and field ion sources with their extraordinary properties. Single- and few-atom sources exhibit spectacular features: their brightness at 100 keV exceeds that of conventional field emitters by two orders in magnitude. Due to the extremely small aberrations of diode field emitter extraction optics, the virtual source size of single-atom tips is on the order of 0.2 nm. As a consequence it illuminates an area 7 cm in diameter on a screen at a distance of 15 cm coherently. Projection electron micrographs taken with these sources reach spatial resolutions of atomic dimensions and in-line holograms are—due to the absence of lenses with their aberrations—not blurred. Their reconstruction is straightforward. By addition of a carbon nanotube biprism into the beam path of a projection microscope a lensless electron interferometer has been realized. In extremely ultrahigh vacuum systems flicker noise is practically absent in the new sources. In the context of holography, methods have been developed to record holograms without modulation of the biprism fringes by waves diffracted at the edges of the biprism filament. This simplifies the reconstruction of holograms and the evaluation of interferograms (taken, e.g. to extract a spectrum by Fourier analysis of the fringe system) significantly. A major section is devoted to the influence of electromagnetic and gravito-inertial potentials and fields on the quantum mechanical phase of matter waves: the Aharonov-Bohm effect, the inertial Aharonov-Bohm effect and its realization, the Sagnac effect and Sagnac experiments with atoms, superfluid helium, Bose-Einstein condensates, electrons and ions and their potential as rotation sensors are discussed. Möllenstedt and Wohland discovered in a crossed beam analyzer (Wien filter) an optical element for charged particles that shifts wave packets longitudinally that transverse a Wien filter on laterally separated paths. This new optical element rendered it possible to measure coherence lengths and the spectrum of charged particle waves by visibility- and Fourier-spectroscopy, to perform a 'Welcher Weg' experiment, to re-establish seemingly lost longitudinal coherence in an interferometer for charged particles and to realize a decoherence free quantum eraser. A precision test of decoherence according to a proposal from Anglin and Zurek and biprism interferences with helium atoms close the section on first-order coherence experiments. The topics of the last section are Hanbury Brown-Twiss correlations and an antibuching experiment of free electrons.

3D structure of individual nanocrystals in solution by electron microscopy

NASA Astrophysics Data System (ADS)

Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

2015-07-01

Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

Oxidation of GaSb(100) and its control studied by scanning tunneling microscopy and spectroscopy

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

Mäkelä, J., E-mail: jaakko.m.makela@utu.fi, E-mail: pekka.laukkanen@utu.fi, E-mail: rmwallace@utdallas.edu; Tuominen, M.; Yasir, M.

2015-08-10

Atomic-scale knowledge and control of oxidation of GaSb(100), which is a potential interface for energy-efficient transistors, are still incomplete, largely due to an amorphous structure of GaSb(100) oxides. We elucidate these issues with scanning-tunneling microscopy and spectroscopy. The unveiled oxidation-induced building blocks cause defect states above Fermi level around the conduction-band edge. By interconnecting the results to previous photoemission findings, we suggest that the oxidation starts with substituting second-layer Sb sites by oxygen. Adding small amount of indium on GaSb(100), resulting in a (4 × 2)-In reconstruction, before oxidation produces a previously unreported, crystalline oxidized layer of (1 × 3)-O free of gap states.

Controlling the surface termination of NdGaO3 (110): the role of the gas atmosphere.

PubMed

Cavallaro, Andrea; Harrington, George F; Skinner, Stephen J; Kilner, John A

2014-07-07

In this work the effect of gas atmosphere on the surface termination reconstruction of single crystal NdGaO3 (110) (NGO) during thermal annealing was analyzed. Using Low Energy Ion Scattering (LEIS) it has been possible to study the chemical composition of the first atomic layer of treated NGO single crystal samples. NGO has been analyzed both as-received and after a specific thermal treatment at 1000 °C under different gas fluxes (argon, nitrogen, static air, synthetic air, nitrogen plus 5% hydrogen and wet synthetic air respectively). Thermal annealing of perovskite single crystals, as already reported in the literature, is used to obtain a fully A-cation surface termination. Nevertheless the effect of the gas-atmosphere on this process has not been previously reported. By the use of sequential low energy Ar(+) sputtering combined with the primary ion LEIS analysis, the reconstruction of the outermost atomic layers has allowed the clarification of the mechanism of NGO neodymium surface enrichment. It is proposed that the gallium at the surface is submitted to a reduction/evaporation mechanism caused by low oxygen partial pressure and/or high water pressure in the vector gas. Below the first surface atomic layers of an as-received NGO single-crystal a gallium-rich phase has also been observed.

Revealing the correlation between real-space structure and chiral magnetic order at the atomic scale

NASA Astrophysics Data System (ADS)

Hauptmann, Nadine; Dupé, Melanie; Hung, Tzu-Chao; Lemmens, Alexander K.; Wegner, Daniel; Dupé, Bertrand; Khajetoorians, Alexander A.

2018-03-01

We image simultaneously the geometric, the electronic, and the magnetic structures of a buckled iron bilayer film that exhibits chiral magnetic order. We achieve this by combining spin-polarized scanning tunneling microscopy and magnetic exchange force microscopy (SPEX) to independently characterize the geometric as well as the electronic and magnetic structures of nonflat surfaces. This new SPEX imaging technique reveals the geometric height corrugation of the reconstruction lines resulting from strong strain relaxation in the bilayer, enabling the decomposition of the real-space from the electronic structure at the atomic level and the correlation with the resultant spin-spiral ground state. By additionally utilizing adatom manipulation, we reveal the chiral magnetic ground state of portions of the unit cell that were not previously imaged with spin-polarized scanning tunneling microscopy alone. Using density functional theory, we investigate the structural and electronic properties of the reconstructed bilayer and identify the favorable stoichiometry regime in agreement with our experimental result.

Reconstructing Ion Spectra from Low-Altitude ENAs: Moderate to Large Storms.

NASA Astrophysics Data System (ADS)

LLera, K.; Goldstein, J.; McComas, D. J.; Valek, P. W.

2015-12-01

Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) Energetic neutral atom (ENA) imagers regularly observe Low-altitude Emission (LAE) intensifications during geomagnetic storm intervals. Since LAEs are produced by the interaction between ions and the near-Earth exosphere (altitudes ~200-800 km), they are a global signature of how the ring current decays in response to solar wind conditions. In this "optically thick" region, an ENA readily becomes reionized, and an ion is readily neutralized. Therefore, emerging ENAs that contribute to the LAE signal (detectable several RE away) have undergone multiple charge exchange and electron stripping interactions. Accounting for the ~36 eV energy loss per interaction, we developed a model to quantify the total energy lost by emergent LAEs. The analytical tool is applied to an ensemble of moderate to large storms (including the recent 17 March and 23 June storms in 2015) to reconstruct the parent ion spectra from TWINS ENA images. We examine the ion spectra energy characteristics among the various storm events.

Enhanced Resolution Maps of Energetic Neutral Atoms from IBEX

NASA Astrophysics Data System (ADS)

Teodoro, L. A.; Elphic, R. C.; Janzen, P.; Reisenfeld, D.; Wilson, J. T.

2017-12-01

The discovery by the Interstellar Boundary Explorer (IBEX) of a "Ribbon" in the measurements of Energetic Neutral Particles (ENA) was a major surprise that lead to the re-thinking of the Physics underpinning the heliosphere-intergalactic medium boundary dynamics. Several physical models have been proposed and tested in their ability to mimic the IBEX observations. Some of the ENA IBEX's include the following features: 1) The presence of fine structure within the ribbon suggests that the physical properties of it exhibit small-scale spacial structure and possibly rapid small-scale variations. 2) The ribbon is a fairly narrow feature at low energies and broadens with increasing energy;The IBEX detectors were designed to maximize count rate by incorporating wide angular and broad energy acceptance. Thus far, the existing mapping software used by the IBEX Science Operation Center has not been design with the "Ribbon" ( 20o wide) in mind: the current generation of maps are binned in 6o longitude pixels by 6o latitude pixels (so the pixels are all of the same size in angle and are quite "blocky"). Furthermore, the instrumental point spread function has not been deconvolved, making any potential narrow features broader than they are. An improvement in the spatial resolution of the IBEX maps would foster a better understanding of the Ribbon and its substructure, and thus reply to some of the basic and profound questions related to its origin, the nature of the outer boundaries of the our solar system and the surrounding interstellar Galactic medium.Here we report on the application of the Bayesian image reconstruction algorithm "Speedy Pixons" to the ENA data with the aim to sharpen the ENA IBEX maps. A preliminary application allow us to conclude that: The peaks in the count rate do appear to be more enhanced in the reconstruction; The reconstruction is clearly denoised; The "Ribbon" is better defined in the reconstruction. We are currently studying the implications of our preliminary results in the current generation of models. Potentially, our results can also be used in the design and planning of future missions whose aim is to produce higher resolution maps of the interstellar medium (e.g. IMAP).

Determination of scattering structures from spatial coherence measurements.

PubMed

Zarubin, A M

1996-03-01

A new method of structure determination and microscopic imaging with short-wavelength radiations (charged particles, X-rays, neutrons), based on measurements of the modulus and the phase of the degree of spatial coherence of the scattered radiation, is developed. The underlying principle of the method--transfer of structural information about the scattering potential via spatial coherence of the secondary (scattering) source of radiation formed by this potential--is expressed by the generalization of the van Cittert-Zernike theorem to wave and particle scattering [A.M. Zarubin, Opt. Commun. 100 (1993) 491; Opt. Commun. 102 (1993) 543]. Shearing interferometric techniques are proposed for implementing the above measurements; the limits of spatial resolution attainable by reconstruction of the absolute square of a 3D scattering potential and its 2D projections from the measurements are analyzed. It is shown theoretically that 3D imaging with atomic resolution can be realized in a "synthetic aperture" electron or ion microscope and that a 3D resolution of about 6 nm can be obtained with a "synthetic aperture" X-ray microscope. A proof-of-principle optical experiment is presented.

Planar regions of GaAs (001) prepared by Ga droplet motion

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

Zheng, Changxi, E-mail: changxi.zheng@monash.edu; Tang, Wen-Xin; Jesson, David E., E-mail: jessonDE@cardiff.ac.uk

2016-07-15

The authors describe a simple method for obtaining planar regions of GaAs (001) suitable for surface science studies. The technique, which requires no buffer layer growth, atomic hydrogen source, or the introduction of As flux, employs controllable Ga droplet motion to create planar trail regions during Langmuir evaporation. Low-energy electron microscopy/diffraction techniques are applied to monitor the droplet motion and characterize the morphology and the surface reconstruction. It is found that the planar regions exhibit atomic flatness at the level of a high-quality buffer layer.

Three dimensional atom probe imaging of GaAsSb quantum rings.

PubMed

Beltrán, A M; Marquis, E A; Taboada, A G; Ripalda, J M; García, J M; Molina, S I

2011-07-01

Unambiguous evidence of ring-shaped self-assembled GaSb nanostructures grown by molecular beam epitaxy is presented on the basis of atom-probe tomography reconstructions and dark field transmission electron microscopy imaging. The GaAs capping process causes a strong segregation of Sb out of the center of GaSb quantum dots, leading to the self-assembled GaAs(x)Sb(1-x) quantum rings of 20-30 nm in diameter with x ∼ 0.33. Copyright © 2011 Elsevier B.V. All rights reserved.

Measuring qutrit-qutrit entanglement of orbital angular momentum states of an atomic ensemble and a photon.

PubMed

Inoue, R; Yonehara, T; Miyamoto, Y; Koashi, M; Kozuma, M

2009-09-11

Three-dimensional entanglement of orbital angular momentum states of an atomic qutrit and a single photon qutrit has been observed. Their full state was reconstructed using quantum state tomography. The fidelity to the maximally entangled state of Schmidt rank 3 exceeds the threshold 2/3. This result confirms that the density matrix cannot be decomposed into an ensemble of pure states of Schmidt rank 1 or 2. That is, the Schmidt number of the density matrix must be equal to or greater than 3.

Reconstruction of magnetic resonance imaging by three-dimensional dual-dictionary learning.

PubMed

Song, Ying; Zhu, Zhen; Lu, Yang; Liu, Qiegen; Zhao, Jun

2014-03-01

To improve the magnetic resonance imaging (MRI) data acquisition speed while maintaining the reconstruction quality, a novel method is proposed for multislice MRI reconstruction from undersampled k-space data based on compressed-sensing theory using dictionary learning. There are two aspects to improve the reconstruction quality. One is that spatial correlation among slices is used by extending the atoms in dictionary learning from patches to blocks. The other is that the dictionary-learning scheme is used at two resolution levels; i.e., a low-resolution dictionary is used for sparse coding and a high-resolution dictionary is used for image updating. Numerical experiments are carried out on in vivo 3D MR images of brains and abdomens with a variety of undersampling schemes and ratios. The proposed method (dual-DLMRI) achieves better reconstruction quality than conventional reconstruction methods, with the peak signal-to-noise ratio being 7 dB higher. The advantages of the dual dictionaries are obvious compared with the single dictionary. Parameter variations ranging from 50% to 200% only bias the image quality within 15% in terms of the peak signal-to-noise ratio. Dual-DLMRI effectively uses the a priori information in the dual-dictionary scheme and provides dramatically improved reconstruction quality. Copyright © 2013 Wiley Periodicals, Inc.

New constraints and discovery potential of sub-GeV dark matter with xenon detectors

NASA Astrophysics Data System (ADS)

McCabe, Christopher

2017-08-01

Existing xenon dark matter (DM) direct detection experiments can probe the DM-nucleon interaction of DM with a sub-GeV mass through a search for photon emission from the recoiling xenon atom. We show that LUX's constraints on sub-GeV DM, which utilize the scintillation (S1) and ionization (S2) signals, are approximately 3 orders of magnitude more stringent than previous xenon constraints in this mass range, derived from the XENON10 and XENON100 S2-only searches. The new LUX constraints provide the most stringent direct detection constraints for DM particles with a mass below 0.5 GeV. In addition, the photon emission signal in LUX and its successor LZ maintain the discrimination between background and signal events so that an unambiguous discovery of sub-GeV DM is possible. We show that LZ has the potential to reconstruct the DM mass with ≃20 % accuracy for particles lighter than 0.5 GeV.

The structure of reconstructed chalcopyrite surfaces

NASA Astrophysics Data System (ADS)

Thinius, Sascha; Islam, Mazharul M.; Bredow, Thomas

2018-03-01

Chalcopyrite (CuFeS2) surfaces are of major interest for copper exploitation in aqueous solution, called leaching. Since leaching is a surface process knowledge of the surface structure, bonding pattern and oxidation states is important for improving the efficiency. At present such information is not available from experimental studies. Therefore a detailed computational study of chalcopyrite surfaces is performed. The structures of low-index stoichiometric chalcopyrite surfaces {hkl} h, k, l ∈ {0, 1, 2} have been studied with density functional theory (DFT) and global optimization strategies. We have applied ab initio molecular dynamics (MD) in combination with simulated annealing (SA) in order to explore possible reconstructions via a minima hopping (MH) algorithm. In almost all cases reconstruction involving substantial rearrangement has occurred accompanied by reduction of the surface energy. The analysis of the change in the coordination sphere and migration during reconstruction reveals that S-S dimers are formed on the surface. Further it was observed that metal atoms near the surface move toward the bulk forming metal alloys passivated by sulfur. The obtained surface energies of reconstructed surfaces are in the range of 0.53-0.95 J/m2.

Atomic study on the ordered structure in Al melts induced by liquid/substrate interface with Ti solute

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

Zhang, H. L.; Han, Y. F., E-mail: yfhan@sjtu.edu.cn, E-mail: bdsun@sjtu.edu.cn; Zhou, W.

2015-01-26

Atomic ordering in Al melts induced by liquid/substrate interface with Ti solute was investigated by ab initio molecular dynamics simulations and in-situ synchrotron X-ray diffraction. It is predicted that deformed nanoscale ordering Al layers with a rhombohedral-centered hexagonal structure (R3{sup ¯}m space group) instead of the intrinsic fcc structure (Fm3{sup ¯}m space group) form on substrate at temperature above Al liquids. With Al atoms stacking away from the interface, the ordering structure reaches a critical thickness, which inhibits the consecutive stacking of Al atoms on substrates. The locally stacking reconstruction induced by Ti atom relieves the accumulated elastic strain energymore » in ordered Al layers, facilitating fully heterogeneous nucleation on substrate beyond the deformed ordering Al layer around the melting point. The roles of liquid/substrate interface with Ti solute in the physical behavior of heterogeneous nucleation on substrate were discussed.« less

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

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

Atomic intercalation to measure adhesion of graphene on graphite

PubMed Central

Wang, Jun; Sorescu, Dan C.; Jeon, Seokmin; Belianinov, Alexei; Kalinin, Sergei V.; Baddorf, Arthur P.; Maksymovych, Petro

2016-01-01

The interest in mechanical properties of two-dimensional materials has emerged in light of new device concepts taking advantage of flexing, adhesion and friction. Here we demonstrate an effective method to measure adhesion of graphene atop highly ordered pyrolytic graphite, utilizing atomic-scale ‘blisters' created in the top layer by neon atom intercalates. Detailed analysis of scanning tunnelling microscopy images is used to reconstruct atomic positions and the strain map within the deformed graphene layer, and demonstrate the tip-induced subsurface translation of neon atoms. We invoke an analytical model, originally devised for graphene macroscopic deformations, to determine the graphite adhesion energy of 0.221±0.011 J m−2. This value is in excellent agreement with reported macroscopic values and our atomistic simulations. This implies mechanical properties of graphene scale down to a few-nanometre length. The simplicity of our method provides a unique opportunity to investigate the local variability of nanomechanical properties in layered materials. PMID:27796294

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

PubMed Central

Baker, Matthew L.; Hryc, Corey F.; Zhang, Qinfen; Wu, Weimin; Jakana, Joanita; Haase-Pettingell, Cameron; Afonine, Pavel V.; Adams, Paul D.; King, Jonathan A.; Jiang, Wen; Chiu, Wah

2013-01-01

High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3–5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit–subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages. PMID:23840063

Nanoscale Chemical Imaging of Zeolites Using Atom Probe Tomography.

PubMed

Weckhuysen, Bert Marc; Schmidt, Joel; Peng, Linqing; Poplawsky, Jonathan

2018-05-02

Understanding structure-composition-property relationships in zeolite-based materials is critical to engineering improved solid catalysts. However, this can be difficult to realize as even single zeolite crystals can exhibit heterogeneities spanning several orders of magnitude, with consequences for e.g. reactivity, diffusion as well as stability. Great progress has been made in characterizing these porous solids using tomographic techniques, though each method has an ultimate spatial resolution limitation. Atom Probe Tomography (APT) is the only technique so far capable of producing 3-D compositional reconstructions with sub-nm-scale resolution, and has only recently been applied to zeolite-based catalysts. Herein, we discuss the use of APT to study zeolites, including the critical aspects of sample preparation, data collection, assignment of mass spectral peaks including the predominant CO peak, the limitations of spatial resolution for the recovery of crystallographic information, and proper data analysis. All sections are illustrated with examples from recent literature, as well as previously unpublished data and analyses to demonstrate practical strategies to overcome potential pitfalls in applying APT to zeolites, thereby highlighting new insights gained from the APT method. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dalton's disputed nitric oxide experiments and the origins of his atomic theory.

PubMed

Usselman, Melvyn C; Leaist, Derek G; Watson, Katherine D

2008-01-11

In 1808 John Dalton published his first general account of chemical atomic theory, a cornerstone of modern chemistry. The theory originated in his earlier studies of the properties of atmospheric gases. In 1803 Dalton discovered that oxygen combined with either one or two volumes of nitric oxide in closed vessels over water and this pioneering observation of integral multiple proportions provided important experimental evidence for his incipient atomic ideas. Previous attempts to reproduce Dalton's experiments have been unsuccessful and some commentators have concluded the results were fraudulent. We report a successful reconstruction of Dalton's experiments and provide an analysis exonerating him of any scientific misconduct. But we conclude that Dalton, already thinking atomistically, adjusted experimental conditions to obtain the integral combining proportions.

Storing a single photon as a spin wave entangled with a flying photon in the telecommunication bandwidth

NASA Astrophysics Data System (ADS)

Zhang, Wei; Ding, Dong-Sheng; Shi, Shuai; Li, Yan; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2016-02-01

Quantum memory is an essential building block for quantum communication and scalable linear quantum computation. Storing two-color entangled photons with one photon being at the telecommunication (telecom) wavelength while the other photon is compatible with quantum memory has great advantages toward the realization of the fiber-based long-distance quantum communication with the aid of quantum repeaters. Here, we report an experimental realization of storing a photon entangled with a telecom photon in polarization as an atomic spin wave in a cold atomic ensemble, thus establishing the entanglement between the telecom-band photon and the atomic-ensemble memory in a polarization degree of freedom. The reconstructed density matrix and the violation of the Clauser-Horne-Shimony-Holt inequality clearly show the preservation of quantum entanglement during storage. Our result is very promising for establishing a long-distance quantum network based on cold atomic ensembles.

Determination of matrix composition based on solute-solute nearest-neighbor distances in atom probe tomography.

PubMed

De Geuser, F; Lefebvre, W

2011-03-01

In this study, we propose a fast automatic method providing the matrix concentration in an atom probe tomography (APT) data set containing two phases or more. The principle of this method relies on the calculation of the relative amount of isolated solute atoms (i.e., not surrounded by a similar solute atom) as a function of a distance d in the APT reconstruction. Simulated data sets have been generated to test the robustness of this new tool and demonstrate that rapid and reproducible results can be obtained without the need of any user input parameter. The method has then been successfully applied to a ternary Al-Zn-Mg alloy containing a fine dispersion of hardening precipitates. The relevance of this method for direct estimation of matrix concentration is discussed and compared with the existing methodologies. Copyright © 2010 Wiley-Liss, Inc.

Singular Atom Optics with Spinor BECs

NASA Astrophysics Data System (ADS)

Schultz, Justin T.; Hansen, Azure; Bigelow, Nicholas P.

2015-05-01

We create and study singular spin textures in pseudo-spin-1/2 BECs. A series of two-photon Raman interactions allows us to not only engineer the spinor wavefunction but also perform the equivalent of atomic polarimetry on the BEC. Adapting techniques from optical polarimetry, we can image two-dimensional maps of the atomic Stokes parameters, thereby fully reconstructing the atomic wavefunction. In a spin-1/2 system, we can represent the local spin superposition with ellipses in a Cartesian basis. The patterns that emerge from the major axes of the ellipses provide fingerprints of the singularities that enable us to classify them as lemons, stars, saddles, or spirals similar to classification schemes for singularities in singular optics, condensed matter, and liquid crystals. These techniques may facilitate the study of geometric Gouy phases in matter waves as well as provide an avenue for utilizing topological structures as quantum gates.

Direct Visualization of Local Electromagnetic Field Structures by Scanning Transmission Electron Microscopy.

PubMed

Shibata, Naoya; Findlay, Scott D; Matsumoto, Takao; Kohno, Yuji; Seki, Takehito; Sánchez-Santolino, Gabriel; Ikuhara, Yuichi

2017-07-18

The functional properties of materials and devices are critically determined by the electromagnetic field structures formed inside them, especially at nanointerface and surface regions, because such structures are strongly associated with the dynamics of electrons, holes and ions. To understand the fundamental origin of many exotic properties in modern materials and devices, it is essential to directly characterize local electromagnetic field structures at such defect regions, even down to atomic dimensions. In recent years, rapid progress in the development of high-speed area detectors for aberration-corrected scanning transmission electron microscopy (STEM) with sub-angstrom spatial resolution has opened new possibilities to directly image such electromagnetic field structures at very high-resolution. In this Account, we give an overview of our recent development of differential phase contrast (DPC) microscopy for aberration-corrected STEM and its application to many materials problems. In recent years, we have developed segmented-type STEM detectors which divide the detector plane into 16 segments and enable simultaneous imaging of 16 STEM images which are sensitive to the positions and angles of transmitted/scattered electrons on the detector plane. These detectors also have atomic-resolution imaging capability. Using these segmented-type STEM detectors, we show DPC STEM imaging to be a very powerful tool for directly imaging local electromagnetic field structures in materials and devices in real space. For example, DPC STEM can clearly visualize the local electric field variation due to the abrupt potential change across a p-n junction in a GaAs semiconductor, which cannot be observed by normal in-focus bright-field or annular type dark-field STEM imaging modes. DPC STEM is also very effective for imaging magnetic field structures in magnetic materials, such as magnetic domains and skyrmions. Moreover, real-time imaging of electromagnetic field structures can now be realized through very fast data acquisition, processing, and reconstruction algorithms. If we use DPC STEM for atomic-resolution imaging using a sub-angstrom size electron probe, it has been shown that we can directly observe the atomic electric field inside atoms within crystals and even inside single atoms, the field between the atomic nucleus and the surrounding electron cloud, which possesses information about the atomic species, local chemical bonding and charge redistribution between bonded atoms. This possibility may open an alternative way for directly visualizing atoms and nanostructures, that is, seeing atoms as an entity of electromagnetic fields that reflect the intra- and interatomic electronic structures. In this Account, the current status of aberration-corrected DPC STEM is highlighted, along with some applications in real material and device studies.

Photoemission studies of CdTe(100) and the Ag-CdTe(100) interface: Surface structure, growth behavior, Schottky barrier, and surface photovoltage

NASA Astrophysics Data System (ADS)

John, P.; Miller, T.; Hsieh, T. C.; Shapiro, A. P.; Wachs, A. L.; Chiang, T.-C.

1986-11-01

The clean CdTe(100) surface prepared by sputtering and annealing was studied with high-energy electron diffraction (HEED) and photoemission. HEED showed the surface to be a one-domain, (2×1) reconstruction. Photoemission spectra showed two surface-shifted components for the Cd 4d core level, with an intensity ratio of about 1:3, accounting for nearly an entire atomic layer. No surface-induced shifts for the Te 4d core level were detected. A model is proposed for the surface structure in which the surface layer is free of Te, and Cd atoms form dimers resulting in a (2×1) reconstruction; in addition, about (1/4) of the surface area is covered by excess loosely attached Cd atoms. Ag was evaporated on the surface at room temperature and found to grow three dimensionally in the [111] direction. The Ag was found to interact only weakly with the substrate, although the Cd atoms originally loosely bound on top of the surface were found to float on the evaporated Ag islands. A small coverage-dependent surface photovoltage, induced by the synchrotron radiation used for photoemission, was observed; with this effect taken into account, band bending was monitored, the final Fermi-level position being near 0.96 eV above the valence-band maximum. This corresponds to a Schottky-barrier height of about 0.60 eV for the n-type sample used in this experiment. The mechanism for generation of the surface photovoltage will be discussed.

Atomic-Scale Structure of the Hematite α-Fe2O3(11̅02) “R-Cut” Surface

PubMed Central

2017-01-01

The α-Fe2O3(11̅02) surface (also known as the hematite r-cut or (012) surface) was studied using low-energy electron diffraction (LEED), X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning tunneling microscopy (STM), noncontact atomic force microscopy (nc-AFM), and ab initio density functional theory (DFT)+U calculations. Two surface structures are stable under ultrahigh vacuum (UHV) conditions; a stoichiometric (1 × 1) surface can be prepared by annealing at 450 °C in ≈10–6 mbar O2, and a reduced (2 × 1) reconstruction is formed by UHV annealing at 540 °C. The (1 × 1) surface is close to an ideal bulk termination, and the undercoordinated surface Fe atoms reduce the surface bandgap by ≈0.2 eV with respect to the bulk. The work function is measured to be 5.7 ± 0.2 eV, and the VBM is located 1.5 ± 0.1 eV below EF. The images obtained from the (2 × 1) reconstruction cannot be reconciled with previously proposed models, and a new “alternating trench” structure is proposed based on an ordered removal of lattice oxygen atoms. DFT+U calculations show that this surface is favored in reducing conditions and that 4-fold-coordinated Fe2+ cations at the surface introduce gap states approximately 1 eV below EF. The work function on the (2 × 1) termination is 5.4 ± 0.2 eV. PMID:29492182

40 CFR 63.2550 - What definitions apply to this subpart?

Code of Federal Regulations, 2012 CFR

2012-07-01

... definition of reconstruction in § 63.2. Consumption means the quantity of all HAP raw materials entering a... the process as well as added as a raw material, consumption includes the quantity generated in the... contain primarily carbon, hydrogen, and oxygen atoms. Organic peroxides means organic compounds containing...

40 CFR 63.2550 - What definitions apply to this subpart?

Code of Federal Regulations, 2014 CFR

2014-07-01

... definition of reconstruction in § 63.2. Consumption means the quantity of all HAP raw materials entering a... the process as well as added as a raw material, consumption includes the quantity generated in the... contain primarily carbon, hydrogen, and oxygen atoms. Organic peroxides means organic compounds containing...

40 CFR 63.2550 - What definitions apply to this subpart?

Code of Federal Regulations, 2011 CFR

2011-07-01

... definition of reconstruction in § 63.2. Consumption means the quantity of all HAP raw materials entering a... the process as well as added as a raw material, consumption includes the quantity generated in the... contain primarily carbon, hydrogen, and oxygen atoms. Organic peroxides means organic compounds containing...

40 CFR 63.2550 - What definitions apply to this subpart?

Code of Federal Regulations, 2013 CFR

2013-07-01

... definition of reconstruction in § 63.2. Consumption means the quantity of all HAP raw materials entering a... the process as well as added as a raw material, consumption includes the quantity generated in the... contain primarily carbon, hydrogen, and oxygen atoms. Organic peroxides means organic compounds containing...

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

PubMed

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S; Subramanian, Hariharan; Dravid, Vinayak P; Backman, Vadim

2017-06-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

PubMed Central

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A.; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S.; Subramanian, Hariharan; Dravid, Vinayak P.; Backman, Vadim

2018-01-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes. PMID:28416035

Transition from Reconstruction toward Thin Film on the (110) Surface of Strontium Titanate

PubMed Central

2016-01-01

The surfaces of metal oxides often are reconstructed with a geometry and composition that is considerably different from a simple termination of the bulk. Such structures can also be viewed as ultrathin films, epitaxed on a substrate. Here, the reconstructions of the SrTiO3 (110) surface are studied combining scanning tunneling microscopy (STM), transmission electron diffraction, and X-ray absorption spectroscopy (XAS), and analyzed with density functional theory calculations. Whereas SrTiO3 (110) invariably terminates with an overlayer of titania, with increasing density its structure switches from n × 1 to 2 × n. At the same time the coordination of the Ti atoms changes from a network of corner-sharing tetrahedra to a double layer of edge-shared octahedra with bridging units of octahedrally coordinated strontium. This transition from the n × 1 to 2 × n reconstructions is a transition from a pseudomorphically stabilized tetrahedral network toward an octahedral titania thin film with stress-relief from octahedral strontia units at the surface. PMID:26954064

Micro-stress dominant displacive reconstructive transition in lithium aluminate

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

Hu, Qiwei; Yan, Xiaozhi; Zhang, Leilei

It is supposed that diffusive reconstructive transitions usually take place under hydrostatic pressure or low stresses, and displacive reconstructive phase transitions easily occur at nonhydrostatic pressure. Here, by in-situ high pressure synchrotron X-ray diffraction and single-crystal Raman scattering studies on lithium aluminate at room temperature, we show that the reconstructive transition mechanism is dependent on the internal microscopic stresses rather than the macroscopic stresses. In this case, even hydrostatic pressure can favor the displacive transition if the compressibility of crystal is anisotropic. During hydrostatic compression, γ-LiAlO{sub 2} transforms to δ-LiAlO{sub 2} at about 4 GPa, which is much lower than thatmore » in previous nonhydrostatic experiments (above 9 GPa). In the region where both phases coexist, there are enormous microscopic stresses stemming from the lattice mismatch, suggesting that this transition is displacive. Furthermore, the atomic picture is drawn with the help of the shear Raman modes.« less

Probing the Properties of the Molecular Adlayers on Metal Substrates: Scanning Tunneling Microscopy Study of Amine Adsorption on Gold(111) and Graphene Nanoislands on Cobalt(0001)

NASA Astrophysics Data System (ADS)

Zhou, Hui

In this thesis, we present our findings on two major topics, both of which are studies of molecules on metal surfaces by scanning tunneling microscopy (STM). The first topic is on adsorption of a model amine compound, 1,4-benzenediamine (BDA), on the reconstructed Au(111) surface, chosen for its potential application as a molecular electronic device. The molecules were deposited in the gas phase onto the substrate in the vacuum chamber. Five different patterns of BDA molecules on the surface at different coverages, and the preferred adsorption sites of BDA molecules on reconstructed Au(111) surface, were observed. In addition, BDA molecules were susceptible to tip-induced movement, suggesting that BDA molecules on metal surfaces can be a potential candidate in STM molecular manipulations. We also studied graphene nanoislands on Co(0001) in the hope of understanding interaction of expitaxially grown graphene and metal substrates. This topic can shed a light on the potential application of graphene as an electronic device, especially in spintronics. The graphene nanoislands were formed by annealing contorted hexabenzocoronene (HBC) on the Co(0001) surface. In our experiments, we have determined atop registry of graphene atoms with respect to the underlying Co surface. We also investigated the low-energy electronic structures of graphene nanoislands by scanning tunneling spectroscopy. The result was compared with a first-principle calculation using density functional theory (DFT) which suggested strong coupling between graphene pi-bands and cobalt d-electrons. We also observed that the islands exhibit zigzag edges, which exhibits unique electronic structures compared with the center areas of the islands.

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Entanglement with negative Wigner function of three thousand atoms heralded by one photon

NASA Astrophysics Data System (ADS)

McConnell, Robert; Zhang, Hao; Hu, Jiazhong; Ćuk, Senka; Vuletić, Vladan

2016-06-01

Quantum-mechanically correlated (entangled) states of many particles are of interest in quantum information, quantum computing and quantum metrology. Metrologically useful entangled states of large atomic ensembles have been experimentally realized [1, 2, 3, 4, 5, 6, 7, 8, 9, 10], but these states display Gaussian spin distribution functions with a non-negative Wigner function. Non-Gaussian entangled states have been produced in small ensembles of ions [11, 12], and very recently in large atomic ensembles [13, 14, 15]. Here, we generate entanglement in a large atomic ensemble via the interaction with a very weak laser pulse; remarkably, the detection of a single photon prepares several thousand atoms in an entangled state. We reconstruct a negative-valued Wigner function, an important hallmark of nonclassicality, and verify an entanglement depth (minimum number of mutually entangled atoms) of 2910 ± 190 out of 3100 atoms. Attaining such a negative Wigner function and the mutual entanglement of virtually all atoms is unprecedented for an ensemble containing more than a few particles. While the achieved purity of the state is slightly below the threshold for entanglement-induced metrological gain, further technical improvement should allow the generation of states that surpass this threshold, and of more complex Schrödinger cat states for quantum metrology and information processing.

Tomographic reconstruction of storm time RC ion distribution from ENA images on board multiple spacecraft

NASA Astrophysics Data System (ADS)

Ma, Shu-Ying; Yan, Wei-Nan; Xu, Liang

2015-11-01

A quantitative retrieval of 3-D distribution of energetic ions as energetic neutral atoms (ENA) sources is a challenging task. In this paper the voxel computerized tomography (CT) method is initially applied to reconstruct the 3-D distribution of energetic ions in the magnetospheric ring current (RC) region from ENA emission images on board multiple spacecraft. To weaken the influence of low-altitude emission (LAE) on the reconstruction, the LAE-associated ENA intensities are corrected by invoking the thick-target approximation. To overcome the divergence in iteration due to discordant instrument biases, a differential ENA voxel CT method is developed. The method is proved reliable and advantageous by numerical simulation for the case of constant bias independent of viewing angle. Then this method is implemented with ENA data measured by the Two Wide-angle Imaging Neutral-atom Spectrometers mission which performs stereoscopic ENA imaging. The 3-D spatial distributions and energy spectra of RC ion flux intensity are reconstructed for energies of 4-50 keV during the main phase of a major magnetic storm. The retrieved ion flux distributions seem to correspond to an asymmetric partial RC, located mainly around midnight favoring the postmidnight with L = 3.5-7.0 in the equatorial plane. The RC ion distributions with magnetic local time depend on energy, with major equatorial flux peak for lower energy located east of that for higher energy. In comparison with the ion energy spectra measured by Time History of Events and Macroscale Interactions during Substorms-D satellite flying in the RC region, the retrieved spectrum from remotely sensed ENA images are well matched with the in situ measurements.

Anisotropic conductivity imaging with MREIT using equipotential projection algorithm.

PubMed

Değirmenci, Evren; Eyüboğlu, B Murat

2007-12-21

Magnetic resonance electrical impedance tomography (MREIT) combines magnetic flux or current density measurements obtained by magnetic resonance imaging (MRI) and surface potential measurements to reconstruct images of true conductivity with high spatial resolution. Most of the biological tissues have anisotropic conductivity; therefore, anisotropy should be taken into account in conductivity image reconstruction. Almost all of the MREIT reconstruction algorithms proposed to date assume isotropic conductivity distribution. In this study, a novel MREIT image reconstruction algorithm is proposed to image anisotropic conductivity. Relative anisotropic conductivity values are reconstructed iteratively, using only current density measurements without any potential measurement. In order to obtain true conductivity values, only either one potential or conductivity measurement is sufficient to determine a scaling factor. The proposed technique is evaluated on simulated data for isotropic and anisotropic conductivity distributions, with and without measurement noise. Simulation results show that the images of both anisotropic and isotropic conductivity distributions can be reconstructed successfully.

3D structure of individual nanocrystals in solution by electron microscopy

DOE PAGES

Park, Jungwok; Elmlund, Hans; Ercius, Peter; ...

2015-07-17

Here, knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unorderedmore » nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.« less

Nanoparticle imaging. 3D structure of individual nanocrystals in solution by electron microscopy.

PubMed

Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A; Zettl, A; Alivisatos, A Paul

2015-07-17

Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale. Copyright © 2015, American Association for the Advancement of Science.

3D structure of individual nanocrystals in solution by electron microscopy

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

Park, Jungwok; Elmlund, Hans; Ercius, Peter

Here, knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unorderedmore » nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.« less

Atomic structure of the GaAs(001)-c(4x4) surface: first-principles evidence for diversity of heterodimer motifs.

PubMed

Penev, E; Kratzer, P; Scheffler, M

2004-10-01

The GaAs(001)-c(4x4) surface was studied using ab initio atomistic thermodynamics based on density-functional theory calculations. We demonstrate that in a range of stoichiometries, between those of the conventional three As-dimer and the new three Ga-As-dimer models, there exists a diversity of atomic structures featuring Ga-As heterodimers. These results fully explain the experimental scanning tunneling microscopy images and are likely to be relevant also to the c(4x4)-reconstructed (001) surfaces of other III-V semiconductors.

Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-12-21

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

The reconstruction of atomic co-ordinates from a protein stereo ribbon diagram when additional information for sufficient sidechain positions is available

NASA Astrophysics Data System (ADS)

Lopes de Oliveira, Paulo Sérgio; Garratt, Richard Charles

1998-11-01

We describe the application of a method for the reconstruction of three-dimensional atomic co-ordinates from a stereo ribbon diagram of a protein when additional information for some of the sidechain positions is available. The method has applications in cases where the 3D co-ordinates have not been made available by any means other than the original publication and are of interest as models for molecular replacement, homology modelling etc. The approach is, on the one hand, more general than other methods which are based on stereo figures which present specific atomic positions, but on the other hand relies on input from a specialist. Its exact implementation will depend on the figure of interest. We have applied the method to the case of the α-d-galactose-binding lectin jacalin with a resultant RMS deviation, compared to the crystal structure, of 1.5 Å for the 133 Cα positions of the α-chain and 2.6 Å for the less regular β-chain. The success of the method depends on the secondary structure of the protein under consideration and the orientation of the stereo diagram itself but can be expected to reproduce the mainchain co-ordinates more accurately than the sidechains. Some ways in which the method may be generalised to other cases are discussed.

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

Spectra of helium clusters with up to six atoms using soft-core potentials

NASA Astrophysics Data System (ADS)

Gattobigio, M.; Kievsky, A.; Viviani, M.

2011-11-01

In this paper, we investigate small clusters of helium atoms using the hyperspherical harmonic basis. We consider systems with A=2,3,4,5,6 atoms with an interparticle potential which does not present a strong repulsion at short distances. We use an attractive Gaussian potential that reproduces the values of the dimer binding energy, the atom-atom scattering length, and the effective range obtained with one of the widely used He-He interactions, the Aziz and Slaman potential, called LM2M2. In systems with more than two atoms, we consider a repulsive three-body force that, by construction, reproduces the trimer binding energy of the LM2M2 potential. With this model, consisting of the sum of a two- and three-body potential, we have calculated the spectrum of clusters formed by four, five, and six helium atoms. We have found that these systems present two bound states, one deep and one shallow, close to the threshold fixed by the energy of the (A-1)-atom system. Universal relations between the energies of the excited state of the A-atom system and the ground-state energy of the (A-1)-atom system are extracted, as well as the ratio between the ground state of the A-atom system and the ground-state energy of the trimer.

Non-equilibrium phase behavior and friction of confined molecular films under shear: A non-equilibrium molecular dynamics study.

PubMed

Maćkowiak, Sz; Heyes, D M; Dini, D; Brańka, A C

2016-10-28

The phase behavior of a confined liquid at high pressure and shear rate, such as is found in elastohydrodynamic lubrication, can influence the traction characteristics in machine operation. Generic aspects of this behavior are investigated here using Non-equilibrium Molecular Dynamics (NEMD) simulations of confined Lennard-Jones (LJ) films under load with a recently proposed wall-driven shearing method without wall atom tethering [C. Gattinoni et al., Phys. Rev. E 90, 043302 (2014)]. The focus is on thick films in which the nonequilibrium phases formed in the confined region impact on the traction properties. The nonequilibrium phase and tribological diagrams are mapped out in detail as a function of load, wall sliding speed, and atomic scale surface roughness, which is shown can have a significant effect. The transition between these phases is typically not sharp as the external conditions are varied. The magnitude of the friction coefficient depends strongly on the nonequilibrium phase adopted by the confined region of molecules, and in general does not follow the classical friction relations between macroscopic bodies, e.g., the frictional force can decrease with increasing load in the Plug-Slip (PS) region of the phase diagram owing to structural changes induced in the confined film. The friction coefficient can be extremely low (∼0.01) in the PS region as a result of incommensurate alignment between a (100) face-centered cubic wall plane and reconstructed (111) layers of the confined region near the wall. It is possible to exploit hysteresis to retain low friction PS states well into the central localization high wall speed region of the phase diagram. Stick-slip behavior due to periodic in-plane melting of layers in the confined region and subsequent annealing is observed at low wall speeds and moderate external loads. At intermediate wall speeds and pressure values (at least) the friction coefficient decreases with increasing well depth of the LJ potential between the wall atoms, but increases when the attractive part of the potential between wall atoms and confined molecules is made larger.

Selective growth of Pb islands on graphene/SiC buffer layers

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

Liu, X. T.; Miao, Y. P.; Ma, D. Y.

2015-02-14

Graphene is fabricated by thermal decomposition of silicon carbide (SiC) and Pb islands are deposited by Pb flux in molecular beam epitaxy chamber. It is found that graphene domains and SiC buffer layer coexist. Selective growth of Pb islands on SiC buffer layer rather than on graphene domains is observed. It can be ascribed to the higher adsorption energy of Pb atoms on the 6√(3) reconstruction of SiC. However, once Pb islands nucleate on graphene domains, they will grow very large owing to the lower diffusion barrier of Pb atoms on graphene. The results are consistent with first-principle calculations. Sincemore » Pb atoms on graphene are nearly free-standing, Pb islands grow in even-number mode.« less

Formation Dynamics of Potassium-Based Graphite Intercalation Compounds: An Ab Initio Study

NASA Astrophysics Data System (ADS)

Jiang, Xiankai; Song, Bo; Tománek, David

2018-04-01

This paper is a contribution to the Physical Review Applied collection in memory of Mildred S. Dresselhaus. We use ab initio molecular dynamics simulations to study the microscopic dynamics of potassium intercalation in graphite. Upon adsorbing on graphite from the vapor phase, K atoms transfer their valence charge to the substrate. K atoms adsorbed on the surface diffuse rapidly along the graphene basal plane and eventually enter the interlayer region following a "U -turn" across the edge, gaining additional energy. This process is promoted at higher coverages associated with higher K pressure, leading to the formation of a stable intercalation compound. We find that the functionalization of graphene edges is an essential prerequisite for intercalation since bare edges reconstruct and reconnect, closing off the entry channels for the atoms.

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

DOE PAGES

Pryor, Alan; Yang, Yongsoo; Rana, Arjun; ...

2017-09-05

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iteratesmore » between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.« less

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

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

Pryor, Alan; Yang, Yongsoo; Rana, Arjun

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iteratesmore » between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.« less

Preliminary frequency-domain analysis for the reconstructed spatial resolution of muon tomography

NASA Astrophysics Data System (ADS)

Yu, B.; Zhao, Z.; Wang, X.; Wang, Y.; Wu, D.; Zeng, Z.; Zeng, M.; Yi, H.; Luo, Z.; Yue, X.; Cheng, J.

2014-11-01

Muon tomography is an advanced technology to non-destructively detect high atomic number materials. It exploits the multiple Coulomb scattering information of muon to reconstruct the scattering density image of the traversed object. Because of the statistics of muon scattering, the measurement error of system and the data incompleteness, the reconstruction is always accompanied with a certain level of interference, which will influence the reconstructed spatial resolution. While statistical noises can be reduced by extending the measuring time, system parameters determine the ultimate spatial resolution that one system can reach. In this paper, an effective frequency-domain model is proposed to analyze the reconstructed spatial resolution of muon tomography. The proposed method modifies the resolution analysis in conventional computed tomography (CT) to fit the different imaging mechanism in muon scattering tomography. The measured scattering information is described in frequency domain, then a relationship between the measurements and the original image is proposed in Fourier domain, which is named as "Muon Central Slice Theorem". Furthermore, a preliminary analytical expression of the ultimate reconstructed spatial is derived, and the simulations are performed for validation. While the method is able to predict the ultimate spatial resolution of a given system, it can also be utilized for the optimization of system design and construction.

Enhancing Eight Grade Students' Scientific Conceptual Change and Scientific Reasoning through a Web-Based Learning Program

ERIC Educational Resources Information Center

Liao, Ya-Wen; She, Hsiao-Ching

2009-01-01

This study reports the impacts of the Scientific Concept Construction and Reconstruction (SCCR) digital learning system on eighth grade students' concept construction, conceptual change, and scientific reasoning involving the topic of "atoms". A two-factorial experimental design was carried out to investigate the effects of the approach…

Interfacial B-site atomic configuration in polar (111) and non-polar (001) SrIrO3/SrTiO3 heterostructures

NASA Astrophysics Data System (ADS)

Anderson, T. J.; Zhou, H.; Xie, L.; Podkaminer, J. P.; Patzner, J. J.; Ryu, S.; Pan, X. Q.; Eom, C. B.

2017-09-01

The precise control of interfacial atomic arrangement in ABO3 perovskite heterostructures is paramount, particularly in cases where the subsequent electronic properties of the material exhibit geometrical preferences along polar crystallographic directions that feature inevitably complex surface reconstructions. Here, we present the B-site interfacial structure in polar (111) and non-polar (001) SrIrO3/SrTiO3 interfaces. The heterostructures were examined using scanning transmission electron microscopy and synchrotron-based coherent Bragg rod analysis. Our results reveal the preference of B-site intermixing across the (111) interface due to the polarity-compensated SrTiO3 substrate surface prior to growth. By comparison, the intermixing at the non-polar (001) interface is negligible. This finding suggests that the intermixing may be necessary to mitigate epitaxy along heavily reconstructed and non-stoichiometric (111) perovskite surfaces. Furthermore, this preferential B-site configuration could allow the geometric design of the interfacial perovskite structure and chemistry to selectively engineer the correlated electronic states of the B-site d-orbital.

Scanning tunneling microscopy study of graphene on Au(111): Growth mechanisms and substrate interactions

NASA Astrophysics Data System (ADS)

Nie, Shu; Bartelt, Norman C.; Wofford, Joseph M.; Dubon, Oscar D.; McCarty, Kevin F.; Thürmer, Konrad

2012-05-01

We use scanning tunneling microscopy to study the structure of graphene islands on Au(111) grown by deposition of elemental carbon at 950 °C. Consistent with low-energy electron microscopic observations, we find that the graphene islands have dendritic shapes. The islands tend to cover depressed regions of the Au surface, suggesting that Au is displaced as the graphene grows. If small tunneling currents are used, it is possible to image simultaneously the graphene/Au moiré and the Au herringbone reconstruction, which forms underneath the graphene on cooling from the growth temperature. The delicate herringbone structure and its periodicity remain unchanged from the bare Au surface. Using a Frenkel-Kontorova model, we deduce that this striking observation is consistent with an attraction between graphene and Au of less than 13 meV per C atom. Raman spectroscopy supports this weak interaction. However, at the tunneling currents necessary for atomic-resolution imaging of graphene, the Au reconstruction is altered, implying influential tip-sample interactions and a mobile Au surface beneath the graphene.

A combined averaging and frequency mixing approach for force identification in weakly nonlinear high-Q oscillators: Atomic force microscope

NASA Astrophysics Data System (ADS)

Sah, Si Mohamed; Forchheimer, Daniel; Borgani, Riccardo; Haviland, David

2018-02-01

We present a polynomial force reconstruction of the tip-sample interaction force in Atomic Force Microscopy. The method uses analytical expressions for the slow-time amplitude and phase evolution, obtained from time-averaging over the rapidly oscillating part of the cantilever dynamics. The slow-time behavior can be easily obtained in either the numerical simulations or the experiment in which a high-Q resonator is perturbed by a weak nonlinearity and a periodic driving force. A direct fit of the theoretical expressions to the simulated and experimental data gives the best-fit parameters for the force model. The method combines and complements previous works (Platz et al., 2013; Forchheimer et al., 2012 [2]) and it allows for computationally more efficient parameter mapping with AFM. Results for the simulated asymmetric piecewise linear force and VdW-DMT force models are compared with the reconstructed polynomial force and show a good agreement. It is also shown that the analytical amplitude and phase modulation equations fit well with the experimental data.

Insight into the collagen assembly in the presence of lysine and glutamic acid: An in vitro study.

PubMed

Liu, Xinhua; Dan, Nianhua; Dan, Weihua

2017-01-01

The aim of this study is to evaluate the effects of two different charged amino acids in collagen chains, lysine and glutamic acid, on the fibrillogenesis process of collagen molecules. The turbidity, zeta potential, and fiber diameter analysis suggest that introducing the positively charged lysine into collagen might improve the sizes or amounts of the self-assembled collagen fibrils significantly. Conversely, the negatively charged glutamic acid might restrict the self-assembly of collagen building blocks into a higher order structure. Meanwhile, the optimal fibrillogenesis condition is achieved when the concentration of lysine reaches to 1mM. Both scanning electron microscopy (SEM) and atomic force microscope (AFM) analysis indicates that compared to pure collagen fibrils, the reconstructed collagen-lysine co-fibrils exhibit a higher degree of inter-fiber entanglements with more straight and longer fibrils. Noted that the specific D-period patterns of the reconstructed collagen fibrils could be clearly discernible and the width of D-banding increases steadily after introducing lysine. Besides, the kinetic and thermodynamic collagen self-assembly analysis confirms that the rate constants of both the first and second assembly phase decrease after introducing lysine, and lysine could promote the process of collagen fibrillogenesis obeying the laws of thermodynamics. Copyright © 2016 Elsevier B.V. All rights reserved.

Strain effects and intermixing at the Si surface: Importance of long-range elastic corrections in first-principles calculations

DOE PAGES

Béland, Laurent Karim; Machado-Charry, Eduardo; Pochet, Pascal; ...

2014-10-06

Here we investigate Ge mixing at the Si(001) surface and characterize the 2 N Si(001) reconstruction by means of hybrid quantum and molecular mechanics calculations (QM/MM). Avoiding fake elastic dampening, this scheme allows to correctly take into account long range deformation induced by reconstructed and defective surfaces. We focus in particular on the dimer vacancy line (DVL) and its interaction with Ge adatoms. We first show that calculated formation energies for these defects are highly dependent on the choice of chemical potential and that the latter must be chosen carefully. Characterizing the effect of the DVL on the deformation field,more » we also find that the DVL favors Ge segregation in the fourth layer close to the DVL. Using the activation-relaxation technique (ART nouveau) and QM/MM, we show that a complex diffusion path permits the substitution of the Ge atom in the fourth layer, with barriers compatible with mixing observed at intermediate temperature. We also show that the use of QM/MM results in much more signi cant corrections at the saddle points (up to 0.5 eV) that at minima, demonstrating its importance for describing kinetics correctly.« less

Reconstructing free-energy landscapes for nonequilibrium periodic potentials

NASA Astrophysics Data System (ADS)

López-Alamilla, N. J.; Jack, Michael W.; Challis, K. J.

2018-03-01

We present a method for reconstructing the free-energy landscape of overdamped Brownian motion on a tilted periodic potential. Our approach exploits the periodicity of the system by using the k -space form of the Smoluchowski equation and we employ an iterative approach to determine the nonequilibrium tilt. We reconstruct landscapes for a number of example potentials to show the applicability of the method to both deep and shallow wells and near-to- and far-from-equilibrium regimes. The method converges logarithmically with the number of Fourier terms in the potential.

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

Paziresh, M.; Kingston, A. M., E-mail: andrew.kingston@anu.edu.au; Latham, S. J.

Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski,more » Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073–2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127–135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260–1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.« less

On the trends of Fukui potential and hardness potential derivatives in isolated atoms vs. atoms in molecules.

PubMed

Bhattacharjee, Rituparna; Roy, Ram Kinkar

2014-10-28

In the present study, trends of electronic contribution to molecular electrostatic potential [Vel(r¯)(r=0)], Fukui potential [v(+)f|(r=0) and v(-)f|(r=0)] and hardness potential derivatives [Δ(+)h(k) and Δ(-)h(k)] for isolated atoms as well as atoms in molecules are investigated. The generated numerical values of these three reactivity descriptors in these two electronically different situations are critically analyzed through the relevant formalism. Values of Vel(r¯) (when r → 0, i.e., on the nucleus) are higher for atoms in molecules than that of isolated atoms. In contrast, higher values of v(+)|(r=0) and v(-)|(r=0) are observed for isolated atoms compared to the values for atoms in a molecule. However, no such regular trend is observed for the Δ(+)h(k) and Δ(-)h(k) values, which is attributed to the uncertainty in the Fukui function values of atoms in molecules. The sum of Fukui potential and the sum of hardness potential derivatives in molecules are also critically analyzed, which shows the efficacy of orbital relaxation effects in quantifying the values of these parameters. The chemical consequence of the observed trends of these descriptors in interpreting electron delocalization, electronic relaxation and non-negativity of atomic Fukui function indices is also touched upon. Several commonly used molecules containing carbon as well as heteroatoms are chosen to make the investigation more insightful.

Application of Tight-Binding Method in Atomistic Simulation of Covalent Materials

NASA Astrophysics Data System (ADS)

Isik, Ahmet

1994-05-01

The primary goal of this thesis is to develop and apply molecular dynamics simulation methods to elemental and binary covalent materials (Si, C, SiC) based on the tight-binding (TB) model of atomic cohesion in studies of bulk and deformation properties far from equilibrium. A second purpose is to compare results with those obtained using empirical interatomic potential functions in order to elucidate the applicability of models of interatomic interactions which do not take into account explicitly electronic structure effects. We have calculated the former by using a basis set consisting of four atomic orbitals, one for the s state and three for the p states, constructing a TB Hamiltonian in the usual Slater-Koster parametrization, and diagonalizing the Hamiltonian matrix at the origin of the Brillouin zone. For the repulsive part of the energy we employ a function in the form of inverse power law with screening which is then fitted to the bulk modulus and lattice parameter of several stable polytypes, results calculated by ab initio methods in the literature. Three types of applications have been investigated to demonstrate the utility of the present TB models and their advantages relative to empirical potentials. In the case of Si we show the calculated cohesive energy agrees to within a few percent with the ab initio local-density approximation (LDA) results. In addition, for clusters up to 10 atoms we find most of the energies and equilibrium structures to be in good agreement with LDA results (the failure of the empirical potential of Stillinger and Weber (SW) is well known). In the case of C clusters our TB model gives ring and chain structures which have been found both experimentally and by LDA calculations. In the second application we have applied our TB model of Si to investigate the core structure and energetics of partial dislocations on the glide plane and reconstruction antiphase defect (APD). For the 90^circ partial we show that the TB description gives the correct asymetric reconstruction previously found by LDA. For the 30^circ partial, TB gives better bond angles in the dislocation core. For the APD we have obtained a binding energy and activation for migration which are somewhat larger than the SW values, but the conclusion remains that APD is a low-energy defect which should be quite mobile. In the third application we formulate a simple TB model for SiC where the coefficients of the two-center integrals in Si-C interactions are taken to be simple averages of Si-Si and C-C integrals. Fitting is done on two polytypes, zincblende and rocksalt structures, and a simulated annealing procedure is used. The TB results are found in good agreement with LDA and experimental results in the cohesive energy, acoustic phonon modes, and elastic constants. (Abstract shortened by UMI.).

Determination of solute site occupancies within γ' precipitates in nickel-base superalloys via orientation-specific atom probe tomography

DOE PAGES

Meher, Subhashish; Rojhirunsakool, Tanaporn; Nandwana, Peeyush; ...

2015-04-28

In this study, the analytical limitations in atom probe tomography such as resolving a desired set of atomic planes, for solving complex materials science problems, have been overcome by employing a well-developed unique and reproducible crystallographic technique, involving synergetic coupling of orientation microscopy with atom probe tomography. The crystallographic information in atom probe reconstructions has been utilized to determine the solute site occupancies in Ni-Al-Cr based superalloys accurately. The structural information in atom probe reveals that both Al and Cr occupy the same sub-lattice within the L1 2-ordered g precipitates to form Ni 3(Al,Cr) precipitates in a Ni-14Al-7Cr(at.%) alloy. Interestingly,more » the addition of Co, which is a solid solution strengthener, to a Ni-14Al-7Cr alloy results in the partial reversal of Al site occupancy within g precipitates to form (Ni,Al) 3(Al,Cr,Co) precipitates. This unique evidence of reversal of Al site occupancy, resulting from the introduction of other solutes within the ordered structures, gives insights into the relative energetics of different sub-lattice sites when occupied by different solutes.« less

Broadband X-ray Imaging in the Near-Field Region of an Airblast Atomizer

NASA Astrophysics Data System (ADS)

Li, Danyu; Bothell, Julie; Morgan, Timothy; Heindel, Theodore

2017-11-01

The atomization process has a close connection to the efficiency of many spray applications. Examples include improved fuel atomization increasing the combustion efficiency of aircraft engines, or controlled droplet size and spray angle enhancing the quality and speed of the painting process. Therefore, it is vital to understand the physics of the atomization process, but the near-field region is typically optically dense and difficult to probe with laser-based or intrusive measurement techniques. In this project, broadband X-ray radiography and X-ray computed tomography (CT) imaging were performed in the near-field region of a canonical coaxial airblast atomizer. The X-ray absorption rate was enhanced by adding 20% by weight of Potassium Iodide to the liquid phase to increase image contrast. The radiographs provided an estimate of the liquid effective mean path length and spray angle at the nozzle exit for different flow conditions. The reconstructed CT images provided a 3D map of the time-average liquid spray distribution. X-ray imaging was used to quantify the changes in the near-field spray characteristics for various coaxial airblast atomizer flow conditions. Office of Naval Research.

Influence of Adsorbed Hydroxyl and Carbon Monoxide on Potential-Induced Reconstruction of Au(100) as Examined by Scanning Tunneling Microscopy

DTIC Science & Technology

1994-02-01

years have witnessed substantial advances in our knowledge of metal reconstruction in electrochemical systems, primarily for low-index gold surfaces in...index gold surfaces, reconstruction can be formed or removed by applying electrode potentials corresponding to negative or positive electronic charge...potential and gold oxidation regions, for Au(100) in 0.1 M KOH, obtained in a conventional electrochemical cell (solid trace). The voltammetric

Limited view angle iterative CT reconstruction

NASA Astrophysics Data System (ADS)

Kisner, Sherman J.; Haneda, Eri; Bouman, Charles A.; Skatter, Sondre; Kourinny, Mikhail; Bedford, Simon

2012-03-01

Computed Tomography (CT) is widely used for transportation security to screen baggage for potential threats. For example, many airports use X-ray CT to scan the checked baggage of airline passengers. The resulting reconstructions are then used for both automated and human detection of threats. Recently, there has been growing interest in the use of model-based reconstruction techniques for application in CT security systems. Model-based reconstruction offers a number of potential advantages over more traditional direct reconstruction such as filtered backprojection (FBP). Perhaps one of the greatest advantages is the potential to reduce reconstruction artifacts when non-traditional scan geometries are used. For example, FBP tends to produce very severe streaking artifacts when applied to limited view data, which can adversely affect subsequent processing such as segmentation and detection. In this paper, we investigate the use of model-based reconstruction in conjunction with limited-view scanning architectures, and we illustrate the value of these methods using transportation security examples. The advantage of limited view architectures is that it has the potential to reduce the cost and complexity of a scanning system, but its disadvantage is that limited-view data can result in structured artifacts in reconstructed images. Our method of reconstruction depends on the formulation of both a forward projection model for the system, and a prior model that accounts for the contents and densities of typical baggage. In order to evaluate our new method, we use realistic models of baggage with randomly inserted simple simulated objects. Using this approach, we show that model-based reconstruction can substantially reduce artifacts and improve important metrics of image quality such as the accuracy of the estimated CT numbers.

Tomography of atomic number and density of materials using dual-energy imaging and the Alvarez and Macovski attenuation model

NASA Astrophysics Data System (ADS)

Paziresh, M.; Kingston, A. M.; Latham, S. J.; Fullagar, W. K.; Myers, G. M.

2016-06-01

Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073-2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127-135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260-1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

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

Faria, Jose P.; Overbeek, Ross; Taylor, Ronald C.

Here, we introduce a manually constructed and curated regulatory network model that describes the current state of knowledge of transcriptional regulation of B. subtilis. The model corresponds to an updated and enlarged version of the regulatory model of central metabolism originally proposed in 2008. We extended the original network to the whole genome by integration of information from DBTBS, a compendium of regulatory data that includes promoters, transcription factors (TFs), binding sites, motifs and regulated operons. Additionally, we consolidated our network with all the information on regulation included in the SporeWeb and Subtiwiki community-curated resources on B. subtilis. Finally, wemore » reconciled our network with data from RegPrecise, which recently released their own less comprehensive reconstruction of the regulatory network for B. subtilis. Our model describes 275 regulators and their target genes, representing 30 different mechanisms of regulation such as TFs, RNA switches, Riboswitches and small regulatory RNAs. Overall, regulatory information is included in the model for approximately 2500 of the ~4200 genes in B. subtilis 168. In an effort to further expand our knowledge of B. subtilis regulation, we reconciled our model with expression data. For this process, we reconstructed the Atomic Regulons (ARs) for B. subtilis, which are the sets of genes that share the same “ON” and “OFF” gene expression profiles across multiple samples of experimental data. We show how atomic regulons for B. subtilis are able to capture many sets of genes corresponding to regulated operons in our manually curated network. Additionally, we demonstrate how atomic regulons can be used to help expand or validate the knowledge of the regulatory networks by looking at highly correlated genes in the ARs for which regulatory information is lacking. During this process, we were also able to infer novel stimuli for hypothetical genes by exploring the genome expression metadata relating to experimental conditions, gaining insights into novel biology.« less

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

DOE PAGES

Faria, Jose P.; Overbeek, Ross; Taylor, Ronald C.; ...

2016-03-18

Here, we introduce a manually constructed and curated regulatory network model that describes the current state of knowledge of transcriptional regulation of B. subtilis. The model corresponds to an updated and enlarged version of the regulatory model of central metabolism originally proposed in 2008. We extended the original network to the whole genome by integration of information from DBTBS, a compendium of regulatory data that includes promoters, transcription factors (TFs), binding sites, motifs and regulated operons. Additionally, we consolidated our network with all the information on regulation included in the SporeWeb and Subtiwiki community-curated resources on B. subtilis. Finally, wemore » reconciled our network with data from RegPrecise, which recently released their own less comprehensive reconstruction of the regulatory network for B. subtilis. Our model describes 275 regulators and their target genes, representing 30 different mechanisms of regulation such as TFs, RNA switches, Riboswitches and small regulatory RNAs. Overall, regulatory information is included in the model for approximately 2500 of the ~4200 genes in B. subtilis 168. In an effort to further expand our knowledge of B. subtilis regulation, we reconciled our model with expression data. For this process, we reconstructed the Atomic Regulons (ARs) for B. subtilis, which are the sets of genes that share the same “ON” and “OFF” gene expression profiles across multiple samples of experimental data. We show how atomic regulons for B. subtilis are able to capture many sets of genes corresponding to regulated operons in our manually curated network. Additionally, we demonstrate how atomic regulons can be used to help expand or validate the knowledge of the regulatory networks by looking at highly correlated genes in the ARs for which regulatory information is lacking. During this process, we were also able to infer novel stimuli for hypothetical genes by exploring the genome expression metadata relating to experimental conditions, gaining insights into novel biology.« less

Adsorption of hydrogen on stable and metastable Ir(100) surfaces

NASA Astrophysics Data System (ADS)

Arman, Mohammad Alif; Klein, Andreas; Ferstl, Pascal; Valookaran, Abhilash; Gustafson, Johan; Schulte, Karina; Lundgren, Edvin; Heinz, Klaus; Schneider, Alexander; Mittendorfer, Florian; Hammer, Lutz; Knudsen, Jan

2017-02-01

Using the combination of high resolution core level spectroscopy and density functional theory we present a detailed spectroscopic study for all clean and hydrogen covered phases of Ir(100). The results are complemented by an investigation of the hydrogen desorption process from various phases using temperature programmed desorption spectroscopy and scanning tunneling microscopy. In total, all experimentally determined core level shifts match very well with those predicted by density functional theory based on established structural models. In particular, we find for the (bridge site) adsorption on the unreconstructed 1×1 phase that the initial core level shift of surface Ir atoms is altered by +0.17 eV for each Ir-H bond formed. In the submonolayer regime we find evidence for island formation at low temperatures. For the H-induced deconstructed 5×1-H phase we identify four different surface core level shifts with two of them being degenerate. Finally, for the reconstructed 5×1-hex phase also four surface components are identified, which undergo a rather rigid core level shift of +0.15 eV upon hydrogen adsorption suggesting a similarly homogeneous charge transfer to all Ir surface atoms. Thermodesorption experiments for the 5×1-H phase reveal two different binding states for hydrogen independent of the total coverage. We conclude that the surface always separates into patches of fully covered deconstructed and uncovered reconstructed phases. We could also show by tunneling microscopy that with the desorption of the last hydrogen atom from the deconstructed unit cell the surface instantaneously reverts into the reconstructed state. Eventually, we could determine the saturation coverage upon molecular adsorption for all phases to be θmax1 × 1 - H = 1.0 ML , θmax5 × 1 - H = 0.8 ML , and θmax5 × 1 - hex - H ≥ 1.0 ML .

Tune-out wavelengths and landscape-modulated polarizabilities of alkali-metal Rydberg atoms in infrared optical lattices

NASA Astrophysics Data System (ADS)

Topcu, Turker; Derevianko, Andrei

2013-11-01

Intensity-modulated optical lattice potentials can change sign for an alkali-metal Rydberg atom, and the atoms are not always attracted to intensity minima in optical lattices with wavelengths near the CO2 laser band. Here we demonstrate that such IR lattices can be tuned so that the trapping potential experienced by the Rydberg atom can be made to vanish for atoms in “targeted” Rydberg states. Such state-selective trapping of Rydberg atoms can be useful in controlled cold Rydberg collisions, cooling Rydberg states, and species-selective trapping and transport of Rydberg atoms in optical lattices. We tabulate wavelengths at which the trapping potential vanishes for the ns, np, and nd Rydberg states of Na and Rb atoms and discuss advantages of using such optical lattices for state-selective trapping of Rydberg atoms. We also develop exact analytical expressions for the lattice-induced polarizability for the mz=0 Rydberg states and derive an accurate formula predicting tune-out wavelengths at which the optical trapping potential becomes invisible to Rydberg atoms in targeted l=0 states.

Direct Determination of the Equilibrium Unbinding Potential Profile for a Short DNA Duplex from Force Spectroscopy Data

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

Noy, A

2004-05-04

Modern force microscopy techniques allow researchers to use mechanical forces to probe interactions between biomolecules. However, such measurements often happen in non-equilibrium regime, which precludes straightforward extraction of the equilibrium energy information. Here we use the work averaging method based on Jarzynski equality to reconstruct the equilibrium interaction potential from the unbinding of a complementary 14-mer DNA duplex from the results of non-equilibrium single-molecule measurements. The reconstructed potential reproduces most of the features of the DNA stretching transition, previously observed only in equilibrium stretching of long DNA sequences. We also compare the reconstructed potential with the thermodynamic parameters of DNAmore » duplex unbinding and show that the reconstruction accurately predicts duplex melting enthalpy.« less

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

Wavelet-sparsity based regularization over time in the inverse problem of electrocardiography.

PubMed

Cluitmans, Matthijs J M; Karel, Joël M H; Bonizzi, Pietro; Volders, Paul G A; Westra, Ronald L; Peeters, Ralf L M

2013-01-01

Noninvasive, detailed assessment of electrical cardiac activity at the level of the heart surface has the potential to revolutionize diagnostics and therapy of cardiac pathologies. Due to the requirement of noninvasiveness, body-surface potentials are measured and have to be projected back to the heart surface, yielding an ill-posed inverse problem. Ill-posedness ensures that there are non-unique solutions to this problem, resulting in a problem of choice. In the current paper, it is proposed to restrict this choice by requiring that the time series of reconstructed heart-surface potentials is sparse in the wavelet domain. A local search technique is introduced that pursues a sparse solution, using an orthogonal wavelet transform. Epicardial potentials reconstructed from this method are compared to those from existing methods, and validated with actual intracardiac recordings. The new technique improves the reconstructions in terms of smoothness and recovers physiologically meaningful details. Additionally, reconstruction of activation timing seems to be improved when pursuing sparsity of the reconstructed signals in the wavelet domain.

Influence of Parameters of a Reactive Interatomic Potential on the Properties of Saturated Hydrocarbons

DTIC Science & Technology

2017-01-01

Methodology 3 2.1 Modified Embedded-Atom Method Theory 3 2.1.1 Embedding Energy Function 3 2.1.2 Screening Factor 8 2.1.3 Modified Embedded-Atom...Simulation Methodology 2.1 Modified Embedded-Atom Method Theory In the EAM and MEAM formalisms1,2,5 the total energy of a system of atoms (Etot) is...An interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a semiempirical many-body potential based on

In-line phase contrast micro-CT reconstruction for biomedical specimens.

PubMed

Fu, Jian; Tan, Renbo

2014-01-01

X-ray phase contrast micro computed tomography (micro-CT) can non-destructively provide the internal structure information of soft tissues and low atomic number materials. It has become an invaluable analysis tool for biomedical specimens. Here an in-line phase contrast micro-CT reconstruction technique is reported, which consists of a projection extraction method and the conventional filter back-projection (FBP) reconstruction algorithm. The projection extraction is implemented by applying the Fourier transform to the forward projections of in-line phase contrast micro-CT. This work comprises a numerical study of the method and its experimental verification using a biomedical specimen dataset measured at an X-ray tube source micro-CT setup. The numerical and experimental results demonstrate that the presented technique can improve the imaging contrast of biomedical specimens. It will be of interest for a wide range of in-line phase contrast micro-CT applications in medicine and biology.

Free energy reconstruction from steered dynamics without post-processing

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

Athenes, Manuel, E-mail: Manuel.Athenes@cea.f; Condensed Matter and Materials Division, Physics and Life Sciences Directorate, LLNL, Livermore, CA 94551; Marinica, Mihai-Cosmin

2010-09-20

Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable one to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes theorem, we propose a more direct method in which a posterior likelihood function is used both to construct the steered dynamics and to infer the contribution to equilibrium of all the sampled states. The method is implemented with two steering schedules. First, using non-autonomous steering, we calculate the migration barrier of the vacancy in Fe-{alpha}. Second, using an autonomous scheduling related to metadynamics and equivalent to temperature-accelerated molecular dynamics, wemore » accurately reconstruct the two-dimensional free energy landscape of the 38-atom Lennard-Jones cluster as a function of an orientational bond-order parameter and energy, down to the solid-solid structural transition temperature of the cluster and without maximum-likelihood post-processing.« less

Plasmonic nanoparticle scattering for color holograms

PubMed Central

Montelongo, Yunuen; Tenorio-Pearl, Jaime Oscar; Williams, Calum; Zhang, Shuang; Milne, William Ireland; Wilkinson, Timothy David

2014-01-01

This work presents an original approach to create holograms based on the optical scattering of plasmonic nanoparticles. By analogy to the diffraction produced by the scattering of atoms in X-ray crystallography, we show that plasmonic nanoparticles can produce a wave-front reconstruction when they are sampled on a diffractive plane. By applying this method, all of the scattering characteristics of the nanoparticles are transferred to the reconstructed field. Hence, we demonstrate that a narrow-band reconstruction can be achieved for direct white light illumination on an array of plasmonic nanoparticles. Furthermore, multicolor capabilities are shown with minimal cross-talk by multiplexing different plasmonic nanoparticles at subwavelength distances. The holograms were fabricated from a single subwavelength thin film of silver and demonstrate that the total amount of binary information stored in the plane can exceed the limits of diffraction and that this wavelength modulation can be detected optically in the far field. PMID:25122675

Plasmonic nanoparticle scattering for color holograms.

PubMed

Montelongo, Yunuen; Tenorio-Pearl, Jaime Oscar; Williams, Calum; Zhang, Shuang; Milne, William Ireland; Wilkinson, Timothy David

2014-09-02

This work presents an original approach to create holograms based on the optical scattering of plasmonic nanoparticles. By analogy to the diffraction produced by the scattering of atoms in X-ray crystallography, we show that plasmonic nanoparticles can produce a wave-front reconstruction when they are sampled on a diffractive plane. By applying this method, all of the scattering characteristics of the nanoparticles are transferred to the reconstructed field. Hence, we demonstrate that a narrow-band reconstruction can be achieved for direct white light illumination on an array of plasmonic nanoparticles. Furthermore, multicolor capabilities are shown with minimal cross-talk by multiplexing different plasmonic nanoparticles at subwavelength distances. The holograms were fabricated from a single subwavelength thin film of silver and demonstrate that the total amount of binary information stored in the plane can exceed the limits of diffraction and that this wavelength modulation can be detected optically in the far field.

Dipolar and spinor bosonic systems

NASA Astrophysics Data System (ADS)

Yukalov, V. I.

2018-05-01

The main properties and methods of describing dipolar and spinor atomic systems, composed of bosonic atoms or molecules, are reviewed. The general approach for the correct treatment of Bose-condensed atomic systems with nonlocal interaction potentials is explained. The approach is applied to Bose-condensed systems with dipolar interaction potentials. The properties of systems with spinor interaction potentials are described. Trapped atoms and atoms in optical lattices are considered. Effective spin Hamiltonians for atoms in optical lattices are derived. The possibility of spintronics with cold atom is emphasized. The present review differs from the previous review articles by concentrating on a thorough presentation of basic theoretical points, helping the reader to better follow mathematical details and to make clearer physical conclusions.

Dictionary learning based noisy image super-resolution via distance penalty weight model

PubMed Central

Han, Yulan; Zhao, Yongping; Wang, Qisong

2017-01-01

In this study, we address the problem of noisy image super-resolution. Noisy low resolution (LR) image is always obtained in applications, while most of the existing algorithms assume that the LR image is noise-free. As to this situation, we present an algorithm for noisy image super-resolution which can achieve simultaneously image super-resolution and denoising. And in the training stage of our method, LR example images are noise-free. For different input LR images, even if the noise variance varies, the dictionary pair does not need to be retrained. For the input LR image patch, the corresponding high resolution (HR) image patch is reconstructed through weighted average of similar HR example patches. To reduce computational cost, we use the atoms of learned sparse dictionary as the examples instead of original example patches. We proposed a distance penalty model for calculating the weight, which can complete a second selection on similar atoms at the same time. Moreover, LR example patches removed mean pixel value are also used to learn dictionary rather than just their gradient features. Based on this, we can reconstruct initial estimated HR image and denoised LR image. Combined with iterative back projection, the two reconstructed images are applied to obtain final estimated HR image. We validate our algorithm on natural images and compared with the previously reported algorithms. Experimental results show that our proposed method performs better noise robustness. PMID:28759633

All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins

PubMed Central

Guttman, Miklos; Weinkam, Patrick; Sali, Andrej; Lee, Kelly K.

2013-01-01

Summary The flexible and heterogeneous nature of carbohydrate chains often renders glycoproteins refractory to traditional structure determination methods. Small Angle X-ray scattering (SAXS) can be a useful tool for obtaining structural information of these systems. All-atom modeling of glycoproteins with flexible glycan chains was applied to interpret the solution SAXS data for a set of glycoproteins. For simpler systems (single glycan, with a well defined protein structure), all-atom modeling generates models in excellent agreement with the scattering pattern, and reveals the approximate spatial occupancy of the glycan chain in solution. For more complex systems (several glycan chains, or unknown protein substructure), the approach can still provide insightful models, though the orientations of glycans become poorly determined. Ab initio shape reconstructions appear to capture the global morphology of glycoproteins, but in most cases offer little information about glycan spatial occupancy. The all-atom modeling methodology is available as a webserver at http://modbase.compbio.ucsf.edu/allosmod-foxs. PMID:23473666

Quantum Degeneracy in Atomic Point Contacts Revealed by Chemical Force and Conductance

NASA Astrophysics Data System (ADS)

Sugimoto, Yoshiaki; Ondráček, Martin; Abe, Masayuki; Pou, Pablo; Morita, Seizo; Perez, Ruben; Flores, Fernando; Jelínek, Pavel

2013-09-01

Quantum degeneracy is an important concept in quantum mechanics with large implications to many processes in condensed matter. Here, we show the consequences of electron energy level degeneracy on the conductance and the chemical force between two bodies at the atomic scale. We propose a novel way in which a scanning probe microscope can detect the presence of degenerate states in atomic-sized contacts even at room temperature. The tunneling conductance G and chemical binding force F between two bodies both tend to decay exponentially with distance in a certain distance range, usually maintaining direct proportionality G∝F. However, we show that a square relation G∝F2 arises as a consequence of quantum degeneracy between the interacting frontier states of the scanning tip and a surface atom. We demonstrate this phenomenon on the Si(111)-(7×7) surface reconstruction where the Si adatom possesses a strongly localized dangling-bond state at the Fermi level.

Constructing oxide interfaces and heterostructures by atomic layer-by-layer laser molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Lei, Qingyu; Golalikhani, Maryam; Davidson, Bruce A.; Liu, Guozhen; Schlom, Darrell G.; Qiao, Qiao; Zhu, Yimei; Chandrasena, Ravini U.; Yang, Weibing; Gray, Alexander X.; Arenholz, Elke; Farrar, Andrew K.; Tenne, Dmitri A.; Hu, Minhui; Guo, Jiandong; Singh, Rakesh K.; Xi, Xiaoxing

2017-12-01

Advancements in nanoscale engineering of oxide interfaces and heterostructures have led to discoveries of emergent phenomena and new artificial materials. Combining the strengths of reactive molecular-beam epitaxy and pulsed-laser deposition, we show here, with examples of Sr1+xTi1-xO3+δ, Ruddlesden-Popper phase Lan+1NinO3n+1 (n = 4), and LaAl1+yO3(1+0.5y)/SrTiO3 interfaces, that atomic layer-by-layer laser molecular-beam epitaxy significantly advances the state of the art in constructing oxide materials with atomic layer precision and control over stoichiometry. With atomic layer-by-layer laser molecular-beam epitaxy we have produced conducting LaAlO3/SrTiO3 interfaces at high oxygen pressures that show no evidence of oxygen vacancies, a capability not accessible by existing techniques. The carrier density of the interfacial two-dimensional electron gas thus obtained agrees quantitatively with the electronic reconstruction mechanism.

A New Approach to the Computer Modeling of Amorphous Nanoporous Structures of Semiconducting and Metallic Materials: A Review

PubMed Central

Romero, Cristina; Noyola, Juan C.; Santiago, Ulises; Valladares, Renela M.; Valladares, Alexander; Valladares, Ariel A.

2010-01-01

We review our approach to the generation of nanoporous materials, both semiconducting and metallic, which leads to the existence of nanopores within the bulk structure. This method, which we have named as the expanding lattice method, is a novel transferable approach which consists first of constructing crystalline supercells with a large number of atoms and a density close to the real value and then lowering the density by increasing the volume. The resulting supercells are subjected to either ab initio or parameterized—Tersoff-based—molecular dynamics processes at various temperatures, all below the corresponding bulk melting points, followed by geometry relaxations. The resulting samples are essentially amorphous and display pores along some of the “crystallographic” directions without the need of incorporating ad hoc semiconducting atomic structural elements such as graphene-like sheets and/or chain-like patterns (reconstructive simulations) or of reproducing the experimental processes (mimetic simulations). We report radial (pair) distribution functions, nanoporous structures of C and Si, and some computational predictions for their vibrational density of states. We present numerical estimates and discuss possible applications of semiconducting materials for hydrogen storage in potential fuel tanks. Nanopore structures for metallic elements like Al and Au also obtained through the expanding lattice method are reported.

Imaging Plasmonic Fields with Atomic Spatiotemporal Resolution

NASA Astrophysics Data System (ADS)

Li, Jianxiong; Saydanzad, Erfan; Thumm, Uwe

2018-06-01

We propose a scheme for the reconstruction of plasmonic near fields at isolated nanoparticles from infrared-streaked extreme-ultraviolet photoemission spectra. Based on quantum-mechanically modeled spectra, we demonstrate and analyze the accurate imaging of the IR-streaking-pulse-induced transient plasmonic fields at the surface of gold nanospheres and nanoshells with subfemtosecond temporal and subnanometer spatial resolution.

Refined potentials for rare gas atom adsorption on rare gas and alkali-halide surfaces

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Heinbockel, J. H.; Outlaw, R. A.

1985-01-01

The utilization of models of interatomic potential for physical interaction to estimate the long range attractive potential for rare gases and ions is discussed. The long range attractive force is calculated in terms of the atomic dispersion properties. A data base of atomic dispersion parameters for rare gas atoms, alkali ion, and halogen ions is applied to the study of the repulsive core; the procedure for evaluating the repulsive core of ion interactions is described. The interaction of rare gas atoms on ideal rare gas solid and alkali-halide surfaces is analyzed; zero coverage absorption potentials are derived.

Improving tritium exposure reconstructions using accelerator mass spectrometry

PubMed Central

Hunt, J. R.; Vogel, J. S.; Knezovich, J. P.

2010-01-01

Direct measurement of tritium atoms by accelerator mass spectrometry (AMS) enables rapid low-activity tritium measurements from milligram-sized samples and permits greater ease of sample collection, faster throughput, and increased spatial and/or temporal resolution. Because existing methodologies for quantifying tritium have some significant limitations, the development of tritium AMS has allowed improvements in reconstructing tritium exposure concentrations from environmental measurements and provides an important additional tool in assessing the temporal and spatial distribution of chronic exposure. Tritium exposure reconstructions using AMS were previously demonstrated for a tree growing on known levels of tritiated water and for trees exposed to atmospheric releases of tritiated water vapor. In these analyses, tritium levels were measured from milligram-sized samples with sample preparation times of a few days. Hundreds of samples were analyzed within a few months of sample collection and resulted in the reconstruction of spatial and temporal exposure from tritium releases. Although the current quantification limit of tritium AMS is not adequate to determine natural environmental variations in tritium concentrations, it is expected to be sufficient for studies assessing possible health effects from chronic environmental tritium exposure. PMID:14735274

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.

Transition from reconstruction toward thin film on the (110) surface of strontium titanate

DOE PAGES

Wang, Z.; Loon, A.; Subramanian, A.; ...

2016-03-08

The surfaces of metal oxides often are reconstructed with a geometry and composition that is considerably different from a simple termination of the bulk. Such structures can also be viewed as ultrathin films, epitaxed on a substrate. Here, the reconstructions of the SrTiO 3 (110) surface are studied combining scanning tunneling microscopy (STM), transmission electron diffraction, and X-ray absorption spectroscopy (XAS), and analyzed with density functional theory calculations. Whereas SrTiO 3 (110) invariably terminates with an overlayer of titania, with increasing density its structure switches from n × 1 to 2 × n. At the same time the coordination ofmore » the Ti atoms changes from a network of corner-sharing tetrahedra to a double layer of edge-shared octahedra with bridging units of octahedrally coordinated strontium. Furthermore, this transition from the n × 1 to 2 × n reconstructions is a transition from a pseudomorphically stabilized tetrahedral network toward an octahedral titania thin film with stress-relief from octahedral strontia units at the surface.« less

Sparse Reconstruction for Temperature Distribution Using DTS Fiber Optic Sensors with Applications in Electrical Generator Stator Monitoring.

PubMed

Bazzo, João Paulo; Pipa, Daniel Rodrigues; da Silva, Erlon Vagner; Martelli, Cicero; Cardozo da Silva, Jean Carlos

2016-09-07

This paper presents an image reconstruction method to monitor the temperature distribution of electric generator stators. The main objective is to identify insulation failures that may arise as hotspots in the structure. The method is based on temperature readings of fiber optic distributed sensors (DTS) and a sparse reconstruction algorithm. Thermal images of the structure are formed by appropriately combining atoms of a dictionary of hotspots, which was constructed by finite element simulation with a multi-physical model. Due to difficulties for reproducing insulation faults in real stator structure, experimental tests were performed using a prototype similar to the real structure. The results demonstrate the ability of the proposed method to reconstruct images of hotspots with dimensions down to 15 cm, representing a resolution gain of up to six times when compared to the DTS spatial resolution. In addition, satisfactory results were also obtained to detect hotspots with only 5 cm. The application of the proposed algorithm for thermal imaging of generator stators can contribute to the identification of insulation faults in early stages, thereby avoiding catastrophic damage to the structure.

Tensor-based Dictionary Learning for Spectral CT Reconstruction

PubMed Central

Zhang, Yanbo; Wang, Ge

2016-01-01

Spectral computed tomography (CT) produces an energy-discriminative attenuation map of an object, extending a conventional image volume with a spectral dimension. In spectral CT, an image can be sparsely represented in each of multiple energy channels, and are highly correlated among energy channels. According to this characteristics, we propose a tensor-based dictionary learning method for spectral CT reconstruction. In our method, tensor patches are extracted from an image tensor, which is reconstructed using the filtered backprojection (FBP), to form a training dataset. With the Candecomp/Parafac decomposition, a tensor-based dictionary is trained, in which each atom is a rank-one tensor. Then, the trained dictionary is used to sparsely represent image tensor patches during an iterative reconstruction process, and the alternating minimization scheme is adapted for optimization. The effectiveness of our proposed method is validated with both numerically simulated and real preclinical mouse datasets. The results demonstrate that the proposed tensor-based method generally produces superior image quality, and leads to more accurate material decomposition than the currently popular popular methods. PMID:27541628

Refining glass structure in two dimensions

NASA Astrophysics Data System (ADS)

Sadjadi, Mahdi; Bhattarai, Bishal; Drabold, D. A.; Thorpe, M. F.; Wilson, Mark

2017-11-01

Recently determined atomistic scale structures of near-two dimensional bilayers of vitreous silica (using scanning probe and electron microscopy) allow us to refine the experimentally determined coordinates to incorporate the known local chemistry more precisely. Further refinement is achieved by using classical potentials of varying complexity: one using harmonic potentials and the second employing an electrostatic description incorporating polarization effects. These are benchmarked against density functional calculations. Our main findings are that (a) there is a symmetry plane between the two disordered layers, a nice example of an emergent phenomena, (b) the layers are slightly tilted so that the Si-O-Si angle between the two layers is not 180∘ as originally thought but rather 175 ±2∘ , and (c) while interior areas that are not completely imagined can be reliably reconstructed, surface areas are more problematic. It is shown that small crystallites that appear are just as expected statistically in a continuous random network. This provides a good example of the value that can be added to disordered structures imaged at the atomic level by implementing computer refinement.

No need for external orthogonality in subsystem density-functional theory.

PubMed

Unsleber, Jan P; Neugebauer, Johannes; Jacob, Christoph R

2016-08-03

Recent reports on the necessity of using externally orthogonal orbitals in subsystem density-functional theory (SDFT) [Annu. Rep. Comput. Chem., 8, 2012, 53; J. Phys. Chem. A, 118, 2014, 9182] are re-investigated. We show that in the basis-set limit, supermolecular Kohn-Sham-DFT (KS-DFT) densities can exactly be represented as a sum of subsystem densities, even if the subsystem orbitals are not externally orthogonal. This is illustrated using both an analytical example and in basis-set free numerical calculations for an atomic test case. We further show that even with finite basis sets, SDFT calculations using accurate reconstructed potentials can closely approach the supermolecular KS-DFT density, and that the deviations between SDFT and KS-DFT decrease as the basis-set limit is approached. Our results demonstrate that formally, there is no need to enforce external orthogonality in SDFT, even though this might be a useful strategy when developing projection-based DFT embedding schemes.

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

PubMed Central

Reddy, Hemanth K.N.; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A.; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Kurta, Ruslan P.; Larsson, Daniel S.D.; Duane Loh, N.; Maia, Filipe R.N.C.; Mancuso, Adrian P.; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A.; Song, Changyong; Spence, John C.H.; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu

2017-01-01

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency. PMID:28654088

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

DOE PAGES

Reddy, Hemanth K. N.; Yoon, Chun Hong; Aquila, Andrew; ...

2017-06-27

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. As a result, themore » data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.« less

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.

PubMed

Reddy, Hemanth K N; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A; Kurta, Ruslan P; Larsson, Daniel S D; Duane Loh, N; Maia, Filipe R N C; Mancuso, Adrian P; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A; Song, Changyong; Spence, John C H; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A; Williams, Garth J; Xavier, P Lourdu

2017-06-27

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

Method for construction of a biased potential for hyperdynamic simulation of atomic systems

NASA Astrophysics Data System (ADS)

Duda, E. V.; Kornich, G. V.

2017-10-01

An approach to constructing a biased potential for hyperdynamic simulation of atomic systems is considered. Using this approach, the diffusion of an atom adsorbed on the surface of a two-dimensional crystal and a vacancy in the bulk of the crystal are simulated. The influence of the variation in the potential barriers due to thermal vibrations of atoms on the results of calculations is discussed. It is shown that the bias of the potential in the hyperdynamic simulation makes it possible to obtain statistical samples of transitions of atomic systems between states, similar to those given by classical molecular dynamics. However, hyperdynamics significantly accelerates computations in comparison with molecular dynamics in the case of temperature-activated transitions and the associated processes in atomic systems.

Scalp reconstruction: an algorithmic approach and systematic review.

PubMed

Desai, Shaun C; Sand, Jordan P; Sharon, Jeffrey D; Branham, Gregory; Nussenbaum, Brian

2015-01-01

Reconstruction of the scalp after acquired defects remains a common challenge for the reconstructive surgeon, especially in a patient with a history of radiation to the area. To review the current literature and describe a novel algorithm to help guide the reconstructive surgeon in determining the optimal reconstruction from a cosmetic and functional standpoint. Pertinent surgical anatomy, considerations for patient and technique selection, reconstructive goals, as well as the reconstructive ladder, are also discussed. A PubMed and Medline search was performed of the entire English literature with respect to scalp reconstruction. Priority of review was given to those studies with higher-quality levels of evidence. Size, location, radiation history, and potential for hairline distortion are important factors in determining the ideal reconstruction. The tighter and looser areas of the scalp play a major role in the potential for primary or local flap closure. Patients with medium to large defects and a history of radiation will likely benefit from free tissue transfer. Ideal reconstruction of scalp defects relies on a comprehensive understanding of scalp anatomy, a full consideration of the armamentarium of surgical techniques, and a detailed appraisal of patient factors and expectations. The simplest reconstruction should be used whenever possible to provide the most functional and aesthetic scalp reconstruction, with the least amount of complexity. NA.

Mixing of MnPc electronic states at the MnPc/Au(110) interface

NASA Astrophysics Data System (ADS)

Gargiani, Pierluigi; Lisi, Simone; Avvisati, Giulia; Mondelli, Pierluigi; Fatale, Sara; Betti, Maria Grazia

2017-10-01

Manganese-phthalocyanines form assembled chains with a variety of ordered super-structures, flat lying along the Au(110) reconstructed channels. The chains first give rise to a ×5 symmetry reconstruction, while further deposition of MnPc leads to a ×7 periodicity at the completion of the first single layer. A net polarization with the formation of an interface dipole is mainly due to the molecular π-states located on the macrocycles pyrrole rings, while the central metal ion induces a reduction in the polarization, whose amount is related to the Mn-Au interaction. The adsorption-induced interface polarization is compared to other 3d-metal phthalocyanines, to unravel the role of the central metal atom configuration in the interaction process of the d-states. The MnPc adsorption on Au(110) induces the re-hybridization of the electronic states localized on the central metal atom, promoting a charge redistribution of the molecular orbitals of the MnPc molecules. The molecule-substrate interaction is controlled by a symmetry-determined mixing between the electronic states, involving also the molecular empty orbitals with d character hybridized with the nitrogen atoms of the pyrrole ring, as deduced by photoemission and X-ray absorption spectroscopy exploiting light polarization. The symmetry-determined mixing between the electronic states of the Mn metal center and of the Au substrate induces a density of states close to the Fermi level for the ×5 phase.

3D tomographic reconstruction of the terrestrial exosphere and its time-dependent coupling to the magnetospheric ring current

NASA Astrophysics Data System (ADS)

Waldrop, L.; Cucho-Padin, G.; Ilie, R.

2017-12-01

Charge exchange collisions between ring current ions and hydrogen (H) atoms in the outer exosphere serve to dissipate magnetospheric energy, particularly during the slow recovery phase of geomagnetic storms, through the generation of energetic neutral atoms (ENAs) which escape the system. As a result, knowledge of the spatial distribution and temporal variability of exospheric H density is critical for reliable interpretation of ENA flux measurements as well as for accurate modeling of the ring current. Although numerous theoretical, numerical, and empirical H distributions have been used for such analyses, their reliance on ad hoc or unphysical assumptions, together with their inherently static formulations, is a source of significant uncertainty. Our recent development of a robust tomographic technique for the model-independent estimation of global exospheric H density from optical remote sensing data overcomes the limitations of past analysis and enables an unprecedented investigation of global exospheric and ring current dynamics. Here, we present sample results of our 3D, time-dependent reconstructions of exospheric structure, derived from measurements of resonantly scattered solar Lyman-alpha (121.6 nm) photons acquired by the Lyman-alpha detectors (LADs) onboard NASA's Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) mission. We use the Hot Electron and Ion Drift Integrator (HEIDI) kinetic model of the ring current to investigate the charge exchange interactions between the resulting H density distribution and ring current ions and generate synthetic images of ENA flux for comparison with those measured by TWINS.

The projected gravitational potential of the galaxy cluster MACS J1206 derived from galaxy kinematics

NASA Astrophysics Data System (ADS)

Stock, Dennis; Meyer, Sven; Sarli, Eleonora; Bartelmann, Matthias; Balestra, Italo; Grillo, Claudio; Koekemoer, Anton; Mercurio, Amata; Nonino, Mario; Rosati, Piero

2015-12-01

We reconstruct the radial profile of the projected gravitational potential of the galaxy cluster MACS J1206 from 592 spectroscopic measurements of velocities of cluster members. To accomplish this, we use a method we have developed recently based on the Richardson-Lucy deprojection algorithm and an inversion of the spherically-symmetric Jeans equation. We find that, within the uncertainties, our reconstruction agrees very well with a potential reconstruction from weak and strong gravitational lensing as well as with a potential obtained from X-ray measurements. In addition, our reconstruction is in good agreement with several common analytic profiles of the lensing potential. Varying the anisotropy parameter in the Jeans equation, we find that isotropy parameters, which are either small, β ≲ 0.2, or decrease with radius, yield potential profiles that strongly disagree with that obtained from gravitational lensing. We achieve the best agreement between our potential profile and the profile from gravitational lensing if the anisotropy parameter rises steeply to β ≈ 0.6 within ≈ 0.5 Mpc and stays constant further out.

Comparison Study of Three Different Image Reconstruction Algorithms for MAT-MI

PubMed Central

Xia, Rongmin; Li, Xu

2010-01-01

We report a theoretical study on magnetoacoustic tomography with magnetic induction (MAT-MI). According to the description of signal generation mechanism using Green’s function, the acoustic dipole model was proposed to describe acoustic source excited by the Lorentz force. Using Green’s function, three kinds of reconstruction algorithms based on different models of acoustic source (potential energy, vectored acoustic pressure, and divergence of Lorenz force) are deduced and compared, and corresponding numerical simulations were conducted to compare these three kinds of reconstruction algorithms. The computer simulation results indicate that the potential energy method and vectored pressure method can directly reconstruct the Lorentz force distribution and give a more accurate reconstruction of electrical conductivity. PMID:19846363

Shell-isolated nanoparticle-enhanced Raman spectroscopy study of the adsorption behaviour of DNA bases on Au(111) electrode surfaces.

PubMed

Wen, Bao-Ying; Jin, Xi; Li, Yue; Wang, Ya-Hao; Li, Chao-Yu; Liang, Miao-Miao; Panneerselvam, Rajapandiyan; Xu, Qing-Chi; Wu, De-Yin; Yang, Zhi-Lin; Li, Jian-Feng; Tian, Zhong-Qun

2016-06-21

For the first time, we used the electrochemical shell-isolated nanoparticle-enhanced Raman spectroscopy (EC-SHINERS) technique to in situ characterize the adsorption behaviour of four DNA bases (adenine, guanine, thymine, and cytosine) on atomically flat Au(111) electrode surfaces. The spectroscopic results of the various molecules reveal similar features, such as the adsorption-induced reconstruction of the Au(111) surface and the drastic Raman intensity reduction of the ring breathing modes after the lifting reconstruction. As a preliminary study of the photo-induced charge transfer (PICT) mechanism, the in situ spectroscopic results obtained on single crystal surfaces are excellently illustrated with electrochemical data.

Physically representative atomistic modeling of atomic-scale friction

NASA Astrophysics Data System (ADS)

Dong, Yalin

Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the interesting physical process is buried between the two contact interfaces, thus makes a direct measurement more difficult. Atomistic simulation is able to simulate the process with the dynamic information of each single atom, and therefore provides valuable interpretations for experiments. In this, we will systematically to apply Molecular Dynamics (MD) simulation to optimally model the Atomic Force Microscopy (AFM) measurement of atomic friction. Furthermore, we also employed molecular dynamics simulation to correlate the atomic dynamics with the friction behavior observed in experiments. For instance, ParRep dynamics (an accelerated molecular dynamic technique) is introduced to investigate velocity dependence of atomic friction; we also employ MD simulation to "see" how the reconstruction of gold surface modulates the friction, and the friction enhancement mechanism at a graphite step edge. Atomic stick-slip friction can be treated as a rate process. Instead of running a direction simulation of the process, we can apply transition state theory to predict its property. We will have a rigorous derivation of velocity and temperature dependence of friction based on the Prandtl-Tomlinson model as well as transition theory. A more accurate relation to prediction velocity and temperature dependence is obtained. Furthermore, we have included instrumental noise inherent in AFM measurement to interpret two discoveries in experiments, suppression of friction at low temperature and the attempt frequency discrepancy between AFM measurement and theoretical prediction. We also discuss the possibility to treat wear as a rate process.

Preclinical Models in Vascularized Composite Allotransplantation

DTIC Science & Technology

2015-06-28

VCA) has the potential to reconstruct any non-visceral tissue defect, using like for like tissue, delivering optimal form and function. Over 150 VCA... Reconstructive transplantation Introduction To date, over 150 VCA transplants have been performed,most commonly of the hand and face, but also abdominal wall...larynx, lower limb, uterus and penis [1, 2]. Any non-visceral tissue defect can potentially be reconstructed in this manner using like for like tissue

Errors and Uncertainties in Dose Reconstruction for Radiation Effects Research

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

Strom, Daniel J.

Dose reconstruction for studies of the health effects of ionizing radiation have been carried out for many decades. Major studies have included Japanese bomb survivors, atomic veterans, downwinders of the Nevada Test Site and Hanford, underground uranium miners, and populations of nuclear workers. For such studies to be credible, significant effort must be put into applying the best science to reconstructing unbiased absorbed doses to tissues and organs as a function of time. In many cases, more and more sophisticated dose reconstruction methods have been developed as studies progressed. For the example of the Japanese bomb survivors, the dose surrogatemore » “distance from the hypocenter” was replaced by slant range, and then by TD65 doses, DS86 doses, and more recently DS02 doses. Over the years, it has become increasingly clear that an equal level of effort must be expended on the quantitative assessment of uncertainty in such doses, and to reducing and managing uncertainty. In this context, this paper reviews difficulties in terminology, explores the nature of Berkson and classical uncertainties in dose reconstruction through examples, and proposes a path forward for Joint Coordinating Committee for Radiation Effects Research (JCCRER) Project 2.4 that requires a reasonably small level of effort for DOSES-2008.« less

Use of the ventricular propagated excitation model in the magnetocardiographic inverse problem for reconstruction of electrophysiological properties.

PubMed

Ohyu, Shigeharu; Okamoto, Yoshiwo; Kuriki, Shinya

2002-06-01

A novel magnetocardiographic inverse method for reconstructing the action potential amplitude (APA) and the activation time (AT) on the ventricular myocardium is proposed. This method is based on the propagated excitation model, in which the excitation is propagated through the ventricle with nonuniform height of action potential. Assumption of stepwise waveform on the transmembrane potential was introduced in the model. Spatial gradient of transmembrane potential, which is defined by APA and AT distributed in the ventricular wall, is used for the computation of a current source distribution. Based on this source model, the distributions of APA and AT are inversely reconstructed from the QRS interval of magnetocardiogram (MCG) utilizing a maximum a posteriori approach. The proposed reconstruction method was tested through computer simulations. Stability of the methods with respect to measurement noise was demonstrated. When reference APA was provided as a uniform distribution, root-mean-square errors of estimated APA were below 10 mV for MCG signal-to-noise ratios greater than, or equal to, 20 dB. Low-amplitude regions located at several sites in reference APA distributions were correctly reproduced in reconstructed APA distributions. The goal of our study is to develop a method for detecting myocardial ischemia through the depression of reconstructed APA distributions.

Tomography of a Probe Potential Using Atomic Sensors on Graphene.

PubMed

Wyrick, Jonathan; Natterer, Fabian D; Zhao, Yue; Watanabe, Kenji; Taniguchi, Takashi; Cullen, William G; Zhitenev, Nikolai B; Stroscio, Joseph A

2016-12-27

Our ability to access and explore the quantum world has been greatly advanced by the power of atomic manipulation and local spectroscopy with scanning tunneling and atomic force microscopes, where the key technique is the use of atomically sharp probe tips to interact with an underlying substrate. Here we employ atomic manipulation to modify and quantify the interaction between the probe and the system under study that can strongly affect any measurement in low charge density systems, such as graphene. We transfer Co atoms from a graphene surface onto a probe tip to change and control the probe's physical structure, enabling us to modify the induced potential at a graphene surface. We utilize single Co atoms on a graphene field-effect device as atomic scale sensors to quantitatively map the modified potential exerted by the scanning probe over the whole relevant spatial and energy range.

Resolution Quality and Atom Positions in Sub-?ngstr?m Electron Microscopy

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

O'Keefe, Michael A.; Allard Jr, Lawrence Frederick; Blom, Douglas Allen

2005-01-01

John Cowley pioneered use of transmission electron microscopy (TEM) for high-resolution imaging and helped spur improvements in resolution that enabled researchers to pinpoint the positions of all but the lightest atoms within a crystal structure. Sub-{angstrom} capabilities allow imaging of even the lightest atoms. Initially achieved with software aberration correction (focal-series reconstruction of the specimen exit-surface wave), sub-{angstrom} imaging will become commonplace for next-generation electron microscopes with hardware-corrected lenses and monochromated electron beams. Currently, advanced HR-TEMs can image columns of light atoms (carbon, oxygen, nitrogen) in complex structures, including the lithium atoms present in battery materials. The ability to determinemore » whether an image peak represents one single atom (or atom column) instead of several depends on the resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to determine whether an image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation.« less

Stimulated transitions in resonant atom Majorana mixing

NASA Astrophysics Data System (ADS)

Bernabéu, José; Segarra, Alejandro

2018-02-01

Massive neutrinos demand to ask whether they are Dirac or Majorana particles. Majorana neutrinos are an irrefutable proof of physics beyond the Standard Model. Neutrinoless double electron capture is not a process but a virtual Δ L = 2 mixing between a parent A Z atom and a daughter A ( Z - 2) excited atom with two electron holes. As a mixing between two neutral atoms and the observable signal in terms of emitted two-hole X-rays, the strategy, experimental signature and background are different from neutrinoless double beta decay. The mixing is resonantly enhanced for almost degeneracy and, under these conditions, there is no irreducible background from the standard two-neutrino channel. We reconstruct the natural time history of a nominally stable parent atom since its production either by nature or in the laboratory. After the time periods of atom oscillations and the decay of the short-lived daughter atom, at observable times the relevant "stationary" states are the mixed metastable long-lived state and the non-orthogonal short-lived excited state, as well as the ground state of the daughter atom. We find that they have a natural population inversion which is most appropriate for exploiting the bosonic nature of the observed atomic transitions radiation. Among different observables of the atom Majorana mixing, we include the enhanced rate of stimulated X-ray emission from the long-lived metastable state by a high-intensity X-ray beam: a gain factor of 100 can be envisaged at current XFEL facilities. On the other hand, the historical population of the daughter atom ground state can be probed by exciting it with a current pulsed optical laser, showing the characteristic absorption lines: the whole population can be excited in a shorter time than typical pulse duration.

Multimodal Task-Driven Dictionary Learning for Image Classification

DTIC Science & Technology

2015-12-18

1 Multimodal Task-Driven Dictionary Learning for Image Classification Soheil Bahrampour, Student Member, IEEE, Nasser M. Nasrabadi, Fellow, IEEE...Asok Ray, Fellow, IEEE, and W. Kenneth Jenkins, Life Fellow, IEEE Abstract— Dictionary learning algorithms have been suc- cessfully used for both...reconstructive and discriminative tasks, where an input signal is represented with a sparse linear combination of dictionary atoms. While these methods are

Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1992-01-01

The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

Real time dynamics of Si magic clusters mediating phase transformation: Si(111)-(1 × 1) to (7 × 7) reconstruction revisited

NASA Astrophysics Data System (ADS)

Ong, Wei Jie; Tok, Eng Soon

2012-07-01

Using Scanning Tunneling Microscope (STM), we show that the surface undergoes phase transformation from disordered "1 × 1" to (7 × 7) reconstruction which is mediated by the formation of Si magic clusters. Mono-disperse Si magic clusters of size ~ 13.5 ± 0.5 Å can be formed by heating the Si(111) surface to 1200 °C and quenching it to room temperature at cooling rates of at least 100 °C/min. The structure consists of 3 tetra-clusters of size ~ 4.5 Ǻ similar to the Si magic clusters that were formed from Si adatoms deposited by Si solid source on Si(111)-(7 × 7) [1]. Using real time STM scanning to probe the surface at ~ 400 °C, we show that Si magic clusters pop up from the (1 × 1) surface and form spontaneously during the phase transformation. This is attributed to the difference in atomic density between "disordered 1 × 1" and (7 × 7) surface structures which lead to the release of excess Si atoms onto the surface as magic clusters.

Systematic implementation of spectral CT with a photon counting detector for liquid security inspection

NASA Astrophysics Data System (ADS)

Xu, Xiaofei; Xing, Yuxiang; Wang, Sen; Zhang, Li

2018-06-01

X-ray liquid security inspection system plays an important role in homeland security, while the conventional dual-energy CT (DECT) system may have a big deviation in extracting the atomic number and the electron density of materials in various conditions. Photon counting detectors (PCDs) have the capability of discriminating the incident photons of different energy. The technique becomes more and more mature in nowadays. In this work, we explore the performance of a multi-energy CT imaging system with a PCD for liquid security inspection in material discrimination. We used a maximum-likelihood (ML) decomposition method with scatter correction based on a cross-energy response model (CERM) for PCDs so that to improve the accuracy of atomic number and electronic density imaging. Experimental study was carried to examine the effectiveness and robustness of the proposed system. Our results show that the concentration of different solutions in physical phantoms can be reconstructed accurately, which could improve the material identification compared to current available dual-energy liquid security inspection systems. The CERM-base decomposition and reconstruction method can be easily used to different applications such as medical diagnosis.

Gctf: Real-time CTF determination and correction

PubMed Central

Zhang, Kai

2016-01-01

Accurate estimation of the contrast transfer function (CTF) is critical for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction. Here, a GPU-accelerated computer program, Gctf, for accurate and robust, real-time CTF determination is presented. The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction. Novel approaches in Gctf improve both speed and accuracy. In addition to GPU acceleration (e.g. 10–50×), a fast ‘1-dimensional search plus 2-dimensional refinement (1S2R)’ procedure further speeds up Gctf. Based on the global CTF determination, the local defocus for each particle and for single frames of movies is accurately refined, which improves CTF parameters of all particles for subsequent image processing. Novel diagnosis method using equiphase averaging (EPA) and self-consistency verification procedures have also been implemented in the program for practical use, especially for aims of near-atomic reconstruction. Gctf is an independent program and the outputs can be easily imported into other cryoEM software such as Relion (Scheres, 2012) and Frealign (Grigorieff, 2007). The results from several representative datasets are shown and discussed in this paper. PMID:26592709

First-Principles Study of Superconductivity in Ultra- thin Pb Films

NASA Astrophysics Data System (ADS)

Noffsinger, Jesse; Cohen, Marvin L.

2010-03-01

Recently, superconductivity in ultrathin layered Pb has been confirmed in samples with as few as two atomic layers [S. Qin, J. Kim, Q. Niu, and C.-K. Shih, Science 2009]. Interestingly, the prototypical strong-coupling superconductor exhibits different Tc's for differing surface reconstructions in samples with only two monolayers. Additionally, Tc is seen to oscillate as the number of atomic layers is increased. Using first principles techniques based on Wannier functions, we analyze the electronic structure, lattice dynamics and electron-phonon coupling for varying thicknesses and surface reconstructions of layered Pb. We discuss results as they relate to superconductivity in the bulk, for which accurate calculations of superconducting properties can be compared to experiment [W. L. McMillan and J.M. Rowell, PRL 1965]. This work was supported by National Science Foundation Grant No. DMR07-05941, the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Computational resources have been provided by the Lawrencium computational cluster resource provided by the IT Division at the Lawrence Berkeley National Laboratory (Supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231)

Si(111) strained layers on Ge(111): Evidence for c (2 ×4 ) domains

NASA Astrophysics Data System (ADS)

Zhachuk, R.; Coutinho, J.; Dolbak, A.; Cherepanov, V.; Voigtländer, B.

2017-08-01

The tensile-strained Si (111 ) layers grown on top of Ge (111 ) substrates are studied by combining scanning tunneling microscopy, low-energy electron diffraction, and first-principles calculations. It is shown that the layers exhibit c (2 ×4 ) domains, which are separated by domain walls along <1 ¯10 > directions. A model structure for the c (2 ×4 ) domains is proposed, which shows low formation energy and good agreement with the experimental data. The results of our calculations suggest that Ge atoms are likely to replace Si atoms with dangling bonds on the surface (rest-atoms and adatoms), thus significantly lowering the surface energy and inducing the formation of domain walls. The experiments and calculations demonstrate that when surface strain changes from compressive to tensile, the (111) reconstruction converts from dimer-adatom-stacking fault-based to adatom-based structures.

Diatomic Metasurface for Vectorial Holography.

PubMed

Deng, Zi-Lan; Deng, Junhong; Zhuang, Xin; Wang, Shuai; Li, Kingfai; Wang, Yao; Chi, Yihui; Ye, Xuan; Xu, Jian; Wang, Guo Ping; Zhao, Rongkuo; Wang, Xiaolei; Cao, Yaoyu; Cheng, Xing; Li, Guixin; Li, Xiangping

2018-05-09

The emerging metasurfaces with the exceptional capability of manipulating an arbitrary wavefront have revived the holography with unprecedented prospects. However, most of the reported metaholograms suffer from limited polarization controls for a restrained bandwidth in addition to their complicated meta-atom designs with spatially variant dimensions. Here, we demonstrate a new concept of vectorial holography based on diatomic metasurfaces consisting of metamolecules formed by two orthogonal meta-atoms. On the basis of a simply linear relationship between phase and polarization modulations with displacements and orientations of identical meta-atoms, active diffraction of multiple polarization states and reconstruction of holographic images are simultaneously achieved, which is robust against both incident angles and wavelengths. Leveraging this appealing feature, broadband vectorial holographic images with spatially varying polarization states and dual-way polarization switching functionalities have been demonstrated, suggesting a new route to achromatic diffractive elements, polarization optics, and ultrasecure anticounterfeiting.

Optical vector network analysis of ultranarrow transitions in 166Er3+ : 7LiYF4 crystal.

PubMed

Kukharchyk, N; Sholokhov, D; Morozov, O; Korableva, S L; Cole, J H; Kalachev, A A; Bushev, P A

2018-02-15

We present optical vector network analysis (OVNA) of an isotopically purified Er166 3+ :LiYF 4 7 crystal. The OVNA method is based on generation and detection of a modulated optical sideband by using a radio-frequency vector network analyzer. This technique is widely used in the field of microwave photonics for the characterization of optical responses of optical devices such as filters and high-Q resonators. However, dense solid-state atomic ensembles induce a large phase shift on one of the optical sidebands that results in the appearance of extra features on the measured transmission response. We present a simple theoretical model that accurately describes the observed spectra and helps to reconstruct the absorption profile of a solid-state atomic ensemble as well as corresponding change of the refractive index in the vicinity of atomic resonances.

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage

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

Walen, Holly, E-mail: hwalen@iastate.edu; Liu, Da-Jiang; Oh, Junepyo

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derivedmore » using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.« less

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage

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

Walen, Holly; Liu, Da -Jiang; Oh, Junepyo

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed cleansurface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, we derivedmore » using a limited cluster expansion based on density functional theory energetics. Furthermore, models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.« less

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage

DOE PAGES

Walen, Holly; Liu, Da -Jiang; Oh, Junepyo; ...

2015-07-06

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed cleansurface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, we derivedmore » using a limited cluster expansion based on density functional theory energetics. Furthermore, models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.« less

Study of α-Cu 0.82Al 0.18(100) using low energy ion scattering

NASA Astrophysics Data System (ADS)

Zhu, L.; Muhlen, E. Zur; O'Connor, D. J.; King, B. V.; MacDonald, R. J.

1996-07-01

The clean α-Cu 0.82Al 0.18(100) surface has been investigated using low energy ion scattering. The surface structure was found to be similar to the structure of the Cu(100) surface. By measuring the first layer concentration of Al using He + and Ne + beams and standard calibration procedure, the α-Cu 0.82Al 0.18(100) surface was found to be slightly Al-rich. Analysis of multiple scattering of ions suggests that Al atoms do not form islands. It was also found that Al atoms sit higher than the Cu atoms on the surface. By comparison with computer simulations (SABRE and FAN2D), the buckling of Al was found to be 0.16 ± 0.07 Å. No reconstructions were observed on the surface by low energy ion scattering which is in agreement with previous LEED studies.

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage.

PubMed

Walen, Holly; Liu, Da-Jiang; Oh, Junepyo; Lim, Hyunseob; Evans, J W; Kim, Yousoo; Thiel, P A

2015-07-07

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derived using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

PubMed Central

Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

2013-01-01

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems. PMID:23665897

Atomic level characterization in corrosion studies

NASA Astrophysics Data System (ADS)

Marcus, Philippe; Maurice, Vincent

2017-06-01

Atomic level characterization brings fundamental insight into the mechanisms of self-protection against corrosion of metals and alloys by oxide passive films and into how localized corrosion is initiated on passivated metal surfaces. This is illustrated in this overview with selected data obtained at the subnanometre, i.e. atomic or molecular, scale and also at the nanometre scale on single-crystal copper, nickel, chromium and stainless steel surfaces passivated in well-controlled conditions and analysed in situ and/or ex situ by scanning tunnelling microscopy/spectroscopy and atomic force microscopy. A selected example of corrosion modelling by ab initio density functional theory is also presented. The discussed aspects include the surface reconstruction induced by hydroxide adsorption and formation of two-dimensional (hydr)oxide precursors, the atomic structure, orientation and surface hydroxylation of three-dimensional ultrathin oxide passive films, the effect of grain boundaries in polycrystalline passive films acting as preferential sites of passivity breakdown, the differences in local electronic properties measured at grain boundaries of passive films and the role of step edges at the exposed surface of oxide grains on the dissolution of the passive film. This article is part of the themed issue 'The challenges of hydrogen and metals'.

Atomic Structures of Silicene Layers Grown on Ag(111): Scanning Tunneling Microscopy and Noncontact Atomic Force Microscopy Observations

PubMed Central

Resta, Andrea; Leoni, Thomas; Barth, Clemens; Ranguis, Alain; Becker, Conrad; Bruhn, Thomas; Vogt, Patrick; Le Lay, Guy

2013-01-01

Silicene, the considered equivalent of graphene for silicon, has been recently synthesized on Ag(111) surfaces. Following the tremendous success of graphene, silicene might further widen the horizon of two-dimensional materials with new allotropes artificially created. Due to stronger spin-orbit coupling, lower group symmetry and different chemistry compared to graphene, silicene presents many new interesting features. Here, we focus on very important aspects of silicene layers on Ag(111): First, we present scanning tunneling microscopy (STM) and non-contact Atomic Force Microscopy (nc-AFM) observations of the major structures of single layer and bi-layer silicene in epitaxy with Ag(111). For the (3 × 3) reconstructed first silicene layer nc-AFM represents the same lateral arrangement of silicene atoms as STM and therefore provides a timely experimental confirmation of the current picture of the atomic silicene structure. Furthermore, both nc-AFM and STM give a unifying interpretation of the second layer (√3 × √3)R ± 30° structure. Finally, we give support to the conjectured possible existence of less stable, ~2% stressed, (√7 × √7)R ± 19.1° rotated silicene domains in the first layer. PMID:23928998

An interface capturing scheme for modeling atomization in compressible flows

NASA Astrophysics Data System (ADS)

Garrick, Daniel P.; Hagen, Wyatt A.; Regele, Jonathan D.

2017-09-01

The study of atomization in supersonic flow is critical to ensuring reliable ignition of scramjet combustors under startup conditions. Numerical methods incorporating surface tension effects have largely focused on the incompressible regime as most atomization applications occur at low Mach numbers. Simulating surface tension effects in compressible flow requires robust numerical methods that can handle discontinuities caused by both shocks and material interfaces with high density ratios. In this work, a shock and interface capturing scheme is developed that uses the Harten-Lax-van Leer-Contact (HLLC) Riemann solver while a Tangent of Hyperbola for INterface Capturing (THINC) interface reconstruction scheme retains the fluid immiscibility condition in the volume fraction and phasic densities in the context of the five equation model. The approach includes the effects of compressibility, surface tension, and molecular viscosity. One and two-dimensional benchmark problems demonstrate the desirable interface sharpening and conservation properties of the approach. Simulations of secondary atomization of a cylindrical water column after its interaction with a shockwave show good qualitative agreement with experimentally observed behavior. Three-dimensional examples of primary atomization of a liquid jet in a Mach 2 crossflow demonstrate the robustness of the method.

ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures.

PubMed

Park, Jungkap; Saitou, Kazuhiro

2014-09-18

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures. In this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named "rotamer-dependent atomic statistical potential" (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality. A new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.

Entanglement with negative Wigner function of almost 3,000 atoms heralded by one photon.

PubMed

McConnell, Robert; Zhang, Hao; Hu, Jiazhong; Ćuk, Senka; Vuletić, Vladan

2015-03-26

Quantum-mechanically correlated (entangled) states of many particles are of interest in quantum information, quantum computing and quantum metrology. Metrologically useful entangled states of large atomic ensembles have been experimentally realized, but these states display Gaussian spin distribution functions with a non-negative Wigner quasiprobability distribution function. Non-Gaussian entangled states have been produced in small ensembles of ions, and very recently in large atomic ensembles. Here we generate entanglement in a large atomic ensemble via an interaction with a very weak laser pulse; remarkably, the detection of a single photon prepares several thousand atoms in an entangled state. We reconstruct a negative-valued Wigner function--an important hallmark of non-classicality--and verify an entanglement depth (the minimum number of mutually entangled atoms) of 2,910 ± 190 out of 3,100 atoms. Attaining such a negative Wigner function and the mutual entanglement of virtually all atoms is unprecedented for an ensemble containing more than a few particles. Although the achieved purity of the state is slightly below the threshold for entanglement-induced metrological gain, further technical improvement should allow the generation of states that surpass this threshold, and of more complex Schrödinger cat states for quantum metrology and information processing. More generally, our results demonstrate the power of heralded methods for entanglement generation, and illustrate how the information contained in a single photon can drastically alter the quantum state of a large system.

3D Surface Reconstruction and Automatic Camera Calibration

NASA Technical Reports Server (NTRS)

Jalobeanu, Andre

2004-01-01

Illustrations in this view-graph presentation are presented on a Bayesian approach to 3D surface reconstruction and camera calibration.Existing methods, surface analysis and modeling,preliminary surface reconstruction results, and potential applications are addressed.

Effects of laser radiation field on energies of hydrogen atom in plasmas

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

Bahar, M. K., E-mail: mussiv58@gmail.com

2015-09-15

In this study, for the first time, the Schrödinger equation with more general exponential cosine screened Coulomb (MGECSC) potential is solved numerically in the presence of laser radiation field within the Ehlotzky approximation using the asymptotic iteration method. The MGECSC potential includes four different potential forms in consideration of different sets of the parameters in the potential. By applying laser field, the total interaction potential of hydrogen atom embedded in plasmas converts to double well-type potential. The plasma screening effects under the influence of laser field as well as confinement effects of laser field on hydrogen atom in Debye andmore » quantum plasmas are investigated by solving the Schrödinger equation with the laser-dressed MGECSC potential. It is resulted that since applying a monochromatic laser field on hydrogen atom embedded in a Debye and quantum plasma causes to shift in the profile of the total interaction potential, the confinement effects of laser field on hydrogen atom in plasmas modeled by the MGECSC potential change localizations of energy states.« less

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

PubMed Central

Schmidt, Michael W.; Ivanic, Joseph; Ruedenberg, Klaus

2014-01-01

An analysis based on the variation principle shows that in the molecules H2+, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation. PMID:24880263

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion.

PubMed

Schmidt, Michael W; Ivanic, Joseph; Ruedenberg, Klaus

2014-05-28

An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

Regular and Chaotic Spatial Distribution of Bose-Einstein Condensed Atoms in a Ratchet Potential

NASA Astrophysics Data System (ADS)

Li, Fei; Xu, Lan; Li, Wenwu

2018-02-01

We study the regular and chaotic spatial distribution of Bose-Einstein condensed atoms with a space-dependent nonlinear interaction in a ratchet potential. There exists in the system a space-dependent atomic current that can be tuned via Feshbach resonance technique. In the presence of the space-dependent atomic current and a weak ratchet potential, the Smale-horseshoe chaos is studied and the Melnikov chaotic criterion is obtained. Numerical simulations show that the ratio between the intensities of optical potentials forming the ratchet potential, the wave vector of the laser producing the ratchet potential or the wave vector of the modulating laser can be chosen as the controlling parameters to result in or avoid chaotic spatial distributional states.

Deciphering chemical order/disorder and material properties at the single-atom level.

PubMed

Yang, Yongsoo; Chen, Chien-Chun; Scott, M C; Ophus, Colin; Xu, Rui; Pryor, Alan; Wu, Li; Sun, Fan; Theis, Wolfgang; Zhou, Jihan; Eisenbach, Markus; Kent, Paul R C; Sabirianov, Renat F; Zeng, Hao; Ercius, Peter; Miao, Jianwei

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction.

PubMed

Pittman, Nikéa; Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S; D'Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-10-30

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism.

Digital imaging mass spectrometry.

PubMed

Bamberger, Casimir; Renz, Uwe; Bamberger, Andreas

2011-06-01

Methods to visualize the two-dimensional (2D) distribution of molecules by mass spectrometric imaging evolve rapidly and yield novel applications in biology, medicine, and material surface sciences. Most mass spectrometric imagers acquire high mass resolution spectra spot-by-spot and thereby scan the object's surface. Thus, imaging is slow and image reconstruction remains cumbersome. Here we describe an imaging mass spectrometer that exploits the true imaging capabilities by ion optical means for the time of flight mass separation. The mass spectrometer is equipped with the ASIC Timepix chip as an array detector to acquire the position, mass, and intensity of ions that are imaged by matrix-assisted laser desorption/ionization (MALDI) directly from the target sample onto the detector. This imaging mass spectrometer has a spatial resolving power at the specimen of (84 ± 35) μm with a mass resolution of 45 and locates atoms or organic compounds on a surface area up to ~2 cm(2). Extended laser spots of ~5 mm(2) on structured specimens allows parallel imaging of selected masses. The digital imaging mass spectrometer proves high hit-multiplicity, straightforward image reconstruction, and potential for high-speed readout at 4 kHz or more. This device demonstrates a simple way of true image acquisition like a digital photographic camera. The technology may enable a fast analysis of biomolecular samples in near future.

Internal Energy Transfer and Dissociation Model Development using Accelerated First-Principles Simulations of Hypersonic Flow Features

DTIC Science & Technology

2013-07-11

in Fig. 3) is simulated. Each atom interacts with its neighboring atoms through a potential energy surface (PES), such as the simple Lennard - Jones ... Lennard -­‐ Jones  (LJ)   potential  energy  surface  (PES)  dictating  atomic  interaction  forces. The main point of this section is to...the potential energy surface (PES) that governs individual atomic interaction forces. In contrast to existing rotational energy models, we found

Optimization-based reconstruction for reduction of CBCT artifact in IGRT

NASA Astrophysics Data System (ADS)

Xia, Dan; Zhang, Zheng; Paysan, Pascal; Seghers, Dieter; Brehm, Marcus; Munro, Peter; Sidky, Emil Y.; Pelizzari, Charles; Pan, Xiaochuan

2016-04-01

Kilo-voltage cone-beam computed tomography (CBCT) plays an important role in image guided radiation therapy (IGRT) by providing 3D spatial information of tumor potentially useful for optimizing treatment planning. In current IGRT CBCT system, reconstructed images obtained with analytic algorithms, such as FDK algorithm and its variants, may contain artifacts. In an attempt to compensate for the artifacts, we investigate optimization-based reconstruction algorithms such as the ASD-POCS algorithm for potentially reducing arti- facts in IGRT CBCT images. In this study, using data acquired with a physical phantom and a patient subject, we demonstrate that the ASD-POCS reconstruction can significantly reduce artifacts observed in clinical re- constructions. Moreover, patient images reconstructed by use of the ASD-POCS algorithm indicate a contrast level of soft-tissue improved over that of the clinical reconstruction. We have also performed reconstructions from sparse-view data, and observe that, for current clinical imaging conditions, ASD-POCS reconstructions from data collected at one half of the current clinical projection views appear to show image quality, in terms of spatial and soft-tissue-contrast resolution, higher than that of the corresponding clinical reconstructions.

MRI diffusion tensor reconstruction with PROPELLER data acquisition.

PubMed

Cheryauka, Arvidas B; Lee, James N; Samsonov, Alexei A; Defrise, Michel; Gullberg, Grant T

2004-02-01

MRI diffusion imaging is effective in measuring the diffusion tensor in brain, cardiac, liver, and spinal tissue. Diffusion tensor tomography MRI (DTT MRI) method is based on reconstructing the diffusion tensor field from measurements of projections of the tensor field. Projections are obtained by appropriate application of rotated diffusion gradients. In the present paper, the potential of a novel data acquisition scheme, PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction), is examined in combination with DTT MRI for its capability and sufficiency for diffusion imaging. An iterative reconstruction algorithm is used to reconstruct the diffusion tensor field from rotated diffusion weighted blades by appropriate rotated diffusion gradients. DTT MRI with PROPELLER data acquisition shows significant potential to reduce the number of weighted measurements, avoid ambiguity in reconstructing diffusion tensor parameters, increase signal-to-noise ratio, and decrease the influence of signal distortion.

Two-point motional Stark effect diagnostic for Madison Symmetric Torus

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

Ko, J.; Den Hartog, D. J.; Caspary, K. J.

2010-10-15

A high-precision spectral motional Stark effect (MSE) diagnostic provides internal magnetic field measurements for Madison Symmetric Torus (MST) plasmas. Currently, MST uses two spatial views - on the magnetic axis and on the midminor (off-axis) radius, the latter added recently. A new analysis scheme has been developed to infer both the pitch angle and the magnitude of the magnetic field from MSE spectra. Systematic errors are reduced by using atomic data from atomic data and analysis structure in the fit. Reconstructed current density and safety factor profiles are more strongly and globally constrained with the addition of the off-axis radiusmore » measurement than with the on-axis one only.« less

TED analysis of the Si(113) surface structure

NASA Astrophysics Data System (ADS)

Suzuki, T.; Minoda, H.; Tanishiro, Y.; Yagi, K.

1999-09-01

We carried out a TED (transmission electron diffraction) analysis of the Si(113) surface structure. The TED patterns taken at room temperature showed reflections due to the 3×2 reconstructed structure. The TED pattern indicated that a glide plane parallel to the <332> direction suggested in some models is excluded. We calculated the R-factors (reliability factors) for six surface structure models proposed previously. All structure models with energy-optimized atomic positions have large R-factors. After revision of the atomic positions, the R-factors of all the structure models decreased below 0.3, and the revised version of Dabrowski's 3×2 model has the smallest R-factor of 0.17.

Paleotopographic Reconstruction of the Tharsis Magmatic Complex Reveals Potential Ancient Drainage Basin/Aquifer System

NASA Technical Reports Server (NTRS)

Dohm, J. M.; Ferris, J.; Anderson, R. C.; Baker, V.; Hare, T.; Barlow, N. G.; Strom, R. G.; Tanaka, K. L.; Scott, D. H.

2001-01-01

Paleotopographic reconstructions reveal the potential existence of an enormous Noachian drainage basin in the eastern part of the Tharsis region of significant geologic and paleohydrologic implications. Additional information is contained in the original extended abstract.

Automatic selection of atomic fingerprints and reference configurations for machine-learning potentials

NASA Astrophysics Data System (ADS)

Imbalzano, Giulio; Anelli, Andrea; Giofré, Daniele; Klees, Sinja; Behler, Jörg; Ceriotti, Michele

2018-06-01

Machine learning of atomic-scale properties is revolutionizing molecular modeling, making it possible to evaluate inter-atomic potentials with first-principles accuracy, at a fraction of the costs. The accuracy, speed, and reliability of machine learning potentials, however, depend strongly on the way atomic configurations are represented, i.e., the choice of descriptors used as input for the machine learning method. The raw Cartesian coordinates are typically transformed in "fingerprints," or "symmetry functions," that are designed to encode, in addition to the structure, important properties of the potential energy surface like its invariances with respect to rotation, translation, and permutation of like atoms. Here we discuss automatic protocols to select a number of fingerprints out of a large pool of candidates, based on the correlations that are intrinsic to the training data. This procedure can greatly simplify the construction of neural network potentials that strike the best balance between accuracy and computational efficiency and has the potential to accelerate by orders of magnitude the evaluation of Gaussian approximation potentials based on the smooth overlap of atomic positions kernel. We present applications to the construction of neural network potentials for water and for an Al-Mg-Si alloy and to the prediction of the formation energies of small organic molecules using Gaussian process regression.

Algorithm-enabled exploration of image-quality potential of cone-beam CT in image-guided radiation therapy

NASA Astrophysics Data System (ADS)

Han, Xiao; Pearson, Erik; Pelizzari, Charles; Al-Hallaq, Hania; Sidky, Emil Y.; Bian, Junguo; Pan, Xiaochuan

2015-06-01

Kilo-voltage (KV) cone-beam computed tomography (CBCT) unit mounted onto a linear accelerator treatment system, often referred to as on-board imager (OBI), plays an increasingly important role in image-guided radiation therapy. While the FDK algorithm is currently used for reconstructing images from clinical OBI data, optimization-based reconstruction has also been investigated for OBI CBCT. An optimization-based reconstruction involves numerous parameters, which can significantly impact reconstruction properties (or utility). The success of an optimization-based reconstruction for a particular class of practical applications thus relies strongly on appropriate selection of parameter values. In the work, we focus on tailoring the constrained-TV-minimization-based reconstruction, an optimization-based reconstruction previously shown of some potential for CBCT imaging conditions of practical interest, to OBI imaging through appropriate selection of parameter values. In particular, for given real data of phantoms and patient collected with OBI CBCT, we first devise utility metrics specific to OBI-quality-assurance tasks and then apply them to guiding the selection of parameter values in constrained-TV-minimization-based reconstruction. The study results show that the reconstructions are with improvement, relative to clinical FDK reconstruction, in both visualization and quantitative assessments in terms of the devised utility metrics.

Tunneling and traversal of ultracold three-level atoms through vacuum-induced potentials

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

Badshah, Fazal; Irfan, Muhammad; Qamar, Shahid

2011-09-15

The passage of ultracold three-level atoms through the potential induced by the vacuum cavity mode is discussed using cascade atomic configuration. We study the tunneling or traversal time of the ultracold atoms via a bimodal high-Q cavity. It is found that the phase time, which may be considered as a measure for the time required to traverse the cavity, exhibits superclassical and subclassical behaviors. Further, the dark states and interference effects in cascade atomic configuration may influence the passage time of the atom through the cavity.

Pursuit of the Kramers-Henneberger atom

NASA Astrophysics Data System (ADS)

Wei, Qi; Wang, Pingxiao; Kais, Sabre; Herschbach, Dudley

2017-09-01

Superstrong femtosecond pulsed lasers can profoundly alter electronic structure of atoms and molecules. The oscillating laser field drives one or more electrons almost free. When averaged over, the rapid oscillations combine with the static Coulomb potential to create an effective binding potential. The consequent array of bound states comprises the ;Kramers-Henneberger Atom;. Theorists have brought forth many properties of KH atoms, yet convincing experimental evidence is meager. We examine a remarkable experiment accelerating atoms (Eichmann et al., 2009). It offers tantalizing evidence for the KH atom, with prospects for firm confirmation by adjustment of laser parameters.

Using tree ring cellulose as a tool to estimate past tritium inputs to the ocean

NASA Astrophysics Data System (ADS)

Stark, S.; Statham, P. J.; Stanley, R.; Jenkins, W. J.

2005-09-01

Tritium ( 3H) concentrations in tree rings should reflect ambient precipitation. Thus, to improve knowledge of the 3H input to the oceans, we developed a new technique to measure 3H concentrations in annual tree rings. Measurements of 3H were made on cellulose, the primary constituent of wood, as the isotopic signal of its carbon bound hydrogen atoms should be unchanged since biosynthesis. Traditional cellulose extraction techniques from softwoods are slow and were found to not yield reproducibly pure cellulose. Therefore, a new microwave method was developed which reduces extraction times from 3-5 days to approximately 3 h. Potential 3H contamination from the hydroxyl groups of the cellulose molecule was subsequently removed by exchange with 3H-free NaOH, thus avoiding the dangers of working with large amounts of cellulose nitrate. The validity of the technique was tested by presenting a 3H time series from a cedar tree which grew in Tollymore Forest Park, Northern Ireland, for comparison with 3H data from the Valentia weather station. We find that the 3H in the cellulose clearly reflects the 3H in precipitation with no significant smearing of the bomb signal. A simple box model illustrates that the maximum reservoir residence time of source water for the tree is less than 1 yr, suggesting that groundwater is not a major source of water for this tree. In general, however, the groundwater input needs to be quantified for accurate 3H reconstructions to be made. This work demonstrates the potential of using 3H in wood cellulose as a proxy for 3H in precipitation and, thus, opens the door to reconstruction of past 3H inputs to the ocean.

SU-E-J-02: 4D Digital Tomosynthesis Based On Algebraic Image Reconstruction and Total-Variation Minimization for the Improvement of Image Quality

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

Kim, D; Kang, S; Kim, T

2014-06-01

Purpose: In this paper, we implemented the four-dimensional (4D) digital tomosynthesis (DTS) imaging based on algebraic image reconstruction technique and total-variation minimization method in order to compensate the undersampled projection data and improve the image quality. Methods: The projection data were acquired as supposed the cone-beam computed tomography system in linear accelerator by the Monte Carlo simulation and the in-house 4D digital phantom generation program. We performed 4D DTS based upon simultaneous algebraic reconstruction technique (SART) among the iterative image reconstruction technique and total-variation minimization method (TVMM). To verify the effectiveness of this reconstruction algorithm, we performed systematic simulation studiesmore » to investigate the imaging performance. Results: The 4D DTS algorithm based upon the SART and TVMM seems to give better results than that based upon the existing method, or filtered-backprojection. Conclusion: The advanced image reconstruction algorithm for the 4D DTS would be useful to validate each intra-fraction motion during radiation therapy. In addition, it will be possible to give advantage to real-time imaging for the adaptive radiation therapy. This research was supported by Leading Foreign Research Institute Recruitment Program (Grant No.2009-00420) and Basic Atomic Energy Research Institute (BAERI); (Grant No. 2009-0078390) through the National Research Foundation of Korea(NRF) funded by the Ministry of Science, ICT and Future Planning (MSIP)« less

Repulsive Casimir-Polder potential by a negative reflecting surface

NASA Astrophysics Data System (ADS)

Yuan, Qi-Zhang

2015-07-01

We present a scheme to generate an all-range long repulsive Casimir-Polder potential between a perfect negative reflecting surface and a ground-state atom. The repulsive potential is stable and does not decay with time. The Casimir-Polder potential is proportional to z-2 at short atom-surface distances and to z-4 at long atom-surface distances. Because of these advantages, this potential can help in building quantum reflectors, quantum levitating devices, and waveguides for matter waves.

Incorporating nitrogen atoms into cobalt nanosheets as a strategy to boost catalytic activity toward CO2 hydrogenation

NASA Astrophysics Data System (ADS)

Wang, Liangbing; Zhang, Wenbo; Zheng, Xusheng; Chen, Yizhen; Wu, Wenlong; Qiu, Jianxiang; Zhao, Xiangchen; Zhao, Xiao; Dai, Yizhou; Zeng, Jie

2017-11-01

Hydrogenation of CO2 into fuels and useful chemicals could help to reduce reliance on fossil fuels. Although great progress has been made over the past decades to improve the activity of catalysts for CO2 hydrogenation, more efficient catalysts, especially those based on non-noble metals, are desired. Here we incorporate N atoms into Co nanosheets to boost the catalytic activity toward CO2 hydrogenation. For the hydrogenation of CO2, Co4N nanosheets exhibited a turnover frequency of 25.6 h-1 in a slurry reactor under 32 bar pressure at 150 °C, which was 64 times that of Co nanosheets. The activation energy for Co4N nanosheets was 43.3 kJ mol-1, less than half of that for Co nanosheets. Mechanistic studies revealed that Co4N nanosheets were reconstructed into Co4NHx, wherein the amido-hydrogen atoms directly interacted with the CO2 to form HCOO* intermediates. In addition, the adsorbed H2O* activated amido-hydrogen atoms via the interaction of hydrogen bonds.

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

Anterior cruciate ligament- and hamstring tendon-derived cells: in vitro differential properties of cells involved in ACL reconstruction.

PubMed

Ghebes, Corina Adriana; Kelder, Cindy; Schot, Thomas; Renard, Auke J; Pakvis, Dean F M; Fernandes, Hugo; Saris, Daniel B

2017-04-01

Anterior cruciate ligament (ACL) reconstruction involves the replacement of the torn ligament with a new graft, often a hamstring tendon (HT). Described as similar, the ACL and HT have intrinsic differences related to their distinct anatomical locations. From a cellular perspective, identifying these differences represents a step forward in the search for new cues that enhance recovery after the reconstruction. The purpose of this study was to characterize the phenotype and multilineage potential of ACL- and HT-derived cells. ACL- and HT-derived cells were isolated from tissue harvest from patients undergoing total knee arthroplasty (TKA) or ACL reconstruction. In total, three ACL and three HT donors were investigated. Cell morphology, self-renewal potential (CFU-F), surface marker profiling, expression of tendon/ligament-related markers (PCR) and multilineage potential were analysed for both cell types; both had fibroblast-like morphology and low self-renewal potential. No differences in the expression of tendon/ligament-related genes or a selected set of surface markers were observed between the two cell types. However, differences in their multilineage potential were observed: while ACL-derived cells showed a high potential to differentiate into chondrocytes and adipocytes, but not osteoblasts, HT-derived cells showed poor potential to form adipocytes, chondrocytes and osteoblasts. Our results demonstrated that HT-derived cells have low multilineage potential compared to ACL-derived cells, further highlighting the need for extrinsic signals to fully restore the function of the ACL upon reconstruction. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Recent developments in trapping and manipulation of atoms with adiabatic potentials

NASA Astrophysics Data System (ADS)

Garraway, Barry M.; Perrin, Hélène

2016-09-01

A combination of static and oscillating magnetic fields can be used to ‘dress’ atoms with radio-frequency (RF), or microwave, radiation. The spatial variation of these fields can be used to create an enormous variety of traps for ultra-cold atoms and quantum gases. This article reviews the type and character of these adiabatic traps and the applications which include atom interferometry and the study of low-dimensional quantum systems. We introduce the main concepts of magnetic traps leading to adiabatic dressed traps. The concept of adiabaticity is discussed in the context of the Landau-Zener model. The first bubble trap experiment is reviewed together with the method used for loading it. Experiments based on atom chips show the production of double wells and ring traps. Dressed atom traps can be evaporatively cooled with an additional RF field, and a weak RF field can be used to probe the spectroscopy of the adiabatic potentials. Several approaches to ring traps formed from adiabatic potentials are discussed, including those based on atom chips, time-averaged adiabatic potentials and induction methods. Several proposals for adiabatic lattices with dressed atoms are also reviewed.

STM studies of GeSi thin layers epitaxially grown on Si(111)

NASA Astrophysics Data System (ADS)

Motta, N.; Sgarlata, A.; De Crescenzi, M.; Derrien, J.

1996-08-01

Ge/Si alloys were prepared in UHV by solid phase epitaxy on Si(111) substrates. The alloy formation, as a function of the evaporation rate and the Ge layer thickness has been followed in situ by RHEED and scanning tunneling microscopy. The 5 × 5 surface reconstruction appeared after annealing at 450°C Ge layers (up to 10 Å thick), obtained from a low rate Knudsen cell evaporator. In this case a nearly flat and uniform layer of reconstructed alloy was observed. When using an e-gun high rate evaporator we needed to anneal the Ge layer up to 780°C to obtain a 5 × 5 reconstruction. The grown layer was not flat, with many steps and Ge clusters; at high coverages (10 Å and more) large Ge islands appeared. Moreover, we then succeeded in visualizing at atomic resolution the top of some of these Ge islands which displayed a 2 × 1 reconstruction, probably induced from the high compressive strain due to the lattice mismatch with the substrate. We suggest that this unusual behavior could be connected to the high evaporation rate, which helped the direct formation of Ge microcrystals on the Si substrate during the deposition process.

The atomistic mechanism for Sb segregation and As displacement of Sb in InSb(001) surfaces

NASA Astrophysics Data System (ADS)

Anderson, Evan M.; Millunchick, Joanna M.

2018-01-01

Interfacial broadening occurs in mixed-anion alloy heterostructures such as InAs/InAsSb due to both Sb-segregation and As-for-Sb exchange. In order to determine the atomistic mechanisms for these processes, we conduct ab initio calculations coupled with a cluster expansion formalism to determine the surface reconstructions of the pure and As-exposed InSb(001) surfaces. This approach provides a predicted phase diagram for pure InSb that is in better agreement with experiments. Namely, the α2(2 × 4) and α3c(4 × 4) structures are ultimately stable at 0K, but the α(4 × 3) and α2c(2 × 6) are within 1 meV/Å2. Exposure of the InSb(001) surface to As results in the As atoms infiltrating into the crystal and displacing subsurface Sb, thus providing the atomistic mechanisms for experimental observations of the As-for-Sb exchange reaction and Sb segregation. Experiments show that the widely reported A-(1 × 3) reconstruction is actually comprised of multiple reconstructions, which is consistent with the prediction of several nearly stable possible reconstructions.

Self-passivation rule and structure of CdTe Σ3 (112) grain boundaries

NASA Astrophysics Data System (ADS)

Liu, Cheng-yan; Zhang, Yue-yu; Hou, Yu-sheng; Chen, Shi-you; Xiang, Hong-jun; Gong, Xin-gao

2016-05-01

The theoretical study of grain boundaries (GBs) in polycrystalline semiconductors is currently stalemated by their complicated nature, which is difficult to extract from any direct experimental characterization. Usually, coincidence-site-lattice models are constructed simply by aligning two symmetric planes ignoring various possible reconstructions. Here, we propose a general self-passivation rule to determine the low-energy GB reconstruction and find new configurations for the CdTe Σ3 (112) GBs. First-principles calculations show that it has lower formation energies than the prototype GBs adopted widely in previous studies. Surprisingly, the reconstructed GBs show self-passivated electronic properties without deep-level states in the band gap. Based on the reconstructed configurations, we revisited the influence of CdC l2 post-treatment on the CdTe GBs and found that the addition of both Cd and Cl atoms in the GB improves the photovoltaic properties by promoting self-passivation and inducing n -type levels, respectively. The present study provides a new route for further studies of GBs in covalent polycrystalline semiconductors and highlights that previous studies on the GBs of multinary semiconductors, which are based on the unreconstructed prototype GB models, should be revisited.

Sparse Reconstruction for Temperature Distribution Using DTS Fiber Optic Sensors with Applications in Electrical Generator Stator Monitoring

PubMed Central

Bazzo, João Paulo; Pipa, Daniel Rodrigues; da Silva, Erlon Vagner; Martelli, Cicero; Cardozo da Silva, Jean Carlos

2016-01-01

This paper presents an image reconstruction method to monitor the temperature distribution of electric generator stators. The main objective is to identify insulation failures that may arise as hotspots in the structure. The method is based on temperature readings of fiber optic distributed sensors (DTS) and a sparse reconstruction algorithm. Thermal images of the structure are formed by appropriately combining atoms of a dictionary of hotspots, which was constructed by finite element simulation with a multi-physical model. Due to difficulties for reproducing insulation faults in real stator structure, experimental tests were performed using a prototype similar to the real structure. The results demonstrate the ability of the proposed method to reconstruct images of hotspots with dimensions down to 15 cm, representing a resolution gain of up to six times when compared to the DTS spatial resolution. In addition, satisfactory results were also obtained to detect hotspots with only 5 cm. The application of the proposed algorithm for thermal imaging of generator stators can contribute to the identification of insulation faults in early stages, thereby avoiding catastrophic damage to the structure. PMID:27618040

Accelerating the reconstruction of magnetic resonance imaging by three-dimensional dual-dictionary learning using CUDA.

PubMed

Jiansen Li; Jianqi Sun; Ying Song; Yanran Xu; Jun Zhao

2014-01-01

An effective way to improve the data acquisition speed of magnetic resonance imaging (MRI) is using under-sampled k-space data, and dictionary learning method can be used to maintain the reconstruction quality. Three-dimensional dictionary trains the atoms in dictionary in the form of blocks, which can utilize the spatial correlation among slices. Dual-dictionary learning method includes a low-resolution dictionary and a high-resolution dictionary, for sparse coding and image updating respectively. However, the amount of data is huge for three-dimensional reconstruction, especially when the number of slices is large. Thus, the procedure is time-consuming. In this paper, we first utilize the NVIDIA Corporation's compute unified device architecture (CUDA) programming model to design the parallel algorithms on graphics processing unit (GPU) to accelerate the reconstruction procedure. The main optimizations operate in the dictionary learning algorithm and the image updating part, such as the orthogonal matching pursuit (OMP) algorithm and the k-singular value decomposition (K-SVD) algorithm. Then we develop another version of CUDA code with algorithmic optimization. Experimental results show that more than 324 times of speedup is achieved compared with the CPU-only codes when the number of MRI slices is 24.

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

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbonmore » nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.« less

Experimental demonstration of multiple monoenergetic gamma radiography for effective atomic number identification in cargo inspection

NASA Astrophysics Data System (ADS)

Henderson, Brian S.; Lee, Hin Y.; MacDonald, Thomas D.; Nelson, Roberts G.; Danagoulian, Areg

2018-04-01

The smuggling of special nuclear materials (SNMs) through international borders could enable nuclear terrorism and constitutes a significant threat to global security. This paper presents the experimental demonstration of a novel radiographic technique for quantitatively reconstructing the density and type of material present in commercial cargo containers, as a means of detecting such threats. Unlike traditional techniques which use sources of bremsstrahlung photons with a continuous distribution of energies, multiple monoenergetic gamma radiography utilizes monoenergetic photons from nuclear reactions, specifically the 4.4 and 15.1 MeV photons from the 11B(d,nγ)12C reaction. By exploiting the Z-dependence of the photon interaction cross sections at these two specific energies, it is possible to simultaneously determine the areal density and the effective atomic number as a function of location for a 2D projection of a scanned object. The additional information gleaned from using and detecting photons of specific energies for radiography substantially increases the resolving power between different materials. This paper presents results from the imaging of mock cargo materials ranging from Z ≈5 -92 , demonstrating accurate reconstruction of the effective atomic number and areal density of the materials over the full range. In particular, the system is capable of distinguishing pure materials with Z ≳ 70 , such as lead and uranium—a critical requirement of a system designed to detect SNM. This methodology could be used to screen commercial cargoes with high material specificity, to distinguish most benign materials from SNM, such as uranium and plutonium.

Limiting factors in atomic resolution cryo electron microscopy: No simple tricks

PubMed Central

Zhang, Xing; Zhou, Z. Hong

2013-01-01

To bring cryo electron microscopy (cryoEM) of large biological complexes to atomic resolution, several factors – in both cryoEM image acquisition and 3D reconstruction – that may be neglected at low resolution become significantly limiting. Here we present thorough analyses of four limiting factors: (a) electron-beam tilt, (b) inaccurate determination of defocus values, (c) focus gradient through particles, and (d) particularly for large particles, dynamic (multiple) scattering of electrons. We also propose strategies to cope with these factors: (a) the divergence and direction tilt components of electron-beam tilt could be reduced by maintaining parallel illumination and by using a coma-free alignment procedure, respectively. Moreover, the effect of all beam tilt components, including spiral tilt, could be eliminated by use of a spherical aberration corrector. (b) More accurate measurement of defocus value could be obtained by imaging areas adjacent to the target area at high electron dose and by measuring the image shift induced by tilting the electron beam. (c) Each known Fourier coefficient in the Fourier transform of a cryoEM image is the sum of two Fourier coefficients of the 3D structure, one on each of two curved ‘characteristic surfaces’ in 3D Fourier space. We describe a simple model-based iterative method that could recover these two Fourier coefficients on the two characteristic surfaces. (d) The effect of dynamic scattering could be corrected by deconvolution of a transfer function. These analyses and our proposed strategies offer useful guidance for future experimental designs targeting atomic resolution cryoEM reconstruction. PMID:21627992

Facet Dependent Disorder in the Pristine High Voltage Lithium-Manganese-Rich Cathode Material

DOE PAGES

Dixit, Hemant M.; Zhou, Wu; Idrobo Tapia, Juan Carlos; ...

2014-11-21

Defects and surface reconstructions are thought to be crucial for the long term stability of high-voltage lithium-manganese-rich cathodes. Unfortunately, many of these defects arise only after electrochemical cycling which occur under harsh conditions making it difficult to fully comprehend the role they play in degrading material performance. Recently, it has been observed that defects are present even in the pristine material. This study, therefore, focuses on examining the nature of the disorder observed in pristine Limore » $$_{1.2}$$Ni$$_{0.175}$$Mn$$_{0.525}$$Co$$_{0.1}$$O$$_2$$ (LNMCO) particles. Using atomic resolution Z-contrast imaging and electron energy-loss spectroscopy measurements we show that there are indeed a significant amount of anti-site defects present in this material; with transition metals substituting on Li metal sites. Furthermore, we find a strong tendency of segregation of these types of defects towards open facets (surfaces perpendicular to the layered arrangement of atoms), rather than closed facets (surfaces parallel to the layered arrangement of atoms). First principles calculations identify anti-site defect pairs of Ni swapping with Li ions as the predominant defect in the material. Furthermore, energetically favorable swapping of Ni on the Mn sites were observed to lead to Mn depletion at open facets. Relatively, low Ni migration barriers also support the notion that Ni are the predominant cause of disorder. These insights suggests that certain facets of the LNMCO particles may be more useful for inhibiting surface reconstruction and improving the stability of these materials through careful consideration of the exposed surface.« less

Chaotic behavior of light-assisted physical aging in arsenoselenide glasses

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

Shpotyuk, O., E-mail: shpotyuk@novas.lviv.ua; Institute of Physics of Jan Dlugosz University, 13/15, al. Armii Krajowej, Czestochowa 42201; Balitska, V.

2014-12-15

The theory of strange attractors is shown to be adequately applicable for analyzing the kinetics of light-assisted physical aging revealed in structural relaxation of Se-rich As-Se glasses below glass transition. Kinetics of enthalpy losses is used to determine the phase space reconstruction parameters. Observed chaotic behaviour (involving chaos and fractal consideration such as detrended fluctuation analysis, attractor identification using phase space representation, delay coordinates, mutual information, false nearest neighbours, etc.) reconstructed via the TISEAN program package is treated within a microstructure model describing multistage aging behaviour in arsenoselenide glasses. This simulation testifies that photoexposure acts as an initiating factor onlymore » at the beginning stage of physical aging, thus facilitating further atomic shrinkage of a glassy backbone.« less

A comparison of manual neuronal reconstruction from biocytin histology or 2-photon imaging: morphometry and computer modeling

PubMed Central

Blackman, Arne V.; Grabuschnig, Stefan; Legenstein, Robert; Sjöström, P. Jesper

2014-01-01

Accurate 3D reconstruction of neurons is vital for applications linking anatomy and physiology. Reconstructions are typically created using Neurolucida after biocytin histology (BH). An alternative inexpensive and fast method is to use freeware such as Neuromantic to reconstruct from fluorescence imaging (FI) stacks acquired using 2-photon laser-scanning microscopy during physiological recording. We compare these two methods with respect to morphometry, cell classification, and multicompartmental modeling in the NEURON simulation environment. Quantitative morphological analysis of the same cells reconstructed using both methods reveals that whilst biocytin reconstructions facilitate tracing of more distal collaterals, both methods are comparable in representing the overall morphology: automated clustering of reconstructions from both methods successfully separates neocortical basket cells from pyramidal cells but not BH from FI reconstructions. BH reconstructions suffer more from tissue shrinkage and compression artifacts than FI reconstructions do. FI reconstructions, on the other hand, consistently have larger process diameters. Consequently, significant differences in NEURON modeling of excitatory post-synaptic potential (EPSP) forward propagation are seen between the two methods, with FI reconstructions exhibiting smaller depolarizations. Simulated action potential backpropagation (bAP), however, is indistinguishable between reconstructions obtained with the two methods. In our hands, BH reconstructions are necessary for NEURON modeling and detailed morphological tracing, and thus remain state of the art, although they are more labor intensive, more expensive, and suffer from a higher failure rate due to the occasional poor outcome of histological processing. However, for a subset of anatomical applications such as cell type identification, FI reconstructions are superior, because of indistinguishable classification performance with greater ease of use, essentially 100% success rate, and lower cost. PMID:25071470

The Emergence of Atomic-Level Structural Information for Ordered Metal-Solution Interfaces: Some Recent Contributions from In-Situ Infrared Spectroscopy and Scanning Tunneling Microscopy

DTIC Science & Technology

1992-02-28

Distribution/ Availabilit Codes jAval’ an~d/or Dist Speoial (19. cont.) reconstruction at gold-aqueous interfaces. All three low-index gold surfaces are...uncharged (vide supra). This difference may well be due to the influence of the interfacial water , or conceivably to adsorbed perchlorate anions. Both Au

Evaluation of kangaroo pericardium as an alternative substitute for reconstructive cardiac surgery.

PubMed

Neethling, W M L; Cooper, S; Van Den Heever, J J; Hough, J; Hodge, A J

2002-06-01

Bioprosthetic materials (human, bovine and porcine) are used in various cardio-thoracic repair and replacement procedures because of excellent performance and low thrombogenicity. These bioprosthetic substitutes fail due to degeneration and calcification. This study examines the morphology, tensile properties and calcification potential of kangaroo pericardium in vitro and in vivo. Bovine (control tissue) and kangaroo pericardium, fixed in 0.625% buffered glutaraldehyde, were examined by light and scanning electron microscopy. A standard method was used for biaxial testing. Pericardial strips (10 x 5 mm) were implanted subcutaneously into male Wistar rats and retrieved after 4, 6 and 8 weeks and examined by Von Kossa's stain technique and atomic absorption spectrophotometry. Histology revealed serosa and fibrosa cell layers in both tissues. Electron microscopy showed a densely arranged collagen matrix in kangaroo pericardium. Kangaroo pericardium calcified significantly less than bovine pericardium at 4 weeks (0.80+/-0.28 versus 21.60+/-4.80 microg/mg) at 6 weeks (0.48+/-0.08 versus 32.80+/-14.4 microg/mg) and at 8 weeks (2.40+/-1.20 versus 30.40+/-17.20 microg/mg), respectively. Kangaroo pericardium has a densely arranged collagen matrix with a higher extensibility and significantly lower calcification potential. Therefore, kangaroo pericardium could be used as an alternative substitute in cardiac surgery because of its low calcification potential.

Spectral asymmetry of atoms in the van der Waals potential of an optical nanofiber

NASA Astrophysics Data System (ADS)

Patterson, B. D.; Solano, P.; Julienne, P. S.; Orozco, L. A.; Rolston, S. L.

2018-03-01

We measure the modification of the transmission spectra of cold 87Rb atoms in the proximity of an optical nanofiber (ONF). Van der Waals interactions between the atoms an the ONF surface decrease the resonance frequency of atoms closer to the surface. An asymmetric spectra of the atoms holds information of their spatial distribution around the ONF. We use a far-detuned laser beam coupled to the ONF to thermally excite atoms at the ONF surface. We study the change of transmission spectrum of these atoms as a function of heating laser power. A semiclassical phenomenological model for the thermal excitation of atoms in the atom-surface van der Waals bound states is in good agreement with the measurements. This result suggests that van der Waals potentials could be used to trap and probe atoms at few nanometers from a dielectric surface, a key tool for hybrid photonic-atomic quantum systems.

Coherent wave packet dynamics in a double-well potential in cavity

NASA Astrophysics Data System (ADS)

Zheng, Li; Li, Gang; Ding, Ming-Song; Wang, Yong-Liang; Zhang, Yun-Cui

2018-02-01

We investigate the coherent wave packet dynamics of a two-level atom trapped in a symmetric double-well potential in a near-resonance cavity. Prepared on one side of the double-well potential, the atom wave packet oscillates between the left and right wells, while recoil induced by the emitted photon from the atom entangles the atomic internal and external degrees of freedom. The collapse and revival of the tunneling occurs. Adjusting the width of the wave packets, one can modify the tunneling frequency and suppress the tunneling.

Physico-Chemical Properties of MgGa Mixed Oxides and Reconstructed Layered Double Hydroxides and Their Performance in Aldol Condensation of Furfural and Acetone

PubMed Central

Kikhtyanin, Oleg; Čapek, Libor; Tišler, Zdeněk; Velvarská, Romana; Panasewicz, Adriana; Diblíková, Petra; Kubička, David

2018-01-01

MgGa layered double hydroxides (Mg/Ga = 2–4) were synthesized and used for the preparation of MgGa mixed oxides and reconstructed hydrotalcites. The properties of the prepared materials were examined by physico-chemical methods (XRD, TGA, NH3-TPD, CO2-TPD, SEM, and DRIFT) and tested in aldol condensation of furfural and acetone. The as-prepared phase-pure MgGa samples possessed hydrotalcite structure, and their calcination resulted in mixed oxides with MgO structure with a small admixture phase characterized by a reflection at 2θ ≈ 36.0°. The interaction of MgGa mixed oxides with pure water resulted in reconstruction of the HTC structure already after 15 s of the rehydration with maximum crystallinity achieved after 60 s. TGA-MS experiments proved a substantial decrease in carbonates in all rehydrated samples compared with their as-prepared counterparts. This allowed suggesting presence of interlayer hydroxyls in the samples. Acido-basic properties of MgGa mixed oxides determined by TPD technique did not correlate with Mg/Ga ratio which was explained by the specific distribution of Ga atoms on the external surface of the samples. CO2-TPD method was also used to evaluate the basic properties of the reconstructed MgGa samples. In these experiments, an intensive peak at T = 450°C on CO2-TPD curve was attributed to the decomposition of carbonates newly formed by CO2 interaction with interlayer carbonates rather than to CO2 desorption from basic sites. Accordingly, CO2-TPD method quantitatively characterized the interlayer hydroxyls only indirectly. Furfural conversion on reconstructed MgGa materials was much larger compared with MgGa mixed oxides confirming that Brønsted basic sites in MgGa catalysts, like MgAl catalysts, were active in the reaction. Mg/Ga ratio in mixed oxides influenced product selectivity which was explained by the difference in textural properties of the samples. In contrast, Mg/Ga ratio in reconstructed catalysts had practically no effect on the composition of reaction products suggesting that the basic sites in these catalysts acted similarly in aldol condensation of acetone with furfural. It was concluded that the properties of MgGa samples resembled in a great extent those of MgAl hydrotalcite-based materials and demonstrated their potential as catalysts for base-catalyzed reactions. PMID:29881721

Physico-Chemical Properties of MgGa Mixed Oxides and Reconstructed Layered Double Hydroxides and Their Performance in Aldol Condensation of Furfural and Acetone.

PubMed

Kikhtyanin, Oleg; Čapek, Libor; Tišler, Zdeněk; Velvarská, Romana; Panasewicz, Adriana; Diblíková, Petra; Kubička, David

2018-01-01

MgGa layered double hydroxides (Mg/Ga = 2-4) were synthesized and used for the preparation of MgGa mixed oxides and reconstructed hydrotalcites. The properties of the prepared materials were examined by physico-chemical methods (XRD, TGA, NH 3 -TPD, CO 2 -TPD, SEM, and DRIFT) and tested in aldol condensation of furfural and acetone. The as-prepared phase-pure MgGa samples possessed hydrotalcite structure, and their calcination resulted in mixed oxides with MgO structure with a small admixture phase characterized by a reflection at 2θ ≈ 36.0°. The interaction of MgGa mixed oxides with pure water resulted in reconstruction of the HTC structure already after 15 s of the rehydration with maximum crystallinity achieved after 60 s. TGA-MS experiments proved a substantial decrease in carbonates in all rehydrated samples compared with their as-prepared counterparts. This allowed suggesting presence of interlayer hydroxyls in the samples. Acido-basic properties of MgGa mixed oxides determined by TPD technique did not correlate with Mg/Ga ratio which was explained by the specific distribution of Ga atoms on the external surface of the samples. CO 2 -TPD method was also used to evaluate the basic properties of the reconstructed MgGa samples. In these experiments, an intensive peak at T = 450°C on CO 2 -TPD curve was attributed to the decomposition of carbonates newly formed by CO 2 interaction with interlayer carbonates rather than to CO 2 desorption from basic sites. Accordingly, CO 2 -TPD method quantitatively characterized the interlayer hydroxyls only indirectly. Furfural conversion on reconstructed MgGa materials was much larger compared with MgGa mixed oxides confirming that Brønsted basic sites in MgGa catalysts, like MgAl catalysts, were active in the reaction. Mg/Ga ratio in mixed oxides influenced product selectivity which was explained by the difference in textural properties of the samples. In contrast, Mg/Ga ratio in reconstructed catalysts had practically no effect on the composition of reaction products suggesting that the basic sites in these catalysts acted similarly in aldol condensation of acetone with furfural. It was concluded that the properties of MgGa samples resembled in a great extent those of MgAl hydrotalcite-based materials and demonstrated their potential as catalysts for base-catalyzed reactions.

Physico-chemical properties of MgGa mixed oxides and reconstructed layered double hydroxides and their performance in aldol condensation of furfural and acetone

NASA Astrophysics Data System (ADS)

Kikhtyanin, Oleg; Čapek, Libor; Tišler, Zdeněk; Velvarská, Romana; Panasewicz, Adriana; Diblíková, Petra; Kubička, David

2018-05-01

MgGa layered double hydroxides (Mg/Ga=2-4) were synthesized and used for the preparation of MgGa mixed oxides and reconstructed hydrotalcites. The properties of the prepared materials were examined by physico-chemical methods (XRD, TGA, NH3-TPD, CO2-TPD, SEM and DRIFT) and tested in aldol condensation of furfural and acetone. The as-prepared phase-pure MgGa samples possessed hydrotalcite structure, and their calcination resulted in mixed oxides with MgO structure with a small admixture phase characterized by a reflection at 2θ ≈ 36.0°. The interaction of MgGa mixed oxides with pure water resulted in reconstruction of the HTC structure already after 15 s of the rehydration with maximum crystallinity achieved after 60 s. TGA-MS experiments proved a substantial decrease in carbonates in all rehydrated samples compared with their as-prepared counterparts. This allowed suggesting presence of interlayer hydroxyls in the samples. Acido-basic properties of MgGa mixed oxides determined by TPD technique did not correlate with Mg/Ga ratio which was explained by the specific distribution of Ga atoms on the external surface of the samples. CO2-TPD method was also used to evaluate the basic properties of the reconstructed MgGa samples. In these experiments, an intensive peak at T=450 °C on CO2-TPD curve was attributed to the decomposition of carbonates newly formed by CO2 interaction with interlayer carbonates rather than to CO2 desorption from basic sites. Accordingly, CO2-TPD method quantitatively characterized the interlayer hydroxyls only indirectly. Furfural conversion on reconstructed MgGa materials was much larger compared with MgGa mixed oxides confirming that Brønsted basic sites in MgGa catalysts, like MgAl catalysts, were active in the reaction. Mg/Ga ratio in mixed oxides influenced product selectivity which was explained by the difference in textural properties of the samples. In contrast, Mg/Ga ratio in reconstructed catalysts had practically no effect on the composition of reaction products suggesting that the basic sites in these catalysts acted similarly in aldol condensation of acetone with furfural. It was concluded that the properties of MgGa samples resembled in a great extent those of MgAl hydrotalcite-based materials and demonstrated their potential as catalysts for base-catalyzed reactions.

Anisotropic interaction and stereoreactivity in a chemi-ionization process of OCS by collision with He*(2(3)S) metastable atoms.

PubMed

Horio, Takuya; Maeda, Satoshi; Kishimoto, Naoki; Ohno, Koichi

2006-09-28

Ionic-state-resolved collision energy dependence of Penning ionization cross sections for OCS with He*(2(3)S) metastable atoms was measured in a wide collision energy range from 20 to 350 meV. Anisotropic interaction potential for the OCS-He*(2(3)S) system was obtained by comparison of the experimental data with classical trajectory simulations. It has been found that attractive potential wells around the O and S atoms are clearly different in their directions. Around the O atom, the collinear approach is preferred (the well depth is ca. 90 meV), while the perpendicular approach is favored around the S atom (the well depth is ca. 40 meV). On the basis of the optimized potential energy surface and theoretical simulations, stereo reactivity around the O and S atoms was also investigated. The results were discussed in terms of anisotropy of the potential energy surface and the electron density distribution of molecular orbitals to be ionized.

Reduction of Metal Artifact in Single Photon-Counting Computed Tomography by Spectral-Driven Iterative Reconstruction Technique

PubMed Central

Nasirudin, Radin A.; Mei, Kai; Panchev, Petar; Fehringer, Andreas; Pfeiffer, Franz; Rummeny, Ernst J.; Fiebich, Martin; Noël, Peter B.

2015-01-01

Purpose The exciting prospect of Spectral CT (SCT) using photon-counting detectors (PCD) will lead to new techniques in computed tomography (CT) that take advantage of the additional spectral information provided. We introduce a method to reduce metal artifact in X-ray tomography by incorporating knowledge obtained from SCT into a statistical iterative reconstruction scheme. We call our method Spectral-driven Iterative Reconstruction (SPIR). Method The proposed algorithm consists of two main components: material decomposition and penalized maximum likelihood iterative reconstruction. In this study, the spectral data acquisitions with an energy-resolving PCD were simulated using a Monte-Carlo simulator based on EGSnrc C++ class library. A jaw phantom with a dental implant made of gold was used as an object in this study. A total of three dental implant shapes were simulated separately to test the influence of prior knowledge on the overall performance of the algorithm. The generated projection data was first decomposed into three basis functions: photoelectric absorption, Compton scattering and attenuation of gold. A pseudo-monochromatic sinogram was calculated and used as input in the reconstruction, while the spatial information of the gold implant was used as a prior. The results from the algorithm were assessed and benchmarked with state-of-the-art reconstruction methods. Results Decomposition results illustrate that gold implant of any shape can be distinguished from other components of the phantom. Additionally, the result from the penalized maximum likelihood iterative reconstruction shows that artifacts are significantly reduced in SPIR reconstructed slices in comparison to other known techniques, while at the same time details around the implant are preserved. Quantitatively, the SPIR algorithm best reflects the true attenuation value in comparison to other algorithms. Conclusion It is demonstrated that the combination of the additional information from Spectral CT and statistical reconstruction can significantly improve image quality, especially streaking artifacts caused by the presence of materials with high atomic numbers. PMID:25955019

Total Reconstruction of the Auricle: Our Experiences on Indications and Recent Techniques

PubMed Central

Storck, K.; Staudenmaier, R.; Buchberger, M.; Strenger, T.; Kreutzer, K.; von Bomhard, A.; Stark, T.

2014-01-01

Introduction. Auricular reconstruction is a great challenge in facial plastic surgery. With the advances in surgical techniques and biotechnology, different options are available for consideration. The aim of this paper is to review the knowledge about the various techniques for total auricular reconstruction based on the literature and our experience. Methods. Approximately 179 articles published from 1980 to 2013 were identified, and 59 articles were included. We have focused on the current status of total auricular reconstruction based on our personal experience and on papers of particular interest, published within the period of review. We have also included a prospective view on the tissue engineering of cartilage. Results. Most surgeons still practice total auricular reconstruction by employing techniques developed by Brent, Nagata, and Firmin with autologous rib cartilage. Within the last years, alloplastic frameworks for reconstruction have become well established. Choosing the reconstruction techniques depends mainly on the surgeon's preference and experience. Prosthetic reconstruction is still reserved for special conditions, even though the material is constantly improving. Tissue engineering has a growing potential for clinical applicability. Conclusion. Auricular reconstruction still receives attention of plastic/maxillofacial surgeons and otolaryngologists. Even though clinical applicability lags behind initial expectations, the development of tissue-engineered constructs continues its potential development. PMID:24822198

Investigation of optimization-based reconstruction with an image-total-variation constraint in PET

NASA Astrophysics Data System (ADS)

Zhang, Zheng; Ye, Jinghan; Chen, Buxin; Perkins, Amy E.; Rose, Sean; Sidky, Emil Y.; Kao, Chien-Min; Xia, Dan; Tung, Chi-Hua; Pan, Xiaochuan

2016-08-01

Interest remains in reconstruction-algorithm research and development for possible improvement of image quality in current PET imaging and for enabling innovative PET systems to enhance existing, and facilitate new, preclinical and clinical applications. Optimization-based image reconstruction has been demonstrated in recent years of potential utility for CT imaging applications. In this work, we investigate tailoring the optimization-based techniques to image reconstruction for PET systems with standard and non-standard scan configurations. Specifically, given an image-total-variation (TV) constraint, we investigated how the selection of different data divergences and associated parameters impacts the optimization-based reconstruction of PET images. The reconstruction robustness was explored also with respect to different data conditions and activity up-takes of practical relevance. A study was conducted particularly for image reconstruction from data collected by use of a PET configuration with sparsely populated detectors. Overall, the study demonstrates the robustness of the TV-constrained, optimization-based reconstruction for considerably different data conditions in PET imaging, as well as its potential to enable PET configurations with reduced numbers of detectors. Insights gained in the study may be exploited for developing algorithms for PET-image reconstruction and for enabling PET-configuration design of practical usefulness in preclinical and clinical applications.

Reconstruction of the mass distribution of galaxy clusters from the inversion of the thermal Sunyaev-Zel'dovich effect

NASA Astrophysics Data System (ADS)

Majer, C. L.; Meyer, S.; Konrad, S.; Sarli, E.; Bartelmann, M.

2016-07-01

This paper continues a series in which we intend to show how all observables of galaxy clusters can be combined to recover the two-dimensional, projected gravitational potential of individual clusters. Our goal is to develop a non-parametric algorithm for joint cluster reconstruction taking all cluster observables into account. For this reason we focus on the line-of-sight projected gravitational potential, proportional to the lensing potential, in order to extend existing reconstruction algorithms. In this paper, we begin with the relation between the Compton-y parameter and the Newtonian gravitational potential, assuming hydrostatic equilibrium and a polytropic stratification of the intracluster gas. Extending our first publication we now consider a spheroidal rather than a spherical cluster symmetry. We show how a Richardson-Lucy deconvolution can be used to convert the intensity change of the CMB due to the thermal Sunyaev-Zel'dovich effect into an estimate for the two-dimensional gravitational potential. We apply our reconstruction method to a cluster based on an N-body/hydrodynamical simulation processed with the characteristics (resolution and noise) of the ALMA interferometer for which we achieve a relative error of ≲20 per cent for a large fraction of the virial radius. We further apply our method to an observation of the galaxy cluster RXJ1347 for which we can reconstruct the potential with a relative error of ≲20 per cent for the observable cluster range.

Pressure induced solid-solid reconstructive phase transition in LiGa O2 dominated by elastic strain

NASA Astrophysics Data System (ADS)

Hu, Qiwei; Yan, Xiaozhi; Lei, Li; Wang, Qiming; Feng, Leihao; Qi, Lei; Zhang, Leilei; Peng, Fang; Ohfuji, Hiroaki; He, Duanwei

2018-01-01

Pressure induced solid-solid reconstructive phase transitions for graphite-diamond, and wurtzite-rocksalt in GaN and AlN occur at significantly higher pressure than expected from equilibrium coexistence and their transition paths are always inconsistent with each other. These indicate that the underlying nucleation and growth mechanism in the solid-solid reconstructive phase transitions are poorly understood. Here, we propose an elastic-strain dominated mechanism in a reconstructive phase transition, β -LiGa O2 to γ -LiGa O2 , based on in situ high-pressure angle dispersive x-ray diffraction and single-crystal Raman scattering. This mechanism suggests that the pressure induced solid-solid reconstructive phase transition is neither purely diffusionless nor purely diffusive, as conventionally assumed, but a combination. The large elastic strains are accumulated, with the coherent nucleation, in the early stage of the transition. The elastic strains along the 〈100 〉 and 〈001 〉 directions are too large to be relaxed by the shear stress, so an intermediate structure emerges reducing the elastic strains and making the transition energetically favorable. At higher pressures, when the elastic strains become small enough to be relaxed, the phase transition to γ -LiGa O2 begins and the coherent nucleation is substituted with a semicoherent one with Li and Ga atoms disordered.

Fiber Orientation Estimation Guided by a Deep Network.

PubMed

Ye, Chuyang; Prince, Jerry L

2017-09-01

Diffusion magnetic resonance imaging (dMRI) is currently the only tool for noninvasively imaging the brain's white matter tracts. The fiber orientation (FO) is a key feature computed from dMRI for tract reconstruction. Because the number of FOs in a voxel is usually small, dictionary-based sparse reconstruction has been used to estimate FOs. However, accurate estimation of complex FO configurations in the presence of noise can still be challenging. In this work we explore the use of a deep network for FO estimation in a dictionary-based framework and propose an algorithm named Fiber Orientation Reconstruction guided by a Deep Network (FORDN). FORDN consists of two steps. First, we use a smaller dictionary encoding coarse basis FOs to represent diffusion signals. To estimate the mixture fractions of the dictionary atoms, a deep network is designed to solve the sparse reconstruction problem. Second, the coarse FOs inform the final FO estimation, where a larger dictionary encoding a dense basis of FOs is used and a weighted ℓ 1 -norm regularized least squares problem is solved to encourage FOs that are consistent with the network output. FORDN was evaluated and compared with state-of-the-art algorithms that estimate FOs using sparse reconstruction on simulated and typical clinical dMRI data. The results demonstrate the benefit of using a deep network for FO estimation.

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

Taylor, Sandra D.; Liu, Jia; Arey, Bruce W.

The distribution of iron resulting from the autocatalytic interaction of aqueous Fe(II) with the hematite (001) surface was directly mapped in three dimensions (3D) for the first time, using iron isotopic labelling and atom probe tomography (APT). Analyses of the mass spectrum showed that natural abundance ratios in 56Fe-dominant hematite are recovered at depth with good accuracy, whereas at the relict interface with 57Fe(II) solution evidence for hematite growth by oxidative adsorption of Fe(II) was found. 3D reconstructions of the isotope positions along the surface normal direction showed a zone enriched in 57Fe, which was consistent with an average netmore » adsorption of 3.2 – 4.3 57Fe atoms nm–2. Statistical analyses utilizing grid-based frequency distribution analyses show a heterogeneous, non-random distribution of oxidized Fe on the (001) surface, consistent with Volmer-Weber-like island growth. The unique 3D nature of the APT data provides an unprecedented means to quantify the atomic-scale distribution of sorbed 57Fe atoms and the extent of segregation on the hematite surface. This new ability to spatially map growth on single crystal faces at the atomic scale will enable resolution to long-standing unanswered questions about the underlying mechanisms for electron and atom exchange involved in a wide variety of redox-catalyzed processes at this archetypal and broadly relevant interface.« less

Electronic and magnetic properties of nonmetal atoms adsorbed ReS{sub 2} monolayers

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

Zhang, Xiaoou; Li, Qingfang, E-mail: qingfangli@nuist.edu.cn; Department of Physics, Nanjing University of Information Science and Technology, Nanjing 210044

2015-08-14

The stable configurations and electronic and magnetic properties of nonmetal atoms (H, N, P, O, S, F, and Cl) adsorbed ReS{sub 2} monolayers have been investigated by first-principles calculations. It is found that H, O, S, F, and Cl prefer to occupy the peak sites of S atoms, while both N and P atoms favor the valley sites of S atoms. The ReS{sub 2} sheet exhibits a good adsorption capability to nonmetal atoms. The reconstruction of the surface is pronounced in N- and P-adsorbed ReS{sub 2} monolayers. In H-adsorbed case, the Fermi level is pulled into the conduction band, whichmore » results in the semiconductor-metal transition. The same magnetic moment of 1μ{sub B} is found in the N-, P-, F-, and Cl-adsorbed ReS{sub 2} monolayers, while the mechanisms of forming magnetic moment for N (P)- and F (Cl)-adsorbed cases are different. In addition, the spatial extensions of spin density in P-, F-, and Cl-adsorbed cases are larger than that in N-adsorbed case, which is more suitable to achieve long-range magnetic coupling interaction at low defect concentrations. Our results provide insight for achieving metal-free magnetism and a tunable band gap for various electronic and spintronic devices based on ReS{sub 2}.« less

Atomically resolved scanning force studies of vicinal Si(111)

NASA Astrophysics Data System (ADS)

Pérez León, Carmen; Drees, Holger; Wippermann, Stefan Martin; Marz, Michael; Hoffmann-Vogel, Regina

2017-06-01

Well-ordered stepped semiconductor surfaces attract intense attention owing to the regular arrangements of their atomic steps that makes them perfect templates for the growth of one-dimensional systems, e.g., nanowires. Here, we report on the atomic structure of the vicinal Si (111 ) surface with 10∘ miscut investigated by a joint frequency-modulation scanning force microscopy (FM-SFM) and ab initio approach. This popular stepped surface contains 7 ×7 -reconstructed terraces oriented along the Si (111 ) direction, separated by a stepped region. Recently, the atomic structure of this triple step based on scanning tunneling microscopy (STM) images has been subject of debate. Unlike STM, SFM atomic resolution capability arises from chemical bonding of the tip apex with the surface atoms. Thus, for surfaces with a corrugated density of states such as semiconductors, SFM provides complementary information to STM and partially removes the dependency of the topography on the electronic structure. Our FM-SFM images with unprecedented spatial resolution on steps coincide with the model based on a (7 7 10 ) orientation of the surface and reveal structural details of this surface. Two different FM-SFM contrasts together with density functional theory calculations explain the presence of defects, buckling, and filling asymmetries on the surface. Our results evidence the important role of charge transfers between adatoms, restatoms, and dimers in the stabilisation of the structure of the vicinal surface.

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

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

Integrated optical dipole trap for cold neutral atoms with an optical waveguide coupler

NASA Astrophysics Data System (ADS)

Lee, J.; Park, D. H.; Mittal, S.; Dagenais, M.; Rolston, S. L.

2013-04-01

An integrated optical dipole trap uses two-color (red and blue-detuned) traveling evanescent wave fields for trapping cold neutral atoms. To achieve longitudinal confinement, we propose using an integrated optical waveguide coupler, which provides a potential gradient along the beam propagation direction sufficient to confine atoms. This integrated optical dipole trap can support an atomic ensemble with a large optical depth due to its small mode area. Its quasi-TE0 waveguide mode has an advantage over the HE11 mode of a nanofiber, with little inhomogeneous Zeeman broadening at the trapping region. The longitudinal confinement eliminates the need for a one dimensional optical lattice, reducing collisional blockaded atomic loading, potentially producing larger ensembles. The waveguide trap allows for scalability and integrability with nano-fabrication technology. We analyze the potential performance of such integrated atom traps.

Investigation of quartz grain surface textures by atomic force microscopy for forensic analysis.

PubMed

Konopinski, D I; Hudziak, S; Morgan, R M; Bull, P A; Kenyon, A J

2012-11-30

This paper presents a study of quartz sand grain surface textures using atomic force microscopy (AFM) to image the surface. Until now scanning electron microscopy (SEM) has provided the primary technique used in the forensic surface texture analysis of quartz sand grains as a means of establishing the provenance of the grains for forensic reconstructions. The ability to independently corroborate the grain type classifications is desirable and provides additional weight to the findings of SEM analysis of the textures of quartz grains identified in forensic soil/sediment samples. AFM offers a quantitative means of analysis that complements SEM examination, and is a non-destructive technique that requires no sample preparation prior to scanning. It therefore has great potential to be used for forensic analysis where sample preservation is highly valuable. By taking quantitative topography scans, it is possible to produce 3D representations of microscopic surface textures and diagnostic features for examination. Furthermore, various empirical measures can be obtained from analysing the topography scans, including arithmetic average roughness, root-mean-square surface roughness, skewness, kurtosis, and multiple gaussian fits to height distributions. These empirical measures, combined with qualitative examination of the surfaces can help to discriminate between grain types and provide independent analysis that can corroborate the morphological grain typing based on the surface textures assigned using SEM. Furthermore, the findings from this study also demonstrate that quartz sand grain surfaces exhibit a statistically self-similar fractal nature that remains unchanged across scales. This indicates the potential for a further quantitative measure that could be utilised in the discrimination of quartz grains based on their provenance for forensic investigations. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Deciphering chemical order/disorder and material properties at the single-atom level

DOE PAGES

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.; ...

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

Challenges and constraints of dynamically emerged source and sink in atomtronic circuits: From closed-system to open-system approaches

PubMed Central

Lai, Chen-Yen; Chien, Chih-Chun

2016-01-01

While batteries offer electronic source and sink for electronic devices, atomic analogues of source and sink and their theoretical descriptions have been a challenge in cold-atom systems. Here we consider dynamically emerged local potentials as controllable source and sink for bosonic atoms. Although a sink potential can collect bosons in equilibrium and indicate its usefulness in the adiabatic limit, sudden switching of the potential exhibits low effectiveness in pushing bosons into it. This is due to conservation of energy and particle in isolated systems such as cold atoms. By varying the potential depth and interaction strength, the systems can further exhibit averse response, where a deeper emerged potential attracts less bosonic atoms into it. To explore possibilities for improving the effectiveness, we investigate what types of system-environment coupling can help bring bosons into a dynamically emerged sink, and a Lindblad operator corresponding to local cooling is found to serve the purpose. PMID:27849034

Quantum control and measurement of atomic spins in polarization spectroscopy

NASA Astrophysics Data System (ADS)

Deutsch, Ivan H.; Jessen, Poul S.

2010-03-01

Quantum control and measurement are two sides of the same coin. To affect a dynamical map, well-designed time-dependent control fields must be applied to the system of interest. To read out the quantum state, information about the system must be transferred to a probe field. We study a particular example of this dual action in the context of quantum control and measurement of atomic spins through the light-shift interaction with an off-resonant optical probe. By introducing an irreducible tensor decomposition, we identify the coupling of the Stokes vector of the light field with moments of the atomic spin state. This shows how polarization spectroscopy can be used for continuous weak measurement of atomic observables that evolve as a function of time. Simultaneously, the state-dependent light shift induced by the probe field can drive nonlinear dynamics of the spin, and can be used to generate arbitrary unitary transformations on the atoms. We revisit the derivation of the master equation in order to give a unified description of spin dynamics in the presence of both nonlinear dynamics and photon scattering. Based on this formalism, we review applications to quantum control, including the design of state-to-state mappings, and quantum-state reconstruction via continuous weak measurement on a dynamically controlled ensemble.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Growth mechanism of isolated indium nanowires formed on Si(5 5 12)-2 × 1 templates

NASA Astrophysics Data System (ADS)

Zhu, Yong-Zhe; Kim, Hidong; Seo, Jae M.

2012-08-01

Through self-assembly of In atoms on a reconstructed Si(5 5 12)-2×1 surface, nanowires of a width less than 5 nm have been formed. One specific site of the one-dimensional structure of the substrate turns out to be inert to arriving In atoms so that the self-assembled nanowires are well-isolated from each other, resulting in a high aspect ratio. In addition to such an isolation, keeping the same periodicity as the substrate ( i.e., 5.35 nm) during such self-assembly is another interesting point of the present system. In the present study, the detailed growth mechanism has been disclosed by using scanning tunneling microscopy.

Mechanical properties of biological specimens explored by atomic force microscopy

NASA Astrophysics Data System (ADS)

Kasas, S.; Longo, G.; Dietler, G.

2013-04-01

The atomic force microscope is a widely used surface scanning apparatus capable of reconstructing at a nanometric scale resolution the 3D morphology of biological samples. Due to its unique sensitivity, it is now increasingly used as a force sensor, to characterize the mechanical properties of specimens with a similar lateral resolution. This unique capability has produced, in the last years, a vast increase in the number of groups that have exploited the versatility and sensitivity of the instrument to explore the nanomechanics of various samples in the fields of biology, microbiology and medicine. In this review we outline the state of the art in this field, reporting the most interesting recent works involving the exploration of the nanomechanical properties of various biological samples.

Analysis of compositional uniformity in Al{sub x}Ga{sub 1−x}N thin films using atom probe tomography and electron microscopy

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

Liu, Fang; Huang, Li; Porter, Lisa M.

2016-07-15

Calculated frequency distributions of atom probe tomography reconstructions (∼80 nm field of view) of very thin Al{sub x}Ga{sub 1−x}N (0.18 ≤ x ≤ 0.51) films grown via metalorganic vapor phase epitaxy on both (0001) GaN/AlN/SiC and (0001) GaN/sapphire heterostructures revealed homogeneous concentrations of Al and chemically abrupt Al{sub x}Ga{sub 1−x}N/GaN interfaces. The results of scanning transmission electron microscopy and selected area diffraction corroborated these results and revealed that neither superlattice ordering nor phase separation was present at nanometer length scales.

A Gaussian Approximation Potential for Silicon

NASA Astrophysics Data System (ADS)

Bernstein, Noam; Bartók, Albert; Kermode, James; Csányi, Gábor

We present an interatomic potential for silicon using the Gaussian Approximation Potential (GAP) approach, which uses the Gaussian process regression method to approximate the reference potential energy surface as a sum of atomic energies. Each atomic energy is approximated as a function of the local environment around the atom, which is described with the smooth overlap of atomic environments (SOAP) descriptor. The potential is fit to a database of energies, forces, and stresses calculated using density functional theory (DFT) on a wide range of configurations from zero and finite temperature simulations. These include crystalline phases, liquid, amorphous, and low coordination structures, and diamond-structure point defects, dislocations, surfaces, and cracks. We compare the results of the potential to DFT calculations, as well as to previously published models including Stillinger-Weber, Tersoff, modified embedded atom method (MEAM), and ReaxFF. We show that it is very accurate as compared to the DFT reference results for a wide range of properties, including low energy bulk phases, liquid structure, as well as point, line, and plane defects in the diamond structure.

Computed tomography imaging with the Adaptive Statistical Iterative Reconstruction (ASIR) algorithm: dependence of image quality on the blending level of reconstruction.

PubMed

Barca, Patrizio; Giannelli, Marco; Fantacci, Maria Evelina; Caramella, Davide

2018-06-01

Computed tomography (CT) is a useful and widely employed imaging technique, which represents the largest source of population exposure to ionizing radiation in industrialized countries. Adaptive Statistical Iterative Reconstruction (ASIR) is an iterative reconstruction algorithm with the potential to allow reduction of radiation exposure while preserving diagnostic information. The aim of this phantom study was to assess the performance of ASIR, in terms of a number of image quality indices, when different reconstruction blending levels are employed. CT images of the Catphan-504 phantom were reconstructed using conventional filtered back-projection (FBP) and ASIR with reconstruction blending levels of 20, 40, 60, 80, and 100%. Noise, noise power spectrum (NPS), contrast-to-noise ratio (CNR) and modulation transfer function (MTF) were estimated for different scanning parameters and contrast objects. Noise decreased and CNR increased non-linearly up to 50 and 100%, respectively, with increasing blending level of reconstruction. Also, ASIR has proven to modify the NPS curve shape. The MTF of ASIR reconstructed images depended on tube load/contrast and decreased with increasing blending level of reconstruction. In particular, for low radiation exposure and low contrast acquisitions, ASIR showed lower performance than FBP, in terms of spatial resolution for all blending levels of reconstruction. CT image quality varies substantially with the blending level of reconstruction. ASIR has the potential to reduce noise whilst maintaining diagnostic information in low radiation exposure CT imaging. Given the opposite variation of CNR and spatial resolution with the blending level of reconstruction, it is recommended to use an optimal value of this parameter for each specific clinical application.

Magnetic conveyor belt for transporting and merging trapped atom clouds.

PubMed

Hänsel, W; Reichel, J; Hommelhoff, P; Hänsch, T W

2001-01-22

We demonstrate an integrated magnetic device which transports cold atoms near a surface with very high positioning accuracy. Time-dependent currents in a lithographic conductor pattern create a moving chain of potential wells; atoms are transported in these wells while remaining confined in all three dimensions. We achieve mean fluxes up to 10(6) s(-1) with a negligible heating rate. An extension of this device allows merging of atom clouds by unification of two Ioffe-Pritchard potentials. The unification, which we demonstrate experimentally, can be performed without loss of phase space density. This novel, all-magnetic atom manipulation offers exciting perspectives, such as trapped-atom interferometry.

The role of place-exchange, dislocations and substrate symmetry in nickel/gold(111) heteroepitaxy

NASA Astrophysics Data System (ADS)

Cullen, William Grady

1999-12-01

The epitaxial growth of Ni on Au(111) in ultrahigh vacuum was investigated using scanning tunneling microscopy (STM) and Auger electron spectroscopy (AES). Films in the coverage range 0--2 monolayers were studied. The goals were to investigate the influence of the substrate reconstruction on the morphology of the growing film and also the possibility of intermixing between Ni and Au. Deposition of Ni at room temperature led to the growth of two-dimensional islands which nucleate at the point dislocations of the Au(111) herringbone reconstruction, as found in previous studies. Anisotropic growth features were identified and shown to result from basic symmetry properties of the Au(111) reconstruction. In addition, significant internal structure was observed within the islands, indicating that the islands are of mixed composition, and that the overlayer is not pseudomorphic. Two-dimensional island ripening was observed after deposition of Ni at room temperature, followed by moderate annealing. Results of STM and AES experiments indicate that the mass transport during ripening is due to mobile Au atoms which have detached from the original islands. Deposition at high temperature was shown to result in the formation of large epitaxial Au islands due to Ni-Au place exchange and subsequent collision-mediated nucleation of Au atoms. Island size distributions were analyzed for comparison with scaling theories, and data collapse onto a common curve was observed at different coverages and temperatures. Based on the scaling analysis, a critical nucleus of i = 2 was inferred. The annealing and high-temperature deposition experiments demonstrated that a Ni monolayer is metastable at the Au(111) surface, i.e. Au tends to segregate and cover the Ni.

Do's and don'ts of cryo-electron microscopy: a primer on sample preparation and high quality data collection for macromolecular 3D reconstruction.

PubMed

Cabra, Vanessa; Samsó, Montserrat

2015-01-09

Cryo-electron microscopy (cryoEM) entails flash-freezing a thin layer of sample on a support, and then visualizing the sample in its frozen hydrated state by transmission electron microscopy (TEM). This can be achieved with very low quantity of protein and in the buffer of choice, without the use of any stain, which is very useful to determine structure-function correlations of macromolecules. When combined with single-particle image processing, the technique has found widespread usefulness for 3D structural determination of purified macromolecules. The protocol presented here explains how to perform cryoEM and examines the causes of most commonly encountered problems for rational troubleshooting; following all these steps should lead to acquisition of high quality cryoEM images. The technique requires access to the electron microscope instrument and to a vitrification device. Knowledge of the 3D reconstruction concepts and software is also needed for computerized image processing. Importantly, high quality results depend on finding the right purification conditions leading to a uniform population of structurally intact macromolecules. The ability of cryoEM to visualize macromolecules combined with the versatility of single particle image processing has proven very successful for structural determination of large proteins and macromolecular machines in their near-native state, identification of their multiple components by 3D difference mapping, and creation of pseudo-atomic structures by docking of x-ray structures. The relentless development of cryoEM instrumentation and image processing techniques for the last 30 years has resulted in the possibility to generate de novo 3D reconstructions at atomic resolution level.

Theoretical studies of positron states and annihilation characteristics at the oxidized Cu(100) surface

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Weiss, A. H.

2013-04-01

In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. An ab-initio study of the electronic properties of the Cu(100) missing row reconstructed surface at various on surface and sub-surface oxygen coverages has been performed on the basis of the density functional theory (DFT) using the Dmol3 code and the generalized gradient approximation (GGA). Surface structures in calculations have been constructed by adding oxygen atoms to various surface hollow and sub-surface octahedral sites of the 0.5 monolayer (ML) missing row reconstructed phase of the Cu(100) surface with oxygen coverages ranging from 0.5 to 1.5 ML. The charge redistribution at the surface and variations in atomic structure and chemical composition of the topmost layers associated with oxidation and surface reconstruction have been found to affect the spatial extent and localization of the positron surface state wave function and annihilation probabilities of surface trapped positrons with relevant core electrons. Theoretical results are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES). It has been shown that positron annihilation probabilities with Cu 3s and 3p core electrons decrease when total (on-surface and sub-surface) oxygen coverage of the Cu(100) surface increases up to 1 ML. The calculations show that for high oxygen coverage when total oxygen coverage is 1. 5 ML the positron is not bound to the surface.

Theoretical studies of positron states and annihilation characteristics at the oxidized Cu(100) surface

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

Fazleev, N. G.; Weiss, A. H.

2013-04-19

In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. An ab-initio study of the electronic properties of the Cu(100) missing row reconstructed surface at various on surface and sub-surface oxygen coverages has been performed on the basis of the density functional theory (DFT) using the Dmol3 code and the generalized gradient approximation (GGA). Surface structures in calculations have been constructed by adding oxygen atoms to various surface hollow and sub-surface octahedral sitesmore » of the 0.5 monolayer (ML) missing row reconstructed phase of the Cu(100) surface with oxygen coverages ranging from 0.5 to 1.5 ML. The charge redistribution at the surface and variations in atomic structure and chemical composition of the topmost layers associated with oxidation and surface reconstruction have been found to affect the spatial extent and localization of the positron surface state wave function and annihilation probabilities of surface trapped positrons with relevant core electrons. Theoretical results are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES). It has been shown that positron annihilation probabilities with Cu 3s and 3p core electrons decrease when total (on-surface and sub-surface) oxygen coverage of the Cu(100) surface increases up to 1 ML. The calculations show that for high oxygen coverage when total oxygen coverage is 1. 5 ML the positron is not bound to the surface.« less

The (2×2) reconstructions on the surface of cobalt silicides: Atomic configuration at the annealed Co/Si(111) interface

NASA Astrophysics Data System (ADS)

Kotlyar, V. G.; Alekseev, A. A.; Olyanich, D. A.; Utas, T. V.; Zotov, A. V.; Saranin, A. A.

2017-08-01

We have used scanning tunneling microscopy (STM) and ab initio total-energy calculations to characterize surface and interfacial structure of Co-Si(111) system. It has been found experimentally that two different types of the (2×2) surface structures occur. The coexistence of two phases is demonstrated by the example of STM image of the surface formed at the early stages of cobalt silicide formation under moderate annealing temperatures (500 °C). The measured height difference between the adjacent (2×2) reconstructed patches equal to about 1.0 Å (as determined from the filled-state STM images). In addition, the shift of the atomic rows by half of the row spacing is observed. Two adatom models of the (2×2) surface structures are developed. According to our data, these structures are assigned to CaF2-type CoSi2 and CsCl-type CoSi with a (2×2) array of Si adatoms on their surfaces. If the latter is the case, it has а coherent double interface CoSi/CoSi2/Si(111) with a two-layer CoSi2. Both of these interfaces are characterized by the eightfold cobalt coordination and incorporate a grown-in stacking fault.

Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.

PubMed

Rusu, Mirabela; Birmanns, Stefan

2010-04-01

A structural characterization of multi-component cellular assemblies is essential to explain the mechanisms governing biological function. Macromolecular architectures may be revealed by integrating information collected from various biophysical sources - for instance, by interpreting low-resolution electron cryomicroscopy reconstructions in relation to the crystal structures of the constituent fragments. A simultaneous registration of multiple components is beneficial when building atomic models as it introduces additional spatial constraints to facilitate the native placement inside the map. The high-dimensional nature of such a search problem prevents the exhaustive exploration of all possible solutions. Here we introduce a novel method based on genetic algorithms, for the efficient exploration of the multi-body registration search space. The classic scheme of a genetic algorithm was enhanced with new genetic operations, tabu search and parallel computing strategies and validated on a benchmark of synthetic and experimental cryo-EM datasets. Even at a low level of detail, for example 35-40 A, the technique successfully registered multiple component biomolecules, measuring accuracies within one order of magnitude of the nominal resolutions of the maps. The algorithm was implemented using the Sculptor molecular modeling framework, which also provides a user-friendly graphical interface and enables an instantaneous, visual exploration of intermediate solutions. (c) 2009 Elsevier Inc. All rights reserved.

Native gallium adatoms discovered on atomically-smooth gallium nitride surfaces at low temperature.

PubMed

Alam, Khan; Foley, Andrew; Smith, Arthur R

2015-03-11

In advanced compound semiconductor devices, such as in quantum dot and quantum well systems, detailed atomic configurations at the growth surfaces are vital in determining the structural and electronic properties. Therefore, it is important to investigate the surface reconstructions in order to make further technological advancements. Usually, conventional semiconductor surfaces (e.g., arsenides, phosphides, and antimonides) are highly reactive due to the existence of a high density of group V (anion) surface dangling bonds. However, in the case of nitrides, group III rich growth conditions in molecular beam epitaxy are usually preferred leading to group III (Ga)-rich surfaces. Here, we use low-temperature scanning tunneling microscopy to reveal a uniform distribution of native gallium adatoms with a density of 0.3%-0.5% of a monolayer on the clean, as-grown surface of nitrogen polar GaN(0001̅) having the centered 6 × 12 reconstruction. Unseen at room temperature, these Ga adatoms are strongly bound to the surface but move with an extremely low surface diffusion barrier and a high density saturation coverage in thermodynamic equilibrium with Ga droplets. Furthermore, the Ga adatoms reveal an intrinsic surface chirality and an asymmetric site occupation. These observations can have important impacts in the understanding of gallium nitride surfaces.

Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

PubMed

A Rohrdanz, Mary; Zheng, Wenwei; Lambeth, Bradley; Vreede, Jocelyne; Clementi, Cecilia

2014-10-01

The nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.

Interplay between Mechanics, Electronics, and Energetics in Atomic-Scale Junctions

NASA Astrophysics Data System (ADS)

Aradhya, Sriharsha V.

The physical properties of materials at the nanoscale are controlled to a large extent by their interfaces. While much knowledge has been acquired about the properties of material in the bulk, there are many new and interesting phenomena at the interfaces that remain to be better understood. This is especially true at the scale of their constituent building blocks - atoms and molecules. Studying materials at this intricate level is a necessity at this point in time because electronic devices are rapidly approaching the limits of what was once thought possible, both in terms of their miniaturization as well as our ability to design their behavior. In this thesis I present our explorations of the interplay between mechanical properties, electronic transport and binding energetics of single atomic contacts and single-molecule junctions. Experimentally, we use a customized conducting atomic force microscope (AFM) that simultaneously measures the current and force across atomic-scale junctions. We use this instrument to study single atomic contacts of gold and silver and single-molecule junctions formed in the gap between two gold metallic point contacts, with molecules with a variety of backbones and chemical linker groups. Combined with density functional theory based simulations and analytical modeling, these experiments provide insight into the correlations between mechanics and electronic structure at the atomic level. In carrying out these experimental studies, we repeatedly form and pull apart nanoscale junctions between a metallized AFM cantilever tip and a metal-coated substrate. The force and conductance of the contact are simultaneously measured as each junction evolves through a series of atomic-scale rearrangements and bond rupture events, frequently resulting in single atomic contacts before rupturing completely. The AFM is particularly optimized to achieve high force resolution with stiff probes that are necessary to create and measure forces across atomic-size junctions that are otherwise difficult to fabricate using conventional lithographic techniques. In addition to the instrumentation, we have developed new algorithmic routines to perform statistical analyses of force data, with varying degrees of reliance on the conductance signatures. The key results presented in this thesis include our measurements with gold metallic contacts, through which we are able to rigorously characterize the stiffness and maximum forces sustained by gold single atomic contacts and many different gold-molecule-gold single-molecule junctions. In our experiments with silver metallic contacts we use statistical correlations in conductance to distinguish between pristine and oxygen-contaminated silver single atomic contacts. This allows us to separately obtain mechanical information for each of these structural motifs. The independently measured force data also provides new insights about atomic-scale junctions that are not possible to obtain through conductance measurements alone. Using a systematically designed set of molecules, we are able to demonstrate that quantum interference is not quenched in single-molecule junctions even at room temperature and ambient conditions. We have also been successful in conducting one of the first quantitative measurements of van der Waals forces at the metal-molecule interface at the single-molecule level. Finally, towards the end of this thesis, we present a general analytical framework to quantitatively reconstruct the binding energy curves of atomic-scale junctions directly from experiments, thereby unifying all of our mechanical measurements. I conclude with a summary of the work presented in this thesis, and an outlook for potential future studies that could be guided by this work.

STIR-Physics: Cold Atoms and Nanocrystals in Tapered Nanofiber and High-Q Resonator Potentials

DTIC Science & Technology

2016-11-02

STIR- Physics : Cold Atoms and Nanocrystals in Tapered Nanofiber and High-Q Resonator Potentials We worked on a tapered fiber in cold atomic cloud...reviewed journals: Number of Papers published in non peer-reviewed journals: Final Report: STIR- Physics : Cold Atoms and Nanocrystals in Tapered Nanofiber...other than abstracts): Number of Peer-Reviewed Conference Proceeding publications (other than abstracts): Books Number of Manuscripts: 0.00Number of

Scattering of particles in the presence of harmonic confinement perturbed by a complex absorbing potential

NASA Astrophysics Data System (ADS)

Maghari, A.; Kermani, M. M.

2018-04-01

A system of two interacting atoms confined in 1D harmonic trap and perturbed by an absorbing boundary potential is studied using the Lippmann-Schwinger formalism. The atom-atom interaction potential was considered as a nonlocal separable model. The perturbed absorbing boundary potential was also assumed in the form of Scarf II complex absorbing potential. The model is used for the study of 1D optical lattices that support the trapping of a pair atom within a unit cell. Moreover, it allows to describe the scattering particles in a tight smooth trapping surface and to analyze the bound and resonance states. The analytical expressions for wavefunctions and transition matrix as well as the absorption probabilities are calculated. A demonstration of how the complex absorbing potential affecting the bound states and resonances of particles confined in a harmonic trap is described.

Electronic Bandgap and Edge Reconstruction in Phosphorene Materials

DOE PAGES

Liang, Liangbo; Wang, Jun; Lin, Wenzhi; ...

2014-11-12

Single-layer black phosphorous (BP), or phosphorene, is a highly-anisotropic two-dimensional elemental material possessing promising semiconductor properties for flexible electronics. However, the direct bandgap of single-layer black phosphorus predicted theoretically has not been directly measured, and the properties of its edges have not been considered in detail. Here we report atomic scale electronic variation related to strain-induced anisotropic deformation of the puckered honeycomb structure of freshly cleaved black phosphorus using a highresolved scanning tunneling spectroscopy (STS) survey along the light (x) and heavy (y) effective mass directions. Through a combination of STS measurements and first-principles calculations, a model for edge reconstructionmore » is also determined. The reconstruction is shown to self-passivate any dangling bond by switching the oxidation state of phosphorous from +3 to +5.« less

Characterizing inner-shell with spectral phase interferometry for direct electric-field reconstruction

PubMed Central

Mashiko, Hiroki; Yamaguchi, Tomohiko; Oguri, Katsuya; Suda, Akira; Gotoh, Hideki

2014-01-01

In many atomic, molecular and solid systems, Lorentzian and Fano profiles are commonly observed in a broad research fields throughout a variety of spectroscopies. As the profile structure is related to the phase of the time-dependent dipole moment, it plays an important role in the study of quantum properties. Here we determine the dipole phase in the inner-shell transition using spectral phase interferometry for direct electric-field reconstruction (SPIDER) with isolated attosecond pulses (IAPs). In addition, we propose a scheme for pulse generation and compression by manipulating the inner-shell transition. The electromagnetic radiation generated by the transition is temporally compressed to a few femtoseconds in the extreme ultraviolet (XUV) region. The proposed pulse-compression scheme may provide an alternative route to producing attosecond pulses of light. PMID:25510971

Optically Unraveling the Edge Chirality-Dependent Band Structure and Plasmon Damping in Graphene Edges.

PubMed

Duan, Jiahua; Chen, Runkun; Cheng, Yuan; Yang, Tianzhong; Zhai, Feng; Dai, Qing; Chen, Jianing

2018-05-01

The nontrivial topological origin and pseudospinorial character of electron wavefunctions make edge states possess unusual electronic properties. Twenty years ago, the tight-binding model calculation predicted that zigzag termination of 2D sheets of carbon atoms have peculiar edge states, which show potential application in spintronics and modern information technologies. Although scanning probe microscopy is employed to capture this phenomenon, the experimental demonstration of its optical response remains challenging. Here, the propagating graphene plasmon provides an edge-selective polaritonic probe to directly detect and control the electronic edge state at ambient condition. Compared with armchair, the edge-band structure in the bandgap gives rise to additional optical absorption and strongly absorbed rim at zigzag edge. Furthermore, the optical conductivity is reconstructed and the anisotropic plasmon damping in graphene systems is revealed. The reported approach paves the way for detecting edge-specific phenomena in other van der Waals materials and topological insulators. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction potential between a helium atom and metal surfaces

NASA Technical Reports Server (NTRS)

Takada, Y.; Kohn, W.

1985-01-01

By employing an S-matrix theory for evanescent waves, the repulsive potential between a helium atom and corrugated metal surfaces has been calculated. P-wave interactions and intra-atomic correlation effects were found to be very important. The corrugation part of the interaction potential is much weaker than predicted by the effective-medium theory. Application to Cu, Ni, and Ag (110) surfaces gives good agreement with experiment without any adjustable parameters.

FI-STM study of hydrogen adsorption on Si(100) surface

NASA Astrophysics Data System (ADS)

Hua, Lu; Xiang-dong, Wang; Motai, K.; Hashizume, T.; Sakurai, T.

1992-11-01

Chemisorption of atomic hydrogen on the Si(100)2 × 1 surface has been investigated in detail by using a field ion-scanning tunneling microscope (FI-STM). The results showed that the adsorption geometry changed from the 2 × 1 monohydride phase to the 1 × 1 dihydride phase with increasing exposure of hydrogen. The data of desorption of the hydrogen-saturated Si surface showed that on annealing at 670 K the surface becomes highly disordered: the 1 × 1 dihydride structure is eliminated and the 2 × 1 reconstructed monohydride is also hardly to identify. When the temperature rises to as high as 730 K, the surface is dominated by the 2 × 1 structure with missing dimer rows, and some adatom chains occur on the Si substrate terraces. We attribute the formation of these atomic chains to an epitaxial growth of Si atoms which are formed by the dissociation of SiHx (x = 1, 2, 3 or 4) compounds on the Si surface.

Long-term Radiation-Related Health Effects in a Unique Human Population: Lessons Learned from the Atomic Bomb Survivors of Hiroshima and Nagasaki

PubMed Central

Douple, Evan B.; Mabuchi, Kiyohiko; Cullings, Harry M.; Preston, Dale L.; Kodama, Kazunori; Shimizu, Yukiko; Fujiwara, Saeko; Shore, Roy E.

2014-01-01

For 63 years scientists in the Atomic Bomb Casualty Commission and its successor, the Radiation Effects Research Foundation, have been assessing the long-term health effects in the survivors of the atomic bombings of Hiroshima and Nagasaki and in their children. The identification and follow-up of a large population (approximately a total of 200 000, of whom more than 40% are alive today) that includes a broad range of ages and radiation exposure doses, and healthy representatives of both sexes; establishment of well-defined cohorts whose members have been studied longitudinally, including some with biennial health examinations and a high survivor participation rate; and careful reconstructions of individual radiation doses have resulted in reliable excess relative risk estimates for radiation-related health effects, including cancer and noncancer effects in humans, for the benefit of the survivors and for all humankind. This article reviews those risk estimates and summarizes what has been learned from this historic and unique study. PMID:21402804

Structural, electronic and magnetic properties of carbon doped boron nitride nanowire: Ab initio study

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

Jalilian, Jaafar, E-mail: JaafarJalilian@gmail.com; Kanjouri, Faramarz, E-mail: kanjouri@khu.ac.ir

2016-11-15

Using spin-polarized density functional theory calculations, we demonstrated that carbon doped boron nitride nanowire (C-doped BNNW) has diverse electronic and magnetic properties depending on position of carbon atoms and their percentages. Our results show that only when one carbon atom is situated on the edge of the nanowire, C-doped BNNW is transformed into half-metal. The calculated electronic structure of the C-doped BNNW suggests that doping carbon can induce localized edge states around the Fermi level, and the interaction among localized edge states leads to semiconductor to half-metal transition. Overall, the bond reconstruction causes of appearance of different electronic behavior suchmore » as semiconducting, half-metallicity, nonmagnetic metallic, and ferromagnetic metallic characters. The formation energy of the system shows that when a C atom is doped on surface boron site, system is more stable than the other positions of carbon impurity. Our calculations show that C-doped BNNW may offer unique opportunities for developing nanoscale spintronic materials.« less

Initial stages of Lutetium growth on Si (111)-7 × 7 probed by STM and core-level photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Smykalla, Lars; Shukrynau, Pavel; Hietschold, Michael

2017-09-01

The interaction of small amounts of Lutetium with the Si (111)-7 × 7 reconstructed surface was investigated in detail using a combination of Scanning Tunneling Microscopy (STM) and Photoelectron Spectroscopy (XPS and UPS). Various immobile and also fastly moving atoms and nanocluster were found in the initial growth of the Lu/Si interface. Density functional theory calculations and photoelectron spectroscopy results suggest that the most attractive adsorption sites for the Lu atoms are basins around Si rest-atoms and there is no strong interaction between Lu and Si at the initial steps of film growth. However Lu nanocluster could also be found on other adsorption sites which results in a different voltage dependence in STM. Coverage-dependent STM images reveal the growth of a closed Lu metal overlayer by joining of the clusters. The existence of a stoichiometric Lu silicide compound was not detected on the surface in the initial growth for deposition at room temperature.

Double-image storage optimized by cross-phase modulation in a cold atomic system

NASA Astrophysics Data System (ADS)

Qiu, Tianhui; Xie, Min

2017-09-01

A tripod-type cold atomic system driven by double-probe fields and a coupling field is explored to store double images based on the electromagnetically induced transparency (EIT). During the storage time, an intensity-dependent signal field is applied further to extend the system with the fifth level involved, then the cross-phase modulation is introduced for coherently manipulating the stored images. Both analytical analysis and numerical simulation clearly demonstrate a tunable phase shift with low nonlinear absorption can be imprinted on the stored images, which effectively can improve the visibility of the reconstructed images. The phase shift and the energy retrieving rate of the probe fields are immune to the coupling intensity and the atomic optical density. The proposed scheme can easily be extended to the simultaneous storage of multiple images. This work may be exploited toward the end of EIT-based multiple-image storage devices for all-optical classical and quantum information processings.

High-Energy Trauma and Damage Control in the Lower Limb

DTIC Science & Technology

2010-01-01

Reconstruction : From Microsurgery Reconstruction to Transplantation; Guest Editors, Chih-Hung Lin, M.D., and Fu-Chan Wei, M.D. Semin Plast Surg...continue intraoperatively.12–14 The goal is to achieve hemostasis, restore normal physiology, and potentially complete a vascular reconstruction upon...injuries and the need for vascular reconstruction at the time of admission is crucial to the success of grafting and maximizes the chances of limb

MO-DE-207A-10: One-Step CT Reconstruction for Metal Artifact Reduction by a Modification of Penalized Weighted Least-Squares (PWLS)

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

Kim, H; Chen, J

Purpose: Metal objects create severe artifacts in kilo-voltage (kV) CT image reconstructions due to the high attenuation coefficients of high atomic number objects. Most of the techniques devised to reduce this artifact utilize a two-step approach, which do not reliably yield the qualified reconstructed images. Thus, for accuracy and simplicity, this work presents a one-step reconstruction method based on a modified penalized weighted least-squares (PWLS) technique. Methods: Existing techniques for metal artifact reduction mostly adopt a two-step approach, which conduct additional reconstruction with the modified projection data from the initial reconstruction. This procedure does not consistently perform well due tomore » the uncertainties in manipulating the metal-contaminated projection data by thresholding and linear interpolation. This study proposes a one-step reconstruction process using a new PWLS operation with total-variation (TV) minimization, while not manipulating the projection. The PWLS for CT reconstruction has been investigated using a pre-defined weight, based on the variance of the projection datum at each detector bin. It works well when reconstructing CT images from metal-free projection data, which does not appropriately penalize metal-contaminated projection data. The proposed work defines the weight at each projection element under the assumption of a Poisson random variable. This small modification using element-wise penalization has a large impact in reducing metal artifacts. For evaluation, the proposed technique was assessed with two noisy, metal-contaminated digital phantoms, against the existing PWLS with TV minimization and the two-step approach. Result: The proposed PWLS with TV minimization greatly improved the metal artifact reduction, relative to the other techniques, by watching the results. Numerically, the new approach lowered the normalized root-mean-square error about 30 and 60% for the two cases, respectively, compared to the two-step method. Conclusion: A new PWLS operation shows promise for improving metal artifact reduction in CT imaging, as well as simplifying the reconstructing procedure.« less

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

PubMed

Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

2016-05-01

The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. Copyright © 2016 Elsevier Inc. All rights reserved.

Wavelet-promoted sparsity for non-invasive reconstruction of electrical activity of the heart.

PubMed

Cluitmans, Matthijs; Karel, Joël; Bonizzi, Pietro; Volders, Paul; Westra, Ronald; Peeters, Ralf

2018-05-12

We investigated a novel sparsity-based regularization method in the wavelet domain of the inverse problem of electrocardiography that aims at preserving the spatiotemporal characteristics of heart-surface potentials. In three normal, anesthetized dogs, electrodes were implanted around the epicardium and body-surface electrodes were attached to the torso. Potential recordings were obtained simultaneously on the body surface and on the epicardium. A CT scan was used to digitize a homogeneous geometry which consisted of the body-surface electrodes and the epicardial surface. A novel multitask elastic-net-based method was introduced to regularize the ill-posed inverse problem. The method simultaneously pursues a sparse wavelet representation in time-frequency and exploits correlations in space. Performance was assessed in terms of quality of reconstructed epicardial potentials, estimated activation and recovery time, and estimated locations of pacing, and compared with performance of Tikhonov zeroth-order regularization. Results in the wavelet domain obtained higher sparsity than those in the time domain. Epicardial potentials were non-invasively reconstructed with higher accuracy than with Tikhonov zeroth-order regularization (p < 0.05), and recovery times were improved (p < 0.05). No significant improvement was found in terms of activation times and localization of origin of pacing. Next to improved estimation of recovery isochrones, which is important when assessing substrate for cardiac arrhythmias, this novel technique opens potentially powerful opportunities for clinical application, by allowing to choose wavelet bases that are optimized for specific clinical questions. Graphical Abstract The inverse problem of electrocardiography is to reconstruct heart-surface potentials from recorded bodysurface electrocardiograms (ECGs) and a torso-heart geometry. However, it is ill-posed and solving it requires additional constraints for regularization. We introduce a regularization method that simultaneously pursues a sparse wavelet representation in time-frequency and exploits correlations in space. Our approach reconstructs epicardial (heart-surface) potentials with higher accuracy than common methods. It also improves the reconstruction of recovery isochrones, which is important when assessing substrate for cardiac arrhythmias. This novel technique opens potentially powerful opportunities for clinical application, by allowing to choose wavelet bases that are optimized for specific clinical questions.

Dynamic of cold-atom tips in anharmonic potentials

PubMed Central

Menold, Tobias; Federsel, Peter; Rogulj, Carola; Hölscher, Hendrik; Fortágh, József

2016-01-01

Background: Understanding the dynamics of ultracold quantum gases in an anharmonic potential is essential for applications in the new field of cold-atom scanning probe microscopy. Therein, cold atomic ensembles are used as sensitive probe tips to investigate nanostructured surfaces and surface-near potentials, which typically cause anharmonic tip motion. Results: Besides a theoretical description of this anharmonic tip motion, we introduce a novel method for detecting the cold-atom tip dynamics in situ and real time. In agreement with theory, the first measurements show that particle interactions and anharmonic motion have a significant impact on the tip dynamics. Conclusion: Our findings will be crucial for the realization of high-sensitivity force spectroscopy with cold-atom tips and could possibly allow for the development of advanced spectroscopic techniques such as Q-control. PMID:28144505

Performance comparison between total variation (TV)-based compressed sensing and statistical iterative reconstruction algorithms.

PubMed

Tang, Jie; Nett, Brian E; Chen, Guang-Hong

2009-10-07

Of all available reconstruction methods, statistical iterative reconstruction algorithms appear particularly promising since they enable accurate physical noise modeling. The newly developed compressive sampling/compressed sensing (CS) algorithm has shown the potential to accurately reconstruct images from highly undersampled data. The CS algorithm can be implemented in the statistical reconstruction framework as well. In this study, we compared the performance of two standard statistical reconstruction algorithms (penalized weighted least squares and q-GGMRF) to the CS algorithm. In assessing the image quality using these iterative reconstructions, it is critical to utilize realistic background anatomy as the reconstruction results are object dependent. A cadaver head was scanned on a Varian Trilogy system at different dose levels. Several figures of merit including the relative root mean square error and a quality factor which accounts for the noise performance and the spatial resolution were introduced to objectively evaluate reconstruction performance. A comparison is presented between the three algorithms for a constant undersampling factor comparing different algorithms at several dose levels. To facilitate this comparison, the original CS method was formulated in the framework of the statistical image reconstruction algorithms. Important conclusions of the measurements from our studies are that (1) for realistic neuro-anatomy, over 100 projections are required to avoid streak artifacts in the reconstructed images even with CS reconstruction, (2) regardless of the algorithm employed, it is beneficial to distribute the total dose to more views as long as each view remains quantum noise limited and (3) the total variation-based CS method is not appropriate for very low dose levels because while it can mitigate streaking artifacts, the images exhibit patchy behavior, which is potentially harmful for medical diagnosis.

Embedded-atom-method study of structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys

NASA Astrophysics Data System (ADS)

Asta, Mark; Morgan, Dane; Hoyt, J. J.; Sadigh, Babak; Althoff, J. D.; de Fontaine, D.; Foiles, S. M.

1999-06-01

Structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys have been studied by Monte Carlo and molecular-dynamics simulations based upon three different embedded-atom method (EAM) interatomic potentials, namely those due to Foiles and Daw (FD) [J. Mater. Res. 2, 5 (1987)], Voter and Chen (VC) [in Characterization of Defects in Materials, edited by R. W. Siegel et al. MRS Symposia Proceedings. No. 82 (Materials Research Society, Pittsburgh, 1987), p.175] and Ludwig and Gumbsch (LG) [Model. Simul. Mater. Sci. Eng. 3, 533 (1995)]. We present detailed comparisons between calculated results and experimental data for structure factors, atomic volumes, enthalpies of mixing, activities, and viscosities. Calculated partial structure factors are found to be in semiquantitative agreement with published neutron scattering measurements for Ni20Al80 alloys, indicating that short-range order in the liquid phase is qualitatively well described. Calculated thermodynamic properties of mixing are found to agree very well with experimental data for Ni compositions greater than 75 atomic %, while for alloys richer in Al the magnitudes of the enthalpies and entropies of mixing are significantly underestimated. The VC and LG potentials give atomic densities and viscosities in good agreement with experiment for Ni-rich compositions, while FD potentials consistently underestimate both properties at all concentrations. The results of this study demonstrate that VC and LG potentials provide a realistic description of the thermodynamic and atomic transport properties for NixAl1-x liquid alloys with x>=0.75, and point to the limitations of EAM potentials for alloys richer in Al.

3D-atom probe characterization of nano-precipitates in a PM processed tool steels

NASA Astrophysics Data System (ADS)

Niederkofler, M.; Leisch, M.

2004-07-01

The microstructure of a powder metallurgical processed high speed steel (nom. composition (wt.%): 1.6 C, 4.8 Cr, 2.0 Mo, 5.0 V, 105 W, 8.0 Co and balance Fe) has been examined using 3D-atom probe technique. By the depth profiling of the time to flight mass spectrometer and position sensitive recording, cylindrical volumes of 10-15 nm in diameter and up to 40 nm in depth have been probed and characterized. The depth profiling measurements of the samples show generally a very homogeneous structure which was expected by the powder metallurgical processing of the material. Different morphologies of the precipitates were recorded. Besides the needle shaped precipitates with an extend up to 20 nm and thickness of few atomic layers, platelets and spherical particles are observed as well. The species which can be assigned to the precipitates appear to some extend as MC molecules in the mass histogram, while the leading constituents in this MC are Mo, V and Cr. Beside distinct particles agglomerations like one-dimensional atomic chains of the alloy components are also observed in the 3D reconstructions of the tool steel matrix.

The role of Ag buffer layer in Fe islands growth on Ge (111) surfaces

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

Fu, Tsu-Yi, E-mail: phtifu@phy.ntnu.edu.tw; Wu, Jia-Yuan; Jhou, Ming-Kuan

2015-05-07

Sub-monolayer iron atoms were deposited at room temperature on Ge (111)-c(2 × 8) substrates with and without Ag buffer layers. The behavior of Fe islands growth was investigated by using scanning tunneling microscope (STM) after different annealing temperatures. STM images show that iron atoms will cause defects and holes on substrates at room temperature. As the annealing temperature rises, iron atoms pull out germanium to form various kinds of alloyed islands. However, the silver layer can protect the Ag/Ge(111)-(√3×√3) reconstruction from forming defects. The phase diagram shows that ring, dot, and triangular defects were only found on Ge (111)-c(2 × 8) substrates. The kindsmore » of islands found in Fe/Ge system are similar to Fe/Ag/Ge system. It indicates that Ge atoms were pulled out to form islands at high annealing temperatures whether there was a Ag layer or not. But a few differences in big pyramidal or strip islands show that the silver layer affects the development of islands by changing the surface symmetry and diffusion coefficient. The structure characters of various islands are also discussed.« less

Self-diffusion on iridium (100). A structure investigation by field-ion microscopy

NASA Astrophysics Data System (ADS)

Friedl, A.; Schütz, O.; Müller, K.

1992-04-01

An iridium atom was thermally activated for diffusion on the (100) terrace of an Ir tip. The residence sites of the atom between diffusion cycles were recorded by means of a computer-controlled video system which generates a map of all occupied sites. For a field evaporated tip at low temperature this map is a c(2 × 2) grid indicating that only every other fourfold hollow in every other row of an undistor ted (100) surface can be occupied by a diffusing atom. This extraordinary behaviour was already reported by Chen and Tsong [Phys. Rev. Lett. 64 (1990) 3147]. The authors base their interpretation on an exchange diffusion mechanism. As an alternative explanation we propose a local adsorbate induced (2 × 2) reconstruction of the substrate. After heating the same terrace to temperatures above 500 K the residence map of the Ir atom indicates a (1 × 1) structure which, however, contains residues of a c(2 × 2) diffusion pattern: while the diffusion still takes place mainly on a c(2 × 2) sublattice, the diffusion path changes occasionally from one sublattice to the other. This can also be understood by local adsorbate induced distortions.

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction

PubMed Central

Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J. Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S.; D’Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-01-01

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism. PMID:29084163

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.

Opposing effects of humidity on rhodochrosite surface oxidation.

PubMed

Na, Chongzheng; Tang, Yuanzhi; Wang, Haitao; Martin, Scot T

2015-03-03

Rhodochrosite (MnCO3) is a model mineral representing carbonate aerosol particles containing redox-active elements that can influence particle surface reconstruction in humid air, thereby affecting the heterogeneous transformation of important atmospheric constituents such as nitric oxides, sulfur dioxides, and organic acids. Using in situ atomic force microscopy, we show that the surface reconstruction of rhodochrosite in humid oxygen leads to the formation and growth of oxide nanostructures. The oxidative reconstruction consists of two consecutive processes with distinctive time scales, including a long waiting period corresponding to slow nucleation and a rapid expansion phase corresponding to fast growth. By varying the relative humidity from 55 to 78%, we further show that increasing humidity has opposing effects on the two processes, accelerating nucleation from 2.8(±0.2) × 10(-3) to 3.0(±0.2) × 10(-2) h(-1) but decelerating growth from 7.5(±0.3) × 10(-3) to 3.1(±0.1) × 10(-3) μm(2) h(-1). Through quantitative analysis, we propose that nanostructure nucleation is controlled by rhodochrosite surface dissolution, similar to the dissolution-precipitation mechanism proposed for carbonate mineral surface reconstruction in aqueous solution. To explain nanostructure growth in humid oxygen, a new Cabrera-Mott mechanism involving electron tunneling and solid-state diffusion is proposed.

Three-dimensional atom probe tomography of oxide, anion, and alkanethiolate coatings on gold.

PubMed

Zhang, Yi; Hillier, Andrew C

2010-07-15

We have used three-dimensional atom probe tomography to analyze several nanometer-thick and monomolecular films on gold surfaces. High-purity gold wire was etched by electropolishing to create a sharp tip suitable for field evaporation with a radius of curvature of <100 nm. The near-surface region of a freshly etched gold tip was examined with the atom probe at subnanometer spatial resolution and with atom-level composition accuracy. A thin contaminant layer, primarily consisting of water and atmospheric gases, was observed on a fresh tip. This sample exhibited crystalline lattice spacings consistent with the interlayer spacing of {200} lattice planes of bulk gold. A thin oxide layer was created on the gold surface via plasma oxidation, and the thickness and composition of this layer was measured. Clear evidence of a nanometer-thick oxide layer was seen coating the gold tip, and the atomic composition of the oxide layer was consistent with the expected stoichiometry for gold oxide. Monomolecular anions layers of Br(-) and I(-) were created via adsorption from aqueous solutions onto the gold. Atom probe data verified the presence of the monomolecular anion layers on the gold surface, with ion density values consistent with literature values. A hexanethiolate monolayer was coated onto the gold tip, and atom probe analysis revealed a thin film whose ion fragments were consistent with the molecular composition of the monolayer and a surface coverage similar to that expected from literature. Details of the various coating compositions and structures are presented, along with discussion of the reconstruction issues associated with properly analyzing these thin-film systems.

Recurrence spectra of a helium atom in parallel electric and magnetic fields

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

Wang, Dehua; Department of Mathematics and Physics, Shandong Architecture and Engineering Institute, Jinan 250014, People's Republic of China; Ding, Shiliang

2003-08-01

A model potential for the general Rydberg atom is put forward, which includes not only the Coulomb interaction potential and the core-attractive potential, but also the exchange potential between the excited electron and other electrons. Using the region-splitting consistent and iterative method, we calculated the scaled recurrence spectra of the helium atom in parallel electric and magnetic fields and the closed orbits in the corresponding classical system have also been obtained. In order to remove the Coulomb singularity of the classical motion of Hamiltonian, we implement the Kustaanheimo-Stiefel transformation, which transforms the system from a three-dimensional to a four-dimensional one.more » The Fourier-transformed spectra of the helium atom has allowed direct comparison between peaks in such a plot and the scaled action values of closed orbits. Considering the exchange potential, the number of the closed orbits increased, which led to more peaks in the recurrence spectra. The results are compared with those of the hydrogen case, which shows that the core-scattered effects and the electron exchange potential play an important role in the multielectron Rydberg atom.« less

Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials

PubMed Central

Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

2009-01-01

Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all-atom distance-dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT-TS score, but decreased the Z-score of the native structure. The attractiveness of potential improved both the correlation and Z-score for template-based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states. PMID:19588493

Dynamics of a single-atom electron pump.

PubMed

van der Heijden, J; Tettamanzi, G C; Rogge, S

2017-03-15

Single-electron pumps based on isolated impurity atoms have recently been experimentally demonstrated. In these devices the Coulomb potential of an atom creates a localised electron state with a large charging energy and considerable orbital level spacings, enabling robust charge capturing processes. In contrast to the frequently used gate-defined quantum dot pumps, which experience a strongly time-dependent potential, the confinement potential in these single-atom pumps is hardly affected by the periodic driving of the system. Here we describe the behaviour and performance of an atomic, single parameter, electron pump. This is done by considering the loading, isolating and unloading of one electron at the time, on a phosphorous atom embedded in a silicon double gate transistor. The most important feature of the atom pump is its very isolated ground state, which is populated through the fast loading of much higher lying excited states and a subsequent fast relaxation process. This leads to a substantial increase in pumping accuracy, and is opposed to the adverse role of excited states observed for quantum dot pumps due to non-adiabatic excitations. The pumping performance is investigated as a function of dopant position, revealing a pumping behaviour robust against the expected variability in atomic position.

Dynamics of a single-atom electron pump

PubMed Central

van der Heijden, J.; Tettamanzi, G. C.; Rogge, S.

2017-01-01

Single-electron pumps based on isolated impurity atoms have recently been experimentally demonstrated. In these devices the Coulomb potential of an atom creates a localised electron state with a large charging energy and considerable orbital level spacings, enabling robust charge capturing processes. In contrast to the frequently used gate-defined quantum dot pumps, which experience a strongly time-dependent potential, the confinement potential in these single-atom pumps is hardly affected by the periodic driving of the system. Here we describe the behaviour and performance of an atomic, single parameter, electron pump. This is done by considering the loading, isolating and unloading of one electron at the time, on a phosphorous atom embedded in a silicon double gate transistor. The most important feature of the atom pump is its very isolated ground state, which is populated through the fast loading of much higher lying excited states and a subsequent fast relaxation process. This leads to a substantial increase in pumping accuracy, and is opposed to the adverse role of excited states observed for quantum dot pumps due to non-adiabatic excitations. The pumping performance is investigated as a function of dopant position, revealing a pumping behaviour robust against the expected variability in atomic position. PMID:28295055

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces.

PubMed

Hong, Ie-Hong; Liao, Yung-Cheng; Tsai, Yung-Feng

2013-11-05

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process.

Template-directed atomically precise self-organization of perfectly ordered parallel cerium silicide nanowire arrays on Si(110)-16 × 2 surfaces

PubMed Central

2013-01-01

The perfectly ordered parallel arrays of periodic Ce silicide nanowires can self-organize with atomic precision on single-domain Si(110)-16 × 2 surfaces. The growth evolution of self-ordered parallel Ce silicide nanowire arrays is investigated over a broad range of Ce coverages on single-domain Si(110)-16 × 2 surfaces by scanning tunneling microscopy (STM). Three different types of well-ordered parallel arrays, consisting of uniformly spaced and atomically identical Ce silicide nanowires, are self-organized through the heteroepitaxial growth of Ce silicides on a long-range grating-like 16 × 2 reconstruction at the deposition of various Ce coverages. Each atomically precise Ce silicide nanowire consists of a bundle of chains and rows with different atomic structures. The atomic-resolution dual-polarity STM images reveal that the interchain coupling leads to the formation of the registry-aligned chain bundles within individual Ce silicide nanowire. The nanowire width and the interchain coupling can be adjusted systematically by varying the Ce coverage on a Si(110) surface. This natural template-directed self-organization of perfectly regular parallel nanowire arrays allows for the precise control of the feature size and positions within ±0.2 nm over a large area. Thus, it is a promising route to produce parallel nanowire arrays in a straightforward, low-cost, high-throughput process. PMID:24188092

Integrated Optical Dipole Trap for Cold Neutral Atoms with an Optical Waveguide Coupler

NASA Astrophysics Data System (ADS)

Lee, J.; Park, D. H.; Mittal, S.; Meng, Y.; Dagenais, M.; Rolston, S. L.

2013-05-01

Using an optical waveguide, an integrated optical dipole trap uses two-color (red and blue-detuned) traveling evanescent wave fields for trapping cold neutral atoms. To achieve longitudinal confinement, we propose using an integrated optical waveguide coupler, which provides a potential gradient along the beam propagation direction sufficient to confine atoms. This integrated optical dipole trap can support an atomic ensemble with a large optical depth due to its small mode area. Its quasi-TE0 waveguide mode has an advantage over the HE11 mode of a nanofiber, with little inhomogeneous Zeeman broadening at the trapping region. The longitudinal confinement eliminates the need for a 1D optical lattice, reducing collisional blockaded atomic loading, potentially producing larger ensembles. The waveguide trap allows for scalability and integrability with nano-fabrication technology. We analyze the potential performance of such integrated atom traps and present current research progress towards a fiber-coupled silicon nitride optical waveguide integrable with atom chips. Work is supported by the ARO Atomtronics MURI. Work is supported by the ARO Atomtronics MURI.

Potential of transition metal atoms embedded in buckled monolayer g-C3N4 as single-atom catalysts.

PubMed

Li, Shu-Long; Yin, Hui; Kan, Xiang; Gan, Li-Yong; Schwingenschlögl, Udo; Zhao, Yong

2017-11-15

We use first-principles calculations to systematically explore the potential of transition metal atoms (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au) embedded in buckled monolayer g-C 3 N 4 as single-atom catalysts. We show that clustering of Sc and Ti on g-C 3 N 4 is thermodynamically impeded and that V, Cr, Mn, and Cu are much less susceptible to clustering than the other TM atoms under investigation. Strong bonding of the transition metal atoms in the cavities of g-C 3 N 4 and high diffusion barriers together are responsible for single-atom fixation. Analysis of the CO oxidation process indicates that embedding of Cr and Mn in g-C 3 N 4 gives rise to promising single-atom catalysts at low temperature.

Stem cell regenerative potential for plastic and reconstructive surgery.

PubMed

Boháč, Martin; Csöbönyeiová, Mária; Kupcová, Ida; Zamborský, Radoslav; Fedeleš, Jozef; Koller, Ján

2016-12-01

Stem cells represent heterogeneous population of undifferentiated cells with unique characteristics of long term self renewal and plasticity. Moreover, they are capable of active migration to diseased tissues, secretion of different bioactive molecules, and they have immunosuppressive potential as well. They occur in all tissues through life and are involved in process of embryogenesis and regeneration. During last decades stem cells attracted significant attention in each field of medicine, including plastic and reconstructive surgery. The main goal of the present review article is to present and discuss the potential of stem cells and to provide information about their safe utilization in chronic wounds and fistulae healing, scar management, breast reconstruction, as well as in bone, tendon and peripheral nerve regeneration.

Correlation energy, correlated electron density, and exchange-correlation potential in some spherically confined atoms.

PubMed

Vyboishchikov, Sergei F

2016-12-05

We report correlation energies, electron densities, and exchange-correlation potentials obtained from configuration interaction and density functional calculations on spherically confined He, Be, Be 2+ , and Ne atoms. The variation of the correlation energy with the confinement radius R c is relatively small for the He, Be 2+ , and Ne systems. Curiously, the Lee-Yang-Parr (LYP) functional works well for weak confinements but fails completely for small R c . However, in the neutral beryllium atom the CI correlation energy increases markedly with decreasing R c . This effect is less pronounced at the density-functional theory level. The LYP functional performs very well for the unconfined Be atom, but fails badly for small R c . The standard exchange-correlation potentials exhibit significant deviation from the "exact" potential obtained by inversion of Kohn-Sham equation. The LYP correlation potential behaves erratically at strong confinements. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

DOE PAGES

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun; ...

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbonmore » nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.« less

Wave packet interferometry and quantum state reconstruction by acousto-optic phase modulation

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

Tekavec, Patrick F.; Dyke, Thomas R.; Marcus, Andrew H.

2006-11-21

Studies of wave packet dynamics often involve phase-selective measurements of coherent optical signals generated from sequences of ultrashort laser pulses. In wave packet interferometry (WPI), the separation between the temporal envelopes of the pulses must be precisely monitored or maintained. Here we introduce a new (and easy to implement) experimental scheme for phase-selective measurements that combines acousto-optic phase modulation with ultrashort laser excitation to produce an intensity-modulated fluorescence signal. Synchronous detection, with respect to an appropriately constructed reference, allows the signal to be simultaneously measured at two phases differing by 90 deg. Our method effectively decouples the relative temporal phasemore » from the pulse envelopes of a collinear train of optical pulse pairs. We thus achieve a robust and high signal-to-noise scheme for WPI applications, such as quantum state reconstruction and electronic spectroscopy. The validity of the method is demonstrated, and state reconstruction is performed, on a model quantum system - atomic Rb vapor. Moreover, we show that our measurements recover the correct separation between the absorptive and dispersive contributions to the system susceptibility.« less

Electrophilic surface sites as precondition for the chemisorption of pyrrole on GaAs(001) surfaces

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

Bruhn, Thomas; Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Albert-Einstein-Str.9, 12489 Berlin; Fimland, Bjørn-Ove

We report how the presence of electrophilic surface sites influences the adsorption mechanism of pyrrole on GaAs(001) surfaces. For this purpose, we have investigated the adsorption behavior of pyrrole on different GaAs(001) reconstructions with different stoichiometries and thus different surface chemistries. The interfaces were characterized by x-ray photoelectron spectroscopy, scanning tunneling microscopy, and by reflectance anisotropy spectroscopy in a spectral range between 1.5 and 5 eV. On the As-rich c(4 × 4) reconstruction that exhibits only nucleophilic surface sites, pyrrole was found to physisorb on the surface without any significant modification of the structural and electronic properties of the surface. Onmore » the Ga-rich GaAs(001)-(4 × 2)/(6 × 6) reconstructions which exhibit nucleophilic as well as electrophilic surface sites, pyrrole was found to form stable covalent bonds mainly to the electrophilic (charge deficient) Ga atoms of the surface. These results clearly demonstrate that the existence of electrophilic surface sites is a crucial precondition for the chemisorption of pyrrole on GaAs(001) surfaces.« less

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.

PubMed

Levin, Barnaby D A; Padgett, Elliot; Chen, Chien-Chun; Scott, M C; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D; Robinson, Richard D; Ercius, Peter; Kourkoutis, Lena F; Miao, Jianwei; Muller, David A; Hovden, Robert

2016-06-07

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

PubMed Central

Levin, Barnaby D.A.; Padgett, Elliot; Chen, Chien-Chun; Scott, M.C.; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D.; Robinson, Richard D.; Ercius, Peter; Kourkoutis, Lena F.; Miao, Jianwei; Muller, David A.; Hovden, Robert

2016-01-01

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data. PMID:27272459

Novel Fourier-domain constraint for fast phase retrieval in coherent diffraction imaging.

PubMed

Latychevskaia, Tatiana; Longchamp, Jean-Nicolas; Fink, Hans-Werner

2011-09-26

Coherent diffraction imaging (CDI) for visualizing objects at atomic resolution has been realized as a promising tool for imaging single molecules. Drawbacks of CDI are associated with the difficulty of the numerical phase retrieval from experimental diffraction patterns; a fact which stimulated search for better numerical methods and alternative experimental techniques. Common phase retrieval methods are based on iterative procedures which propagate the complex-valued wave between object and detector plane. Constraints in both, the object and the detector plane are applied. While the constraint in the detector plane employed in most phase retrieval methods requires the amplitude of the complex wave to be equal to the squared root of the measured intensity, we propose a novel Fourier-domain constraint, based on an analogy to holography. Our method allows achieving a low-resolution reconstruction already in the first step followed by a high-resolution reconstruction after further steps. In comparison to conventional schemes this Fourier-domain constraint results in a fast and reliable convergence of the iterative reconstruction process. © 2011 Optical Society of America

Reconstruction of low-index graphite surfaces

NASA Astrophysics Data System (ADS)

Thinius, Sascha; Islam, Mazharul M.; Bredow, Thomas

2016-07-01

The low-index graphite surfaces (10 1 -0), (10 1 -1), (11 2 -0) and (11 2 - 1) have been studied by density functional theory (DFT) including van-der-Waals (vdW) corrections. Different from the (0001) surface which has been extensively investigated both experimentally and theoretically, there is no comprehensive study on the (10 1 -0)- (10 1 -1)-, (11 2 -0)- and (11 2 - 1)-surfaces available, although they are of relevance for Li insertion processes, e.g. in Li-ion batteries. In this study the structure and stability of all non-(0001) low-index surfaces were calculated with RPBE-D3 and converged slab models. In all cases reconstruction involving bond formation between unsaturated carbon atoms of two neighboring graphene sheets reduces the surface energy dramatically. Two possible reconstruction patterns have been considered. The first possibility leads to formation of oblong nanotubes. Alternatively, the graphene sheets form bonds to different neighboring sheets at the upper and lower sides and sinusoidal structures are formed. Both structure types have similar stabilities. Based on the calculated surface energies the Gibbs-Wulff theorem was applied to construct the macroscopic shape of graphite single crystals.

Magnetic resonance imaging after anterior cruciate ligament reconstruction: A practical guide

PubMed Central

Grassi, Alberto; Bailey, James R; Signorelli, Cecilia; Carbone, Giuseppe; Tchonang Wakam, Andy; Lucidi, Gian Andrea; Zaffagnini, Stefano

2016-01-01

Anterior cruciate ligament (ACL) reconstruction is one of the most common orthopedic procedures performed worldwide. In this regard, magnetic resonance imaging (MRI) represents a useful pre-operative tool to confirm a disruption of the ACL and to assess for potential associated injuries. However, MRI is also valuable post-operatively, as it is able to identify, in a non-invasive way, a number of aspects and situations that could suggest potential problems to clinicians. Graft signal and integrity, correct tunnel placement, tunnel widening, and problems with fixation devices or the donor site could all compromise the surgical outcomes and potentially predict the failure of the ACL reconstruction. Furthermore, several anatomical features of the knee could be associated to worst outcomes or higher risk of failure. This review provides a practical guide for the clinician to evaluate the post-surgical ACL through MRI, and to analyze all the parameters and features directly or indirectly related to ACL reconstruction, in order to assess for normal or pathologic conditions. PMID:27795945

Oxide surfaces and metal/oxide interfaces studied by grazing incidence X-ray scattering

NASA Astrophysics Data System (ADS)

Renaud, Gilles

Experimental determinations of the atomic structure of insulating oxide surfaces and metal/oxide interfaces are scarce, because surface science techniques are often limited by the insulating character of the substrate. Grazing incidence X-ray scattering (GIXS), which is not subject to charge effects, can provide very precise information on the atomic structure of oxide surfaces: roughness, relaxation and reconstruction. It is also well adapted to analyze the atomic structure, the registry, the misfit relaxation, elastic or plastic, the growth mode and the morphology of metal/oxide interfaces during their growth, performed in situ. GIXS also allows the analysis of thin films and buried interfaces, in a non-destructive way, yielding the epitaxial relationships, and, by variation of the grazing incidence angle, the lattice parameter relaxation along the growth direction. On semi-coherent interfaces, the existence of an ordered network of interfacial misfit dislocations can be demonstrated, its Burger's vector determined, its ordering during in situ annealing cycles followed, and sometimes even its atomic structure can be addressed. Careful analysis during growth allows the modeling of the dislocation nucleation process. This review emphasizes the new information that GIXS can bring to oxide surfaces and metal/oxide interfaces by comparison with other surface science techniques. The principles of X-ray diffraction by surfaces and interfaces are recalled, together with the advantages and properties of grazing angles. The specific experimental requirements are discussed. Recent results are presented on the determination of the atomic structure of relaxed or reconstructed oxide surfaces. A description of results obtained during the in situ growth of metal on oxide surfaces is also given, as well as investigations of thick metal films on oxide surfaces, with lattice parameter misfit relaxed by an array of dislocations. Recent work performed on oxide thin films having important physical properties such as superconductivity or magnetism is also briefly reviewed. The strengths and limitations of the technique, such as the need for single crystals and surfaces of high crystalline quality are discussed. Finally, an outlook of future prospects in the field is given, such as the study of more complex oxide surfaces, vicinal surfaces, reactive metal/oxide interfaces, metal oxidation processes, the use of surfactants to promote wetting of a metal deposited on an oxide surface or the study of oxide/liquid interfaces in a non-UHV environment.

Semiempirical potentials for positron scattering by atoms

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

Assafrao, Denise; Walters, H. R. J.; Arretche, Felipe

2011-08-15

We report calculations of differential and integral cross sections for positron scattering by noble gas and alkaline-earth atoms within the same methodology. The scattering potentials are constructed by scaling adiabatic potentials so that their minima coincide with the covalent radii of the target atoms. Elastic differential and integral cross sections are calculated for Ne, Ar, Be, and Mg, and the results are very close to experimental and best theoretical data. Particularly, elastic differential cross sections for Be and Mg at low energies are reported.

Assessment of the generalization of learned image reconstruction and the potential for transfer learning.

PubMed

Knoll, Florian; Hammernik, Kerstin; Kobler, Erich; Pock, Thomas; Recht, Michael P; Sodickson, Daniel K

2018-05-17

Although deep learning has shown great promise for MR image reconstruction, an open question regarding the success of this approach is the robustness in the case of deviations between training and test data. The goal of this study is to assess the influence of image contrast, SNR, and image content on the generalization of learned image reconstruction, and to demonstrate the potential for transfer learning. Reconstructions were trained from undersampled data using data sets with varying SNR, sampling pattern, image contrast, and synthetic data generated from a public image database. The performance of the trained reconstructions was evaluated on 10 in vivo patient knee MRI acquisitions from 2 different pulse sequences that were not used during training. Transfer learning was evaluated by fine-tuning baseline trainings from synthetic data with a small subset of in vivo MR training data. Deviations in SNR between training and testing led to substantial decreases in reconstruction image quality, whereas image contrast was less relevant. Trainings from heterogeneous training data generalized well toward the test data with a range of acquisition parameters. Trainings from synthetic, non-MR image data showed residual aliasing artifacts, which could be removed by transfer learning-inspired fine-tuning. This study presents insights into the generalization ability of learned image reconstruction with respect to deviations in the acquisition settings between training and testing. It also provides an outlook for the potential of transfer learning to fine-tune trainings to a particular target application using only a small number of training cases. © 2018 International Society for Magnetic Resonance in Medicine.

Current strategies with 1-stage prosthetic breast reconstruction

PubMed Central

2015-01-01

Background 1-stage prosthetic breast reconstruction is gaining traction as a preferred method of breast reconstruction in select patients who undergo mastectomy for cancer or prevention. Methods Critical elements to the procedure including patient selection, technique, surgical judgment, and postoperative care were reviewed. Results Outcomes series reveal that in properly selected patients, direct-to-implant (DTI) reconstruction has similar low rates of complications and high rates of patient satisfaction compared to traditional 2-stage reconstruction. Conclusions 1-stage prosthetic breast reconstruction may be the procedure of choice in select patients undergoing mastectomy. Advantages include the potential for the entire reconstructive process to be complete in one surgery, the quick return to normal activities, and lack of donor site morbidity. PMID:26005643

Non-autonomous matter-wave solitons in hybrid atomic-molecular Bose-Einstein condensates with tunable interactions and harmonic potential

NASA Astrophysics Data System (ADS)

Wang, Deng-Shan; Liu, Jiang; Wang, Lizhen

2018-03-01

In this paper, we investigate matter-wave solitons in hybrid atomic-molecular Bose-Einstein condensates with tunable interactions and external potentials. Three types of time-modulated harmonic potentials are considered and, for each of them, two groups of exact non-autonomous matter-wave soliton solutions of the coupled Gross-Pitaevskii equation are presented. Novel nonlinear structures of these non-autonomous matter-wave solitons are analyzed by displaying their density distributions. It is shown that the time-modulated nonlinearities and external potentials can support exact non-autonomous atomic-molecular matter-wave solitons.

Potential Energy Curves and Collisions Integrals of Air Components. 2; Interactions Involving Ionized Atoms

NASA Technical Reports Server (NTRS)

Stallcop, James R.; Partridge, Harry; Levin, Eugene; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Collision integrals are fundamental quantities required to determine the transport properties of the environment surrounding aerospace vehicles in the upper atmosphere. These collision integrals can be determined as a function of temperature from the potential energy curves describing the atomic and molecular collisions. Ab initio calculations provide a practical method of computing the required interaction potentials. In this work we will discuss recent advances in scattering calculations with an emphasis on the accuracy that is obtainable. Results for interactions of the atoms and ionized atoms of nitrogen and oxygen will be reviewed and their application to the determination of transport properties, such as diffusion and viscosity coefficients, will be examined.

Phonon dispersion and local density of states in NiPd alloy using modified embedded atom method potential

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

Joshi, Subodh, E-mail: subodhssgk@gmail.com; Chand, Manesh, E-mail: maneshchand@gmail.com; Dabral, Krishna, E-mail: kmkrishna.dabral@gmail.com

2016-05-06

A modified embedded atom method (MEAM) potential model up to second neighbours has been used to calculate the phonon dispersions for Ni{sub 0.55}Pd{sub 0.45} alloy in which Pd is introduced as substitutional impurity. Using the force-constants obtained from MEAM potential, the local vibrational density of states in host Ni and substitutional Pd atoms using Green’s function method has been calculated. The calculation of phonon dispersions of NiPd alloy shows a good agreement with the experimental results. Condition of resonance mode has also been investigated and resonance mode in the frequency spectrum of impurity atom at low frequency is observed.

A protocol for generating a high-quality genome-scale metabolic reconstruction.

PubMed

Thiele, Ines; Palsson, Bernhard Ø

2010-01-01

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

A protocol for generating a high-quality genome-scale metabolic reconstruction

PubMed Central

Thiele, Ines; Palsson, Bernhard Ø.

2011-01-01

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have developed over the past 10 years. These reconstructions represent structured knowledge-bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates myriad computational biological studies including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics, and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge-bases. Here, we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction as well as common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process. PMID:20057383

On the Failure of Correlating Partitioned Electrostatic Surface Potentials Using Bader’s Atoms-in-Molecules Theory to Impact Sensitivities

DTIC Science & Technology

2013-04-01

atoms labeled. ......................................................................................25 Figure A-15. Picric acid with atoms labeled...217 Table A-47. DATB atom specific Politzer parameters using PBE/6-31G**..............................218 Table A-48. Picric acid atom specific...weighted atom specific Politzer parameters using PBE/6-31G**. .....272 Table A-96. Picric acid area weighted atom specific Politzer parameters using PBE

Eulerian velocity reconstruction in ideal atmospheric dynamics using potential vorticity and potential temperature

NASA Astrophysics Data System (ADS)

Blender, R.

2009-04-01

An approach for the reconstruction of atmospheric flow is presented which uses space- and time-dependent fields of density ?, potential vorticity Q and potential temperature Î& cedil;[J. Phys. A, 38, 6419 (2005)]. The method is based on the fundamental equations without approximation. The basic idea is to consider the time-dependent continuity equation as a condition for zero divergence of momentum in four dimensions (time and space, with unit velocity in time). This continuity equation is solved by an ansatz for the four-dimensional momentum using three conserved stream functions, the potential vorticity, potential temperature and a third field, denoted as ?-potential. In zonal flows, the ?-potential identifies the initial longitude of particles, whereas potential vorticity and potential temperature identify mainly meridional and vertical positions. Since the Lagrangian tracers Q, Î&,cedil; and ? determine the Eulerian velocity field, the reconstruction combines the Eulerian and the Lagrangian view of hydrodynamics. In stationary flows, the ?-potential is related to the Bernoulli function. The approach requires that the gradients of the potential vorticity and potential temperature do not vanish when the velocity remains finite. This behavior indicates a possible interrelation with stability conditions. Examples with analytical solutions are presented for a Rossby wave and zonal and rotational shear flows.

Rubidium distribution at atomic scale in high efficient Cu(In,Ga)Se2 thin-film solar cells

NASA Astrophysics Data System (ADS)

Vilalta-Clemente, Arantxa; Raghuwanshi, Mohit; Duguay, Sébastien; Castro, Celia; Cadel, Emmanuel; Pareige, Philippe; Jackson, Philip; Wuerz, Roland; Hariskos, Dimitrios; Witte, Wolfram

2018-03-01

The introduction of a rubidium fluoride post deposition treatment (RbF-PDT) for Cu(In,Ga)Se2 (CIGS) absorber layers has led to a record efficiency up to 22.6% for thin-film solar cell technology. In the present work, high efficiency CIGS samples with RbF-PDT have been investigated by atom probe tomography (APT) to reveal the atomic distribution of all alkali elements present in CIGS layers and compared with non-treated samples. A Scanning Electron Microscopy Dual beam station (Focused Ion Beam-Gas Injection System) as well as Transmission Kikuchi diffraction is used for atom probe sample preparation and localization of the grain boundaries (GBs) in the area of interest. The analysis of the 3D atomic scale APT reconstructions of CIGS samples with RbF-PDT shows that inside grains, Rb is under the detection limit, but the Na concentration is enhanced as compared to the reference sample without Rb. At the GBs, a high concentration of Rb reaching 1.5 at. % was found, and Na and K (diffusing from the glass substrate) are also segregated at GBs but at lower concentrations as compared to Rb. The intentional introduction of Rb leads to significant changes in the chemical composition of CIGS matrix and at GBs, which might contribute to improve device efficiency.

Influence of beta instabilities on the early stages of nucleation and growth of alpha in beta titanium alloys

NASA Astrophysics Data System (ADS)

Nag, Soumya

Microstructural evolution in beta Titanium alloys is an important factor that governs the properties exhibited by them. Intricate understanding of complex phase transformations in these alloys is vital to tailor their microstructures and in turn their properties to our advantage. One such important subject of study is the nucleation and growth of alpha precipitates triggered by the compositional instabilities in the beta matrix, instilled in them during non equilibrium heat treatments. The present work is an effort to investigate such a phenomenon. Here studies have been conducted primarily on two different beta-Titanium alloys of commercial relevance- Ti5553 (Ti-5Al-5Mo-5V-3Cr-0.5Fe), an alloy used in the aerospace industry for landing gear applications and, TNZT (Ti-35Nb-7Zr-5Ta), a potential load bearing orthopedic implant alloy. Apart from the effect of thermal treatment on these alloys, the focus of this work is to study the interplay between different alpha and beta stabilizers present in them. For this, advanced nano-scale characterization tools such as High Resolution STEM, High Resolution TEM, EFTEM and 3D Atom Probe have been used to determine the structure, distribution and composition of the non equilibrium instabilities such as beta' and o, and also to investigate the subsequent nucleation of stable alpha. Thus in this work, very early stages of phase separation via spinodal decomposition and second phase nucleation in titanium alloys are successfully probed at an atomic resolution. For the first time, atomically resolved HRSTEM 'Z'-contrast image is recorded showing modulated structures within the as-quenched beta matrix. Also in the same condition HRTEM results showed the presence of nanoscale alpha regions. These studies are revalidated by conventional selected area diffraction and 3D atom probe reconstruction results. Also TEM dark field and selected are diffraction studies are conducted to understand the effect of quenching and subsequent aging of o precipitates. Using 3D atom probe tomography, the elemental partitioning involved in coarsening of o is investigated in detail. Finally by performing a series of well planned heat treatments, an effort is made to reason out the influence of these instabilities on the morphology, volume fraction and nucleation site of alpha.

The reconstruction of tachyon inflationary potentials

NASA Astrophysics Data System (ADS)

Fei, Qin; Gong, Yungui; Lin, Jiong; Yi, Zhu

2017-08-01

We derive a lower bound on the field excursion for the tachyon inflation, which is determined by the amplitude of the scalar perturbation and the number of e-folds before the end of inflation. Using the relation between the observables like ns and r with the slow-roll parameters, we reconstruct three classes of tachyon potentials. The model parameters are determined from the observations before the potentials are reconstructed, and the observations prefer the concave potential. We also discuss the constraints from the reheating phase preceding the radiation domination for the three classes of models by assuming the equation of state parameter wre during reheating is a constant. Depending on the model parameters and the value of wre, the constraints on Nre and Tre are different. As ns increases, the allowed reheating epoch becomes longer for wre=-1/3, 0 and 1/6 while the allowed reheating epoch becomes shorter for wre=2/3.

Genome scale metabolic reconstruction of Chlorella variabilis for exploring its metabolic potential for biofuels.

PubMed

Juneja, Ankita; Chaplen, Frank W R; Murthy, Ganti S

2016-08-01

A compartmentalized genome scale metabolic network was reconstructed for Chlorella variabilis to offer insight into various metabolic potentials from this alga. The model, iAJ526, was reconstructed with 1455 reactions, 1236 metabolites and 526 genes. 21% of the reactions were transport reactions and about 81% of the total reactions were associated with enzymes. Along with gap filling reactions, 2 major sub-pathways were added to the model, chitosan synthesis and rhamnose metabolism. The reconstructed model had reaction participation of 4.3 metabolites per reaction and average lethality fraction of 0.21. The model was effective in capturing the growth of C. variabilis under three light conditions (white, red and red+blue light) with fair agreement. This reconstructed metabolic network will serve an important role in systems biology for further exploration of metabolism for specific target metabolites and enable improved characteristics in the strain through metabolic engineering. Copyright © 2016 Elsevier Ltd. All rights reserved.

Measuring nanometre-scale electric fields in scanning transmission electron microscopy using segmented detectors.

PubMed

Brown, H G; Shibata, N; Sasaki, H; Petersen, T C; Paganin, D M; Morgan, M J; Findlay, S D

2017-11-01

Electric field mapping using segmented detectors in the scanning transmission electron microscope has recently been achieved at the nanometre scale. However, converting these results to quantitative field measurements involves assumptions whose validity is unclear for thick specimens. We consider three approaches to quantitative reconstruction of the projected electric potential using segmented detectors: a segmented detector approximation to differential phase contrast and two variants on ptychographical reconstruction. Limitations to these approaches are also studied, particularly errors arising from detector segment size, inelastic scattering, and non-periodic boundary conditions. A simple calibration experiment is described which corrects the differential phase contrast reconstruction to give reliable quantitative results despite the finite detector segment size and the effects of plasmon scattering in thick specimens. A plasmon scattering correction to the segmented detector ptychography approaches is also given. Avoiding the imposition of periodic boundary conditions on the reconstructed projected electric potential leads to more realistic reconstructions. Copyright © 2017 Elsevier B.V. All rights reserved.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.

PubMed

Wang, Jimin

2017-06-01

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. © 2017 The Protein Society.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

PubMed Central

2017-01-01

Abstract Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement. PMID:28370507

A Novel Pairwise Comparison-Based Method to Determine Radiation Dose Reduction Potentials of Iterative Reconstruction Algorithms, Exemplified Through Circle of Willis Computed Tomography Angiography.

PubMed

Ellmann, Stephan; Kammerer, Ferdinand; Brand, Michael; Allmendinger, Thomas; May, Matthias S; Uder, Michael; Lell, Michael M; Kramer, Manuel

2016-05-01

The aim of this study was to determine the dose reduction potential of iterative reconstruction (IR) algorithms in computed tomography angiography (CTA) of the circle of Willis using a novel method of evaluating the quality of radiation dose-reduced images. This study relied on ReconCT, a proprietary reconstruction software that allows simulating CT scans acquired with reduced radiation dose based on the raw data of true scans. To evaluate the performance of ReconCT in this regard, a phantom study was performed to compare the image noise of true and simulated scans within simulated vessels of a head phantom. That followed, 10 patients scheduled for CTA of the circle of Willis were scanned according to our institute's standard protocol (100 kV, 145 reference mAs). Subsequently, CTA images of these patients were reconstructed as either a full-dose weighted filtered back projection or with radiation dose reductions down to 10% of the full-dose level and Sinogram-Affirmed Iterative Reconstruction (SAFIRE) with either strength 3 or 5. Images were marked with arrows pointing on vessels of different sizes, and image pairs were presented to observers. Five readers assessed image quality with 2-alternative forced choice comparisons. In the phantom study, no significant differences were observed between the noise levels of simulated and true scans in filtered back projection, SAFIRE 3, and SAFIRE 5 reconstructions.The dose reduction potential for patient scans showed a strong dependence on IR strength as well as on the size of the vessel of interest. Thus, the potential radiation dose reductions ranged from 84.4% for the evaluation of great vessels reconstructed with SAFIRE 5 to 40.9% for the evaluation of small vessels reconstructed with SAFIRE 3. This study provides a novel image quality evaluation method based on 2-alternative forced choice comparisons. In CTA of the circle of Willis, higher IR strengths and greater vessel sizes allowed higher degrees of radiation dose reduction.

Lipid biomarkers in surface sediments from the Gulf of Genoa (Ligurian Sea) and their potential for palaeo-environmental reconstructions

NASA Astrophysics Data System (ADS)

Ruggieri, Nicoletta; Kaiser, Jérôme; Arz, Helge W.; Hefter, Jens; Siegel, Herbert; Mollenhauer, Gesine; Lamy, Frank

2014-05-01

A series of molecular organic markers were determined in surface sediments from the Gulf of Genoa (Ligurian Sea) in order to evaluate their potential for palaeo-environmental reconstructions. The interest for the Gulf of Genoa lies in its contrasting coastal and central areas in terms of terrestrial input, oligotrophy, primary production and surface temperature gradient. Moreover, the Gulf of Genoa contains a large potential for climate reconstruction as it is one of the four major Mediterranean centres for cyclogenesis and the ultra high sedimentation rates on the shelf make this area suitable for high resolution environmental reconstruction. Initial results from sediment cores in the coastal area indeed reveal the potential for Holocene environmental reconstruction on up to decadal timescales (see Poster "Reconstruction of late Holocene flooding events in the Gulf of Genoa, Ligurian Sea" by Lamy et al.). During R/V Poseidon cruise P413 (May 2011), ca. 60 sediment cores were taken along the Ligurian shelf, continental slope, and in the basin between off Livorno and the French border. Results based on surface sediments suggest that some biomarker-based proxies are well-suited to reconstruct sea surface temperature (SST), the input of terrestrial organic material (TOM), and marine primary productivity (PP). The estimated UK'37 SST reflects very closely the autumnal mean satellite-based SST distribution, while TEXH86 SSTs correspond to summer SST at offshore sites and to winter SST for the nearshore sites. Using both SST proxies together may thus allow reconstructing past seasonality changes. Proxies for TOM input (terrestrial n-alkane and n-alkanol concentrations, BIT index) have higher values close to the major river mouths and decrease offshore suggesting that these may be used as proxy for the variability in TOM input by runoff. Interestingly, high n-alkane average chain length in the most offshore sites may result from aeolian input from northern Africa. Finally, high concentrations of crenarchaeol and isoprenoid GDGTs in the open basin illustrate the preference of Thaumarchaeota for oligotrophic waters. This study represents a major prerequisite for the future application of lipid biomarkers on sediment cores from the Gulf of Genoa.

Theoretical aspects of graphene-like group IV semiconductors

NASA Astrophysics Data System (ADS)

Houssa, M.; van den Broek, B.; Scalise, E.; Ealet, B.; Pourtois, G.; Chiappe, D.; Cinquanta, E.; Grazianetti, C.; Fanciulli, M.; Molle, A.; Afanas'ev, V. V.; Stesmans, A.

2014-02-01

Silicene and germanene are the silicon and germanium counterparts of graphene, respectively. Recent experimental works have reported the growth of silicene on (1 1 1)Ag surfaces with different atomic configurations, depending on the growth temperature and surface coverage. We first theoretically study the structural and electronic properties of silicene on (1 1 1)Ag surfaces, focusing on the (4 × 4)silicene/Ag structure. Due to symmetry breaking in the silicene layer (nonequivalent number of top and bottom Si atoms), the corrugated silicene layer, with the Ag substrate removed, is predicted to be semiconducting, with a computed energy bandgap of about 0.3 eV. However, the hybridization between the Si 3p orbitals and the Ag 5s orbital in the silicene/(1 1 1)Ag slab model leads to an overall metallic system, with a distribution of local electronic density of states, which is related to the slightly disordered structure of the silicene layer on the (1 1 1)Ag surface. We next study the interaction of silicene and germanene with different hexagonal non-metallic substrates, namely ZnS and ZnSe. On reconstructed (0 0 0 1)ZnS or ZnSe surfaces, which should be more energetically stable for very thin layers, silicene and germanene are found to be semiconducting. Remarkably, the nature and magnitude of their energy bandgap can be controlled by an out-of-plane electric field, an important finding for the potential use of these materials in nanoelectronic devices.

Synchrotron x-ray scattering study of charge-density-wave order in HgBa2CuO4 +δ

NASA Astrophysics Data System (ADS)

Tabis, W.; Yu, B.; Bialo, I.; Bluschke, M.; Kolodziej, T.; Kozlowski, A.; Blackburn, E.; Sen, K.; Forgan, E. M.; Zimmermann, M. v.; Tang, Y.; Weschke, E.; Vignolle, B.; Hepting, M.; Gretarsson, H.; Sutarto, R.; He, F.; Le Tacon, M.; Barišić, N.; Yu, G.; Greven, M.

2017-10-01

We present a detailed synchrotron x-ray scattering study of the charge-density-wave (CDW) order in simple tetragonal HgBa2CuO4 +δ (Hg1201). Resonant soft x-ray scattering measurements reveal that short-range order appears at a temperature that is distinctly lower than the pseudogap temperature and in excellent agreement with a prior transient reflectivity result. Despite considerable structural differences between Hg1201 and YBa2Cu3O6 +δ , the CDW correlations exhibit similar doping dependencies, and we demonstrate a universal relationship between the CDW wave vector and the size of the reconstructed Fermi pocket observed in quantum oscillation experiments. The CDW correlations in Hg1201 vanish already below optimal doping, once the correlation length is comparable to the CDW modulation period, and they appear to be limited by the disorder potential from unit cells hosting two interstitial oxygen atoms. A complementary hard x-ray diffraction measurement, performed on an underdoped Hg1201 sample in magnetic fields along the crystallographic c axis of up to 16 T, provides information on the form factor of the CDW order. As expected from the single-CuO2-layer structure of Hg1201, the CDW correlations vanish at half-integer values of L and appear to be peaked at integer L . We conclude that the atomic displacements associated with the short-range CDW order are mainly planar, within the CuO2 layers.

The use of cone beam computed tomography in the postoperative assessment of orbital wall fracture reconstruction.

PubMed

Tsao, Kim; Cheng, Andrew; Goss, Alastair; Donovan, David

2014-07-01

Computed tomography (CT) is currently the standard in postoperative evaluation of orbital wall fracture reconstruction, but cone beam computed tomography (CBCT) offers potential advantages including reduced radiation dose and cost. The purpose of this study is to examine objectively the image quality of CBCT in the postoperative evaluation of orbital fracture reconstruction, its radiation dose, and cost compared with CT. Four consecutive patients with orbital wall fractures in whom surgery was indicated underwent orbital reconstruction with radio-opaque grafts (bone, titanium-reinforced polyethylene, and titanium plate) and were assessed postoperatively with orbital CBCT. CBCT was evaluated for its ability to provide objective information regarding the adequacy of orbital reconstruction, radiation dose, and cost. In all patients, CBCT was feasible and provided hard tissue image quality comparable to CT with significantly reduced radiation dose and cost. However, it has poorer soft tissue resolution, which limits its ability to identify the extraocular muscles, their relationship to the reconstructive graft, and potential muscle entrapment. CBCT is a viable alternative to CT in the routine postoperative evaluation of orbital fracture reconstruction. However, in the patient who develops gaze restriction postoperatively, conventional CT is preferred over CBCT for its superior soft tissue resolution to exclude extraocular muscle entrapment.

Trends in Materials Science for Ligament Reconstruction.

PubMed

Sava, Oana Roxana; Sava, Daniel Florin; Radulescu, Marius; Albu, Madalina Georgiana; Ficai, Denisa; Veloz-Castillo, Maria Fernanda; Mendez-Rojas, Miguel Angel; Ficai, Anton

2017-01-01

The number of ligament injuries increases every year and concomitantly the need for materials or systems that can reconstruct the ligament. Limitations imposed by autografts and allografts in ligament reconstruction together with the advances in materials science and biology have attracted a lot of interest for developing systems and materials for ligament replacement or reconstruction. This review intends to synthesize the major steps taken in the development of polymer-based materials for anterior cruciate ligament, their advantages and drawbacks and the results of different in vitro and in vivo tests. Until present, there is no successful polymer system for ligament reconstruction implanted in humans. The developing field of synthetic polymers for ligament reconstruction still has a lot of potential. In addition, several nano-structured materials, made of nanofibers or in the form of ceramic/polymeric nanocomposites, are attracting the interest of several groups due to their potential use as engineered scaffolds that mimic the native environment of cells, increasing the chances for tissue regeneration. Here, we review the last 15 years of literature in order to obtain a better understanding on the state-of-the-art that includes the usage of nano- and poly-meric materials for ligament reconstruction, and to draw perspectives on the future development of the field. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A modern pollen-climate dataset from the Darjeeling area, eastern Himalaya: Assessing its potential for past climate reconstruction

NASA Astrophysics Data System (ADS)

Ghosh, Ruby; Bruch, Angela A.; Portmann, Felix; Bera, Subir; Paruya, Dipak Kumar; Morthekai, P.; Ali, Sheikh Nawaz

2017-10-01

Relying on the ability of pollen assemblages to differentiate among elevationally stratified vegetation zones, we assess the potential of a modern pollen-climate dataset from the Darjeeling area, eastern Himalaya, in past climate reconstructions. The dataset includes 73 surface samples from 25 sites collected from a c. 130-3600 m a.s.l. elevation gradient along a horizontal distance of c. 150 km and 124 terrestrial pollen taxa, which are analysed with respect to various climatic and environmental variables such as mean annual temperature (MAT), mean annual precipitation (MAP), mean temperature of coldest quarter (MTCQ), mean temperature of warmest quarter (MTWQ), mean precipitation of driest quarter (MPDQ), mean precipitation of wettest quarter (MPWQ), AET (actual evapotranspiration) and MI (moisture index). To check the reliability of the modern pollen-climate relationships different ordination methods are employed and subsequently tested with Huisman-Olff-Fresco (HOF) models. A series of pollen-climate parameter transfer functions using weighted-averaging regression and calibration partial least squares (WA-PLS) models are developed to reconstruct past climate changes from modern pollen data, and have been cross-validated. Results indicate that three of the environmental variables i.e., MTCQ, MPDQ and MI have strong potential for past climate reconstruction based on the available surface pollen dataset. The potential of the present modern pollen-climate relationship for regional quantitative paleoclimate reconstruction is further tested on a Late Quaternary fossil pollen profile from the Darjeeling foothill region with previously reconstructed and quantified climate. The good agreement with existing data allows for new insights in the hydroclimatic conditions during the Last glacial maxima (LGM) with (winter) temperature being the dominant controlling factor for glacial changes during the LGM in the eastern Himalaya.

Three-Dimensional Reconstruction and Solar Energy Potential Estimation of Buildings

NASA Astrophysics Data System (ADS)

Chen, Y.; Li, M.; Cheng, L.; Xu, H.; Li, S.; Liu, X.

2017-12-01

In the context of the construction of low-carbon cities, green cities and eco-cities, the ability of the airborne and mobile LiDAR should be explored in urban renewable energy research. As the main landscape in urban environment, buildings have large regular envelopes could receive a huge amount of solar radiation. In this study, a relatively complete calculation scheme about building roof and façade solar utilization potential is proposed, using building three-dimensional geometric feature information. For measuring the city-level building solar irradiance, the precise three-dimensional building roof and façade models should be first reconstructed from the airborne and mobile LiDAR, respectively. In order to obtaining the precise geometric structure of building facades from the mobile LiDAR data, a new method for structure detection and the three-dimensional reconstruction of building façades from mobile LiDAR data is proposed. The method consists of three steps: the preprocessing of façade points, the detection of façade structure, the restoration and reconstruction of building façade. As a result, the reconstruction method can effectively deal with missing areas caused by occlusion, viewpoint limitation, and uneven point density, as well as realizing the highly complete 3D reconstruction of a building façade. Furthermore, the window areas can be excluded for more accurate estimation of solar utilization potential. After then, the solar energy utilization potential of global building roofs and facades is estimate by using the solar irradiance model, which combine the analysis of the building shade and sky diffuse, based on the analysis of the geometrical structure of buildings.

The Evolution of Complex Microsurgical Midface Reconstruction: A Classification Scheme and Reconstructive Algorithm.

PubMed

Alam, Daniel; Ali, Yaseen; Klem, Christopher; Coventry, Daniel

2016-11-01

Orbito-malar reconstruction after oncological resection represents one of the most challenging facial reconstructive procedures. Until the last few decades, rehabilitation was typically prosthesis based with a limited role for surgery. The advent of microsurgical techniques allowed large-volume tissue reconstitution from a distant donor site, revolutionizing the potential approaches to these defects. The authors report a novel surgery-based algorithm and a classification scheme for complete midface reconstruction with a foundation in the Gillies principles of like-to-like reconstruction and with a significant role of computer-aided virtual planning. With this approach, the authors have been able to achieve significantly better patient outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

Sparse Reconstruction Techniques in MRI: Methods, Applications, and Challenges to Clinical Adoption

PubMed Central

Yang, Alice Chieh-Yu; Kretzler, Madison; Sudarski, Sonja; Gulani, Vikas; Seiberlich, Nicole

2016-01-01

The family of sparse reconstruction techniques, including the recently introduced compressed sensing framework, has been extensively explored to reduce scan times in Magnetic Resonance Imaging (MRI). While there are many different methods that fall under the general umbrella of sparse reconstructions, they all rely on the idea that a priori information about the sparsity of MR images can be employed to reconstruct full images from undersampled data. This review describes the basic ideas behind sparse reconstruction techniques, how they could be applied to improve MR imaging, and the open challenges to their general adoption in a clinical setting. The fundamental principles underlying different classes of sparse reconstructions techniques are examined, and the requirements that each make on the undersampled data outlined. Applications that could potentially benefit from the accelerations that sparse reconstructions could provide are described, and clinical studies using sparse reconstructions reviewed. Lastly, technical and clinical challenges to widespread implementation of sparse reconstruction techniques, including optimization, reconstruction times, artifact appearance, and comparison with current gold-standards, are discussed. PMID:27003227

Jaw In A Day™ – State of the Art in Maxillary Reconstruction

PubMed Central

Runyan, Christopher M.; Sharma, Vishal; Staffenberg, David A.; Levine, Jamie P.; Brecht, Lawrence E.; Wexler, Leonard H.; Hirsch, David L.

2017-01-01

Background Reconstruction of maxillary defects following tumor extirpation is challenging because of combined aesthetic and functional roles of the maxilla. One-stage reconstruction combining osseous free flaps with immediate osseointegrated implants are becoming the standard for mandibular defects, and have similar potential for maxillary reconstruction. Methods A woman with maxillary Ewing’s sarcoma successfully treated at age nine with neoadjuvant chemotherapy, right hemi-maxillectomy and obturator prosthetic reconstruction presented for definitive reconstruction, complaining of poor obturator fit and hypernasality. Her reconstruction was computer-simulated by a multi-disciplinary team, consisting of left hemi-Lefort I advancement and right maxillary reconstruction with a free fibula flap with immediate osseointegrated implants and dental prosthesis. Results Full dental restoration, midface projection and oral fistula corrections were achieved in one operative stage using this approach. Conclusions This case demonstrates a successful approach for maxillary reconstruction using computer-planned orthognathic surgery with free fibula reconstruction and immediate osseointegrated implants with dental prosthesis. PMID:28005762

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

Macroscopic quantum interference from atomic tunnel arrays

PubMed

Anderson; Kasevich

1998-11-27

Interference of atomic de Broglie waves tunneling from a vertical array of macroscopically populated traps has been observed. The traps were located in the antinodes of an optical standing wave and were loaded from a Bose-Einstein condensate. Tunneling was induced by acceleration due to gravity, and interference was observed as a train of falling pulses of atoms. In the limit of weak atomic interactions, the pulse frequency is determined by the gravitational potential energy difference between adjacent potential wells. The effect is closely related to the ac Josephson effect observed in superconducting electronic systems.

Artificial electromagnetism for neutral atoms: Escher staircase and Laughlin liquids

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

Mueller, Erich J.

2004-10-01

We present a method for creating fields that couple to neutral atoms in the same way that electromagnetic fields couple to charged particles. We show that this technique opens the door for a range of neutral atom experiments, including probing the interplay between periodic potentials and quantum Hall effects. Furthermore, we propose, and analyze, seemingly paradoxical geometries which can be engineered through these techniques. For example, we show how to create a ring of sites where an atom continuously reduces its potential energy by moving in a clockwise direction.

Visual saliency detection based on in-depth analysis of sparse representation

NASA Astrophysics Data System (ADS)

Wang, Xin; Shen, Siqiu; Ning, Chen

2018-03-01

Visual saliency detection has been receiving great attention in recent years since it can facilitate a wide range of applications in computer vision. A variety of saliency models have been proposed based on different assumptions within which saliency detection via sparse representation is one of the newly arisen approaches. However, most existing sparse representation-based saliency detection methods utilize partial characteristics of sparse representation, lacking of in-depth analysis. Thus, they may have limited detection performance. Motivated by this, this paper proposes an algorithm for detecting visual saliency based on in-depth analysis of sparse representation. A number of discriminative dictionaries are first learned with randomly sampled image patches by means of inner product-based dictionary atom classification. Then, the input image is partitioned into many image patches, and these patches are classified into salient and nonsalient ones based on the in-depth analysis of sparse coding coefficients. Afterward, sparse reconstruction errors are calculated for the salient and nonsalient patch sets. By investigating the sparse reconstruction errors, the most salient atoms, which tend to be from the most salient region, are screened out and taken away from the discriminative dictionaries. Finally, an effective method is exploited for saliency map generation with the reduced dictionaries. Comprehensive evaluations on publicly available datasets and comparisons with some state-of-the-art approaches demonstrate the effectiveness of the proposed algorithm.

Improved osseointegration properties of hierarchical microtopographic/nanotopographic coatings fabricated on titanium implants.

PubMed

Zemtsova, Elena G; Yudintceva, Natalia M; Morozov, Pavel E; Valiev, Ruslan Z; Smirnov, Vladimir M; Shevtsov, Maxim A

2018-01-01

Titanium (Ti) implants are extensively used in reconstructive surgery and orthopedics. However, the intrinsic inertness of untreated Ti implants usually results in insufficient osseointegration. In order to improve the osteoconductivity properties of the implants, they are coated with hierarchical microtopographic/nanotopographic coatings employing the method of molecular layering of atomic layer deposition (ML-ALD). The analysis of the fabricated nanostructured relief employing scanning electron microscopy, atomic force microscopy, and electron spectroscopy for chemical analysis clearly demonstrated the formation of the nanotopographic (<100 nm) and microtopographic (0.1-0.5 μm) titano-organic structures on the surface of the nanograined Ti implants. Subsequent coincubation of the MC3T3-E1 mouse osteoblasts on the microtopographic/nanotopographic surface of the implants resulted in enhanced osteogenic cell differentiation (the production of alkaline phosphatase, osteopontin, and osteocalcin). In vivo assessment of the osseointegrative properties of the microtopographically/nanotopographically coated implants in a model of below-knee amputation in New Zealand rabbits demonstrated enhanced new bone formation in the zone of the bone-implant contact (as measured by X-ray study) and increased osseointegration strength (removal torque measurements). The fabrication of the hierarchical microtopographic/nanotopographic coatings on the nanograined Ti implants significantly improves the osseointegrative properties of the intraosseous Ti implants. This effect could be employed in both translational and clinical studies in orthopedic and reconstructive surgery.

Current Limitations of Surgical Robotics in Reconstructive Plastic Microsurgery.

PubMed

Tan, Youri P A; Liverneaux, Philippe; Wong, Jason K F

2018-01-01

Surgical robots have the potential to provide surgeons with increased capabilities, such as removing physiologic tremor, scaling motion and increasing manual dexterity. Several surgical specialties have subsequently integrated robotic surgery into common clinical practice. Plastic and reconstructive microsurgical procedures have not yet  benefitted significantly from technical developments observed over the last two decades. Several studies have successfully demonstrated the feasibility of utilising surgical robots in plastic surgery procedures, yet limited work has been done to identify and analyse current barriers that have prevented wide-scale adaptation of surgical robots for microsurgery. Therefore, a systematic review using PubMed, MEDLINE, Embase and Web of Science databases was performed, in order to evaluate current state of surgical robotics within the field of reconstructive microsurgery and their limitations. Despite the theoretical potential of surgical robots, current commercially available robotic systems are suboptimal for plastic or reconstructive microsurgery. Absence of bespoke microsurgical instruments, increases in operating time, and high costs associated with robotic-assisted provide a barrier to using such systems effectively for reconstructive microsurgery. Consequently, surgical robots provide currently little overall advantage over conventional microsurgery. Nevertheless, if current barriers can be addressed and systems are specifically designed for microsurgery, surgical robots may have the potential of meaningful impact on clinical outcomes within  this surgical subspeciality.

Current Limitations of Surgical Robotics in Reconstructive Plastic Microsurgery

PubMed Central

Tan, Youri P. A.; Liverneaux, Philippe; Wong, Jason K. F.

2018-01-01

Surgical robots have the potential to provide surgeons with increased capabilities, such as removing physiologic tremor, scaling motion and increasing manual dexterity. Several surgical specialties have subsequently integrated robotic surgery into common clinical practice. Plastic and reconstructive microsurgical procedures have not yet  benefitted significantly from technical developments observed over the last two decades. Several studies have successfully demonstrated the feasibility of utilising surgical robots in plastic surgery procedures, yet limited work has been done to identify and analyse current barriers that have prevented wide-scale adaptation of surgical robots for microsurgery. Therefore, a systematic review using PubMed, MEDLINE, Embase and Web of Science databases was performed, in order to evaluate current state of surgical robotics within the field of reconstructive microsurgery and their limitations. Despite the theoretical potential of surgical robots, current commercially available robotic systems are suboptimal for plastic or reconstructive microsurgery. Absence of bespoke microsurgical instruments, increases in operating time, and high costs associated with robotic-assisted provide a barrier to using such systems effectively for reconstructive microsurgery. Consequently, surgical robots provide currently little overall advantage over conventional microsurgery. Nevertheless, if current barriers can be addressed and systems are specifically designed for microsurgery, surgical robots may have the potential of meaningful impact on clinical outcomes within  this surgical subspeciality. PMID:29740585

Exploring a potential energy surface by machine learning for characterizing atomic transport

NASA Astrophysics Data System (ADS)

Kanamori, Kenta; Toyoura, Kazuaki; Honda, Junya; Hattori, Kazuki; Seko, Atsuto; Karasuyama, Masayuki; Shitara, Kazuki; Shiga, Motoki; Kuwabara, Akihide; Takeuchi, Ichiro

2018-03-01

We propose a machine-learning method for evaluating the potential barrier governing atomic transport based on the preferential selection of dominant points for atomic transport. The proposed method generates numerous random samples of the entire potential energy surface (PES) from a probabilistic Gaussian process model of the PES, which enables defining the likelihood of the dominant points. The robustness and efficiency of the method are demonstrated on a dozen model cases for proton diffusion in oxides, in comparison with a conventional nudge elastic band method.

Characterization of Incidental Renal Mass With Dual-Energy CT: Diagnostic Accuracy of Effective Atomic Number Maps for Discriminating Nonenhancing Cysts From Enhancing Masses.

PubMed

Mileto, Achille; Allen, Brian C; Pietryga, Jason A; Farjat, Alfredo E; Zarzour, Jessica G; Bellini, Davide; Ebner, Lukas; Morgan, Desiree E

2017-10-01

The purpose of this study was to assess the diagnostic accuracy of effective atomic number maps reconstructed from dual-energy contrast-enhanced data for discriminating between nonenhancing renal cysts and enhancing masses. Two hundred six patients (128 men, 78 women; mean age, 64 years) underwent a CT renal mass protocol (single-energy unenhanced and dual-energy contrast-enhanced nephrographic imaging) at two different hospitals. For each set of patients, two blinded, independent observers performed measurements on effective atomic number maps from contrast-enhanced dual-energy data. Renal mass assessment on unenhanced and nephrographic images, corroborated by imaging and medical records, was the reference standard. The diagnostic accuracy of effective atomic number maps was assessed with ROC analysis. Significant differences in mean effective atomic numbers (Z eff ) were observed between nonenhancing and enhancing masses (set A, 8.19 vs 9.59 Z eff ; set B, 8.05 vs 9.19 Z eff ; sets combined, 8.13 vs 9.37 Z eff ) (p < 0.0001). An effective atomic number value of 8.36 Z eff was the optimal threshold, rendering an AUC of 0.92 (95% CI, 0.89-0.94), sensitivity of 90.8% (158/174 [95% CI, 85.5-94.7%]), specificity of 85.2% (445/522 [95% CI, 81.9-88.2%]), and overall diagnostic accuracy of 86.6% (603/696 [95% CI, 83.9-89.1%]). Nonenhancing renal cysts, including hyperattenuating cysts, can be discriminated from enhancing masses on effective atomic number maps generated from dual-energy contrast-enhanced CT data. This technique may be of clinical usefulness when a CT protocol for comprehensive assessment of renal masses is not available.

Hirshfeld atom refinement for modelling strong hydrogen bonds.

PubMed

Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

2014-09-01

High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

Alignment relaxation of Ne*(2pi [J = 1]) atoms in He-Ne* glow discharges

NASA Astrophysics Data System (ADS)

Bahrim, Cristian; Khadilkar, Vaibhav; Matsukuma, Hiraku; Hasuo, Masahiro

2009-11-01

Alignment relaxation of the Ne*(2p5 3p; 2pi [J = 1]) atoms (where i = 2, 5, 7 or 10) induced by collisions with He atoms in glow discharges at 77 K < T < 1,000 K are reported. Close-coupling many-channel quantum calculations using a model potential for the Ne*(2p5 3p) - He system are compared with measurements of the alignment relaxation using the LIFS technique and the Hanle effect. The addition of the dipole polarization potential of the Ne*(2pi [J = 1]) atoms to the spin-orbit coupling and the electrostatic interaction between Ne* and He atoms leads to good agreement between theory and experiment.

Stretching of short monatomic gold chains-some model calculations

NASA Astrophysics Data System (ADS)

Sumali, Priyanka, Verma, Veena; Dharamvir, Keya

2012-06-01

The Mechanical properties of zig-zag monatomic gold chains containing 5 and 7 atoms were studied using the Siesta Code (SC), which works within the framework of DFT formalism and Gupta Potential (GP), which is an effective atom-atom potential. The zig-zag chains were stretched by keeping the end atoms fixed while rest of the atoms were relaxed till minimum energy is obtained. Energy, Force and Young's Modulus found using GP and SC were plotted as functions of total length. It is found that the breaking force in case of GP is of order of 1.6nN while for SIESTA is of the order of 2.9nN for both the chains.

Elastic cartilage reconstruction by transplantation of cultured hyaline cartilage-derived chondrocytes.

PubMed

Mizuno, M; Takebe, T; Kobayashi, S; Kimura, S; Masutani, M; Lee, S; Jo, Y H; Lee, J I; Taniguchi, H

2014-05-01

Current surgical intervention of craniofacial defects caused by injuries or abnormalities uses reconstructive materials, such as autologous cartilage grafts. Transplantation of autologous tissues, however, places a significant invasiveness on patients, and many efforts have been made for establishing an alternative graft. Recently, we and others have shown the potential use of reconstructed elastic cartilage from ear-derived chondrocytes or progenitors with the unique elastic properties. Here, we examined the differentiation potential of canine joint cartilage-derived chondrocytes into elastic cartilage for expanding the cell sources, such as hyaline cartilage. Articular chondrocytes are isolated from canine joint, cultivated, and compared regarding characteristic differences with auricular chondrocytes, including proliferation rates, gene expression, extracellular matrix production, and cartilage reconstruction capability after transplantation. Canine articular chondrocytes proliferated less robustly than auricular chondrocytes, but there was no significant difference in the amount of sulfated glycosaminoglycan produced from redifferentiated chondrocytes. Furthermore, in vitro expanded and redifferentiated articular chondrocytes have been shown to reconstruct elastic cartilage on transplantation that has histologic characteristics distinct from hyaline cartilage. Taken together, cultured hyaline cartilage-derived chondrocytes are a possible cell source for elastic cartilage reconstruction. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

Image reconstruction and scan configurations enabled by optimization-based algorithms in multispectral CT

NASA Astrophysics Data System (ADS)

Chen, Buxin; Zhang, Zheng; Sidky, Emil Y.; Xia, Dan; Pan, Xiaochuan

2017-11-01

Optimization-based algorithms for image reconstruction in multispectral (or photon-counting) computed tomography (MCT) remains a topic of active research. The challenge of optimization-based image reconstruction in MCT stems from the inherently non-linear data model that can lead to a non-convex optimization program for which no mathematically exact solver seems to exist for achieving globally optimal solutions. In this work, based upon a non-linear data model, we design a non-convex optimization program, derive its first-order-optimality conditions, and propose an algorithm to solve the program for image reconstruction in MCT. In addition to consideration of image reconstruction for the standard scan configuration, the emphasis is on investigating the algorithm’s potential for enabling non-standard scan configurations with no or minimum hardware modification to existing CT systems, which has potential practical implications for lowered hardware cost, enhanced scanning flexibility, and reduced imaging dose/time in MCT. Numerical studies are carried out for verification of the algorithm and its implementation, and for a preliminary demonstration and characterization of the algorithm in reconstructing images and in enabling non-standard configurations with varying scanning angular range and/or x-ray illumination coverage in MCT.

Reconstruction of spatio-temporal temperature from sparse historical records using robust probabilistic principal component regression

USGS Publications Warehouse

Tipton, John; Hooten, Mevin B.; Goring, Simon

2017-01-01

Scientific records of temperature and precipitation have been kept for several hundred years, but for many areas, only a shorter record exists. To understand climate change, there is a need for rigorous statistical reconstructions of the paleoclimate using proxy data. Paleoclimate proxy data are often sparse, noisy, indirect measurements of the climate process of interest, making each proxy uniquely challenging to model statistically. We reconstruct spatially explicit temperature surfaces from sparse and noisy measurements recorded at historical United States military forts and other observer stations from 1820 to 1894. One common method for reconstructing the paleoclimate from proxy data is principal component regression (PCR). With PCR, one learns a statistical relationship between the paleoclimate proxy data and a set of climate observations that are used as patterns for potential reconstruction scenarios. We explore PCR in a Bayesian hierarchical framework, extending classical PCR in a variety of ways. First, we model the latent principal components probabilistically, accounting for measurement error in the observational data. Next, we extend our method to better accommodate outliers that occur in the proxy data. Finally, we explore alternatives to the truncation of lower-order principal components using different regularization techniques. One fundamental challenge in paleoclimate reconstruction efforts is the lack of out-of-sample data for predictive validation. Cross-validation is of potential value, but is computationally expensive and potentially sensitive to outliers in sparse data scenarios. To overcome the limitations that a lack of out-of-sample records presents, we test our methods using a simulation study, applying proper scoring rules including a computationally efficient approximation to leave-one-out cross-validation using the log score to validate model performance. The result of our analysis is a spatially explicit reconstruction of spatio-temporal temperature from a very sparse historical record.

Modulation of electrical potential and conductivity in an atomic-layer semiconductor heterojunction

PubMed Central

Kobayashi, Yu; Yoshida, Shoji; Sakurada, Ryuji; Takashima, Kengo; Yamamoto, Takahiro; Saito, Tetsuki; Konabe, Satoru; Taniguchi, Takashi; Watanabe, Kenji; Maniwa, Yutaka; Takeuchi, Osamu; Shigekawa, Hidemi; Miyata, Yasumitsu

2016-01-01

Semiconductor heterojunction interfaces have been an important topic, both in modern solid state physics and in electronics and optoelectronics applications. Recently, the heterojunctions of atomically-thin transition metal dichalcogenides (TMDCs) are expected to realize one-dimensional (1D) electronic systems at their heterointerfaces due to their tunable electronic properties. Herein, we report unique conductivity enhancement and electrical potential modulation of heterojunction interfaces based on TMDC bilayers consisted of MoS2 and WS2. Scanning tunneling microscopy/spectroscopy analyses showed the formation of 1D confining potential (potential barrier) in the valence (conduction) band, as well as bandgap narrowing around the heterointerface. The modulation of electronic properties were also probed as the increase of current in conducting atomic force microscopy. Notably, the observed band bending can be explained by the presence of 1D fixed charges around the heterointerface. The present findings indicate that the atomic layer heterojunctions provide a novel approach to realizing tunable 1D electrical potential for embedded quantum wires and ultrashort barriers of electrical transport. PMID:27515115

MO-DE-207A-12: Toward Patient-Specific 4DCT Reconstruction Using Adaptive Velocity Binning

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

Morris, E.D.; Glide-Hurst, C.; Wayne State University, Detroit, MI

2016-06-15

Purpose: While 4DCT provides organ/tumor motion information, it often samples data over 10–20 breathing cycles. For patients presenting with compromised pulmonary function, breathing patterns can change over the acquisition time, potentially leading to tumor delineation discrepancies. This work introduces a novel adaptive velocity-modulated binning (AVB) 4DCT algorithm that modulates the reconstruction based on the respiratory waveform, yielding a patient-specific 4DCT solution. Methods: AVB was implemented in a research reconstruction configuration. After filtering the respiratory waveform, the algorithm examines neighboring data to a phase reconstruction point and the temporal gate is widened until the difference between the reconstruction point and waveformmore » exceeds a threshold value—defined as percent difference between maximum/minimum waveform amplitude. The algorithm only impacts reconstruction if the gate width exceeds a set minimum temporal width required for accurate reconstruction. A sensitivity experiment of threshold values (0.5, 1, 5, 10, and 12%) was conducted to examine the interplay between threshold, signal to noise ratio (SNR), and image sharpness for phantom and several patient 4DCT cases using ten-phase reconstructions. Individual phase reconstructions were examined. Subtraction images and regions of interest were compared to quantify changes in SNR. Results: AVB increased signal in reconstructed 4DCT slices for respiratory waveforms that met the prescribed criteria. For the end-exhale phases, where the respiratory velocity is low, patient data revealed a threshold of 0.5% demonstrated increased SNR in the AVB reconstructions. For intermediate breathing phases, threshold values were required to be >10% to notice appreciable changes in CT intensity with AVB. AVB reconstructions exhibited appreciably higher SNR and reduced noise in regions of interest that were photon deprived such as the liver. Conclusion: We demonstrated that patient-specific velocity-based 4DCT reconstruction is feasible. Image noise was reduced with AVB, suggesting potential applications for low-dose acquisitions and to improve 4DCT reconstruction for irregular breathing patients. The submitting institution holds research agreements with Philips Healthcare.« less