Fe and Co nanostructures embedded into the Cu(100) surface: Self-Organization and magnetic properties

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

Kolesnikov, S. V., E-mail: kolesnikov@physics.msu.ru; Klavsyuk, A. L.; Saletsky, A. M.

The self-organization and magnetic properties of small iron and cobalt nanostructures embedded into the first layer of a Cu(100) surface are investigated using the self-learning kinetic Monte Carlo method and density functional theory. The similarities and differences between the Fe/Cu(100) and the Co/Cu(100) are underlined. The time evolution of magnetic properties of a copper monolayer with embedded magnetic atoms at 380 K is discussed.

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

Structural stability and O{sub 2} dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

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

Yang, Mingye; Wang, Lu, E-mail: lwang22@suda.edu.cn, E-mail: yyli@suda.edu.cn; Li, Min

2015-06-15

By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped) graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM) atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N{sub 4}V {sub 2} forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O{sub 2} dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N,more » the graphitic-N is more favorable to dissociate O{sub 2} molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.« less

Adsorption of gas molecules on Cu impurities embedded monolayer MoS2: A first- principles study

NASA Astrophysics Data System (ADS)

Zhao, B.; Li, C. Y.; Liu, L. L.; Zhou, B.; Zhang, Q. K.; Chen, Z. Q.; Tang, Z.

2016-09-01

Adsorption of small gas molecules (O2, NO, NO2 and NH3) on transition-metal Cu atom embedded monolayer MoS2 was investigated by first-principles calculations based on the density-functional theory (DFT). The embedded Cu atom is strongly constrained on the sulfur vacancy of monolayer MoS2 with a high diffusion barrier. The stable adsorption geometry, charge transfer and electronic structures of these gas molecules on monolayer MoS2 embedded with transition-metal Cu atom are discussed in detail. It is found that the monolayer MoS2 with embedded Cu atom can effectively capture these gas molecules with high adsorption energy. The NH3 molecule acts as electron donor after adsorption, which is different from the other gas molecules (O2, NO, and NO2). The results suggest that MoS2-Cu system may be promising for future applications in gas molecules sensing and catalysis, which is similar to those of the transition-metal embedded graphene.

Pressure effect on phonon frequencies in some transition metals: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Kazanc, S.; Ozgen, S.

2005-08-01

It is important to determine the atomic lattice vibrations of metallic materials, under high-pressure conditions, due to its effects on material properties such as thermal, electrical and optical conductions. In this work, we have investigated the changes of acoustic phonon frequencies with hydrostatic pressure for Cu, Ni, Al, Ag and Au transition metals, using molecular dynamics (MD) simulations based on embedded atom method (EAM). For this aim, we have adopted the embedded atom potential proposed by Sutton and Chen. The phonon frequencies have been calculated from the dynamical matrix for [1 0 0], [1 1 0] and [1 1 1] high symmetry directions of the Brillouin zone. The obtained results show that the hydrostatic pressure causes an increment in phonon frequencies, and this rising do not depend linearly on the increasing pressure.

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.

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.

Embedded atom method potential for studying mechanical properties of binary Cu–Au alloys

NASA Astrophysics Data System (ADS)

Gola, Adrien; Pastewka, Lars

2018-07-01

We present an embedded atom method (EAM) potential for the binary Cu–Au system. The unary phases are described by two well-tested unary EAM potentials for Cu and Au. We fitted the interaction between Cu and Au to experimental properties of the binary intermetallic phases Cu3Au, CuAu and CuAu3. Particular attention has been paid to reproducing stacking fault energies in order to obtain a potential suitable for studying deformation in this binary system. The resulting energies, lattice constant, elastic properties and melting points are in good agreement with available experimental data. We use nested sampling to show that our potential reproduces the phase boundaries between intermetallic phases and the disordered face-centered cubic solid solution. We benchmark our potential against four popular Cu–Au EAM parameterizations and density-functional theory calculations.

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

An Embedded Statistical Method for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Saether, E.; Glaessgen, E.H.; Yamakov, V.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Atomistic simulations of the effect of embedded hydrogen and helium on the tensile properties of monocrystalline and nanocrystalline tungsten

NASA Astrophysics Data System (ADS)

Chen, Zhe; Kecskes, Laszlo J.; Zhu, Kaigui; Wei, Qiuming

2016-12-01

Uniaxial tensile properties of monocrystalline tungsten (MC-W) and nanocrystalline tungsten (NC-W) with embedded hydrogen and helium atoms have been investigated using molecular dynamics (MD) simulations in the context of radiation damage evolution. Different strain rates have been imposed to investigate the strain rate sensitivity (SRS) of the samples. Results show that the plastic deformation processes of MC-W and NC-W are dominated by different mechanisms, namely dislocation-based for MC-W and grain boundary-based activities for NC-W, respectively. For MC-W, the SRS increases and a transition appears in the deformation mechanism with increasing embedded atom concentration. However, no obvious embedded atom concentration dependence of the SRS has been observed for NC-W. Instead, in the latter case, the embedded atoms facilitate GB sliding and intergranular fracture. Additionally, a strong strain enhanced He cluster growth has been observed. The corresponding underlying mechanisms are discussed.

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.

Embedded sparse representation of fMRI data via group-wise dictionary optimization

NASA Astrophysics Data System (ADS)

Zhu, Dajiang; Lin, Binbin; Faskowitz, Joshua; Ye, Jieping; Thompson, Paul M.

2016-03-01

Sparse learning enables dimension reduction and efficient modeling of high dimensional signals and images, but it may need to be tailored to best suit specific applications and datasets. Here we used sparse learning to efficiently represent functional magnetic resonance imaging (fMRI) data from the human brain. We propose a novel embedded sparse representation (ESR), to identify the most consistent dictionary atoms across different brain datasets via an iterative group-wise dictionary optimization procedure. In this framework, we introduced additional criteria to make the learned dictionary atoms more consistent across different subjects. We successfully identified four common dictionary atoms that follow the external task stimuli with very high accuracy. After projecting the corresponding coefficient vectors back into the 3-D brain volume space, the spatial patterns are also consistent with traditional fMRI analysis results. Our framework reveals common features of brain activation in a population, as a new, efficient fMRI analysis method.

Interface mobility and the liquid-glass transition in a one-component system described by an embedded atom method potential

NASA Astrophysics Data System (ADS)

Mendelev, M. I.; Schmalian, J.; Wang, C. Z.; Morris, J. R.; Ho, K. M.

2006-09-01

We present molecular dynamics (MD) studies of the liquid structure, thermodynamics, and dynamics in a one-component system described by the Ercolessi-Adams embedded atom method potential for Al. We find two distinct noncrystalline phases in this system. One of them is a liquid phase and the second phase has similar structure but different equation of state. Moreover, this phase has qualitatively different dynamics than that in the liquid phase. The transitions between these two noncrystalline phases can be seen during MD simulation. The hysteresis in this transition suggests that this is a first-order transition. This conclusion is strongly supported by simulations of the two phases that demonstrate that these phases may coexist with a well-defined interface. We find the coexistent temperature and the interface mobility. Finally, we discuss how these results can be explained using modern models of vitrification.

The effect of grading the atomic number at resistive guide element interface on magnetic collimation

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

Alraddadi, R. A. B.; Woolsey, N. C.; Robinson, A. P. L.

2016-07-15

Using 3 dimensional numerical simulations, this paper shows that grading the atomic number and thus the resistivity at the interface between an embedded high atomic number guide element and a lower atomic number substrate enhances the growth of a resistive magnetic field. This can lead to a large integrated magnetic flux density, which is fundamental to confining higher energy fast electrons. This results in significant improvements in both magnetic collimation and fast-electron-temperature uniformity across the guiding. The graded interface target provides a method for resistive guiding that is tolerant to laser pointing.

Applications and assessment of QM:QM electronic embedding using generalized asymmetric Mulliken atomic charges.

PubMed

Parandekar, Priya V; Hratchian, Hrant P; Raghavachari, Krishnan

2008-10-14

Hybrid QM:QM (quantum mechanics:quantum mechanics) and QM:MM (quantum mechanics:molecular mechanics) methods are widely used to calculate the electronic structure of large systems where a full quantum mechanical treatment at a desired high level of theory is computationally prohibitive. The ONIOM (our own N-layer integrated molecular orbital molecular mechanics) approximation is one of the more popular hybrid methods, where the total molecular system is divided into multiple layers, each treated at a different level of theory. In a previous publication, we developed a novel QM:QM electronic embedding scheme within the ONIOM framework, where the model system is embedded in the external Mulliken point charges of the surrounding low-level region to account for the polarization of the model system wave function. Therein, we derived and implemented a rigorous expression for the embedding energy as well as analytic gradients that depend on the derivatives of the external Mulliken point charges. In this work, we demonstrate the applicability of our QM:QM method with point charge embedding and assess its accuracy. We study two challenging systems--zinc metalloenzymes and silicon oxide cages--and demonstrate that electronic embedding shows significant improvement over mechanical embedding. We also develop a modified technique for the energy and analytic gradients using a generalized asymmetric Mulliken embedding method involving an unequal splitting of the Mulliken overlap populations to offer improvement in situations where the Mulliken charges may be deficient.

Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system

NASA Astrophysics Data System (ADS)

Kong, Fantai; Longo, Roberto C.; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae

2017-11-01

To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO2. A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li2CoO2 and Li-deficient LiCo2O4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.

Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system.

PubMed

Kong, Fantai; Longo, Roberto C; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae

2017-11-29

To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO 2 . A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li 2 CoO 2 and Li-deficient LiCo 2 O 4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.

Embedded-atom-method interatomic potentials from lattice inversion.

PubMed

Yuan, Xiao-Jian; Chen, Nan-Xian; Shen, Jiang; Hu, Wangyu

2010-09-22

The present work develops a physically reliable procedure for building the embedded-atom-method (EAM) interatomic potentials for the metals with fcc, bcc and hcp structures. This is mainly based on Chen-Möbius lattice inversion (Chen et al 1997 Phys. Rev. E 55 R5) and first-principles calculations. Following Baskes (Baskes et al 2007 Phys. Rev. B 75 094113), this new version of the EAM eliminates all of the prior arbitrary choices in the determination of the atomic electron density and pair potential functions. Parameterizing the universal form deduced from the calculations within the density-functional scheme for homogeneous electron gas as the embedding function, the new-type EAM potentials for Cu, Fe and Ti metals have successfully been constructed by considering interatomic interactions up to the fifth neighbor, the third neighbor and the seventh neighbor, respectively. The predictions of elastic constants, structural energy difference, vacancy formation energy and migration energy, activation energy of vacancy diffusion, latent heat of melting and relative volume change on melting all satisfactorily agree with the experimental results available or first-principles calculations. The predicted surface energies for low-index crystal faces and the melting point are in agreement with the experimental data to the same extent as those calculated by other EAM-type potentials such as the FBD-EAM, 2NN MEAM and MS-EAM. In addition, the order among the predicted low-index surface energies is also consistent with the experimental information.

Embedded correlated wavefunction schemes: theory and applications.

PubMed

Libisch, Florian; Huang, Chen; Carter, Emily A

2014-09-16

Conspectus Ab initio modeling of matter has become a pillar of chemical research: with ever-increasing computational power, simulations can be used to accurately predict, for example, chemical reaction rates, electronic and mechanical properties of materials, and dynamical properties of liquids. Many competing quantum mechanical methods have been developed over the years that vary in computational cost, accuracy, and scalability: density functional theory (DFT), the workhorse of solid-state electronic structure calculations, features a good compromise between accuracy and speed. However, approximate exchange-correlation functionals limit DFT's ability to treat certain phenomena or states of matter, such as charge-transfer processes or strongly correlated materials. Furthermore, conventional DFT is purely a ground-state theory: electronic excitations are beyond its scope. Excitations in molecules are routinely calculated using time-dependent DFT linear response; however applications to condensed matter are still limited. By contrast, many-electron wavefunction methods aim for a very accurate treatment of electronic exchange and correlation. Unfortunately, the associated computational cost renders treatment of more than a handful of heavy atoms challenging. On the other side of the accuracy spectrum, parametrized approaches like tight-binding can treat millions of atoms. In view of the different (dis-)advantages of each method, the simulation of complex systems seems to force a compromise: one is limited to the most accurate method that can still handle the problem size. For many interesting problems, however, compromise proves insufficient. A possible solution is to break up the system into manageable subsystems that may be treated by different computational methods. The interaction between subsystems may be handled by an embedding formalism. In this Account, we review embedded correlated wavefunction (CW) approaches and some applications. We first discuss our density functional embedding theory, which is formally exact. We show how to determine the embedding potential, which replaces the interaction between subsystems, at the DFT level. CW calculations are performed using a fixed embedding potential, that is, a non-self-consistent embedding scheme. We demonstrate this embedding theory for two challenging electron transfer phenomena: (1) initial oxidation of an aluminum surface and (2) hot-electron-mediated dissociation of hydrogen molecules on a gold surface. In both cases, the interaction between gas molecules and metal surfaces were treated by sophisticated CW techniques, with the remainder of the extended metal surface being treated by DFT. Our embedding approach overcomes the limitations of conventional Kohn-Sham DFT in describing charge transfer, multiconfigurational character, and excited states. From these embedding simulations, we gained important insights into fundamental processes that are crucial aspects of fuel cell catalysis (i.e., O2 reduction at metal surfaces) and plasmon-mediated photocatalysis by metal nanoparticles. Moreover, our findings agree very well with experimental observations, while offering new views into the chemistry. We finally discuss our recently formulated potential-functional embedding theory that provides a seamless, first-principles way to include back-action onto the environment from the embedded region.

Improved method for analysis of RNA present in long-term preserved thyroid cancer tissue of atomic bomb survivors.

PubMed

Hamatani, Kiyohiro; Eguchi, Hidetaka; Mukai, Mayumi; Koyama, Kazuaki; Taga, Masataka; Ito, Reiko; Hayashi, Yuzo; Nakachi, Kei

2010-01-01

Since many thyroid cancer tissue samples from atomic bomb (A-bomb) survivors have been preserved for several decades as unbuffered formalin-fixed, paraffin-embedded specimens, molecular oncological analysis of such archival specimens is indispensable for clarifying the mechanisms of thyroid carcinogenesis in A-bomb survivors. Although RET gene rearrangements are the most important targets, it is a difficult task to examine all of the 13 known types of RET gene rearrangements with the use of the limited quantity of RNA that has been extracted from invaluable paraffin-embedded tissue specimens of A-bomb survivors. In this study, we established an improved 5' rapid amplification of cDNA ends (RACE) method using a small amount of RNA extracted from archival thyroid cancer tissue specimens. Three archival thyroid cancer tissue specimens from three different patients were used as in-house controls to determine the conditions for an improved switching mechanism at 5' end of RNA transcript (SMART) RACE method; one tissue specimen with RET/PTC1 rearrangement and one with RET/PTC3 rearrangement were used as positive samples. One other specimen, used as a negative sample, revealed no detectable expression of the RET gene tyrosine kinase domain. We established a 5' RACE method using an amount of RNA as small as 10 ng extracted from long-term preserved, unbuffered formalin-fixed, paraffin-embedded thyroid cancer tissue by application of SMART technology. This improved SMART RACE method not only identified common RET gene rearrangements, but also isolated a clone containing a 93-bp insert of rare RTE/PTC8 in RNA extracted from formalin-fixed, paraffin-embedded thyroid cancer specimens from one A-bomb survivor who had been exposed to a high radiation dose. In addition, in the papillary thyroid cancer of another high-dose A-bomb survivor, this method detected one novel type of RET gene rearrangement whose partner gene is acyl coenzyme A binding domain 5, located on chromosome 10p. We conclude that our improved SMART RACE method is expected to prove useful in molecular analyses using archival formalin-fixed, paraffin-embedded tissue samples of limited quantity.

Improved Electrostatic Embedding for Fragment-Based Chemical Shift Calculations in Molecular Crystals.

PubMed

Hartman, Joshua D; Balaji, Ashwin; Beran, Gregory J O

2017-12-12

Fragment-based methods predict nuclear magnetic resonance (NMR) chemical shielding tensors in molecular crystals with high accuracy and computational efficiency. Such methods typically employ electrostatic embedding to mimic the crystalline environment, and the quality of the results can be sensitive to the embedding treatment. To improve the quality of this embedding environment for fragment-based molecular crystal property calculations, we borrow ideas from the embedded ion method to incorporate self-consistently polarized Madelung field effects. The self-consistent reproduction of the Madelung potential (SCRMP) model developed here constructs an array of point charges that incorporates self-consistent lattice polarization and which reproduces the Madelung potential at all atomic sites involved in the quantum mechanical region of the system. The performance of fragment- and cluster-based 1 H, 13 C, 14 N, and 17 O chemical shift predictions using SCRMP and density functionals like PBE and PBE0 are assessed. The improved embedding model results in substantial improvements in the predicted 17 O chemical shifts and modest improvements in the 15 N ones. Finally, the performance of the model is demonstrated by examining the assignment of the two oxygen chemical shifts in the challenging γ-polymorph of glycine. Overall, the SCRMP-embedded NMR chemical shift predictions are on par with or more accurate than those obtained with the widely used gauge-including projector augmented wave (GIPAW) model.

First-principles investigation of graphitic carbon nitride monolayer with embedded Fe atom

NASA Astrophysics Data System (ADS)

Abdullahi, Yusuf Zuntu; Yoon, Tiem Leong; Halim, Mohd Mahadi; Hashim, Md. Roslan; Lim, Thong Leng

2018-01-01

Density-functional theory (DFT) calculations with spin-polarized generalized gradient approximation and Hubbard U correction are carried out to investigate the mechanical, structural, electronic and magnetic properties of graphitic heptazine with embedded Fe atom under bi-axial tensile strain and applied perpendicular electric field. It was found that the binding energy of heptazine with embedded Fe atom system decreases as larger tensile strain is applied, while it increases as larger electric field strength is applied. Our calculations also predict a band gap at a peak value of 5% tensile strain but at expense of the structural stability of the system. The band gap open up at 5% tensile strain is due to distortion in the structure caused by the repulsive effect in the cavity between the lone pairs of the edge nitrogen atoms and dxy /dx2 -y2 orbital of Fe atom, forcing the unoccupied pz- orbital is forced to shift toward higher energy. The electronic and magnetic properties of the heptazine with embedded Fe system under perpendicular electric field up to a peak value of 8 V/nm is also well preserved despite an obvious buckled structure. Such properties are desirable for diluted magnetic semiconductors, spintronics, and sensing devices.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

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

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

NASA Astrophysics Data System (ADS)

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; Carter, Emily A.; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2017-02-01

A new modified embedded-atom method (MEAM) force field is developed for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997), 10.1103/PhysRevLett.79.2482], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquid density, self-diffusivity, viscosity, and vapor-liquid surface tension. It is shown that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.

A modified Embedded-Atom Method interatomic potential for uranium-silicide

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

Beeler, Benjamin; Baskes, Michael; Andersson, David

Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel bene ts from higher thermal conductivity and higher ssile density compared to uranium dioxide (UO 2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling e orts are underway to address this gap in knowledge. In this study, a semi-empirical modi ed Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is ttedmore » to the formation energy, defect energies and structural properties of U 3Si 2. The primary phase of interest (U 3Si 2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.« less

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

DOE PAGES

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; ...

2017-02-01

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

A modified Embedded-Atom Method interatomic potential for uranium-silicide

DOE PAGES

Beeler, Benjamin; Baskes, Michael; Andersson, David; ...

2017-08-18

Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel bene ts from higher thermal conductivity and higher ssile density compared to uranium dioxide (UO 2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling e orts are underway to address this gap in knowledge. In this study, a semi-empirical modi ed Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is ttedmore » to the formation energy, defect energies and structural properties of U 3Si 2. The primary phase of interest (U 3Si 2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.« less

Size-Dependent Surface Energy Density of Spherical Face-Centered-Cubic Metallic Nanoparticles.

PubMed

Wei, Yaochi; Chen, Shaohua

2015-12-01

The surface energy density of nano-sized elements exhibits a significantly size-dependent behavior. Spherical nanoparticle, as an important element in nano-devices and nano-composites, has attracted many interesting studies on size effect, most of which are molecular dynamics (MD) simulations. However, the existing MD calculations yield two opposite size-dependent trends of surface energy density of nanoparticles. In order to clarify such a real underlying problem, atomistic calculations are carried out in the present paper for various spherical face-centered-cubic (fcc) metallic nanoparticles. Both the embedded atom method (EAM) potential and the modified embedded atom method (MEAM) one are adopted. It is found that the size-dependent trend of surface energy density of nanoparticles is not governed by the chosen potential function or variation trend of surface energy, but by the defined radius of spherical nanoparticles in MD models. The finding in the present paper should be helpful for further theoretical studies on surface/interface effect of nanoparticles and nanoparticle-reinforced composites.

A modified Embedded-Atom Method interatomic potential for uranium-silicide

NASA Astrophysics Data System (ADS)

Beeler, Benjamin; Baskes, Michael; Andersson, David; Cooper, Michael W. D.; Zhang, Yongfeng

2017-11-01

Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel benefits from higher thermal conductivity and higher fissile density compared to uranium dioxide (UO2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling efforts are underway to address this gap in knowledge. In this study, a semi-empirical modified Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is fitted to the formation energy, defect energies and structural properties of U3Si2. The primary phase of interest (U3Si2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.

Embedding Fragment ab Initio Model Potentials in CASSCF/CASPT2 Calculations of Doped Solids: Implementation and Applications.

PubMed

Swerts, Ben; Chibotaru, Liviu F; Lindh, Roland; Seijo, Luis; Barandiaran, Zoila; Clima, Sergiu; Pierloot, Kristin; Hendrickx, Marc F A

2008-04-01

In this article, we present a fragment model potential approach for the description of the crystalline environment as an extension of the use of embedding ab initio model potentials (AIMPs). The biggest limitation of the embedding AIMP method is the spherical nature of its model potentials. This poses problems as soon as the method is applied to crystals containing strongly covalently bonded structures with highly nonspherical electron densities. The newly proposed method addresses this problem by keeping the full electron density as its model potential, thus allowing one to group sets of covalently bonded atoms into fragments. The implementation in the MOLCAS 7.0 quantum chemistry package of the new method, which we call the embedding fragment ab inito model potential method (embedding FAIMP), is reported here, together with results of CASSCF/CASPT2 calculations. The developed methodology is applied for two test problems: (i) the investigation of the lowest ligand field states (2)A1 and (2)B1 of the Cr(V) defect in the YVO4 crystal and (ii) the investigation of the lowest ligand field and ligand-metal charge transfer (LMCT) states at the Mn(II) substitutional impurity doped into CaCO3. Comparison with similar calculations involving AIMPs for all environmental atoms, including those from covalently bounded units, shows that the FAIMP treatment of the YVO4 units surrounding the CrO4(3-) cluster increases the excitation energy (2)B1 → (2)A1 by ca. 1000 cm(-1) at the CASSCF level of calculation. In the case of the Mn(CO3)6(10-) cluster, the FAIMP treatment of the CO3(2-) units of the environment give smaller corrections, of ca. 100 cm(-1), for the ligand-field excitation energies, which is explained by the larger ligands of this cluster. However, the correction for the energy of the lowest LMCT transition is found to be ca. 600 cm(-1) for the CASSCF and ca. 1300 cm(-1) for the CASPT2 calculation.

Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10(1)0).

PubMed

Hellström, Matti; Spångberg, Daniel; Hermansson, Kersti

2015-12-15

We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10(1)0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10(1)0), as long as care is taken to account for the effects of CT. © 2015 Wiley Periodicals, Inc.

Atom-Photon Coupling from Nitrogen-vacancy Centres Embedded in Tellurite Microspheres

NASA Astrophysics Data System (ADS)

Ruan, Yinlan; Gibson, Brant C.; Lau, Desmond W. M.; Greentree, Andrew D.; Ji, Hong; Ebendorff-Heidepriem, Heike; Johnson, Brett C.; Ohshima, Takeshi; Monro, Tanya M.

2015-06-01

We have developed a technique for creating high quality tellurite microspheres with embedded nanodiamonds (NDs) containing nitrogen-vacancy (NV) centres. This hybrid method allows fluorescence of the NVs in the NDs to be directly, rather than evanescently, coupled to the whispering gallery modes of the tellurite microspheres at room temperature. As a demonstration of its sensing potential, shifting of the resonance peaks is also demonstrated by coating a sphere surface with a liquid layer. This new approach is a robust way of creating cavities for use in quantum and sensing applications.

Depressing thermal conductivity of fullerene by caging rare gas

NASA Astrophysics Data System (ADS)

Li, Jian; Zheng, Dong-Qin; Zhong, Wei-Rong

2016-01-01

We have investigated the thermal conductivity of C60 and its derivatives caged with rare gas by using the nonequilibrium molecular dynamics method. It is reported that embedding C60 with different rare gas atoms has a significant impact on its thermal conductivity. We analyze the phenomenon through the phonon spectra of rare gas atom and the C-C bonds length of C60. When the number of atoms inside the C60 increases, the phonon spectra band width of rare gas expands and the length of C-C bonds becomes longer, which contributes to the depression of the thermal conductivity of C60. The method is applied to control the thermal conductivity of C60 chains, which maybe a kind of potential materials in thermal circuits. Our results also provide a controllable method for the thermal management in nanoscale materials.

Collective dynamics and entanglement of two distant atoms embedded into single-negative index material.

PubMed

Fang, Wei; Li, Gao-Xiang; Yang, Yaping; Ficek, Zbigniew

2017-02-06

We study the dynamics of two two-level atoms embedded near to the interface of paired meta-material slabs, one of negative permeability and the other of negative permittivity. This combination generates a strong surface plasmon field at the interface between the meta-materials. It is found that the symmetric and antisymmetric modes of the two-atom system couple to the plasmonic field with different Rabi frequencies. Including the Ohmic losses of the materials we find that the Rabi frequencies exhibit threshold behaviour which distinguish between the non-Markovian (memory preserving) and Markovian (memoryless) regimes of the evolution. Moreover, it is found that significantly different dynamics occur for the resonant and an off-resonant couplings of the plasmon field to the atoms. In the case of the resonant coupling, the field does not appear as a dissipative reservoir to the atoms. We adopt the image method and show that the dynamics of the two atoms coupled to the plasmon field are analogous to the dynamics of a four-atom system in a rectangular configuration. A large and long living entanglement mediated by the plasmonic field in both Markovian and non-Markovian regimes of the evolution is predicted. We also show that a simultaneous Markovian and non-Markovian regime of the evolution may occur in which the memory effects exist over a finite evolution time. In the case of an off-resonant coupling of the atoms to the plasmon field, the atoms interact with each other by exchanging virtual photons which results in the dynamics corresponding to those of two atoms coupled to a common reservoir. In addition, the entanglement is significantly enhanced.

N2O + CO reaction over single Ga or Ge atom embedded graphene: A DFT study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Vessally, Esmail

2018-01-01

The possibility of using a single Ga or Ge atom embedded graphene as an efficient catalyst for the reduction of N2O molecule by CO is examined. We perform density functional theory calculations to calculate adsorption energies as well as analysis of the structural and electronic properties of different species involved in the N2O + CO reaction. The large activation energy for the diffusion of the single Ga or Ge atom on the C vacancy site of graphene shows the high stability of both Ga- and Ge-embedded graphene sheets in the N2O reduction. The activation energy needed for the decomposition of N2O is calculated to be 18.4 and 14.1 kcal/mol over Ga- and Ge-embedded graphene, respectively. The results indicate that the Ge-embedded graphene may serve as an effective catalyst for the N2O reduction. Moreover, the activation energy for the disproportionation of N2O molecules that generates N2 and O2 is relatively high; so, the generation of these side products may be hindered by decreasing the temperature.

Topochemistry of trace metals in nasal mucosa. Potentialities of some histochemical methods and energy dispersive X-ray microanalysis.

PubMed

Torjussen, W; Haug, F M; Olsen, A; Andersen, I

1978-01-01

Histochemical methods and energy dispersive X-ray micro-analysis (EDX-analysis) were evaluated in model experiments and on tissue sections for their usefulness in detecting traces of metals in biological tissue. The goal for this study was to establish a method for localization of nickel deposits in the nasal mucosa, where it has been found in concentrations between 1 and 40 microgram/g in nickel exposed individuals. The histochemical methods tested were staining with dimethylglyoxime, rubeanic acid and dithizone, the Turnbull and Prussian blue methods and TIMM'S sulphide silver procedure. In model experiments nickel-, cobalt-, copper-, zinc- and ironsalts were applied to thin-layer chromatography sheets (TLC-sheets) and stained by the histochemical methods. Spots containing 500 and 50 ng of these metals represented the smallest amounts that could consistently be detected in these experiments, except for the sulphide silver method which seemed a little more sensitive. With the latter method, moreover, zinc was detected in 40 micrometer thick cryostat sections of gelatine made up with 1 microgram/g of the metal. For nickel the corresponding figure was 10 to 50 microgram/g. On specimens of nasal mucosa from nickel-exposed workers, a faint colour was obtained in 40 micron thick cryostat sections from specimens that had been immersed in dithizone, but the colour was too weak for histological analysis. None of the other coloured chelating agents caused noticeable staining when applied to blocks or to cryostat sections. TIMM'S sulphide silver method caused strong staining of the basal layers of the surface epithelium and of fibroblast-like cells in the underlying connective tissue. This staining pattern is described in more detail in a separate report. Rat liver tissue was analyzed by atomic absorption before and after araldite embedding. Blocks of gelatine made up with nickel, copper, zinc and iron were embedded in epoxy resin and analyzed by atomic absorption. Large changes in the metal concentrations, usually an increase, were found after embedding. Ultrathin sections from this material were used to test the sensitivity of the EDX-equipment. Referring to the concentrations determined by atomic absorption in the embedded material, iron was detected at 1215 microgram/g and 362 microgram/g (gelatine standards) but not at 167 microgram/g (rat liver). Similar values could not be determined for nickel, copper or zinc, because of background radiation resulting from the presence of these metals in the instrument. We did not succeed in establishing a procedure for detecting nickel deposits in nasal mucosa with any of the methods which were tested. The most sensitive but least specific of the tested methods for visualizing heavy metals in the nasal mucosa, was TIMM'S sulphide silver procedure. The preparation of tissue for this method is discussed.

Melting of Cu nanoclusters by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Wang, Li; Zhang, Yanning; Bian, Xiufang; Chen, Ying

2003-04-01

We present a detailed molecular dynamics study of the melting of copper nanoclusters with up to 8628 atoms within the framework of the embedded-atom method. The finding indicates that there exists an intermediate nanocrystal regime above 456 atoms. The linear relation between the cluster size and its thermodynamics properties is obeyed in this regime. Melting first occurs at the surface of the clusters, leading to Tm, N= Tm,Bulk- αN-1/3, dropping from Tm,Bulk=1360 K to Tm,456=990 K. In addition, the size, surface energy as well as the root mean square displacement (RMSD) of the clusters in the intermediate regime have been investigated.

Atomic scale study of nanocontacts

NASA Astrophysics Data System (ADS)

Buldum, A.; Ciraci, S.; Batra, Inder P.; Fong, C. Y.

1998-03-01

Nanocontact and subsequent pulling off a sharp Ni(111) tip on a Cu(110) surface are investigated by using molecular dynamics method with embedded atom model. As the contact is formed, the sharp tip experiences multiple jump to contact in the attractive force range. The contact interface develops discontinuously mainly due to disorder-order transformations which lead to disappearance of a layer and hence abrupt changes in the normal force variation. Atom exchange occurs in the repulsive range. The connective neck is reduced also discontinuously by pulling off the tip. The novel atomic structure of the neck under the tensile force is analyzed. We also presented a comperative study for the contact by a Si(111) tip on Si(111)-(2x1) surface.

Iron-embedded C2N monolayer: a promising low-cost and high-activity single-atom catalyst for CO oxidation.

PubMed

He, B L; Shen, J S; Tian, Z X

2016-09-21

An Fe-embedded C2N monolayer as a promising single-atom catalyst for CO oxidation by O2 has been investigated based on first-principles calculations. It is found that the single Fe atom can be strongly trapped in the cavity of the C2N monolayer with a large adsorption energy of 4.55 eV and a high diffusion barrier of at least 3.00 eV to leave the cavity, indicating that Fe should exist in the isolated single-atom form. Due to the localized metal 3d orbitals near the Fermi level, the embedded Fe single-atom catalyst has a high chemical activity for the adsorption of CO and O2 molecules. CO oxidation by O2 on the catalyst would proceed via a two-step mechanism. The first step of the CO oxidation reaction has been studied via the Langmuir-Hinshelwood and Eley-Rideal mechanisms with energy barriers of 0.46 and 0.65 eV, respectively. The second step of the CO oxidation reaction follows the Eley-Rideal mechanism with a much smaller energy barrier of 0.24 eV. For both the steps, the CO2 molecules produced are weakly adsorbed on the substrates, suggesting that the proposed catalyst will not be poisoned by the generated CO2. Our results indicate that the Fe-embedded C2N monolayer is a promising single-atom catalyst for CO oxidation by O2 at low temperatures.

Atomic Force Microscope Investigations of Bacterial Biofilms Treated with Gas Discharge Plasmas

NASA Astrophysics Data System (ADS)

Vandervoort, Kurt; Zelaya, Anna; Brelles-Marino, Graciela

2012-02-01

We present investigations of bacterial biofilms before and after treatment with gas discharge plasmas. Gas discharge plasmas represent a way to inactivate bacteria under conditions where conventional disinfection methods are often ineffective. These conditions involve biofilm communities, where bacteria grow embedded in an exopolysaccharide matrix, and cooperative interactions between cells make organisms less susceptible to standard inactivation methods. In this study, biofilms formed by the opportunistic bacterium Pseudomonas aeruginosa were imaged before and after plasma treatment using an atomic force microscope (AFM). Through AFM images and micromechanical measurements we observed bacterial morphological damage and reduced AFM tip-sample surface adhesion following plasma treatment.

Self-learning kinetic Monte Carlo simulations of Al diffusion in Mg

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

Nandipati, Giridhar; Govind, Niranjan; Andersen, Amity

2016-03-16

Atomistic on-lattice self-learning kinetic Monte Carlo (SLKMC) method was used to examine the vacancy-mediated diffusion of an Al atom in pure hcp Mg. Local atomic environment dependent activation barriers for vacancy-atom exchange processes were calculated on-the-fly using climbing image nudged-elastic band method (CI-NEB) and using a Mg-Al binary modified embedded-atom method (MEAM) interatomic potential. Diffusivities of vacancy and Al atom in pure Mg were obtained from SLKMC simulations and are compared with values available in the literature that are obtained from experiments and first-principle calculations. Al Diffusivities obtained from SLKMC simulations are lower, due to larger activation barriers and lowermore » diffusivity prefactors, than those available in the literature but have same order of magnitude. We present all vacancy-Mg and vacancy-Al atom exchange processes and their activation barriers that were identified in SLKMC simulations. We will describe a simple mapping scheme to map a hcp lattice on to a simple cubic lattice that would enable hcp lattices to be simulated in an on-lattice KMC framework. We also present the pattern recognition scheme used in SLKMC simulations.« less

Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

PubMed

Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

2013-11-14

We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

Surface characterization of InP trenches embedded in oxide using scanning probe microscopy

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

Mannarino, Manuel, E-mail: manuel.mannarino@imec.be, E-mail: manuelmannarino@gmail.com; Chintala, Ravi; Vandervorst, Wilfried

2015-12-14

Metrology for structural and electrical analyses at device level has been identified as one of the major challenges to be resolved for the sub-14 nm technology nodes. In these advanced nodes, new high mobility semiconductors, such as III–V compounds, are grown in narrow trenches on a Si substrate. Probing the nature of the defects, the defect density, and the role of processing steps on the surface of such structures are prime metrology requirements. In order to enable defect analysis on a (III–V) surface, a proper sample preparation for oxide removal is of primary importance. In this work, the effectiveness of differentmore » chemical cleanings and thermal annealing procedures is investigated on both blanket InP and oxide embedded InP trenches by means of scanning probe microscopy techniques. It is found that the most effective approach is a combination of an HCl-based chemical cleaning combined with a low-temperature thermal annealing leading to an oxide free surface with atomically flat areas. Scanning tunneling microscopy (STM) has been the preferred method for such investigations on blanket films due to its intrinsic sub-nm spatial resolution. However, its application on oxide embedded structures is non-trivial. To perform STM on the trenches of interest (generally <20 nm wide), we propose a combination of non-contact atomic force microscopy and STM using the same conductive atomic force microscopy tip Our results prove that with these procedures, it is possible to perform STM in narrow InP trenches showing stacking faults and surface reconstruction. Significant differences in terms of roughness and terrace formation are also observed between the blanket and the oxide embedded InP.« less

Pre-service Science Teachers (PSTs)’ Creative Thinking Skills on Atoms, Ions and Molecules Digital Media Creation

NASA Astrophysics Data System (ADS)

Agustin, RR; Liliasari, L.; Sinaga, P.; Rochintaniawati, D.

2017-09-01

Atoms, ions and molecules are considered as abstract concepts that often lead to students’ learning difficulties. Th is study aimed at providing description of pre-service science teachers (PSTs)’ creative thinking skills on atoms, elements and compounds digital media creation. Qualitative descriptive method were employed to acquire data. Instruments used were rubric of PSTs’ digital teaching media, open ended question related to PSTs’ technological knowledge and pre-test about atoms, ions and molecules that were given to eighteen PSTs. The study reveals that PSTs’ creative thinking skills were still low and inadequate to create qualified teaching media of atoms, ions and molecules. PSTs’ content and technological knowledge in regard with atoms, ions and molecules are the most contributing factors. This finding support the necessity of developing pre-service and in-service science teachers’ creative thinking skill in digital media that is embedded to development of technological content knowledge.

Confinement boosts CO oxidation on an Ni atom embedded inside boron nitride nanotubes

DOE PAGES

Zhang, Yadong; Liu, Yuzhen; Meng, Zhaoshun; ...

2018-01-01

Because of the confinement effect, Ni embedded on the interior surface of BNNT exhibits a much higher catalytic activity for CO oxidation by comparing with that embedded in h-BN or on the outside surface of BNNT.

Accurate classical short-range forces for the study of collision cascades in Fe–Ni–Cr

DOE PAGES

Béland, Laurent Karim; Tamm, Artur; Mu, Sai; ...

2017-05-10

The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded-atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed.more » The pairwise terms and the embedding terms of the potential are modi ed in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni 50Fe 50, Ni 80Cr 20 and Ni 33Fe 33Cr 33. The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.« less

Development of an interatomic potential for the simulation of defects, plasticity, and phase transformations in titanium

DOE PAGES

Mendelev, M. I.; Underwood, T. L.; Ackland, G. J.

2016-10-17

New interatomic potentials describing defects, plasticity, and high temperature phase transitions for Ti are presented. Fitting the martensitic hcp-bcc phase transformation temperature requires an efficient and accurate method to determine it. We apply a molecular dynamics method based on determination of the melting temperature of competing solid phases, and Gibbs-Helmholtz integration, and a lattice-switch Monte Carlo method: these agree on the hcp-bcc transformation temperatures to within 2 K. We were able to develop embedded atom potentials which give a good fit to either low or high temperature data, but not both. The first developed potential (Ti1) reproduces the hcp-bcc transformationmore » and melting temperatures and is suitable for the simulation of phase transitions and bcc Ti. Two other potentials (Ti2 and Ti3) correctly describe defect properties and can be used to simulate plasticity or radiation damage in hcp Ti. The fact that a single embedded atom method potential cannot describe both low and high temperature phases may be attributed to neglect of electronic degrees of freedom, notably bcc has a much higher electronic entropy. As a result, a temperature-dependent potential obtained from the combination of potentials Ti1 and Ti2 may be used to simulate Ti properties at any temperature.« less

Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

PubMed

Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

2013-02-19

Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of the atom: for an sp(3) carbon atom, we consider the two core 1s electrons and treat that carbon as an atom with three electrons. This results in an LSCF+3 model. Similarly, a nitrogen atom with a lone pair of electrons available for conjugation is treated as an atom with five electrons (LSCF+5). This approach is particularly well suited to splitting peptide bonds and other bonds that include carbon or nitrogen atoms. To embed the induced polarization within the calculation, researchers must use a polarizable force field. However, because the parameters of the usual force fields include an average of the induction effects, researchers typically can obtain satisfactory results without explicitly introducing the polarization. When considering electronic transitions, researchers must take into account the changes in the electronic polarization. One approach is to simulate the electronic cloud of the surroundings by a continuum whose dielectric constant is equal to the square of the refractive index. This Electronic Response of the Surroundings (ERS) methodology allows researchers to model the changes in induced polarization easily. We illustrate this approach by modeling the electronic absorption of tryptophan in human serum albumin (HSA).

Low-energy ion beam synthesis of Ag endotaxial nanostructures in silicon

NASA Astrophysics Data System (ADS)

Nagarajappa, Kiran; Guha, Puspendu; Thirumurugan, Arun; Satyam, Parlapalli V.; Bhatta, Umananda M.

2018-06-01

Coherently, embedded metal nanostructures (endotaxial) are known to have potential applications concerning the areas of plasmonics, optoelectronics and thermoelectronics. Incorporating appropriate concentrations of metal atoms into crystalline silicon is critical for these applications. Therefore, choosing proper dose of low-energy ions, instead of depositing thin film as a source of metal atoms, helps in avoiding surplus concentration of metal atoms that diffuses into the silicon crystal. In this work, 30 keV silver negative ions are implanted into a SiO x /Si(100) at two different fluences: 1 × 1015 and 2.5 × 1015 Ag- ions/cm2. Later, the samples are annealed at 700 °C for 1 h in Ar atmosphere. Embedded silver nanostructures have been characterized using planar and cross-sectional TEM (XTEM) analysis. Planar TEM analysis shows the formation of mostly rectangular silver nanostructures following the fourfold symmetry of the substrate. XTEM analysis confirms the formation of prism-shaped silver nanostructures embedded inside crystalline silicon. Endotaxial nature of the embedded crystals has been discussed using selected area electron diffraction analysis.

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.

Crown oxygen-doping graphene with embedded main-group metal atoms

NASA Astrophysics Data System (ADS)

Wu, Liyuan; Wang, Qian; Yang, Chuanghua; Quhe, Ruge; Guan, Pengfei; Lu, Pengfei

2018-02-01

Different main-group metal atoms embedded in crown oxygen-doping graphene (metal@OG) systems are studied by the density functional theory. The binding energies and electronic structures are calculated by using first-principles calculations. The binding energy of metal@OG system mainly depends on the electronegativity of the metal atom. The lower the value of the electronegativity, the larger the binding energy, indicating the more stable the system. The electronic structure of metal@OG arouses the emergence of bandgap and shift of Dirac point. It is shown that interaction between metal atom and crown oxygen-doping graphene leads to the graphene's stable n-doping, and the metal@OG systems are stable semiconducting materials, which can be used in technological applications.

Optical beams with embedded vortices: building blocks for atom optics and quantum information

NASA Astrophysics Data System (ADS)

Chattrapiban, N.; Arakelyan, I.; Mitra, S.; Hill, W. T., III

2006-05-01

Laser beams with embedded vortices, Bessel or Laguerre-Gaussian modes, provide a unique opportunity for creating elements for atom optics, entangling photons and, potentially, mediating novel quantum interconnects between photons and matter. High-order Bessel modes, for example, contain intensity voids and propagate nearly diffraction-free for tens of meters. These vortices can be exploited to produce dark channels oriented longitudinally (hollow beams) or transversely to the laser propagation direction. Such channels are ideal for generating networks or circuits to guide and manipulate cold neutral atoms, an essential requirement for realizing future applications associated with atom interferometry, atom lithography and even some neutral atom-based quantum computing architectures. Recently, we divided a thermal cloud of neutral atoms moving within a blue-detuned beam into two clouds with two different momenta by crossing two hollow beams. In this presentation, we will describe these results and discuss the prospects for extending the process to coherent ensembles of matter.

Combinatorial Search for High-Activity Hydrogen Catalysts Based on Transition-Metal-Embedded Graphitic Carbons

DOE PAGES

Choi, Woon Ih; Wood, Brandon C.; Schwegler, Eric; ...

2015-09-22

Transition metal (TM) atoms in porphyrin–like complexes play important roles in many protein and enzymetic systems, where crystal–field effects are used to modify d–orbital levels. Inspired by the tunable electronic structure of these motifs, a high–throughput computational search for synthetic hydrogen catalysts is performed based on a similar motif of TM atoms embedded into the lattice of graphene. Based on an initial list of 300 possible embedding geometries, binders, and host atoms, descriptors for stability and catalytic activity are applied to extract ten promising candidates for hydrogen evolution, two of which are expected to exhibit high activity for hydrogen oxidation.more » In several instances, the active TM atoms are earth–abundant elements that show no activity in the bulk phase, highlighting the importance of the coordination environment in tuning the d–orbitals. In conclusion, it is found that the most active candidates involve a hitherto unreported surface reaction pathway that involves a Kubas–complex intermediate, which significantly lowers the kinetic barrier associated with hydrogen dissociation and association.« less

Modelling the atomic structure of Al92U8 metallic glass.

PubMed

Michalik, S; Bednarcik, J; Jóvári, P; Honkimäki, V; Webb, A; Franz, H; Fazakas, E; Varga, L K

2010-10-13

The local atomic structure of the glassy Al(92)U(8) alloy was modelled by the reverse Monte Carlo (RMC) method, fitting x-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) signals. The final structural model was analysed by means of partial pair correlation functions, coordination number distributions and Voronoi tessellation. In our study we found that the most probable atomic separations between Al-Al and U-Al pairs in the glassy Al(92)U(8) alloy are 2.7 Å and 3.1 Å with coordination numbers 11.7 and 17.1, respectively. The Voronoi analysis did not support evidence of the existence of well-defined building blocks directly embedded in the amorphous matrix. The dense-random-packing model seems to be adequate for describing the connection between solvent and solute atoms.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

NASA Astrophysics Data System (ADS)

Konovalenko, Ivan S.; Konovalenko, Igor S.

2015-10-01

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving tool from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.

New Propellants and Cryofuels

NASA Technical Reports Server (NTRS)

Palasezski, Bryan; Sullivan, Neil S.; Hamida, Jaha; Kokshenev, V.

2006-01-01

The proposed research will investigate the stability and cryogenic properties of solid propellants that are critical to NASA s goal of realizing practical propellant designs for future spacecraft. We will determine the stability and thermal properties of a solid hydrogen-liquid helium stabilizer in a laboratory environment in order to design a practical propellant. In particular, we will explore methods of embedding atomic species and metallic nano-particulates in hydrogen matrices suspended in liquid helium. We will also measure the characteristic lifetimes and diffusion of atomic species in these candidate cryofuels. The most promising large-scale advance in rocket propulsion is the use of atomic propellants; most notably atomic hydrogen stabilized in cryogenic environments, and metallized-gelled liquid hydrogen (MGH) or densified gelled hydrogen (DGH). The new propellants offer very significant improvements over classic liquid oxygen/hydrogen fuels because of two factors: (1) the high energy-release, and (ii) the density increase per unit energy release. These two changes can lead to significant reduced mission costs and increased payload to orbit weight ratios. An achievable 5 to 10 percent improvement in specific impulse for the atomic propellants or MGH fuels can result in a doubling or tripling of system payloads. The high-energy atomic propellants must be stored in a stabilizing medium such as solid hydrogen to inhibit or delay their recombination into molecules. The goal of the proposed research is to determine the stability and thermal properties of the solid hydrogen-liquid helium stabilizer. Magnetic resonance techniques will be used to measure the thermal lifetimes and the diffusive motions of atomic species stored in solid hydrogen grains. The properties of metallic nano-particulates embedded in hydrogen matrices will also be studied and analyzed. Dynamic polarization techniques will be developed to enhance signal/noise ratios in order to be able to detect low concentrations of the introduced species. The required lifetimes for atomic hydrogen and other species can only be realized at low temperatures to avoid recombination of atoms before use as a fuel.

Atomic characterization of Si nanoclusters embedded in SiO2 by atom probe tomography

PubMed Central

2011-01-01

Silicon nanoclusters are of prime interest for new generation of optoelectronic and microelectronics components. Physical properties (light emission, carrier storage...) of systems using such nanoclusters are strongly dependent on nanostructural characteristics. These characteristics (size, composition, distribution, and interface nature) are until now obtained using conventional high-resolution analytic methods, such as high-resolution transmission electron microscopy, EFTEM, or EELS. In this article, a complementary technique, the atom probe tomography, was used for studying a multilayer (ML) system containing silicon clusters. Such a technique and its analysis give information on the structure at the atomic level and allow obtaining complementary information with respect to other techniques. A description of the different steps for such analysis: sample preparation, atom probe analysis, and data treatment are detailed. An atomic scale description of the Si nanoclusters/SiO2 ML will be fully described. This system is composed of 3.8-nm-thick SiO layers and 4-nm-thick SiO2 layers annealed 1 h at 900°C. PMID:21711666

Scalable quantum computer architecture with coupled donor-quantum dot qubits

DOEpatents

Schenkel, Thomas; Lo, Cheuk Chi; Weis, Christoph; Lyon, Stephen; Tyryshkin, Alexei; Bokor, Jeffrey

2014-08-26

A quantum bit computing architecture includes a plurality of single spin memory donor atoms embedded in a semiconductor layer, a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, wherein a first voltage applied across at least one pair of the aligned quantum dot and donor atom controls a donor-quantum dot coupling. A method of performing quantum computing in a scalable architecture quantum computing apparatus includes arranging a pattern of single spin memory donor atoms in a semiconductor layer, forming a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, applying a first voltage across at least one aligned pair of a quantum dot and donor atom to control a donor-quantum dot coupling, and applying a second voltage between one or more quantum dots to control a Heisenberg exchange J coupling between quantum dots and to cause transport of a single spin polarized electron between quantum dots.

Atomistic modeling of metallic thin films by modified embedded atom method

NASA Astrophysics Data System (ADS)

Hao, Huali; Lau, Denvid

2017-11-01

Molecular dynamics simulation is applied to investigate the deposition process of metallic thin films. Eight metals, titanium, vanadium, iron, cobalt, nickel, copper, tungsten, and gold, are chosen to be deposited on the aluminum substrate. The second nearest-neighbor modified embedded atom method potential is adopted to predict their thermal and mechanical properties. When quantifying the screening parameters of the potential, the error for Young's modulus and coefficient of thermal expansion between the simulated results and the experimental measurements is less than 15%, demonstrating the reliability of the potential to predict metallic behaviors related to thermal and mechanical properties. A set of potential parameters which governs the interactions between aluminum and other metals in a binary system is also generated from ab initio calculation. The details of interfacial structures between the chosen films and substrate are successfully simulated with the help of these parameters. Our results indicate that the preferred orientation of film growth depends on the film crystal structure, and the inter-diffusion at the interface is correlated the cohesive energy parameter of potential for the binary system. Such finding provides an important basis to further understand the interfacial science, which contributes to the improvement of the mechanical properties, reliability and durability of films.

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.

Tunable meta-atom using liquid metal embedded in stretchable polymer

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

Liu, Peng; Yang, Siming; Wang, Qiugu

2015-07-07

Reconfigurable metamaterials have great potential to alleviate complications involved in using passive metamaterials to realize emerging electromagnetic functions, such as dynamical filtering, sensing, and cloaking. This paper presents a new type of tunable meta-atoms in the X-band frequency range (8–12 GHz) toward reconfigurable metamaterials. The meta-atom is made of all flexible materials compliant to the surface of an interaction object. It uses a liquid metal-based split-ring resonator as its core constituent embedded in a highly flexible elastomer. We demonstrate that simple mechanical stretching of the meta-atom can lead to the great flexibility in reconfiguring its resonance frequency continuously over moremore » than 70% of the X-band frequency range. The presented meta-atom technique provides a simple approach to dynamically tune response characteristics of metamaterials over a broad frequency range.« less

Suppression of planar defects in the molecular beam epitaxy of GaAs/ErAs/GaAs heterostructures

NASA Astrophysics Data System (ADS)

Crook, Adam M.; Nair, Hari P.; Ferrer, Domingo A.; Bank, Seth R.

2011-08-01

We present a growth method that overcomes the mismatch in rotational symmetry of ErAs and conventional III-V semiconductors, allowing for epitaxially integrated semimetal/semiconductor heterostructures. Transmission electron microscopy and reflection high-energy electron diffraction reveal defect-free overgrowth of ErAs layers, consisting of >2× the total amount of ErAs that can be embedded with conventional layer-by-layer growth methods. We utilize epitaxial ErAs nanoparticles, overgrown with GaAs, as a seed to grow full films of ErAs. Growth proceeds by diffusion of erbium atoms through the GaAs spacer, which remains registered to the underlying substrate, preventing planar defect formation during subsequent GaAs growth. This growth method is promising for metal/semiconductor heterostructures that serve as embedded Ohmic contacts to epitaxial layers and epitaxially integrated active plasmonic devices.

Anomalous Insulator-Metal Transition in Boron Nitride-Graphene Hybrid Atomic Layers

DTIC Science & Technology

2012-08-13

REPORT Anomalous insulator-metal transition in boron nitride-graphene hybrid atomic layers 14 . ABSTRACT 16. SECURITY CLASSIFICATION OF: The study of...from the DFT calculation. The calculated transmission through a N terminated zigzag edged h-BN nanodomain embedded in graphene is shown in Fig. 14 , with...Energy ε − ε F (eV) 0 0.5 1 1.5 2 Tr an sm is si on FIG. 14 . (Color online) Transmission through a N terminated zigzag edged h-BN nanodomain embedded in

Nanoscale Subsurface Imaging of Nanocomposites via Resonant Difference-Frequency Atomic Force Ultrasonic Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, Sean A.; Cantrell, John H.; Lillehei, Peter T.

2007-01-01

A scanning probe microscope methodology, called resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), has been developed. The method employs an ultrasonic wave launched from the bottom of a sample while the cantilever of an atomic force microscope engages the sample top surface. The cantilever is driven at a frequency differing from the ultrasonic frequency by one of the contact resonance frequencies of the cantilever. The nonlinear mixing of the oscillating cantilever and the ultrasonic wave at the sample surface generates difference-frequency oscillations at the cantilever contact resonance. The resonance-enhanced difference-frequency signals are used to create amplitude and phase-generated images of nanoscale near-surface and subsurface features. RDF-AFUM phase images of LaRC-CP2 polyimide polymer containing embedded nanostructures are presented. A RDF-AFUM micrograph of a 12.7 micrometer thick film of LaRC-CP2 containing a monolayer of gold nanoparticles embedded 7 micrometers below the specimen surface reveals the occurrence of contiguous amorphous and crystalline phases within the bulk of the polymer and a preferential growth of the crystalline phase in the vicinity of the gold nanoparticles. A RDF-AFUM micrograph of LaRC-CP2 film containing randomly dispersed carbon nanotubes reveals the growth of an interphase region at certain nanotube-polymer interfaces.

The embedded operating system project

NASA Technical Reports Server (NTRS)

Campbell, R. H.

1984-01-01

This progress report describes research towards the design and construction of embedded operating systems for real-time advanced aerospace applications. The applications concerned require reliable operating system support that must accommodate networks of computers. The report addresses the problems of constructing such operating systems, the communications media, reconfiguration, consistency and recovery in a distributed system, and the issues of realtime processing. A discussion is included on suitable theoretical foundations for the use of atomic actions to support fault tolerance and data consistency in real-time object-based systems. In particular, this report addresses: atomic actions, fault tolerance, operating system structure, program development, reliability and availability, and networking issues. This document reports the status of various experiments designed and conducted to investigate embedded operating system design issues.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

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

Konovalenko, Ivan S., E-mail: ivkon@ispms.tsc.ru; Konovalenko, Igor S., E-mail: igkon@ispms.tsc.ru; National Research Tomsk Polytechnic University, Tomsk, 634050

2015-10-27

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving toolmore » from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.« less

Atomistic modeling for interfacial properties of Ni-Al-V ternary system

NASA Astrophysics Data System (ADS)

Dong, Wei-ping; Lee, Byeong-Joo; Chen, Zheng

2014-05-01

Interatomic potentials for Ni-Al-V ternary systems have been developed based on the second-nearest-neighbor modified embedded-atom method potential formalism. The potentials can describe various fundamental physical properties of the relevant materials in good agreement with experimental information. The potential is utilized for an atomistic computation of interfacial properties of Ni-Al-V alloys. It is found that vanadium atoms segregate on the γ-fcc/L12 interface and this segregation affects the interfacial properties. The applicability of the atomistic approach to an elaborate alloy design of advanced Ni-based superalloys through the investigation of the effect of alloying elements on interfacial properties is discussed.

Incorporating isolated molybdenum (Mo) atoms into Bilayer Epitaxial Graphene on 4H-SiC(0001)

NASA Astrophysics Data System (ADS)

Huang, Han; Wan, Wen; Li, Hui; Wong, Swee Liang; Lv, Lu; Gao, Yongli; Wee, Andrew T. S.

2014-03-01

The atomic structures and electronic properties of isolated Mo atoms in bilayer epitaxial graphene (BLEG) on 4H-SiC(0001) are investigated by low temperature scanning tunneling microscopy (LT-STM). LT-STM results reveal that isolated Mo dopants prefer to substitute C atoms at α-sites, and preferentially locate between the graphene bilayers. First-principles calculations confirm that the embedding of single Mo dopants within BLEG is energetically favorable as compared to monolayer graphene. The calculated bandstructures show that Mo-doped BLEG is n-doped, and each Mo atom introduces a local magnetic moment of 1.81 μB. Our findings demonstrate a simple and stable method to incorporate single transition metal dopants into the graphene lattice to tune its electronic and magnetic properties for possible use in graphene spin devices. NRF-CRP (Singapore) grants R-143-000-360-281and R-144-000-295-281. ``Shenghua Professorship'' startup funding from CSU and the support from the NSF of China (Grant No.11304398).

Reinforced silver-embedded silica matrix from the cheap silica source for the controlled release of silver ions

NASA Astrophysics Data System (ADS)

Hilonga, A.; Kim, J. K.; Sarawade, P. B.; Kim, H. T.

2009-07-01

In this study, a reinforced silver-embedded silica matrix was designed by utilizing the interaction between the [AlO 4] - tetrahedral and the Ag + in sol-gel process using sodium silicate as a silica precursor. The Ag + mole ratio in each sample was significantly varied to examine the influence of silver concentration on the properties of the final product. Aluminium ions were added to reinforce and improve the chemical durability of silver-embedded silica. A templated sample at Al/Ag = 1 atomic ratio was also synthesized to attempt a possibility of controlling porosity of the final product. Also, a sample neither embedded with silver nor templated was synthesized and characterized to serve as reference. The material at Al/Ag = 1 was found to have a desirable properties, compared to its counterparts, before and even after calcination up to 1000 °C. The results demonstrate that materials with desirable properties can be obtained by this unprecedented method while utilizing sodium silicate, which is relatively cheap, as a silica precursor. This may significantly boost the industrial production of the silver-embedded silicas for various applications.

Lattice distortion and electron charge redistribution induced by defects in graphene

DOE PAGES

Zhang, Wei; Lu, Wen -Cai; Zhang, Hong -Xing; ...

2016-09-14

Lattice distortion and electronic charge localization induced by vacancy and embedded-atom defects in graphene were studied by tight-binding (TB) calculations using the recently developed three-center TB potential model. We showed that the formation energies of the defects are strongly correlated with the number of dangling bonds and number of embedded atoms, as well as the magnitude of the graphene lattice distortion induced by the defects. Lastly, we also showed that the defects introduce localized electronic states in the graphene which would affect the electron transport properties of graphene.

Embedded dielectric water "atom" array for broadband microwave absorber based on Mie resonance

NASA Astrophysics Data System (ADS)

Gogoi, Dhruba Jyoti; Bhattacharyya, Nidhi Saxena

2017-11-01

A wide band microwave absorber at X-band frequency range is demonstrated numerically and experimentally by embedding a simple rectangular structured dielectric water "atom" in flexible silicone substrate. The absorption peak of the absorber is tuned by manipulating the size of the dielectric water "atom." The frequency dispersive permittivity property of the water "atom" shows broadband absorption covering the entire X-band above 90% efficiency with varying the size of the water "atom." Mie resonance of the proposed absorber provides the desired impedance matching condition at the air-absorber interface across a wide frequency range in terms of electric and magnetic resonances. Multipole decomposition of induced current densities is used to identify the nature of observed resonances. Numerical absorptivity verifies that the designed absorber is polarization insensitive for normal incidence and can maintain an absorption bandwidth of more than 2 GHz in a wide-angle incidence. Additionally, the tunability of absorption property with temperature is shown experimentally.

Cooling rate dependence and local structure in aluminum monatomic metallic glass

NASA Astrophysics Data System (ADS)

Kbirou, M.; Trady, S.; Hasnaoui, A.; Mazroui, M.

2017-10-01

The local atomic structure in aluminium monatomic metallic glass is studied using molecular dynamics simulations combined with the embedded atom method (EAM). We have used a variety of analytical methods to characterise the atomic configurations of our system: the Pair Distribution Function (PDF), the Common Neighbour Analysis (CNA) and the Voronoi Tessellation Analysis. CNA was used to investigate the order change from liquid to amorphous phases, recognising that the amount of icosahedral clusters increases with the decrease of temperature. The Voronoi analysis revealed that the icosahedral-like polyhedral are the predominant ones. It has been observed that the PDF function shows a splitting in the second peak, which cannot be attributed to the only ideal icosahedral polyhedron 〈0, 0, 12, 0〉, but also to the formation of other Voronoi polyhedra 〈0, 1, 10, 2〉 . Further, the PDFs were then integrated giving the cumulative coordination number in order to compute the fractal dimension (df).

Numerical simulations for quantitative analysis of electrostatic interaction between atomic force microscopy probe and an embedded electrode within a thin dielectric: meshing optimization, sensitivity to potential distribution and impact of cantilever contribution

NASA Astrophysics Data System (ADS)

Azib, M.; Baudoin, F.; Binaud, N.; Villeneuve-Faure, C.; Bugarin, F.; Segonds, S.; Teyssedre, G.

2018-04-01

Recent experimental results demonstrated that an electrostatic force distance curve (EFDC) can be used for space charge probing in thin dielectric layers. A main advantage of the method is claimed to be its sensitivity to charge localization, which, however, needs to be substantiated by numerical simulations. In this paper, we have developed a model which permits us to compute an EFDC accurately by using the most sophisticated and accurate geometry for the atomic force microscopy probe. To avoid simplifications and in order to reproduce experimental conditions, the EFDC has been simulated for a system constituted of a polarized electrode embedded in a thin dielectric layer (SiN x ). The individual contributions of forces on the tip and on the cantilever have been analyzed separately to account for possible artefacts. The EFDC sensitivity to potential distribution is studied through the change in electrode shape, namely the width and the depth. Finally, the numerical results have been compared with experimental data.

First row transition metal atoms embedded in multivacancies in a rippled graphene system

NASA Astrophysics Data System (ADS)

Mombrú, Dominique; Faccio, Ricardo; Mombrú, Alvaro W.

2018-03-01

Ab-initio calculations based on density functional theory (DFT) have been performed to study systems where a first row transition metal atom is embedded in a rippled graphene due to the existence of an 8-order multivacancy. In addition to these cases, also the inclusion of a zinc atom, with a 3d10 electron configuration, was also studied. Structural distortions and magnetic response for each system were studied. A correlation was found for the magnitude of the rippling and the distortion in the vacancy. Variation in the trends was found for Cu and Zn cases, which were explained on the basis of the filling of the 3dx2-y2 orbital. All the systems exhibit lower magnetic moment in comparison to the metal-less system. The quenching of the magnetic moment due to the carbon atoms in the vacancy is observed for Sc and Cu.

Study of optical and luminescence properties of silicon — semiconducting silicide — silicon multilayer nanostructures

NASA Astrophysics Data System (ADS)

Galkin, N. G.; Galkin, K. N.; Dotsenko, , S. A.; Goroshko, D. L.; Shevlyagin, A. V.; Chusovitin, E. A.; Chernev, I. M.

2017-01-01

By method of in situ differential spectroscopy it was established that at the formation of monolayer Fe, Cr, Ca, Mg silicide and Mg stannide islands on the atomically clean silicon surface an appearance of loss peaks characteristic for these materials in the energy range of 1.1-2.6 eV is observed. An optimization of growth processes permit to grow monolithic double nanoheterostructures (DNHS) with embedded Fe, Cr and Ca nanocrystals, and also polycrystalline DNHS with NC of Mg silicide and Mg stannide and Ca disilicide. By methods of optical spectroscopy and Raman spectroscopy it was shown that embedded NC form intensive peaks in the reflectance spectra at energies up to 2.5 eV and Raman peaks. In DNS with β-FeSi2 NC a photoluminescence and electroluminescence at room temperature were firstly observed.

Multiple period s-p hybridization in nano-strip embedded photonic crystal.

PubMed

Han, Seunghoon; Lee, Il-Min; Kim, Hwi; Lee, Byoungho

2005-04-04

We report and analyze hybridization of s-state and p-state modes in photonic crystal one-dimensional defect cavity array. When embedding a nano-strip into a dielectric rod photonic crystal, an effective cavity array is made, where each cavity possesses two cavity modes: s-state and p-state. The two modes are laterally even versus the nano-strip direction, and interact with each other, producing defect bands, of which the group velocity becomes zero within the first Brillouin zone. We could model and describe the phenomena by using the tight-binding method, well agreeing with the plane-wave expansion method analysis. We note that the reported s- and p-state mode interaction corresponds to the hybridization of atomic orbital in solid-state physics. The concept of multiple period s-p hybridization and the proposed model can be useful for analyzing and developing novel photonic crystal waveguides and devices.

Positronic probe of vacancy defects on surfaces of Au nanoparticles embedded in MgO

NASA Astrophysics Data System (ADS)

Xu, Jun; Moxom, J.; Somieski, B.; White, C. W.; Mills, A. P., Jr.; Suzuki, R.; Ishibashi, S.

2001-09-01

Clusters of four atomic vacancies were found in Au nanoparticle-embedded MgO by positron lifetime spectroscopy [Phys. Rev. Lett. 83, 4586 (1999)]. These clusters were also suggested to locate at the surface of Au nanoparticles by one-detector measurements of Doppler broadening of annihilation radiation. In this work we provide evidence, using two-detector coincidence experiments of Doppler broadening (2D-DBAR), to clarify that these vacancy clusters reside on the surfaces of Au nanoparticles. This work also demonstrates a method for identifying defects at nanomaterials interfaces: a combination of both positron lifetime spectroscopy, which tells the type of the defects, and 2D-DBAR measurements, which reveals chemical environment of the defects.

Thermomechanical response of NiTi shape-memory nanoprecipitates in TiV alloys

NASA Astrophysics Data System (ADS)

Maisel, S. B.; Ko, W.-S.; Zhang, J.-L.; Grabowski, B.; Neugebauer, J.

2017-08-01

We study the properties of NiTi shape-memory nanoparticles coherently embedded in TiV matrices using three-dimensional atomistic simulations based on the modified embedded-atom method. To this end, we develop and present a suitable NiTiV potential for our simulations. Employing this potential, we identify the conditions under which the martensitic phase transformation of such a nanoparticle is triggered—specifically, how these conditions can be tuned by modifying the size of the particle, the composition of the surrounding matrix, or the temperature and strain state of the system. Using these insights, we establish how the transformation temperature of such particles can be influenced and discuss the practical implications in the context of shape-memory strengthened alloys.

Study on the structural transition of CoNi nanoclusters using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Xia, J. H.; Gao, Xue-Mei

2018-04-01

In this work, the segregation and structural transitions of CoNi clusters, between 1500 and 300 K, have been investigated using molecular dynamics simulations with the embedded atom method potential. The radial distribution function was used to analyze the segregation during the cooling processes. It is found that Co atoms segregate to the inside and Ni atoms preferably to the surface during the cooling processes, the Co147Ni414 cluster becomes a core-shell structure. We discuss the structural transition according to the pair-correction function and pair-analysis technique, and finally the liquid Co147Ni414 crystallizes into the coexistence of hcp and fcc structure at 300 K. At the same time, it is found that the frozen structure of CoNi cluster is strongly related to the Co concentration.

Probing resistivity and doping concentration of semiconductors at the nanoscale using scanning microwave microscopy

NASA Astrophysics Data System (ADS)

Brinciotti, Enrico; Gramse, Georg; Hommel, Soeren; Schweinboeck, Thomas; Altes, Andreas; Fenner, Matthias A.; Smoliner, Juergen; Kasper, Manuel; Badino, Giorgio; Tuca, Silviu-Sorin; Kienberger, Ferry

2015-08-01

We present a new method to extract resistivity and doping concentration of semiconductor materials from Scanning Microwave Microscopy (SMM) S11 reflection measurements. Using a three error parameters de-embedding workflow, the S11 raw data are converted into calibrated capacitance and resistance images where no calibration sample is required. The SMM capacitance and resistance values were measured at 18 GHz and ranged from 0 to 100 aF and from 0 to 1 MΩ, respectively. A tip-sample analytical model that includes tip radius, microwave penetration skin depth, and semiconductor depletion layer width has been applied to extract resistivity and doping concentration from the calibrated SMM resistance. The method has been tested on two doped silicon samples and in both cases the resistivity and doping concentration are in quantitative agreement with the data-sheet values over a range of 10-3 Ω cm to 101 Ω cm, and 1014 atoms per cm3 to 1020 atoms per cm3, respectively. The measured dopant density values, with related uncertainties, are [1.1 +/- 0.6] × 1018 atoms per cm3, [2.2 +/- 0.4] × 1017 atoms per cm3, [4.5 +/- 0.2] × 1016 atoms per cm3, [4.5 +/- 1.3] × 1015 atoms per cm3, [4.5 +/- 1.7] × 1014 atoms per cm3. The method does not require sample treatment like cleavage and cross-sectioning, and high contact imaging forces are not necessary, thus it is easily applicable to various semiconductor and materials science investigations.

Pt Single Atoms Embedded in the Surface of Ni Nanocrystals as Highly Active Catalysts for Selective Hydrogenation of Nitro Compounds.

PubMed

Peng, Yuhan; Geng, Zhigang; Zhao, Songtao; Wang, Liangbing; Li, Hongliang; Wang, Xu; Zheng, Xusheng; Zhu, Junfa; Li, Zhenyu; Si, Rui; Zeng, Jie

2018-06-13

Single-atom catalysts exhibit high selectivity in hydrogenation due to their isolated active sites, which ensure uniform adsorption configurations of substrate molecules. Compared with the achievement in catalytic selectivity, there is still a long way to go in exploiting the catalytic activity of single-atom catalysts. Herein, we developed highly active and selective catalysts in selective hydrogenation by embedding Pt single atoms in the surface of Ni nanocrystals (denoted as Pt 1 /Ni nanocrystals). During the hydrogenation of 3-nitrostyrene, the TOF numbers based on surface Pt atoms of Pt 1 /Ni nanocrystals reached ∼1800 h -1 under 3 atm of H 2 at 40 °C, much higher than that of Pt single atoms supported on active carbon, TiO 2 , SiO 2 , and ZSM-5. Mechanistic studies reveal that the remarkable activity of Pt 1 /Ni nanocrystals derived from sufficient hydrogen supply because of spontaneous dissociation of H 2 on both Pt and Ni atoms as well as facile diffusion of H atoms on Pt 1 /Ni nanocrystals. Moreover, the ensemble composed of the Pt single atom and nearby Ni atoms in Pt 1 /Ni nanocrystals leads to the adsorption configuration of 3-nitrostyrene favorable for the activation of nitro groups, accounting for the high selectivity for 3-vinylaniline.

Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals.

PubMed

Huang, Yanhua; Zong, Wenjun

2014-01-01

In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature.

Monte Carlo simulation of elongating metallic nanowires in the presence of surfactants

NASA Astrophysics Data System (ADS)

Gimenez, M. Cecilia; Reinaudi, Luis; Leiva, Ezequiel P. M.

2015-12-01

Nanowires of different metals undergoing elongation were studied by means of canonical Monte Carlo simulations and the embedded atom method representing the interatomic potentials. The presence of a surfactant medium was emulated by the introduction of an additional stabilization energy, represented by a parameter Q. Several values of the parameter Q and temperatures were analyzed. In general, it was observed for all studied metals that, as Q increases, there is a greater elongation before the nanowire breaks. In the case of silver, linear monatomic chains several atoms long formed at intermediate values of Q and low temperatures. Similar observations were made for the case of silver-gold alloys when the medium interacted selectively with Ag.

Modified Embedded Atom Method Study of the Mechanical Properties of Carbon Nanotube Reinforced Nickel Composites

DTIC Science & Technology

2010-01-01

0188 The public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing...body screening effect. In addition, a radial cutoff function is also applied to reduce calculation time . The MEAM for an alloy system is based on the...moduli Real materials are usually polycrystalline aggregates of randomly oriented single-crystal grains, each exhibiting single-crystalline elastic

Theoretical Investigations of the Electrochemical Reduction of CO on Single Metal Atoms Embedded in Graphene

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

Kirk, Charlotte; Chen, Leanne D.; Siahrostami, Samira

Single transition metal atoms embedded at single vacancies of graphene provide a unique paradigm for catalytic reactions. We present a density functional theory study of such systems for the electrochemical reduction of CO. Theoretical investigations of CO electrochemical reduction are particularly challenging in that electrochemical activation energies are a necessary descriptor of activity. We determined the electrochemical barriers for key proton–electron transfer steps using a state-of-the-art, fully explicit solvent model of the electrochemical interface. The accuracy of GGA-level functionals in describing these systems was also benchmarked against hybrid methods. We find the first proton transfer to form CHO from COmore » to be a critical step in C 1 product formation. On these single atom sites, the corresponding barrier scales more favorably with the CO binding energy than for 211 and 111 transition metal surfaces, in the direction of improved activity. Intermediates and transition states for the hydrogen evolution reaction were found to be less stable than those on transition metals, suggesting a higher selectivity for CO reduction. We present a rate volcano for the production of methane from CO. We identify promising candidates with high activity, stability, and selectivity for the reduction of CO. As a result, this work highlights the potential of these systems as improved electrocatalysts over pure transition metals for CO reduction.« less

Theoretical Investigations of the Electrochemical Reduction of CO on Single Metal Atoms Embedded in Graphene

DOE PAGES

Kirk, Charlotte; Chen, Leanne D.; Siahrostami, Samira; ...

2017-12-18

Single transition metal atoms embedded at single vacancies of graphene provide a unique paradigm for catalytic reactions. We present a density functional theory study of such systems for the electrochemical reduction of CO. Theoretical investigations of CO electrochemical reduction are particularly challenging in that electrochemical activation energies are a necessary descriptor of activity. We determined the electrochemical barriers for key proton–electron transfer steps using a state-of-the-art, fully explicit solvent model of the electrochemical interface. The accuracy of GGA-level functionals in describing these systems was also benchmarked against hybrid methods. We find the first proton transfer to form CHO from COmore » to be a critical step in C 1 product formation. On these single atom sites, the corresponding barrier scales more favorably with the CO binding energy than for 211 and 111 transition metal surfaces, in the direction of improved activity. Intermediates and transition states for the hydrogen evolution reaction were found to be less stable than those on transition metals, suggesting a higher selectivity for CO reduction. We present a rate volcano for the production of methane from CO. We identify promising candidates with high activity, stability, and selectivity for the reduction of CO. As a result, this work highlights the potential of these systems as improved electrocatalysts over pure transition metals for CO reduction.« less

Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2003-02-01

We present a continuum approach for efficient and accurate calculation of reaction field forces and energies in classical molecular-dynamics (MD) simulations of proteins in water. The derivation proceeds in two steps. First, we reformulate the electrostatics of an arbitrarily shaped molecular system, which contains partially charged atoms and is embedded in a dielectric continuum representing the water. A so-called fuzzy partition is used to exactly decompose the system into partial atomic volumes. The reaction field is expressed by means of dipole densities localized at the atoms. Since these densities cannot be calculated analytically for general systems, we introduce and carefully analyze a set of approximations in a second step. These approximations allow us to represent the dipole densities by simple dipoles localized at the atoms. We derive a system of linear equations for these dipoles, which can be solved numerically by iteration. After determining the two free parameters of our approximate method we check its quality by comparisons (i) with an analytical solution, which is available for a perfectly spherical system, (ii) with forces obtained from a MD simulation of a soluble protein in water, and (iii) with reaction field energies of small molecules calculated by a finite difference method.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100-x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-03-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100- x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-06-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Modeling of crack growth under mixed-mode loading by a molecular dynamics method and a linear fracture mechanics approach

NASA Astrophysics Data System (ADS)

Stepanova, L. V.

2017-12-01

Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is the Embedded Atom Method (EAM) potential. Plane specimens with an initial central crack are subjected to mixed-mode loadings. The simulation cell contains 400,000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide range of temperatures (from 0.1 K to 800 K) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields. The multi-parameter fracture criteria are based on the multi-parameter stress field description taking into account the higher order terms of the Williams series expansion of the crack tip fields.

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

Srivastava, Ashish Kumar, E-mail: ashish.memech@gmail.com; Singh, Akhileshwar; Mokhalingam, A.

Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for themore » interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young’s modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young’s modulus of the Al matrix up to 77 % as compared to pure Al.« less

Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)

NASA Astrophysics Data System (ADS)

Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido

2018-04-01

Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.

Studies of Positrons Trapped at Quantum-Dot Like Particles Embedded in Metal Surfaces

NASA Astrophysics Data System (ADS)

Fazleev, N. G.; Nadesalingam, M. P.; Weiss, A. H.

2009-03-01

Experimental studies of the positron annihilation induced Auger electron (PAES) spectra from the Fe-Cu alloy surfaces with quantum-dot like Cu nanoparticles embedded in Fe show that the PAES signal from Cu increase rapidly as the concentration of Cu is enhanced by vacuum annealing. These measurements indicate that almost 75% of positrons that annihilate with core electrons due so with Cu even though the surface concentration of Cu as measured by EAES is only 6%. This result suggests that positrons become localized at sites at the surface containing high concentration of Cu atoms before annihilation. These experimental results are investigated theoretically by performing calculations of the "image-potential" positron surface states and annihilation characteristics of the surface trapped positrons with relevant Fe and Cu core-level electrons for the clean Fe(100) and Cu(100) surfaces and for the Fe(100) surface with quantum-dot like Cu nanoparticles embedded in the top atomic layers of the host substrate. Estimates of the positron binding energy and positron annihilation characteristics reveal their strong sensitivity to the nanoparticle coverage. Computed core annihilation probabilities are compared with experimental ones estimated from the measured Auger peak intensities. The observed behavior of the Fe and Cu PAES signal intensities is explained by theoretical calculations as being due to trapping of positrons in the regions of Cu nanoparticles embedded in the top atomic layers of Fe.

Development of a Modified Embedded Atom Force Field for Zirconium Nitride Using Multi-Objective Evolutionary Optimization

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

Narayanan, Badri; Sasikumar, Kiran; Mei, Zhi-Gang

2016-07-07

Zirconium nitride (ZrN) exhibits exceptional mechanical, chemical, and electrical properties, which make it attractive for a wide range of technological applications, including wear-resistant coatings, protection from corrosion, cutting/shaping tools, and nuclear breeder reactors. Despite its broad usability, an atomic scale understanding of the superior performance of ZrN, and its response to external stimuli, for example, temperature, applied strain, and so on, is not well understood. This is mainly due to the lack of interatomic potential models that accurately describe the interactions between Zr and N atoms. To address this challenge, we develop a modified embedded atom method (MEAM) interatomic potentialmore » for the Zr–N binary system by training against formation enthalpies, lattice parameters, elastic properties, and surface energies of ZrN (and, in some cases, also Zr3N4) obtained from density functional theory (DFT) calculations. The best set of MEAM parameters are determined by employing a multiobjective global optimization scheme driven by genetic algorithms. Our newly developed MEAM potential accurately reproduces structure, thermodynamics, energetic ordering of polymorphs, as well as elastic and surface properties of Zr–N compounds, in excellent agreement with DFT calculations and experiments. As a representative application, we employed molecular dynamics simulations based on this MEAM potential to investigate the atomic scale mechanisms underlying fracture of bulk and nanopillar ZrN under applied uniaxial strains, as well as the impact of strain rate on their mechanical behavior. These simulations indicate that bulk ZrN undergoes brittle fracture irrespective of the strain rate, while ZrN nanopillars show quasi-plasticity owing to amorphization at the crack front. The MEAM potential for Zr–N developed in this work is an invaluable tool to investigate atomic-scale mechanisms underlying the response of ZrN to external stimuli (e.g, temperature, pressure etc.), as well as other interesting phenomena such as precipitation.« less

The role of titanium nitride supports for single-atom platinum-based catalysts in fuel cell technology.

PubMed

Zhang, Ren-Qin; Lee, Tae-Hun; Yu, Byung-Deok; Stampfl, Catherine; Soon, Aloysius

2012-12-28

As a first step towards a microscopic understanding of single-Pt atom-dispersed catalysts on non-conventional TiN supports, we present density-functional theory (DFT) calculations to investigate the adsorption properties of Pt atoms on the pristine TiN(100) surface, as well as the dominant influence of surface defects on the thermodynamic stability of platinized TiN. Optimized atomic geometries, energetics, and analysis of the electronic structure of the Pt/TiN system are reported for various surface coverages of Pt. We find that atomic Pt does not bind preferably to the clean TiN surface, but under typical PEM fuel cell operating conditions, i.e. strongly oxidizing conditions, TiN surface vacancies play a crucial role in anchoring the Pt atom for its catalytic function. Whilst considering the energetic stability of the Pt/TiN structures under varying N conditions, embedding Pt at the surface N-vacancy site is found to be the most favorable under N-lean conditions. Thus, the system of embedding Pt at the surface N-vacancy sites on TiN(100) surfaces could be promising catalysts for PEM fuel cells.

Rydberg aggregates

NASA Astrophysics Data System (ADS)

Wüster, S.; Rost, J.-M.

2018-02-01

We review Rydberg aggregates, assemblies of a few Rydberg atoms exhibiting energy transport through collective eigenstates, considering isolated atoms or assemblies embedded within clouds of cold ground-state atoms. We classify Rydberg aggregates, and provide an overview of their possible applications as quantum simulators for phenomena from chemical or biological physics. Our main focus is on flexible Rydberg aggregates, in which atomic motion is an essential feature. In these, simultaneous control over Rydberg-Rydberg interactions, external trapping and electronic energies, allows Born-Oppenheimer surfaces for the motion of the entire aggregate to be tailored as desired. This is illustrated with theory proposals towards the demonstration of joint motion and excitation transport, conical intersections and non-adiabatic effects. Additional flexibility for quantum simulations is enabled by the use of dressed dipole-dipole interactions or the embedding of the aggregate in a cold gas or Bose-Einstein condensate environment. Finally we provide some guidance regarding the parameter regimes that are most suitable for the realization of either static or flexible Rydberg aggregates based on Li or Rb atoms. The current status of experimental progress towards enabling Rydberg aggregates is also reviewed.

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

Yadav, Satyesh Kumar; Shao, S.; Chen, Youxing

Here, using a newly developed embedded-atom-method potential for Mg–Nb, the semi-coherent Mg/Nb interface with the Kurdjumov–Sachs orientation relationship is studied. Atomistic simulations have been carried out to understand the shear strength of the interface, as well as the interaction between lattice glide dislocations and the interface. The interface shear mechanisms are dependent on the shear loading directions, through either interface sliding between Mg and Nb atomic layers or nucleation and gliding of Shockley partial dislocations in between the first two atomic planes in Mg at the interface. The shear strength for the Mg/Nb interface is found to be generally high,more » in the range of 0.9–1.3 GPa depending on the shear direction. As a consequence, the extents of dislocation core spread into the interface are considerably small, especially when compared to the case of other “weak” interfaces such as the Cu/Nb interface.« less

Extending the accuracy of the SNAP interatomic potential form

NASA Astrophysics Data System (ADS)

Wood, Mitchell A.; Thompson, Aidan P.

2018-06-01

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functions in EAM. The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similar to artificial neural network potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting. The quality of this new potential form is measured through a robust cross-validation analysis.

On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Fu, Yao; Song, Jeong-Hoon

2014-08-01

Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.

Preparation and application of a carbon paste electrode modified with multi-walled carbon nanotubes and boron-embedded molecularly imprinted composite membranes.

PubMed

Wang, Hongjuan; Qian, Duo; Xiao, Xilin; Deng, Chunyan; Liao, Lifu; Deng, Jian; Lin, Ying-Wu

2018-06-01

An innovative electrochemical sensor was fabricated for the sensitive and selective determination of tinidazole (TNZ), based on a carbon paste electrode (CPE) modified with multi-walled carbon nanotubes (MWCNTs) and boron-embedded molecularly imprinted composite membranes (B-MICMs). Density functional theory (DFT) calculations were carried out to investigate the utility of template-monomer interactions to screen appropriate monomers for the rational design of B-MICMs. The distinct synergic effect of MWCNTs and B-MICMs was evidenced by the positive shift of the reduction peak potential of TNZ at B-MICMs/MWCNTs modified CPE (B-MICMs/MWCNTs/CPE) by about 200 mV, and the 12-fold amplification of the peak current, compared with a bare carbon paste electrode (CPE). Moreover, the coordinate interactions between trisubstituted boron atoms embedded in B-MICMs matrix and nitrogen atoms of TNZ endow the sensor with advanced affinity and specific directionality. Thereafter, a highly sensitive electrochemical analytical method for TNZ was established by different pulse voltammetry (DPV) at B-MICMs/MWCNTs/CPE with a lower detection limit (1.25 × 10 -12  mol L -1 ) (S/N = 3). The practical application of the sensor was demonstrated by determining TNZ in pharmaceutical and biological samples with good precision (RSD 1.36% to 3.85%) and acceptable recoveries (82.40%-104.0%). Copyright © 2018 Elsevier B.V. All rights reserved.

Magneto-optical Faraday rotation of semiconductor nanoparticles embedded in dielectric matrices.

PubMed

Savchuk, Andriy I; Stolyarchuk, Ihor D; Makoviy, Vitaliy V; Savchuk, Oleksandr A

2014-04-01

Faraday rotation has been studied for CdS, CdTe, and CdS:Mn semiconductor nanoparticles synthesized by colloidal chemistry methods. Additionally these materials were prepared in a form of semiconductor nanoparticles embedded in polyvinyl alcohol films. Transmission electron microscopy and atomic force microscopy analyses served as confirmation of nanocrystallinity and estimation of the average size of the nanoparticles. Spectral dependence of the Faraday rotation for the studied nanocrystals and nanocomposites is correlated with a blueshift of the absorption edge due to the confinement effect in zero-dimensional structures. Faraday rotation spectra and their temperature behavior in Mn-doped nanocrystals demonstrates peculiarities, which are associated with s, p-d exchange interaction between Mn²⁺ ions and band carriers in diluted magnetic semiconductor nanostructures.

Adsorption mechanism of SF6 decomposed species on pyridine-like PtN3 embedded CNT: A DFT study

NASA Astrophysics Data System (ADS)

Cui, Hao; Zhang, Xiaoxing; Chen, Dachang; Tang, Ju

2018-07-01

Metal-Nx embedded CNT have aroused considerable attention in the field of gas interaction due to their strong catalytic behavior, which provides prospective scopes for gas adsorption and sensing. Detecting SF6 decomposed species in certain devices is essential to guarantee their safe operation. In this work, we performed DFT method and simulated the adsorption of three SF6 decomposed gases (SO2, SOF2 and SO2F2) onto the PtN3 embedded CNT surface, in order to shed light on its adsorption ability and sensing mechanism. Results suggest that the CNT embedded with PtN3 center has strong interaction with these gas molecules, leading to high hybridization between Pt dopant and active atoms inner gas molecules. These interactions are assumed to be chemisorption due to the remarkable Ead and QT, thus resulting in dramatic deformations in electronic structure of PtN3-CNT near the Fermi level. Furthermore, the electronic redistribution cause the conductivity increase of proposed material in three systems, based on frontier molecular orbital theory. Our calculations attempt to suggest novel sensing material that are potentially employed in detection of SF6 decomposed components.

Correlating confocal microscopy and atomic force indentation reveals metastatic cancer cells stiffen during invasion into collagen I matrices

NASA Astrophysics Data System (ADS)

Staunton, Jack R.; Doss, Bryant L.; Lindsay, Stuart; Ros, Robert

2016-01-01

Mechanical interactions between cells and their microenvironment dictate cell phenotype and behavior, calling for cell mechanics measurements in three-dimensional (3D) extracellular matrices (ECM). Here we describe a novel technique for quantitative mechanical characterization of soft, heterogeneous samples in 3D. The technique is based on the integration of atomic force microscopy (AFM) based deep indentation, confocal fluorescence microscopy, finite element (FE) simulations and analytical modeling. With this method, the force response of a cell embedded in 3D ECM can be decoupled from that of its surroundings, enabling quantitative determination of the elastic properties of both the cell and the matrix. We applied the technique to the quantification of the elastic properties of metastatic breast adenocarcinoma cells invading into collagen hydrogels. We found that actively invading and fully embedded cells are significantly stiffer than cells remaining on top of the collagen, a clear example of phenotypical change in response to the 3D environment. Treatment with Rho-associated protein kinase (ROCK) inhibitor significantly reduces this stiffening, indicating that actomyosin contractility plays a major role in the initial steps of metastatic invasion.

Accurate force field for molybdenum by machine learning large materials data

NASA Astrophysics Data System (ADS)

Chen, Chi; Deng, Zhi; Tran, Richard; Tang, Hanmei; Chu, Iek-Heng; Ong, Shyue Ping

2017-09-01

In this work, we present a highly accurate spectral neighbor analysis potential (SNAP) model for molybdenum (Mo) developed through the rigorous application of machine learning techniques on large materials data sets. Despite Mo's importance as a structural metal, existing force fields for Mo based on the embedded atom and modified embedded atom methods do not provide satisfactory accuracy on many properties. We will show that by fitting to the energies, forces, and stress tensors of a large density functional theory (DFT)-computed dataset on a diverse set of Mo structures, a Mo SNAP model can be developed that achieves close to DFT accuracy in the prediction of a broad range of properties, including elastic constants, melting point, phonon spectra, surface energies, grain boundary energies, etc. We will outline a systematic model development process, which includes a rigorous approach to structural selection based on principal component analysis, as well as a differential evolution algorithm for optimizing the hyperparameters in the model fitting so that both the model error and the property prediction error can be simultaneously lowered. We expect that this newly developed Mo SNAP model will find broad applications in large and long-time scale simulations.

Relativistic corrections for screening effects on the energies of hydrogen-like atoms embedded in plasmas

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

Poszwa, A., E-mail: poszwa@matman.uwm.edu.p; Bahar, M. K., E-mail: mussiv58@gmail.com

2015-01-15

The influence of relativistic and plasma screening effects on energies of hydrogen-like atoms embedded in plasmas has been studied. The Dirac equation with a more general exponential cosine screened potential has been solved numerically and perturbatively, by employing the direct perturbation theory. Properties of spectra corresponding to bound states and to different sets of the potential parameters have been studied both in nonrelativistic and relativistic approximations. Binding energies, fine-structure splittings, and relativistic energy shifts have been determined as functions of parameters of the potential. The results have been compared with the ones known from the literature.

Fe doped Magnetic Nanodiamonds made by Ion Implantation.

PubMed

Chen, ChienHsu; Cho, I C; Jian, Hui-Shan; Niu, H

2017-02-09

Here we present a simple physical method to prepare magnetic nanodiamonds (NDs) using high dose Fe ion-implantation. The Fe atoms are embedded into NDs through Fe ion-implantation and the crystal structure of NDs are recovered by thermal annealing. The results of TEM and Raman examinations indicated the crystal structure of the Fe implanted NDs is recovered completely. The SQUID-VSM measurement shows the Fe-NDs possess room temperature ferromagnetism. That means the Fe atoms are distributed inside the NDs without affecting NDs crystal structure, so the NDs can preserve the original physical and chemical properties of the NDs. In addition, the ion-implantation-introduced magnetic property might make the NDs to become suitable for variety of medical applications.

Fe doped Magnetic Nanodiamonds made by Ion Implantation

NASA Astrophysics Data System (ADS)

Chen, Chienhsu; Cho, I. C.; Jian, Hui-Shan; Niu, H.

2017-02-01

Here we present a simple physical method to prepare magnetic nanodiamonds (NDs) using high dose Fe ion-implantation. The Fe atoms are embedded into NDs through Fe ion-implantation and the crystal structure of NDs are recovered by thermal annealing. The results of TEM and Raman examinations indicated the crystal structure of the Fe implanted NDs is recovered completely. The SQUID-VSM measurement shows the Fe-NDs possess room temperature ferromagnetism. That means the Fe atoms are distributed inside the NDs without affecting NDs crystal structure, so the NDs can preserve the original physical and chemical properties of the NDs. In addition, the ion-implantation-introduced magnetic property might make the NDs to become suitable for variety of medical applications.

Monte Carlo simulation of elongating metallic nanowires in the presence of surfactants

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

Gimenez, M. Cecilia; Reinaudi, Luis, E-mail: luis.reinaudi@unc.edu.ar; Leiva, Ezequiel P. M.

2015-12-28

Nanowires of different metals undergoing elongation were studied by means of canonical Monte Carlo simulations and the embedded atom method representing the interatomic potentials. The presence of a surfactant medium was emulated by the introduction of an additional stabilization energy, represented by a parameter Q. Several values of the parameter Q and temperatures were analyzed. In general, it was observed for all studied metals that, as Q increases, there is a greater elongation before the nanowire breaks. In the case of silver, linear monatomic chains several atoms long formed at intermediate values of Q and low temperatures. Similar observations weremore » made for the case of silver-gold alloys when the medium interacted selectively with Ag.« less

First Principles Study on the CO Oxidation on Mn-Embedded Divacancy Graphene

PubMed Central

Jiang, Quanguo; Zhang, Jianfeng; Ao, Zhimin; Huang, Huajie; He, Haiyan; Wu, Yuping

2018-01-01

The CO oxidation mechanism on graphene with divacancy (DG) embedded with transition metal from Sc to Zn has been studied by using first principles calculations. The results indicate that O2 molecule is preferentially adsorbed on Sc, Ti, V, Cr, Mn, and Fe-DG, which can avoid the CO poisoning problem that many catalysts facing and is beneficial to the CO oxidation progress. Further study indicates that Mn-DG shows the best catalytic properties for CO oxidation with consideration of both Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) oxidation mechanisms. Along the ER mechanism, the reaction energy barrier for the first step (CO free + O2 pre-adsorbed → OOCO) is 0.96 eV. Along the LH mechanism, the energy barrier for the rate limiting step (CO adsorbed + O2 adsorbed → OOCO) is only 0.41 eV, indicating that the CO oxidation on Mn-DG will occur along LH mechanism. The Hirshfeld charge distributions of O2 and CO molecules is tuned by the embedded Mn atom, and the charge transfer from the embedded Mn atom to the adsorbed molecules plays an important role for the CO oxidation. The result shows that the Mn-embedded divacancy graphene is a noble-metal free and efficient catalyst for CO oxidation at low temperature.

A New Concurrent Multiscale Methodology for Coupling Molecular Dynamics and Finite Element Analyses

NASA Technical Reports Server (NTRS)

Yamakov, Vesselin; Saether, Erik; Glaessgen, Edward H/.

2008-01-01

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

The uniformity study of non-oxide thin film at device level using electron energy loss spectroscopy

NASA Astrophysics Data System (ADS)

Li, Zhi-Peng; Zheng, Yuankai; Li, Shaoping; Wang, Haifeng

2018-05-01

Electron energy loss spectroscopy (EELS) has been widely used as a chemical analysis technique to characterize materials chemical properties, such as element valence states, atoms/ions bonding environment. This study provides a new method to characterize physical properties (i.e., film uniformity, grain orientations) of non-oxide thin films in the magnetic device by using EELS microanalysis on scanning transmission electron microscope. This method is based on analyzing white line ratio of spectra and related extended energy loss fine structures so as to correlate it with thin film uniformity. This new approach can provide an effective and sensitive method to monitor/characterize thin film quality (i.e., uniformity) at atomic level for thin film development, which is especially useful for examining ultra-thin films (i.e., several nanometers) or embedded films in devices for industry applications. More importantly, this technique enables development of quantitative characterization of thin film uniformity and it would be a remarkably useful technique for examining various types of devices for industrial applications.

Molecular dynamic simulation study of plasma etching L10 FePt media in embedded mask patterning (EMP) process

NASA Astrophysics Data System (ADS)

Zhu, Jianxin; Quarterman, P.; Wang, Jian-Ping

2017-05-01

Plasma etching process of single-crystal L10-FePt media [H. Wang et al., Appl. Phys. Lett. 102(5) (2013)] is studied using molecular dynamic simulation. Embedded-Atom Method [M. S. Daw and M. I. Baskes, Phy. Rev. B 29, 6443 (1984); X. W. Zhou, R. A. Johnson and H. N. G. Wadley, Phy. Rev. B 69, 144113 (2004)] is used to calculate the interatomic potential within atoms in FePt alloy, and ZBL potential [J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon,1985] in comparison with conventional Lennard-Jones "12-6" potential is applied to interactions between etching gas ions and metal atoms. It is shown the post-etch structure defects can include amorphized surface layer and lattice interstitial point defects that caused by etchant ions passed through the surface layer. We show that the amorphized or damaged FePt lattice surface layer (or "magnetic dead-layer") thickness after etching increases with ion energy for Ar ion impacts, but significantly small for He ions at up to 250eV ion energy. However, we showed that He sputtering creates more interstitial defects at lower energy levels and defects are deeper below the surface compared to Ar sputtering. We also calculate the interstitial defect level and depth as dependence on ion energy for both Ar and He ions. Media magnetic property loss due to these defects is also discussed.

Solvation and Spectral Line Shifts of Chromium Atoms in Helium Droplets Based on a Density Functional Theory Approach

PubMed Central

2014-01-01

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y7P, a5S, and y5P excited states. The necessary Cr–He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z7P ← a7S, y7P ← a7S, z5P ← a5S, and y5P ← a5S are compared to recent fluorescence and photoionization experiments. PMID:24906160

Solvation and spectral line shifts of chromium atoms in helium droplets based on a density functional theory approach.

PubMed

Ratschek, Martin; Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2014-08-21

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y(7)P, a(5)S, and y(5)P excited states. The necessary Cr-He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z(7)P ← a(7)S, y(7)P ← a(7)S, z(5)P ← a(5)S, and y(5)P ← a(5)S are compared to recent fluorescence and photoionization experiments.

The embedded operating system project

NASA Technical Reports Server (NTRS)

Campbell, R. H.

1985-01-01

The design and construction of embedded operating systems for real-time advanced aerospace applications was investigated. The applications require reliable operating system support that must accommodate computer networks. Problems that arise in the construction of such operating systems, reconfiguration, consistency and recovery in a distributed system, and the issues of real-time processing are reported. A thesis that provides theoretical foundations for the use of atomic actions to support fault tolerance and data consistency in real-time object-based system is included. The following items are addressed: (1) atomic actions and fault-tolerance issues; (2) operating system structure; (3) program development; (4) a reliable compiler for path Pascal; and (5) mediators, a mechanism for scheduling distributed system processes.

Thermal conductance at atomically clean and disordered silicon/aluminum interfaces: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Ih Choi, Woon; Kim, Kwiseon; Narumanchi, Sreekant

2012-09-01

Thermal resistance between layers impedes effective heat dissipation in electronics packaging applications. Thermal conductance for clean and disordered interfaces between silicon (Si) and aluminum (Al) was computed using realistic Si/Al interfaces and classical molecular dynamics with the modified embedded atom method potential. These realistic interfaces, which include atomically clean as well as disordered interfaces, were obtained using density functional theory. At 300 K, the magnitude of interfacial conductance due to phonon-phonon scattering obtained from the classical molecular dynamics simulations was approximately five times higher than the conductance obtained using analytical elastic diffuse mismatch models. Interfacial disorder reduced the thermal conductance due to increased phonon scattering with respect to the atomically clean interface. Also, the interfacial conductance, due to electron-phonon scattering at the interface, was greater than the conductance due to phonon-phonon scattering. This indicates that phonon-phonon scattering is the bottleneck for interfacial transport at the semiconductor/metal interfaces. The molecular dynamics modeling predictions for interfacial thermal conductance for a 5-nm disordered interface between Si/Al were in-line with recent experimental data in the literature.

Molecular dynamics study of mechanical properties of carbon nanotube reinforced aluminum composites

NASA Astrophysics Data System (ADS)

Srivastava, Ashish Kumar; Mokhalingam, A.; Singh, Akhileshwar; Kumar, Dinesh

2016-05-01

Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for the interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young's modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young's modulus of the Al matrix up to 77 % as compared to pure Al.

Kohn-Sham potentials from electron densities using a matrix representation within finite atomic orbital basis sets

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

We revisit the static response function-based Kohn-Sham (KS) inversion procedure for determining the KS effective potential that corresponds to a given target electron density within finite atomic orbital basis sets. Instead of expanding the potential in an auxiliary basis set, we directly update the potential in its matrix representation. Through numerical examples, we show that the reconstructed density rapidly converges to the target density. Preliminary results are presented to illustrate the possibility of obtaining a local potential in real space from the optimized potential in its matrix representation. We have further applied this matrix-based KS inversion approach to density functional embedding theory. A proof-of-concept study of a solvated proton transfer reaction demonstrates the method's promise.

Atomic-scale Modeling of the Structure and Dynamics of Dislocations in Complex Alloys at High Temperatures

NASA Technical Reports Server (NTRS)

Daw, Murray S.; Mills, Michael J.

2003-01-01

We report on the progress made during the first year of the project. Most of the progress at this point has been on the theoretical and computational side. Here are the highlights: (1) A new code, tailored for high-end desktop computing, now combines modern Accelerated Dynamics (AD) with the well-tested Embedded Atom Method (EAM); (2) The new Accelerated Dynamics allows the study of relatively slow, thermally-activated processes, such as diffusion, which are much too slow for traditional Molecular Dynamics; (3) We have benchmarked the new AD code on a rather simple and well-known process: vacancy diffusion in copper; and (4) We have begun application of the AD code to the diffusion of vacancies in ordered intermetallics.

Electrical properties of films of zinc oxide nanoparticles and its hybrid with reduced graphene oxide

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

Madhuri, K. Priya; Bramhaiah, K.; John, Neena S., E-mail: jsneena@cnsms.res.in

Free-standing films of ZnO nanoparticles (NPs) and reduced graphene oxide (rGO)-ZnO NPs hybrid are prepared at a liquid/liquid interface. The films are characterized by UV-visible spectroscopy, X-ray diffraction, scanning electron microscopy and atomic force microscopy. ZnO film consists of spherical aggregated NPs while the hybrid film contains folded sheets of rGO with embedded ZnO NPs. Electrical properties of the films and its photoresponse in presence of UV radiation are investigated using current sensing atomic force microscopy (CSAFM) at nanoscale and bulk measurements using two probe methods. Enhancement in photocurrent is observed in both cases and the current imaging reveals anmore » inhomogeneous contribution by different ZnO grains in the film.« less

Computer simulation of liquid metals

NASA Astrophysics Data System (ADS)

Belashchenko, D. K.

2013-12-01

Methods for and the results of the computer simulation of liquid metals are reviewed. Two basic methods, classical molecular dynamics with known interparticle potentials and the ab initio method, are considered. Most attention is given to the simulated results obtained using the embedded atom model (EAM). The thermodynamic, structural, and diffusion properties of liquid metal models under normal and extreme (shock) pressure conditions are considered. Liquid-metal simulated results for the Groups I - IV elements, a number of transition metals, and some binary systems (Fe - C, Fe - S) are examined. Possibilities for the simulation to account for the thermal contribution of delocalized electrons to energy and pressure are considered. Solidification features of supercooled metals are also discussed.

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

Song, Jiaming; Hudak, Bethany M.; Sims, Hunter

One-dimensional (1D) nanostructures are highly sought after, both for their novel electronic properties as well as for their improved functionality. However, due to their nanoscale dimensions, these properties are significantly affected by the environment in which they are embedded. Here in this paper, we report on the creation of 1D homo-endotaxial Si nanostructures, i.e. 1D Si nanostructures with a lattice structure that is uniquely different from the Si diamond lattice in which they are embedded. We use scanning tunneling microscopy and spectroscopy, scanning transmission electron microscopy, density functional theory, and conductive atomic force microscopy to elucidate their formation and properties.more » Depending on kinetic constraints during growth, they can be prepared as endotaxial 1D Si nanostructures completely embedded in crystalline Si, or underneath a stripe of amorphous Si containing a large concentration of Bi atoms. Lastly, these homo-endotaxial 1D Si nanostructures have the potential to be useful components in nanoelectronic devices based on the technologically mature Si platform.« less

Homo-endotaxial one-dimensional Si nanostructures

DOE PAGES

Song, Jiaming; Hudak, Bethany M.; Sims, Hunter; ...

2017-11-29

One-dimensional (1D) nanostructures are highly sought after, both for their novel electronic properties as well as for their improved functionality. However, due to their nanoscale dimensions, these properties are significantly affected by the environment in which they are embedded. Here in this paper, we report on the creation of 1D homo-endotaxial Si nanostructures, i.e. 1D Si nanostructures with a lattice structure that is uniquely different from the Si diamond lattice in which they are embedded. We use scanning tunneling microscopy and spectroscopy, scanning transmission electron microscopy, density functional theory, and conductive atomic force microscopy to elucidate their formation and properties.more » Depending on kinetic constraints during growth, they can be prepared as endotaxial 1D Si nanostructures completely embedded in crystalline Si, or underneath a stripe of amorphous Si containing a large concentration of Bi atoms. Lastly, these homo-endotaxial 1D Si nanostructures have the potential to be useful components in nanoelectronic devices based on the technologically mature Si platform.« less

A Locality-Constrained and Label Embedding Dictionary Learning Algorithm for Image Classification.

PubMed

Zhengming Li; Zhihui Lai; Yong Xu; Jian Yang; Zhang, David

2017-02-01

Locality and label information of training samples play an important role in image classification. However, previous dictionary learning algorithms do not take the locality and label information of atoms into account together in the learning process, and thus their performance is limited. In this paper, a discriminative dictionary learning algorithm, called the locality-constrained and label embedding dictionary learning (LCLE-DL) algorithm, was proposed for image classification. First, the locality information was preserved using the graph Laplacian matrix of the learned dictionary instead of the conventional one derived from the training samples. Then, the label embedding term was constructed using the label information of atoms instead of the classification error term, which contained discriminating information of the learned dictionary. The optimal coding coefficients derived by the locality-based and label-based reconstruction were effective for image classification. Experimental results demonstrated that the LCLE-DL algorithm can achieve better performance than some state-of-the-art algorithms.

Mathematical modeling of the crack growth in linear elastic isotropic materials by conventional fracture mechanics approaches and by molecular dynamics method: crack propagation direction angle under mixed mode loading

NASA Astrophysics Data System (ADS)

Stepanova, Larisa; Bronnikov, Sergej

2018-03-01

The crack growth directional angles in the isotropic linear elastic plane with the central crack under mixed-mode loading conditions for the full range of the mixity parameter are found. Two fracture criteria of traditional linear fracture mechanics (maximum tangential stress and minimum strain energy density criteria) are used. Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-scale Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is Embedded Atom Method (EAM) potential. The plane specimens with initial central crack were subjected to Mixed-Mode loadings. The simulation cell contains 400000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide diapason of temperatures (from 0.1 К to 800 К) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics method coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields.

On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation

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

Fu, Yao, E-mail: fu5@mailbox.sc.edu, E-mail: jhsong@cec.sc.edu; Song, Jeong-Hoon, E-mail: fu5@mailbox.sc.edu, E-mail: jhsong@cec.sc.edu

2014-08-07

Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifiesmore » the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.« less

Extending the accuracy of the SNAP interatomic potential form

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

Wood, Mitchell A.; Thompson, Aidan P.

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functionsmore » in EAM. It is also argued that the quadratic SNAP form is a special case of an artificial neural network (ANN). The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similarly to ANN potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting, as measured by cross-validation analysis.« less

Extending the accuracy of the SNAP interatomic potential form

DOE PAGES

Wood, Mitchell A.; Thompson, Aidan P.

2018-03-28

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functionsmore » in EAM. It is also argued that the quadratic SNAP form is a special case of an artificial neural network (ANN). The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similarly to ANN potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting, as measured by cross-validation analysis.« less

Critical assessment of Pt surface energy - An atomistic study

NASA Astrophysics Data System (ADS)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

Atomistic modeling of Mg/Nb interfaces: shear strength and interaction with lattice glide dislocations

DOE PAGES

Yadav, Satyesh Kumar; Shao, S.; Chen, Youxing; ...

2017-10-17

Here, using a newly developed embedded-atom-method potential for Mg–Nb, the semi-coherent Mg/Nb interface with the Kurdjumov–Sachs orientation relationship is studied. Atomistic simulations have been carried out to understand the shear strength of the interface, as well as the interaction between lattice glide dislocations and the interface. The interface shear mechanisms are dependent on the shear loading directions, through either interface sliding between Mg and Nb atomic layers or nucleation and gliding of Shockley partial dislocations in between the first two atomic planes in Mg at the interface. The shear strength for the Mg/Nb interface is found to be generally high,more » in the range of 0.9–1.3 GPa depending on the shear direction. As a consequence, the extents of dislocation core spread into the interface are considerably small, especially when compared to the case of other “weak” interfaces such as the Cu/Nb interface.« less

Molecular dynamics for near melting temperatures simulations of metals using modified embedded-atom method

NASA Astrophysics Data System (ADS)

Etesami, S. Alireza; Asadi, Ebrahim

2018-01-01

Availability of a reliable interatomic potential is one of the major challenges in utilizing molecular dynamics (MD) for simulations of metals at near the melting temperatures and melting point (MP). Here, we propose a novel approach to address this challenge in the concept of modified-embedded-atom (MEAM) interatomic potential; also, we apply the approach on iron, nickel, copper, and aluminum as case studies. We propose adding experimentally available high temperature elastic constants and MP of the element to the list of typical low temperature properties used for the development of MD interatomic potential parameters. We show that the proposed approach results in a reasonable agreement between the MD calculations of melting properties such as latent heat, expansion in melting, liquid structure factor, and solid-liquid interface stiffness and their experimental/computational counterparts. Then, we present the physical properties of mentioned elements near melting temperatures using the new MEAM parameters. We observe that the behavior of elastic constants, heat capacity and thermal linear expansion coefficient at room temperature compared to MP follows an empirical linear relation (α±β × MP) for transition metals. Furthermore, a linear relation between the tetragonal shear modulus and the enthalpy change from room temperature to MP is observed for face-centered cubic materials.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-01

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ɛ(r) is close to one everywhere inside the protein. The Gaussian widths σi of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σi. A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description.

PubMed

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-14

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

A Statistical Approach for the Concurrent Coupling of Molecular Dynamics and Finite Element Methods

NASA Technical Reports Server (NTRS)

Saether, E.; Yamakov, V.; Glaessgen, E.

2007-01-01

Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, increasing the size of the MD domain quickly presents intractable computational demands. A robust approach to surmount this computational limitation has been to unite continuum modeling procedures such as the finite element method (FEM) with MD analyses thereby reducing the region of atomic scale refinement. The challenging problem is to seamlessly connect the two inherently different simulation techniques at their interface. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the typical boundary value problem used to define a coupled domain. The method uses statistical averaging of the atomistic MD domain to provide displacement interface boundary conditions to the surrounding continuum FEM region, which, in return, generates interface reaction forces applied as piecewise constant traction boundary conditions to the MD domain. The two systems are computationally disconnected and communicate only through a continuous update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM) as opposed to a direct coupling method where interface atoms and FEM nodes are individually related. The methodology is inherently applicable to three-dimensional domains, avoids discretization of the continuum model down to atomic scales, and permits arbitrary temperatures to be applied.

Conductivity and structure of ErAs nanoparticles embedded in GaAs pn junctions analyzed via conductive atomic force microscopy

NASA Astrophysics Data System (ADS)

Park, K. W.; Dasika, V. D.; Nair, H. P.; Crook, A. M.; Bank, S. R.; Yu, E. T.

2012-06-01

We have used conductive atomic force microscopy to investigate the influence of growth temperature on local current flow in GaAs pn junctions with embedded ErAs nanoparticles grown by molecular beam epitaxy. Three sets of samples, one with 1 ML ErAs deposited at different growth temperatures and two grown at 530 °C and 575 °C with varying ErAs depositions, were characterized. Statistical analysis of local current images suggests that the structures grown at 575 °C have about 3 times thicker ErAs nanoparticles than structures grown at 530 °C, resulting in degradation of conductivity due to reduced ErAs coverage. These findings explain previous studies of macroscopic tunnel junctions.

Synthesis of Ag and Au nanoparticles embedded in carbon film: Optical, crystalline and topography analysis

NASA Astrophysics Data System (ADS)

Gholamali, Hediyeh; Shafiekhani, Azizollah; Darabi, Elham; Elahi, Seyed Mohammad

2018-03-01

Atomic force microscopy (AFM) images give valuable information about surface roughness of thin films based on the results of power spectral density (PSD) through the fast Fourier transform (FFT) algorithms. In the present work, AFM data are studied for silver and gold nanoparticles (Ag NPs a-C: H and Au NPs a-C: H) embedded in amorphous hydrogenated carbon films and co-deposited on glass substrate via of RF-Sputtering and RF-Plasma Enhanced Chemical Vapor Deposition methods. Here, the working gas is acetylene and the targets are Ag and Au. While time and power are constant, the only variable parameter in this study is initial pressure. In addition, the crystalline structure of Ag NPs a-C: H and Au NPs a-C: H are studied using X-ray diffraction (XRD). UV-visible spectrophotometry will also investigate optical properties and localized surface plasmon resonance (LSPR) of samples.

Fragmentation dynamics of ionized neon clusters (Ne(n), n=3-14) embedded in helium nanodroplets.

PubMed

Bonhommeau, David; Halberstadt, Nadine; Viel, Alexandra

2006-01-14

We report a theoretical study of the nonadiabatic fragmentation dynamics of ionized neon clusters embedded in helium nanodroplets for cluster sizes up to n=14 atoms. The dynamics of the neon atoms is modeled using the molecular dynamics with quantum transitions method of Tully [J. Chem. Phys. 93, 1061 (1990)] with the nuclei treated classically and transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model to which induced dipole-induced dipole interactions are added. The effect of the spin-orbit interaction is also discussed. The helium environment is modeled by a friction force acting on charged atoms whose speed exceeds the critical Landau velocity. The dependence of the fragment size distribution on the friction strength and on the initial nanodroplet size is investigated. By comparing with the available experimental data obtained for Ne3+ and Ne4+, a reasonable value for the friction coefficient, the only parameter of the model, is deduced. This value is then used to predict the effect of the helium environment on the dissociation dynamics of larger neon clusters, n=5-14. The results show stabilization of larger fragments than in the gas phase, but fragmentation is not completely caged. In addition, two types of dynamics are characterized for Ne4+: fast and explosive, therefore leaving no time for friction to cool down the process when dynamics starts on one of the highest electronic states, and slower, therefore leading to some stabilization by helium when it starts on one of the lowest electronic states.

Analytic modified embedded atom potentials for HCP metals

NASA Astrophysics Data System (ADS)

Hu, Wangyu; Zhang, Bangwei; Huang, Baiyun; Gao, Fei; Bacon, David J.

2001-02-01

Analytic modified embedded atom method (AMEAM) type many-body potentials have been constructed for ten hcp metals: Be, Co, Hf, Mg, Re, Ru, Sc, Ti, Y and Zr. The potentials are parametrized using analytic functions and fitted to the cohesive energy, unrelaxed vacancy formation energy, five independent second-order elastic constants and two equilibrium conditions. Hence, each of the constructed potentials represents a stable hexagonal close-packed lattice with a particular non-ideal c/a ratio. In order to treat the metals with negative Cauchy pressure, a modified term has been added to the total energy. For all the metals considered, the hcp lattice is shown to be energetically most stable when compared with the fcc and bcc structure and the hcp lattice with ideal c/a. The activation energy for vacancy diffusion in these metals has been calculated. They agree well with experimental data available and those calculated by other authors for both monovacancy and divacancy mechanisms and the most possible diffusion paths are predicted. Stacking fault and surface energy have also been calculated and their values are lower than typical experimental data. Finally, the self-interstitial atom (SIA) formation energy and volume have been evaluated for eight possible sites. This calculation suggests that the basal split or crowdion is the most stable configuration for metals with a rather large deviation from the ideal c/a value and the non-basal dumbbell (C or S) is the most stable configuration for metals with c/a near ideal. The relationship between SIA formation energy and melting temperature roughly obeys a linear relation for most metals except Ru and Re.

One- and Two-Color Resonant Photoionization Spectroscopy of Chromium-Doped Helium Nanodroplets

PubMed Central

2014-01-01

We investigate the photoinduced relaxation dynamics of Cr atoms embedded into superfluid helium nanodroplets. One- and two-color resonant two-photon ionization (1CR2PI and 2CR2PI, respectively) are applied to study the two strong ground state transitions z7P2,3,4° ← a7S3 and y7P2,3,4° ← a7S3. Upon photoexcitation, Cr* atoms are ejected from the droplet in various excited states, as well as paired with helium atoms as Cr*–Hen exciplexes. For the y7P2,3,4° intermediate state, comparison of the two methods reveals that energetically lower states than previously identified are also populated. With 1CR2PI we find that the population of ejected z5P3° states is reduced for increasing droplet size, indicating that population is transferred preferentially to lower states during longer interaction with the droplet. In the 2CR2PI spectra we find evidence for generation of bare Cr atoms in their septet ground state (a7S3) and metastable quintet state (a5S2), which we attribute to a photoinduced fast excitation–relaxation cycle mediated by the droplet. A fraction of Cr atoms in these ground and metastable states is attached to helium atoms, as indicated by blue wings next to bare atom spectral lines. These relaxation channels provide new insight into the interaction of excited transition metal atoms with helium nanodroplets. PMID:24708058

Effect of interstitial and substitution alloying elements on the intrinsic stacking fault energy of nanocrystalline fcc-iron by atomistic simulation study

NASA Astrophysics Data System (ADS)

Mohammadzadeh, Mina; Mohammadzadeh, Roghayeh

2017-11-01

The stacking fault energy (SFE) is an important parameter in the deformation mechanism of face centered cubic (fcc) iron-based alloy. In this study, the effect of interstitial (C and N) and substitution (Nb and Ti) alloying elements on the intrinsic SFE (ISFE) of nanocrystalline iron were investigated via molecular dynamics (MD) simulation. The modified embedded atom method (MEAM) inter-atomic potential was used in the MD simulations. The results demonstrate a strong dependence of ISFE with addition of interstitial alloying elements but only a mild increase in ISFE with addition of substitution alloying elements in the composition range of 0 < {CNb, CTi} < 3 (at%). Moreover, it is shown that alloying of fcc iron with N decreases ISFE, whereas it increases significantly by addition of carbon element [0 < {CC, CN} < 3.5 (at%)]. The simulation method employed in this work shows reasonable agreement with some published experimental/calculated data.

Hybrid quantum and molecular mechanics embedded cluster models for chemistry on silicon and silicon carbide surfaces

NASA Astrophysics Data System (ADS)

Shoemaker, James Richard

Fabrication of silicon carbide (SiC) semiconductor devices are of interest for aerospace applications because of their high-temperature tolerance. Growth of an insulating SiO2 layer on SiC by oxidation is a poorly understood process, and sometimes produces interface defects that degrade device performance. Accurate theoretical models of surface chemistry, using quantum mechanics (QM), do not exist because of the huge computational cost of solving Schrodinger's equation for a molecular cluster large enough to represent a surface. Molecular mechanics (MM), which describes a molecule as a collection of atoms interacting through classical potentials, is a fast computational method, good at predicting molecular structure, but cannot accurately model chemical reactions. A new hybrid QM/MM computational method for surface chemistry was developed and applied to silicon and SiC surfaces. The addition of MM steric constraints was shown to have a large effect on the energetics of O atom adsorption on SiC. Adsorption of O atoms on Si-terminated SiC(111) favors above surface sites, in contrast to Si(111), but favors subsurface adsorption sites on C- terminated SiC(111). This difference, and the energetics of C atom etching via CO2 desorption, can explain the observed poor performance of SiC devices in which insulating layers were grown on C-terminated surfaces.

Semiclassical neutral atom as a reference system in density functional theory.

PubMed

Constantin, Lucian A; Fabiano, E; Laricchia, S; Della Sala, F

2011-05-06

We use the asymptotic expansions of the semiclassical neutral atom as a reference system in density functional theory to construct accurate generalized gradient approximations (GGAs) for the exchange-correlation and kinetic energies without any empiricism. These asymptotic functionals are among the most accurate GGAs for molecular systems, perform well for solid state, and overcome current GGA state of the art in frozen density embedding calculations. Our results also provide evidence for the conjointness conjecture between exchange and kinetic energies of atomic systems.

Single-Atom Pt as Co-Catalyst for Enhanced Photocatalytic H2 Evolution.

PubMed

Li, Xiaogang; Bi, Wentuan; Zhang, Lei; Tao, Shi; Chu, Wangsheng; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi

2016-03-23

Isolated single-atom platinum (Pt) embedded in the sub-nanoporosity of 2D g-C3 N4 as a new form of co-catalyst is reported. The highly stable single-atom co-catalyst maximizes the atom efficiency and alters the surface trap states of g-C3 N4 , leading to significantly enhanced photocatalytic H2 evolution activity, 8.6 times higher than that of Pt nanoparticles and up to 50 times that for bare g-C3 N4 . © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The application of an atomistic J-integral to a ductile crack.

PubMed

Zimmerman, Jonathan A; Jones, Reese E

2013-04-17

In this work we apply a Lagrangian kernel-based estimator of continuum fields to atomic data to estimate the J-integral for the emission dislocations from a crack tip. Face-centered cubic (fcc) gold and body-centered cubic (bcc) iron modeled with embedded atom method (EAM) potentials are used as example systems. The results of a single crack with a K-loading compare well to an analytical solution from anisotropic linear elastic fracture mechanics. We also discovered that in the post-emission of dislocations from the crack tip there is a loop size-dependent contribution to the J-integral. For a system with a finite width crack loaded in simple tension, the finite size effects for the systems that were feasible to compute prevented precise agreement with theory. However, our results indicate that there is a trend towards convergence.

Development and application of QM/MM methods to study the solvation effects and surfaces

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

Dibya, Pooja Arora

2010-01-01

Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize themore » computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this work. Chapter 2 illustrates the methodology of the interface of the EFP method with the configuration interaction with single excitations (CIS) method to study solvent effects in excited states. Chapter 3 discusses the study of the adiabatic electron affinity of the hydroxyl radical in aqueous solution and in micro-solvated clusters using a QM/EFP method. Chapter 4 describes the study of etching and diffusion of oxygen atom on a reconstructed Si(100)-2 x 1 surface using a hybrid QM/MM embedded cluster model (SIMOMM). Chapter 4 elucidates the application of the EFP method towards the understanding of the aqueous ionization potential of Na atom. Finally, a general conclusion of this dissertation work and prospective future direction are presented in Chapter 6.« less

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

Atomic theory of viscoelastic response and memory effects in metallic glasses

NASA Astrophysics Data System (ADS)

Cui, Bingyu; Yang, Jie; Qiao, Jichao; Jiang, Minqiang; Dai, Lanhong; Wang, Yun-Jiang; Zaccone, Alessio

2017-09-01

An atomic-scale theory of the viscoelastic response of metallic glasses is derived from first principles, using a Zwanzig-Caldeira-Leggett system-bath Hamiltonian as a starting point within the framework of nonaffine linear response to mechanical deformation. This approach provides a generalized Langevin equation (GLE) as the average equation of motion for an atom or ion in the material, from which non-Markovian nonaffine viscoelastic moduli are extracted. These can be evaluated using the vibrational density of states (DOS) as input, where the boson peak plays a prominent role in the mechanics. To compare with experimental data for binary ZrCu alloys, a numerical DOS was obtained from simulations of this system, which also take electronic degrees of freedom into account via the embedded-atom method for the interatomic potential. It is shown that the viscoelastic α -relaxation, including the α -wing asymmetry in the loss modulus, can be very well described by the theory if the memory kernel (the non-Markovian friction) in the GLE is taken to be a stretched-exponential decaying function of time. This finding directly implies strong memory effects in the atomic-scale dynamics and suggests that the α -relaxation time is related to the characteristic time scale over which atoms retain memory of their previous collision history. This memory time grows dramatically below the glass transition.

Mechanistic insight into the enhanced photocatalytic activity of single-atom Pt, Pd or Au-embedded g-C3N4

NASA Astrophysics Data System (ADS)

Tong, Tong; Zhu, Bicheng; Jiang, Chuanjia; Cheng, Bei; Yu, Jiaguo

2018-03-01

Single atoms of platinum (Pt), palladium (Pd) or gold (Au) trapped by two-dimensional graphitic carbon nitride (g-C3N4) exhibit superior photocatalytic performance. However, the underlying mechanism of single-atom noble metal/g-C3N4 photocatalytic system is still unclear. Herein, the structural, electronic and optical properties of single-atom Pt, Pd and Au loaded on bilayer g-C3N4 (BL-g-C3N4) substrate were investigated by density functional theory (DFT) simulations. The results indicate that single-atom Pt/Pd/Au loading can significantly narrow the band gap of g-C3N4 and thus increase its light absorption in the visible-light region. Rather than being adsorbed on the surface, Pt and Pd atoms tend to be embedded into g-C3N4 interlayer and act as bridges to facilitate the interlayer charge carrier transfer due to the effects of conduction band offset. In particular, an internal electric field is generated in Pt/BL-g-C3N4, which is further beneficial for separating charge carrier of photoexcited g-C3N4. By contrast, Au can only be adsorbed on the g-C3N4 surface (in the six-fold cavity) and deliver a limited amount of charge carrier excited in the N-conjugated aromatic pore of g-C3N4 surface. Our finding is conducive to understanding the interactive relationship between single-atom noble metal co-catalysts and g-C3N4 and to the design of high-efficiency photocatalyst.

Positron confinement in embedded lithium nanoclusters

NASA Astrophysics Data System (ADS)

van Huis, M. A.; van Veen, A.; Schut, H.; Falub, C. V.; Eijt, S. W.; Mijnarends, P. E.; Kuriplach, J.

2002-02-01

Quantum confinement of positrons in nanoclusters offers the opportunity to obtain detailed information on the electronic structure of nanoclusters by application of positron annihilation spectroscopy techniques. In this work, positron confinement is investigated in lithium nanoclusters embedded in monocrystalline MgO. These nanoclusters were created by means of ion implantation and subsequent annealing. It was found from the results of Doppler broadening positron beam analysis that approximately 92% of the implanted positrons annihilate in lithium nanoclusters rather than in the embedding MgO, while the local fraction of lithium at the implantation depth is only 1.3 at. %. The results of two-dimensional angular correlation of annihilation radiation confirm the presence of crystalline bulk lithium. The confinement of positrons is ascribed to the difference in positron affinity between lithium and MgO. The nanocluster acts as a potential well for positrons, where the depth of the potential well is equal to the difference in the positron affinities of lithium and MgO. These affinities were calculated using the linear muffin-tin orbital atomic sphere approximation method. This yields a positronic potential step at the MgO||Li interface of 1.8 eV using the generalized gradient approximation and 2.8 eV using the insulator model.

Magnetism from Fe2O3 nanoparticles embedded in amorphous SiO2 matrix

NASA Astrophysics Data System (ADS)

Sendil Kumar, A.; Bhatnagar, Anil K.

2018-02-01

Fe2O3 nanoparticles are embedded in amorphous SiO2 matrix by coprecipitation method with varying concentrations. Conditions are optimized to get almost monodispersed Fe2O3 nanoparticles with high chemical stability. Microstructure of synthesized nanoparticles is well characterized and found that Fe2O3 is in nanocrystalline form and embedded uniformly in amorphous SiO2 matrix. Enhanced surface reactivity is found for nanoparticles which influences physical properties of the SiO2 supported Fe2O3 system due to adsorption. In oxide nanoparticles, significant number of defect sites at the surface is expected but when supported medium such as SiO2 it reduces this defect concentration. Field- and temperature-dependent magnetisation studies on these samples show superparamagnetic behaviour. Superparamagnetic behaviour is seen in all the concentration systems but the coercivity observed in the lower concentration systems is found to be anomalous compared to that of higher concentrations. The observed magnetic behaviour comes from either unsaturated bond existing due to the absence of anions at the surface of nanoparticles or reconstruction of atomic orbitals taking place at interface of Fe2O3-SiO2 system.

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap

NASA Astrophysics Data System (ADS)

Spiwok, Vojtěch; Králová, Blanka

2011-12-01

Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling.

Au-Ge MEAM potential fitted to the binary phase diagram

NASA Astrophysics Data System (ADS)

Wang, Yanming; Santana, Adriano; Cai, Wei

2017-02-01

We have developed a modified embedded atom method potential for the gold-germanium (Au-Ge) binary system that is fitted to the experimental binary phase diagram. The phase diagram is obtained from the common tangent construction of the free energy curves calculated by the adiabatic switching method. While maintaining the accuracy of the melting points of pure Au and Ge, this potential reproduces the eutectic temperature, eutectic composition and the solubility of Ge in solid Au, all in good agreement with the experimental values. To demonstrate the self-consistency of the potential, we performed benchmark molecular dynamics simulations of Ge crystal growth and etching in contact with a Au-Ge liquid alloy.

Molecular dynamics study of the melting curve of NiTi alloy under pressure

NASA Astrophysics Data System (ADS)

Zeng, Zhao-Yi; Hu, Cui-E.; Cai, Ling-Cang; Chen, Xiang-Rong; Jing, Fu-Qian

2011-02-01

The melting curve of NiTi alloy was predicted by using molecular dynamics simulations combining with the embedded atom model potential. The calculated thermal equation of state consists well with our previous results obtained from quasiharmonic Debye approximation. Fitting the well-known Simon form to our Tm data yields the melting curves for NiTi: 1850(1 + P/21.938)0.328 (for one-phase method) and 1575(1 + P/7.476)0.305 (for two-phase method). The two-phase simulations can effectively eliminate the superheating in one-phase simulations. At 1 bar, the melting temperature of NiTi is 1575 ± 25 K and the corresponding melting slope is 64 K/GPa.

Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

PubMed

Arshad, Junaid; Hoffmann, Alexander; Gesing, Sandra; Grunzke, Richard; Krüger, Jens; Kiss, Tamas; Herres-Pawlis, Sonja; Terstyanszky, Gabor

2016-01-01

In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Graphical AbstractMeta-workflows and embedded workflows in the template representation.

Low-power embedded read-only memory using atom switch and silicon-on-thin-buried-oxide transistor

NASA Astrophysics Data System (ADS)

Sakamoto, Toshitsugu; Tada, Munehiro; Tsuji, Yukihide; Makiyama, Hideki; Hasegawa, Takumi; Yamamoto, Yoshiki; Okanishi, Shinobu; Banno, Naoki; Miyamura, Makoto; Okamoto, Koichiro; Iguchi, Noriyuki; Ogasahara, Yasuhiro; Oda, Hidekazu; Kamohara, Shiro; Yamagata, Yasushi; Sugii, Nobuyuki; Hada, Hiromitsu

2015-04-01

We developed an atom-switch read-only memory (ROM) fabricated on silicon-on-thin-buried-oxide (SOTB) for use in a low-power microcontroller for the first time. An atom switch with a low programming voltage and large ON/OFF conductance ratio is suitable for low-power nonvolatile memory. The atom-switch ROM using an SOTB transistor uses a 0.34-1.2 V operating voltage and 12 µA/MHz active current (or 4.5 µW/MHz active power). Furthermore, the sleep current is as low as 0.4 µA when a body bias voltage is applied to the SOTB.

Macrocycles inserted in graphene: from coordination chemistry on graphene to graphitic carbon oxide.

NASA Astrophysics Data System (ADS)

Liu, Wei; Liu, Jingyao; Miao, Maosheng

Tuning the electronic structure and the chemical properties of graphene by binding with metals has become a focus in the area of two dimension materials. Despite many interesting results and promising potentials, the approach suffers from weak binding and the high reactivity of the metal atoms. On the other hand, many macrocyclic molecules such as crown ether show strong and selective binding with metal atoms. The alliance of the two substances will largely benefit the two parallel fields: it will provide a scaffold for coordination chemistry as well as a controllable method for tuning the electronic structure of graphene through strong binding with metals. Here, using crown ether as an example, we demonstrate by first principles calculations that the embedment of macrocyclic molecules into graphene honeycomb lattice can be very thermochemically favored. The embedment of crown ether on graphene can form a family of new two-dimensional materials that possess varying band gaps and band edges. The one with highest O composition (C2O), with similar structure features as graphilic C3N4, shows strong potentials for photolysis and as true two-dimensional superconductor while binding with alkali metals. Calculations are performed on NSF-funded XSEDE resources (TG-DMR130005). This research is also supported by National Natural Science Foundation of China (Grants No. 21373098) in China.

New mechanisms of cluster diffusion on metal fcc(100) surfaces

NASA Astrophysics Data System (ADS)

Trushin, Oleg; Salo, Petri; Alatalo, Matti; Ala-Nissila, Tapio

2001-03-01

We have studied atomic mechanisms of the diffusion of small clusters on the fcc(100) metal surfaces using semi-empirical and ab-initio molecular static calculations. Primary goal of these studies was to investigate possible many-body mechanisms of cluster motion which can contribute to low temperature crystal growth. We used embedded atom and Glue potentials in semi-empirical simulations of Cu and Al. Combination of the Nudged Elastic Band and Eigenvector Following methods allowed us to find all the possible transition paths for cluster movements on flat terrace. In case of Cu(001) we have found several new mechanisms for diffusion of clusters, including mechanisms called row-shearing and dimer-rotating in which a whole row inside an island moves according to a concerted jump and a dimer rotates at the periphery of an island, respectively. In some cases these mechanisms yield a lower energy barrier than the standard mechanisms.

Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate

NASA Astrophysics Data System (ADS)

Khoshouei, Maryam; Radjainia, Mazdak; Baumeister, Wolfgang; Danev, Radostin

2017-06-01

With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with the intrinsically low contrast and beam-induced motion of radiation-sensitive organic materials embedded in amorphous ice, and hence they have enabled the structure determination of many macromolecular assemblies to atomic or near-atomic resolution. Nevertheless, there are still limitations and one of them is the size of the target structure. Here, we report the use of a Volta phase plate in determining the structure of human haemoglobin (64 kDa) at 3.2 Å. Our results demonstrate that this method can be applied to complexes that are significantly smaller than those previously studied by conventional defocus-based approaches. Cryo-EM is now close to becoming a fast and cost-effective alternative to crystallography for high-resolution protein structure determination.

What is the copper thin film thickness effect on thermal properties of NiTi/Cu bi-layer?

NASA Astrophysics Data System (ADS)

Fazeli, Sara; Vahedpour, Morteza; Khatiboleslam Sadrnezhaad, Sayed

2017-02-01

Molecular dynamics (MD) simulation was used to study of thermal properties of NiTi/Cu. Embedded atom method (EAM) potentials for describing of inter-atomic interaction and Nose-Hoover thermostat and barostat are employed. The melting of the bi-layers was considered by studying the temperature dependence of the cohesive energy and mean square displacement. To highlight the differences between bi-layers with various copper layer thickness, the effect of copper film thickness on thermal properties containing the cohesive energy, melting point, isobaric heat capacity and latent heat of fusion was estimated. The results show that thermal properties of bi-layer systems are higher than that of their corresponding of pure NiTi. But, these properties of bi-layer systems approximately are independent of copper film thicknesses. The mean square displacement (MSD) results show that, the diffusion coefficients enhance upon increasing of copper film thickness in a linear performance.

A molecular dynamics study of the role of pressure on the response of reactive materials to thermal initiation

NASA Astrophysics Data System (ADS)

Weingarten, N. Scott; Mattson, William D.; Yau, Anthony D.; Weihs, Timothy P.; Rice, Betsy M.

2010-05-01

To elucidate the mechanisms of energy release in a reacting nickel/aluminum bilayer, we simulate the exothermic alloying reactions using both microcanonical and isoenthalpic-isobaric molecular dynamics simulations and an embedded-atom method type potential. The mechanism of the mixing consists of a sequence of steps in which mixing and reaction first occurs at the interface; the resulting heat generated from the mixing then melts the Al layer; subsequent mixing leads to further heat generation after which the Ni layer melts. The mixing continues until the alloying reactions are completed. The results indicate that pressure has a significant influence on the rates of atomic mixing and alloying reactions. Local pressures and temperatures within the individual layers at the time of melting are calculated, and these results are compared with the pressure-dependent melting curves determined for pure Al and pure Ni using this interaction potential.

Calculation of spontaneous emission from a V-type three-level atom in photonic crystals using fractional calculus

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

Huang, Chih-Hsien; Hsieh, Wen-Feng; Institute of Electro-Optical Science and Engineering, National Cheng Kung University, 1 Dahsueh Rd., Tainan 701, Taiwan

2011-07-15

Fractional time derivative, an abstract mathematical operator of fractional calculus, is used to describe the real optical system of a V-type three-level atom embedded in a photonic crystal. A fractional kinetic equation governing the dynamics of the spontaneous emission from this optical system is obtained as a fractional Langevin equation. Solving this fractional kinetic equation by fractional calculus leads to the analytical solutions expressed in terms of fractional exponential functions. The accuracy of the obtained solutions is verified through reducing the system into the special cases whose results are consistent with the experimental observation. With accurate physical results and avoidingmore » the complex integration for solving this optical system, we propose fractional calculus with fractional time derivative as a better mathematical method to study spontaneous emission dynamics from the optical system with non-Markovian dynamics.« less

Thermophysical properties of liquid Ni around the melting temperature from molecular dynamics simulation

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

Rozas, R. E.; Department of Physics, University of Bío-Bío, Av. Collao 1202, P.O. Box 5C, Concepción; Demiraǧ, A. D.

Thermophysical properties of liquid nickel (Ni) around the melting temperature are investigated by means of classical molecular dynamics (MD) simulation, using three different embedded atom method potentials to model the interactions between the Ni atoms. Melting temperature, enthalpy, static structure factor, self-diffusion coefficient, shear viscosity, and thermal diffusivity are compared to recent experimental results. Using ab initio MD simulation, we also determine the static structure factor and the mean-squared displacement at the experimental melting point. For most of the properties, excellent agreement is found between experiment and simulation, provided the comparison relative to the corresponding melting temperature. We discuss themore » validity of the Hansen-Verlet criterion for the static structure factor as well as the Stokes-Einstein relation between self-diffusion coefficient and shear viscosity. The thermal diffusivity is extracted from the autocorrelation function of a wavenumber-dependent temperature fluctuation variable.« less

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

Zhu, Bo; Zhao, Hongwei, E-mail: hwzhao@jlu.edu.cn, E-mail: khl69@163.com; Zhao, Dan

It has always been a critical issue to understand the material removal behavior of Vibration-Assisted Machining (VAM), especially on atomic level. To find out the effects of vibration frequency on material removal response, a three-dimensional molecular dynamics (MD) model has been established in this research to investigate the effects of scratched groove, crystal defects on the surface quality, comparing with the Von Mises shear strain and tangential force in simulations during nano-scratching process. Comparisons are made among the results of simulations from different vibration frequency with the same scratching feed, depth, amplitude and crystal orientation. Copper potential in this simulationmore » is Embedded-Atom Method (EAM) potential. Interaction between copper and carbon atoms is Morse potential. Simulational results show that higher frequency can make groove smoother. Simulation with high frequency creates more dislocations to improve the machinability of copper specimen. The changing frequency does not have evident effects on Von Mises shear strain. Higher frequency can decrease the tangential force to reduce the consumption of cutting energy and tool wear. In conclusion, higher vibration frequency in VAM on mono-crystalline copper has positive effects on surface finish, machinablility and tool wear reduction.« less

Phase separation in SiGe nanocrystals embedded in SiO{sub 2} matrix during high temperature annealing

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

Mogaddam, N. A. P.; Turan, R.; Alagoz, A. S.

2008-12-15

SiGe nanocrystals have been formed in SiO{sub 2} matrix by cosputtering Si, Ge, and SiO{sub 2} independently on Si substrate. Effects of the annealing time and temperature on structural and compositional properties are studied by transmission electron microscopy, x-ray diffraction (XRD), and Raman spectroscopy measurements. It is observed that Ge-rich Si{sub (1-x)}Ge{sub x} nanocrystals do not hold their compositional uniformity when annealed at high temperatures for enough long time. A segregation process leading to separation of Ge and Si atoms from each other takes place. This process has been evidenced by a double peak formation in the XRD and Ramanmore » spectra. We attributed this phase separation to the differences in atomic size, surface energy, and surface diffusion disparity between Si and Ge atoms leading to the formation of nonhomogenous structure consist of a Si-rich SiGe core covered by a Ge-rich SiGe shell. This experimental observation is consistent with the result of reported theoretical and simulation methods.« less

Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

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

Kryzhevich, Dmitrij S., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Zolnikov, Konstantin P., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Abdrashitov, Andrei V.

2014-11-14

A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

Edge cracks in nickel and aluminium single crystals: A molecular dynamics study

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

Chandra, Sagar, E-mail: sagarc@barc.gov.in; Chavan, V. M.; Patel, R. J.

A molecular dynamics study of edge cracks in Ni and Al single crystals under mode-I loading conditions is presented. Simulations are performed using embedded-atom method potentials for Ni and Al at a temperature of 0.5 K. The results reveal that Ni and Al show different fracture mechanisms. Overall failure behavior of Ni is brittle, while fracture in Al proceeds through void nucleation and coalescence with a zig-zag pattern of crack growth. The qualitative nature of results is discussed in the context of vacancy-formation energies and surface energies of the two FCC metals.

Optical Properties of Free and Embedded Small Nanoparticles

NASA Astrophysics Data System (ADS)

Idrobo, Juan

2008-03-01

It is well known that the absorption spectra, as well as the effective dielectric function, of nanoparticles in vacuum or surrounded by a dielectric medium can be obtained by classical Mie and Maxwell-Garnett theories. A limit as to how the particles can be for the theory to apply has not been established. Here I present theoretical results on the optical properties of small Ag, Au, and Si and Ge nanoparticles with tens of atoms in vacuum and in an embedded dielectric medium obtained from first-principles density-functional calculations. In particular, I will discuss the role that d-electron play on the optical properties of Ag and Au nanoparticles, and the cases when classical Mie and Maxwell-Garnett theories can be applied for nanoparticles of just few atoms in size and whose atoms are in bulk-like and not bulk-like positions. Comparison will be made for nanoparticles in vacuum and embedded in an alumina matrix. The quantum-mechanical results indicate that small nanoparticles in alumina can have an imprint on the effective dielectric function that is several times larger than would be predicted by Maxwell-Garnett theory for same-size particles. This work was supported by a GOALI NSF grant, DOE, the Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, and Alcoa Inc. Collaborators: S. ögüt, K. Jackson, J. Jellinek, A. Halabica. R. F. Haglund, R. Magruder, S.J. Pennycook and S.T. Pantelides.

Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.

PubMed

Mazhab-Jafari, Mohammad T; Rohou, Alexis; Schmidt, Carla; Bueler, Stephanie A; Benlekbir, Samir; Robinson, Carol V; Rubinstein, John L

2016-11-03

Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V 1 region drives proton translocation through the membrane-embedded V O region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V 1 and V O regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the V O complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits ac 8 c'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.

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

Tight-binding study of stacking fault energies and the Rice criterion of ductility in the fcc metals

NASA Astrophysics Data System (ADS)

Mehl, Michael J.; Papaconstantopoulos, Dimitrios A.; Kioussis, Nicholas; Herbranson, M.

2000-02-01

We have used the Naval Research Laboratory (NRL) tight-binding (TB) method to calculate the generalized stacking fault energy and the Rice ductility criterion in the fcc metals Al, Cu, Rh, Pd, Ag, Ir, Pt, Au, and Pb. The method works well for all classes of metals, i.e., simple metals, noble metals, and transition metals. We compared our results with full potential linear-muffin-tin orbital and embedded atom method (EAM) calculations, as well as experiment, and found good agreement. This is impressive, since the NRL-TB approach only fits to first-principles full-potential linearized augmented plane-wave equations of state and band structures for cubic systems. Comparable accuracy with EAM potentials can be achieved only by fitting to the stacking fault energy.

Information-theoretic measures of hydrogen-like ions in weakly coupled Debye plasmas

NASA Astrophysics Data System (ADS)

Zan, Li Rong; Jiao, Li Guang; Ma, Jia; Ho, Yew Kam

2017-12-01

Recent development of information theory provides researchers an alternative and useful tool to quantitatively investigate the variation of the electronic structure when atoms interact with the external environment. In this work, we make systematic studies on the information-theoretic measures for hydrogen-like ions immersed in weakly coupled plasmas modeled by Debye-Hückel potential. Shannon entropy, Fisher information, and Fisher-Shannon complexity in both position and momentum spaces are quantified in high accuracy for the hydrogen atom in a large number of stationary states. The plasma screening effect on embedded atoms can significantly affect the electronic density distributions, in both conjugate spaces, and it is quantified by the variation of information quantities. It is shown that the composite quantities (the Shannon entropy sum and the Fisher information product in combined spaces and Fisher-Shannon complexity in individual space) give a more comprehensive description of the atomic structure information than single ones. The nodes of wave functions play a significant role in the changes of composite information quantities caused by plasmas. With the continuously increasing screening strength, all composite quantities in circular states increase monotonously, while in higher-lying excited states where nodal structures exist, they first decrease to a minimum and then increase rapidly before the bound state approaches the continuum limit. The minimum represents the most reduction of uncertainty properties of the atom in plasmas. The lower bounds for the uncertainty product of the system based on composite information quantities are discussed. Our research presents a comprehensive survey in the investigation of information-theoretic measures for simple atoms embedded in Debye model plasmas.

Theoretical approach to embed nanocrystallites into a bulk crystalline matrix and the embedding influence on the electronic band structure and optical properties of the resulting heterostructures

NASA Astrophysics Data System (ADS)

Balagan, Semyon A.; Nazarov, Vladimir U.; Shevlyagin, Alexander V.; Goroshko, Dmitrii L.; Galkin, Nikolay G.

2018-06-01

We develop an approach and present results of the combined molecular dynamics and density functional theory calculations of the structural and optical properties of the nanometer-sized crystallites embedded in a bulk crystalline matrix. The method is designed and implemented for both compatible and incompatible lattices of the nanocrystallite (NC) and the host matrix, when determining the NC optimal orientation relative to the matrix constitutes a challenging problem. We suggest and substantiate an expression for the cost function of the search algorithm, which is the energy per supercell generalized for varying number of atoms in the latter. The epitaxial relationships at the Si/NC interfaces and the optical properties are obtained and found to be in a reasonable agreement with experimental data. Dielectric functions show significant sensitivity to the NC’s orientation relative to the matrix at energies below 0.5 eV.

High performance SONOS flash memory with in-situ silicon nanocrystals embedded in silicon nitride charge trapping layer

NASA Astrophysics Data System (ADS)

Lim, Jae-Gab; Yang, Seung-Dong; Yun, Ho-Jin; Jung, Jun-Kyo; Park, Jung-Hyun; Lim, Chan; Cho, Gyu-seok; Park, Seong-gye; Huh, Chul; Lee, Hi-Deok; Lee, Ga-Won

2018-02-01

In this paper, SONOS-type flash memory device with highly improved charge-trapping efficiency is suggested by using silicon nanocrystals (Si-NCs) embedded in silicon nitride (SiNX) charge trapping layer. The Si-NCs were in-situ grown by PECVD without additional post annealing process. The fabricated device shows high program/erase speed and retention property which is suitable for multi-level cell (MLC) application. Excellent performance and reliability for MLC are demonstrated with large memory window of ∼8.5 V and superior retention characteristics of 7% charge loss for 10 years. High resolution transmission electron microscopy image confirms the Si-NC formation and the size is around 1-2 nm which can be verified again in X-ray photoelectron spectroscopy (XPS) where pure Si bonds increase. Besides, XPS analysis implies that more nitrogen atoms make stable bonds at the regular lattice point. Photoluminescence spectra results also illustrate that Si-NCs formation in SiNx is an effective method to form deep trap states.

Theoretical approach to embed nanocrystallites into a bulk crystalline matrix and the embedding influence on the electronic band structure and optical properties of the resulting heterostructures.

PubMed

Balagan, Semyon Anatolyevich; Nazarov, Vladimir U; Shevlyagin, Alexander Vladimirovich; Goroshko, Dmitrii L; Galkin, N G

2018-05-03

We develop an approach and present results of the combined molecular dynamics and density functional theory calculations of the structural and optical properties of the nanometer-sized crystallites embedded in a bulk crystalline matrix. The method is designed and implemented for both compatible and incompatible lattices of the nanocrystallite (NC) and the host matrix, when determining the NC optimal orientation relative to the matrix constitutes a challenging problem. We suggest and substantiate an expression for the cost function of the search algorithm, which is the energy per supercell generalized for varying number of atoms in the latter. The epitaxial relationships at the Si/NC interfaces and the optical properties are obtained and found to be in a reasonable agreement with experimental data. Dielectric functions show significant sensitivity to the NC's orientation relative to the matrix at energies below 0.5 eV. © 2018 IOP Publishing Ltd.

Enhanced Ionization of Embedded Clusters by Electron-Transfer-Mediated Decay in Helium Nanodroplets.

PubMed

LaForge, A C; Stumpf, V; Gokhberg, K; von Vangerow, J; Stienkemeier, F; Kryzhevoi, N V; O'Keeffe, P; Ciavardini, A; Krishnan, S R; Coreno, M; Prince, K C; Richter, R; Moshammer, R; Pfeifer, T; Cederbaum, L S; Mudrich, M

2016-05-20

We report the observation of electron-transfer-mediated decay (ETMD) involving magnesium (Mg) clusters embedded in helium (He) nanodroplets. ETMD is initiated by the ionization of He followed by removal of two electrons from the Mg clusters of which one is transferred to the He ion while the other electron is emitted into the continuum. The process is shown to be the dominant ionization mechanism for embedded clusters for photon energies above the ionization potential of He. For Mg clusters larger than five atoms we observe stable doubly ionized clusters. Thus, ETMD provides an efficient pathway to the formation of doubly ionized cold species in doped nanodroplets.

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Control of spontaneous emission from a microwave-field-driven four-level atom in an anisotropic photonic crystal

NASA Astrophysics Data System (ADS)

Zhang, Duo; Li, Jiahua; Ding, Chunling; Yang, Xiaoxue

2012-05-01

The spontaneous emission properties of a microwave-field-driven four-level atom embedded in anisotropic double-band photonic crystals (PCs) are investigated. We discuss the influences of the band-edge positions, Rabi frequency and detuning of the microwave field on the emission spectrum. It is found that several interesting features such as spectral-line enhancement, spectral-line suppression, spectral-line overlap, and multi-peak structures can be observed in the spectra. The proposed scheme can be achieved by use of a microwave-coupled field into hyperfine levels in rubidium atom confined in a photonic crystal. These theoretical investigations may provide more degrees of freedom to manipulate the atomic spontaneous emission.

Grain-Boundary Resistance in Copper Interconnects: From an Atomistic Model to a Neural Network

NASA Astrophysics Data System (ADS)

Valencia, Daniel; Wilson, Evan; Jiang, Zhengping; Valencia-Zapata, Gustavo A.; Wang, Kuang-Chung; Klimeck, Gerhard; Povolotskyi, Michael

2018-04-01

Orientation effects on the specific resistance of copper grain boundaries are studied systematically with two different atomistic tight-binding methods. A methodology is developed to model the specific resistance of grain boundaries in the ballistic limit using the embedded atom model, tight- binding methods, and nonequilibrium Green's functions. The methodology is validated against first-principles calculations for thin films with a single coincident grain boundary, with 6.4% deviation in the specific resistance. A statistical ensemble of 600 large, random structures with grains is studied. For structures with three grains, it is found that the distribution of specific resistances is close to normal. Finally, a compact model for grain-boundary-specific resistance is constructed based on a neural network.

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles

PubMed Central

Haddadian, Esmael J.; Zhang, Hao; Freed, Karl F.; Douglas, Jack F.

2017-01-01

Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to ‘surface-melted’ inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a ‘glassy’ state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations (‘colored’ or ‘pink’ noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains. PMID:28176808

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles

NASA Astrophysics Data System (ADS)

Haddadian, Esmael J.; Zhang, Hao; Freed, Karl F.; Douglas, Jack F.

2017-02-01

Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to ‘surface-melted’ inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a ‘glassy’ state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations (‘colored’ or ‘pink’ noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.

Effect on magnetic properties of germanium encapsulated C60 fullerene

NASA Astrophysics Data System (ADS)

Umran, Nibras Mossa; Kumar, Ranjan

2013-02-01

Structural and electronic properties of Gen(n = 1-4) doped C60 fullerene are investigated with ab initio density functional theory calculations by using an efficient computer code, known as SIESTA. The pseudopotentials are constructed using a Trouiller-Martins scheme, to describe the interaction of valence electrons with the atomic cores. In endohedral doped embedding of more germanium atoms complexes we have seen that complexes are stable and thereafter cage break down. We have also investigated that binding energy, electronic affinity increases and magnetic moment oscillating behavior as the number of semiconductor atoms in C60 fullerene goes on increasing.

Defect energetics of concentrated solid-solution alloys from ab initio calculations: Ni 0.5Co 0.5, Ni 0.5Fe 0.5, Ni 0.8Fe 0.2 and Ni 0.8Cr 0.2

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

Zhao, Shijun; Stocks, George Malcolm; Zhang, Yanwen

2016-08-03

It has been shown that concentrated solid solution alloys possess unusual electronic, magnetic, transport, mechanical and radiation-resistant properties that are directly related to underlying chemical complexity. Because every atom experiences a different local atomic environment, the formation and migration energies of vacancies and interstitials in these alloys exhibit a distribution, rather than a single value as in a pure metal or dilute alloy. In this study, using ab initio calculations based on density functional theory and special quasirandom structure, we have characterized the distribution of defect formation energy and migration barrier in four Ni-based solid-solution alloys: Ni 0.5Co 0.5, Nimore » 0.5Fe 0.5, Ni 0.8Fe 0.2 and Ni 0.8Cr 0.2. As defect formation energies in finite-size models depend sensitively on the elemental chemical potential, we have developed a computationally efficient method for determining it which takes into account the global composition and the local short-range order. In addition we have compared the results of our ab initio calculations to those obtained from available embedded atom method (EAM) potentials. Our results indicate that the defect formation and migration energies are closely related to the specific atomic size in the structure, which further determines the elemental diffusion properties. In conclusion, different EAM potentials yield different features of defect energetics in concentrated alloys, pointing to the need for additional potential development efforts in order to allow spatial and temporal scale-up of defect and simulations, beyond those accessible to ab initio methods.« less

Defect energetics of concentrated solid-solution alloys from ab initio calculations: Ni0.5Co0.5, Ni0.5Fe0.5, Ni0.8Fe0.2 and Ni0.8Cr0.2.

PubMed

Zhao, Shijun; Stocks, G Malcolm; Zhang, Yanwen

2016-09-14

It has been shown that concentrated solid solution alloys possess unusual electronic, magnetic, transport, mechanical and radiation-resistant properties that are directly related to underlying chemical complexity. Because every atom experiences a different local atomic environment, the formation and migration energies of vacancies and interstitials in these alloys exhibit a distribution, rather than a single value as in a pure metal or dilute alloy. Using ab initio calculations based on density functional theory and special quasirandom structures, we have characterized the distribution of defect formation energy and migration barrier in four Ni-based solid-solution alloys: Ni0.5Co0.5, Ni0.5Fe0.5, Ni0.8Fe0.2, and Ni0.8Cr0.2. As defect formation energies in finite-size models depend sensitively on the elemental chemical potential, we have developed a computationally efficient method for determining it which takes into account the global composition and the local short-range order. In addition we have compared the results of our ab initio calculations to those obtained from available embedded atom method (EAM) potentials. Our results indicate that the defect formation and migration energies are closely related to the specific atoms in the structure, which further determines the elemental diffusion properties. Different EAM potentials yield different features of defect energetics in concentrated alloys, pointing to the need for additional potential development efforts in order to allow spatial and temporal scale-up of defect and simulations, beyond those accessible to ab initio methods.

Synthesis of AzPhchitosan-bifenthrin-PVC to protect cables against termites.

PubMed

Zhang, Lingkun; Cai, Weiwei; Chen, Wu-Ya; Zhang, Li; Hu, Kaikai; Guan, Yan-Qing

2016-03-30

The destruction of PVC cables by termites is a continuing and long-standing problem, which can lead to power leakage and power cut. Given the environmental demerits of insecticide overuse, alternative methods of addressing this problem are a highly desirable goal. In this study, we used photo-immobilization to develop a chitosan carrier system to help bifenthrin immobilize on the surface of the PVC substrate. The immobilization was analyzed using nuclear magnetic resonance (NMR), UV absorption, reverse-phase high-performance liquid chromatography (RP-HPLC), Raman absorption spectroscopy, and thermal gravimetric analysis (TGA). The surface structure and biological activity of the embedded and immobilized bifenthrin were examined using scanning electron microscopy (SEM), atomic force microscopy (AFM), and X-ray photon-electron spectroscopy (XPS). Its efficacy was assessed in pest experiments. The results indicate a successful embedding and immobilization of bifenthrin. Furthermore, the chemical bonding network between AzPhchitosan, bifenthrin, and PVC is stable, guaranteeing no environmental release of bifenthrin, and also providing more efficacious protection against termites. The evidence suggests that this photo-immobilization of bifenthrin-embedded chitosan on the surface of PVC substrates is a novel and environmentally friendly technique for termite control. This paper also reports a modification of chitosan with respect to its novel application in environmental protection. Copyright © 2015 Elsevier Ltd. All rights reserved.

Amorphous Ge quantum dots embedded in crystalline Si: ab initio results.

PubMed

Laubscher, M; Küfner, S; Kroll, P; Bechstedt, F

2015-10-14

We study amorphous Ge quantum dots embedded in a crystalline Si matrix through structure modeling and simulation using ab initio density functional theory including spin-orbit interaction and quasiparticle effects. Three models are generated by replacing a spherical region within diamond Si by Ge atoms and creating a disordered bond network with appropriate density inside the Ge quantum dot. After total-energy optimisations of the atomic geometry we compute the electronic and optical properties. We find three major effects: (i) the resulting nanostructures adopt a type-I heterostructure character; (ii) the lowest optical transitions occur only within the Ge quantum dots, and do not involve or cross the Ge-Si interface. (iii) for larger amorphous Ge quantum dots, with diameters of about 2.0 and 2.7 nm, absorption peaks appear in the mid-infrared spectral region. These are promising candidates for intense luminescence at photon energies below the gap energy of bulk Ge.

Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

DOE PAGES

Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; ...

2015-10-22

Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.

PubMed

Berger, Daniel; Logsdail, Andrew J; Oberhofer, Harald; Farrow, Matthew R; Catlow, C Richard A; Sherwood, Paul; Sokol, Alexey A; Blum, Volker; Reuter, Karsten

2014-07-14

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework

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

Berger, Daniel, E-mail: daniel.berger@ch.tum.de; Oberhofer, Harald; Reuter, Karsten

2014-07-14

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capabilitymore » by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO{sub 2}(110)« less

Solid-phase extraction method for the isolation of plant thionins from European mistletoe, wheat and barley using zirconium silicate embedded in poly(styrene-co-divinylbenzene) hollow-monoliths.

PubMed

Hussain, Shah; Güzel, Yüksel; Schönbichler, Stefan A; Rainer, Matthias; Huck, Christian W; Bonn, Günther K

2013-09-01

Thionins are cysteine-rich, biologically active small (∼5 kDa) and basic proteins occurring ubiquitously in the plant kingdom. This study describes an efficient solid-phase extraction (SPE) method for the selective isolation of these pharmacologically active proteins. Hollow-monolithic extraction tips based on poly(styrene-co-divinylbenzene) with embedded zirconium silicate nano-powder were designed, which showed an excellent selectivity for sulphur-rich proteins owing to strong co-ordination between zirconium and the sulphur atoms from the thiol-group of cysteine. The sorbent provides a combination of strong hydrophobic and electrostatic interactions which may help in targeted separation of certain classes of proteins in a complex mixture based upon the binding strength of different proteins. European mistletoe, wheat and barley samples were used for selective isolation of viscotoxins, purothionins and hordothionins, respectively. The enriched fractions were subjected to analysis by matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometer to prove the selectivity of the SPE method towards thionins. For peptide mass-fingerprint analysis, tryptic digests of SPE eluates were examined. Reversed-phase high-performance liquid chromatography hyphenated to diode-array detection was employed for the purification of individual isoforms. The developed method was found to be highly specific for the isolation and purification of thionins.

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.

PubMed

Spiwok, Vojtěch; Králová, Blanka

2011-12-14

Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling. © 2011 American Institute of Physics

Direct observation of interfacial Au atoms on TiO₂ in three dimensions.

PubMed

Gao, Wenpei; Sivaramakrishnan, Shankar; Wen, Jianguo; Zuo, Jian-Min

2015-04-08

Interfacial atoms, which result from interactions between the metal nanoparticles and support, have a large impact on the physical and chemical properties of nanoparticles. However, they are difficult to observe; the lack of knowledge has been a major obstacle toward unraveling their role in chemical transformations. Here we report conclusive evidence of interfacial Au atoms formed on the rutile (TiO2) (110) surfaces by activation using high-temperature (∼500 °C) annealing in air. Three-dimensional imaging was performed using depth-sectioning enabled by aberration-corrected scanning transmission electron microscopy. Results show that the interface between Au nanocrystals and TiO2 (110) surfaces consists of a single atomic layer with Au atoms embedded inside Ti-O. The number of interfacial Au atoms is estimated from ∼1-8 in an interfacial atomic column. Direct impact of interfacial Au atoms is observed on an enhanced Au-TiO2 interaction and the reduction of surface TiO2; both are critical to Au catalysis.

Learning linear transformations between counting-based and prediction-based word embeddings

PubMed Central

Hayashi, Kohei; Kawarabayashi, Ken-ichi

2017-01-01

Despite the growing interest in prediction-based word embedding learning methods, it remains unclear as to how the vector spaces learnt by the prediction-based methods differ from that of the counting-based methods, or whether one can be transformed into the other. To study the relationship between counting-based and prediction-based embeddings, we propose a method for learning a linear transformation between two given sets of word embeddings. Our proposal contributes to the word embedding learning research in three ways: (a) we propose an efficient method to learn a linear transformation between two sets of word embeddings, (b) using the transformation learnt in (a), we empirically show that it is possible to predict distributed word embeddings for novel unseen words, and (c) empirically it is possible to linearly transform counting-based embeddings to prediction-based embeddings, for frequent words, different POS categories, and varying degrees of ambiguities. PMID:28926629

Enhanced etching of tin-doped indium oxide due to surface modification by hydrogen ion injection

NASA Astrophysics Data System (ADS)

Li, Hu; Karahashi, Kazuhiro; Friederich, Pascal; Fink, Karin; Fukasawa, Masanaga; Hirata, Akiko; Nagahata, Kazunori; Tatsumi, Tetsuya; Wenzel, Wolfgang; Hamaguchi, Satoshi

2018-06-01

It is known that the etching yield (i.e., sputtering yield) of tin-doped indium oxide (ITO) by hydrocarbon ions (CH x +) is higher than its corresponding physical sputtering yield [H. Li et al., J. Vac. Sci. Technol. A 33, 060606 (2015)]. In this study, the effects of hydrogen in the incident hydrocarbon ion beam on the etching yield of ITO have been examined experimentally and theoretically with the use of a mass-selected ion beam system and by first-principles quantum mechanical (QM) simulation. As in the case of ZnO [H. Li et al., J. Vac. Sci. Technol. A 35, 05C303 (2017)], mass-selected ion beam experiments have shown that the physical sputtering yield of ITO by chemically inert Ne ions increases after a pretreatment of the ITO film by energetic hydrogen ion injection. First-principles QM simulation of the interaction of In2O3 with hydrogen atoms shows that hydrogen atoms embedded in In2O3 readily form hydroxyl (OH) groups and weaken or break In–O bonds around the hydrogen atoms, making the In2O3 film less resistant to physical sputtering. This is consistent with experimental observation of the enhanced etching yields of ITO by CH x + ions, considering the fact that hydrogen atoms of the incident CH x + ions are embedded into ITO during the etching process.

The determination of temperature stability of silver nanotubes by the molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Filatov, O.; Soldatenko, S.; Soldatenko, O.

2018-04-01

Molecular dynamics simulation using the embedded-atom method is applied to study thermal stability of silver nanotubes and its coefficient of linear thermal expansion. The correspondence of face centered cubic structure potential for this task is tested. Three types of nanotubes are modelled: scrolled from graphene-like plane, scrolled from plane with cubic structure and cut from cylinder. It is established that only the last two of them are stable. The last one describes in details. There is critical temperature when free ends of the nanotube close but the interior surface retains. At higher temperatures, the interior surface collapses and the nanotube is unstable.

Self-consistent calculations for the electronic structure of a vacancy in copper. A solution of the embedding problem

NASA Astrophysics Data System (ADS)

Zeller, R.; Braspenning, P. J.

1982-06-01

The charge density and the local density of states for a vacancy in Cu and for the first shell of Cu neighbours are calculated by the KKR-Green's function technique. The muffin-tin potentials for the vacancy and the neighbour shell atoms are determined self-consistently in the local density approximation of density functional theory. By the use of the proper host Green's function the embedding of this cluster of 13 perturbed muffin-tins into the infinite array of bulk Cu muffin-tin potentials is described rigorously, thus representing a solution of the embedding problem. The calculations demonstrate a rather large charge transfer of 1.1 electrons from the first neighbour shell to the vacancy.

IMPROVEMENTS IN EPOXY RESIN EMBEDDING METHODS

PubMed Central

Luft, John H.

1961-01-01

Epoxy embedding methods of Glauert and Kushida have been modified so as to yield rapid, reproducible, and convenient embedding methods for electron microscopy. The sections are robust and tissue damage is less than with methacrylate embedding. PMID:13764136

Structural evolution and atomic dynamics in Ni-Nb metallic glasses: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Xu, T. D.; Wang, X. D.; Zhang, H.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-10-01

The composition and temperature dependence of static and dynamic structures in NixNb1-x (x = 50-70 at. %) were systematically studied using molecular dynamics with a new-released semi-empirical embedded atom method potential by Mendelev. The calculated pair correlation functions and the structure factor match well with the experimental data, demonstrating the reliability of the potential within relatively wide composition and temperature ranges. The local atomic structures were then characterized by bond angle distributions and Voronoi tessellation methods, demonstrating that the icosahedral ⟨0,0,12,0⟩ is only a small fraction in the liquid state but increases significantly during cooling and becomes dominant at 300 K. The most abundant clusters are identified as ⟨0,0,12,0⟩ and distorted icosahedron ⟨0,2,8,2⟩. The large fraction of these two clusters hints that the relatively good glass forming ability is near the eutectic point. Unlike Cu-Zr alloys, both the self-diffusion coefficient and shear viscosity are insensitive to compositions upon cooling in Ni-Nb alloys. The breakdown of the Stokes-Einstein relation happens at around 1.6Tg (Tg: glass transition temperature). In the amorphous state, the solid and liquid-like atoms can be distinguished based on the Debye-Waller factor ⟨u2⟩. The insensitivity of the dynamic properties of Ni-Nb alloys to compositions may result from the relatively simple solidification process in the phase diagram, in which only one eutectic point exists in the studied composition range.

SU-C-BRC-05: Monte Carlo Calculations to Establish a Simple Relation of Backscatter Dose Enhancement Around High-Z Dental Alloy to Its Atomic Number

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

Utsunomiya, S; Kushima, N; Katsura, K

Purpose: To establish a simple relation of backscatter dose enhancement around a high-Z dental alloy in head and neck radiation therapy to its average atomic number based on Monte Carlo calculations. Methods: The PHITS Monte Carlo code was used to calculate dose enhancement, which is quantified by the backscatter dose factor (BSDF). The accuracy of the beam modeling with PHITS was verified by comparing with basic measured data namely PDDs and dose profiles. In the simulation, a high-Z alloy of 1 cm cube was embedded into a tough water phantom irradiated by a 6-MV (nominal) X-ray beam of 10 cmmore » × 10 cm field size of Novalis TX (Brainlab). The ten different materials of high-Z alloys (Al, Ti, Cu, Ag, Au-Pd-Ag, I, Ba, W, Au, Pb) were considered. The accuracy of calculated BSDF was verified by comparing with measured data by Gafchromic EBT3 films placed at from 0 to 10 mm away from a high-Z alloy (Au-Pd-Ag). We derived an approximate equation to determine the relation of BSDF and range of backscatter to average atomic number of high-Z alloy. Results: The calculated BSDF showed excellent agreement with measured one by Gafchromic EBT3 films at from 0 to 10 mm away from the high-Z alloy. We found the simple linear relation of BSDF and range of backscatter to average atomic number of dental alloys. The latter relation was proven by the fact that energy spectrum of backscatter electrons strongly depend on average atomic number. Conclusion: We found a simple relation of backscatter dose enhancement around high-Z alloys to its average atomic number based on Monte Carlo calculations. This work provides a simple and useful method to estimate backscatter dose enhancement from dental alloys and corresponding optimal thickness of dental spacer to prevent mucositis effectively.« less

Phonon interference control of atomic-scale metamirrors, meta-absorbers, and heat transfer through crystal interfaces

NASA Astrophysics Data System (ADS)

Kosevich, Yu. A.; Potyomina, L. G.; Darinskii, A. N.; Strelnikov, I. A.

2018-03-01

The paper theoretically studies the possibility of using the effects of phonon interference between paths through different interatomic bonds for the control of phonon heat transfer through internal crystal interfaces and for the design of phonon metamirrors and meta-absorbers. These metamirrors and meta-absorbers are considered to be defect nanolayers of atomic-scale thicknesses embedded in a crystal. Several analytically solvable three-dimensional lattice-dynamics models of the phonon metamirrors and meta-absorbers at the internal crystal planes are described. It is shown that due to destructive interference in the two or more phonon paths, the internal crystal planes, fully or partially filled with weakly bound or heavy-isotope defect atoms, can completely reflect or completely absorb phonons at the transmission antiresonances, whose wavelengths are larger than the effective thickness of the metamirror or meta-absorber. Due to cooperative superradiant effect, the spectral widths of the two-path interference antiresonances for the plane waves are given by the square of partial filling fraction in the defect crystal plane. Our analysis reveals that the presence of two or more phonon paths plays the dominant role in the emergence of the transmission antiresonances in phonon scattering at the defect crystal planes and in reduction of the thermal interface conductance in comparison with the Fano-resonance concept. We study analytically phonon transmission through internal crystal plane in a model cubic lattice of Si-like atoms, partially filled with Ge-like defect atoms. Such a plane can serve as interference phonon metamirror with the transmission antiresonances in the vicinities of eigenmode frequencies of Ge-like defect atoms in the terahertz frequency range. We predict the extraordinary phonon transmission induced by the two-path constructive interference of the lattice waves in resonance with the vibrations of rare host atoms, periodically distributed in the crystal plane almost completely filled with heavy-isotope defects. We show that the phonon-interference-induced transparency can be produced by the defect nanolayer with the non-nearest-neighbor interactions, filled with two types of isotopes with relatively small difference in masses or binding force constants. In this case, relatively broad transmission antiresonance is accompanied by the narrow transmission peak close to the antiresonance frequency. We describe the softening of the flexural surface acoustic wave, localized at the embedded defect nanolayer, caused by negative surface stress in the layer. The surface wave softening results in spatially periodic static bending deformation of the embedded nanolayer with the definite wave number. The latter effect is estimated for graphene monolayer embedded in a strained matrix of polyethylene. We analyze the effect of nonlinearity in the dynamics of defect atoms on the one- and two-path phonon interference and show that the interference transmission resonances and antiresonances are shifted in frequencies but not completely suppressed by rather strong anharmonicity of interatomic bonds. The reduction of the Kapitza thermal interface conductance caused by the destructive phonon interference in a defect monolayer is described. We show that the additional relatively weak non-nearest-neighbor interactions through the defect crystal plane filled with heavy isotopes substantially reduces the interface thermal conductance, and this effect is stronger in the three-dimensional system than in the quasi-one-dimensional systems studied previously.

Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2004-01-01

We extend our continuum description of solvent dielectrics in molecular-dynamics (MD) simulations [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)], which has provided an efficient and accurate solution of the Poisson equation, to ionic solvents as described by the linearized Poisson-Boltzmann (LPB) equation. We start with the formulation of a general theory for the electrostatics of an arbitrarily shaped molecular system, which consists of partially charged atoms and is embedded in a LPB continuum. This theory represents the reaction field induced by the continuum in terms of charge and dipole densities localized within the molecular system. Because these densities cannot be calculated analytically for systems of arbitrary shape, we introduce an atom-based discretization and a set of carefully designed approximations. This allows us to represent the densities by charges and dipoles located at the atoms. Coupled systems of linear equations determine these multipoles and can be rapidly solved by iteration during a MD simulation. The multipoles yield the reaction field forces and energies. Finally, we scrutinize the quality of our approach by comparisons with an analytical solution restricted to perfectly spherical systems and with results of a finite difference method.

Single d-metal atoms on F(s) and F(s+) defects of MgO(001): a theoretical study across the periodic table.

PubMed

Neyman, Konstantin M; Inntam, Chan; Matveev, Alexei V; Nasluzov, Vladimir A; Rösch, Notker

2005-08-24

Single d-metal atoms on oxygen defects F(s) and F(s+) of the MgO(001) surface were studied theoretically. We employed an accurate density functional method combined with cluster models, embedded in an elastic polarizable environment, and we applied two gradient-corrected exchange-correlation functionals. In this way, we quantified how 17 metal atoms from groups 6-11 of the periodic table (Cu, Ag, Au; Ni, Pd, Pt; Co, Rh, Ir; Fe, Ru, Os; Mn, Re; and Cr, Mo, W) interact with terrace sites of MgO. We found bonding with F(s) and F(s+) defects to be in general stronger than that with O2- sites, except for Mn-, Re-, and Fe/F(s) complexes. In M/F(s) systems, electron density is accumulated on the metal center in a notable fashion. The binding energy on both kinds of O defects increases from 3d- to 4d- to 5d-atoms of a given group, at variance with the binding energy trend established earlier for the M/O2- complexes, 4d < 3d < 5d. Regarding the evolution of the binding energy along a period, group 7 atoms are slightly destabilized compared to their group 6 congeners in both the F(s) and F(s+) complexes; for later transition elements, the binding energy increases gradually up to group 10 and finally decreases again in group 11, most strongly on the F(s) site. This trend is governed by the negative charge on the adsorbed atoms. We discuss implications for an experimental detection of metal atoms on oxide supports based on computed core-level energies.

Robust Deterministic Controlled Phase-Flip Gate and Controlled-Not Gate Based on Atomic Ensembles Embedded in Double-Sided Optical Cavities

NASA Astrophysics Data System (ADS)

Liu, A.-Peng; Cheng, Liu-Yong; Guo, Qi; Zhang, Shou

2018-02-01

We first propose a scheme for controlled phase-flip gate between a flying photon qubit and the collective spin wave (magnon) of an atomic ensemble assisted by double-sided cavity quantum systems. Then we propose a deterministic controlled-not gate on magnon qubits with parity-check building blocks. Both the gates can be accomplished with 100% success probability in principle. Atomic ensemble is employed so that light-matter coupling is remarkably improved by collective enhancement. We assess the performance of the gates and the results show that they can be faithfully constituted with current experimental techniques.

Study of thermal stability of disordered alloy AgxCu1-x nanoparticles by molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Baidyshev, V. S.; Chepkasov, I. V.; Artemova, N. D.

2018-05-01

In this paper melting processes of particles of disordered AgCu alloy in the size range of D=3-5 nm were investigated. The simulation was carried out with molecular dynamics, using the embedded atom potential. It was defined that for nanoparticles of D=3 nm, the melting process is connected with the formation of the outer layer consisting of Ag atoms as well as with the further transition of the particle into an amorphous state. The increase of the particle size to D=5 nm did not show the processes of redistributing Ag atoms on the particle surface.

Configuration of twins in glass-embedded silver nanoparticles of various origin

NASA Astrophysics Data System (ADS)

Hofmeister, H.; Dubiel, M.; Tan, G. L.; Schicke, K.-D.

2005-09-01

Structural characterization using high resolution electron microscopy and diffractogram analysis of silver nanoparticles embedded in glass by various routes of fabrication was aimed at revealing the characteristic features of twin faults occuring in such particles. Nearly spherical silver nanoparticles well below 10 nm size embedded in commercial soda-lime silicate float glass have been fabricated either by silver/sodium ion exchange or by Ag+ ion implantation. Twinned nanoparticles, besides single crystalline species, have frequently been observed for both fabrication routes, mainly at sizes above 5 nm, but also at smaller sizes, even around 1 nm. The variety of particle forms comprises single crystalline particles of nearly cuboctahedron shape, particles containing single twin faults, and multiply twinned particles containing parallel twin lamellae, or cyclic twinned segments arranged around axes of fivefold symmetry. Parallel twinning is distinctly favoured by ion implantation whereas cyclic twinning preferably occurs upon ion exchange processing. Regardless of single or repeated twinning, parallel or cyclic twin arrangement, one may classify simple twin faults of regular atomic configuration and compound twin faults whose irregular configuration consists of additional planar defects like associated stacking faults or secondary twin faults. Besides, a particular superstructure composed of parallel twin lamellae of only three atomic layers thickness is observed.

Structural properties of CuAu nanoparticles with different type. Molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Chepkasov, I. V.; Baidyshev, V. S.; Baev, A. Y.

2018-05-01

The paper is devoted to the thermal stability of a CuAu nanoparticles structure (D=5 nm) of various type (binary alloy, core-shell, "Janus" type) and of various percentage of copper atoms. The simulation was carried out with molecular dynamics, using the embedded atom potential. The authors defined the most preferable structural options from the standpoint of thermodynamics, as well as studied in detail the influence of different temperatures on the structural stability of CuAu nanoparticles.

Photon absorption potential coefficient as a tool for materials engineering

NASA Astrophysics Data System (ADS)

Akande, Raphael Oluwole; Oyewande, Emmanuel Oluwole

2016-09-01

Different atoms achieve ionizations at different energies. Therefore, atoms are characterized by different responses to photon absorption in this study. That means there exists a coefficient for their potential for photon absorption from a photon source. In this study, we consider the manner in which molecular constituents (atoms) absorb photon from a photon source. We observe that there seems to be a common pattern of variation in the absorption of photon among the electrons in all atoms on the periodic table. We assume that the electrons closest to the nucleus (En) and the electrons closest to the outside of the atom (Eo) do not have as much potential for photon absorption as the electrons at the middle of the atom (Em). The explanation we give to this effect is that the En electrons are embedded within the nuclear influence, and similarly, Eo electrons are embedded within the influence of energies outside the atom that there exists a low potential for photon absorption for them. Unlike En and Eo, Em electrons are conditioned, such that there is a quest for balance between being influenced either by the nuclear force or forces external to the atom. Therefore, there exists a higher potential for photon absorption for Em electrons than for En and Eo electrons. The results of our derivations and analysis always produce a bell-shaped curve, instead of an increasing curve as in the ionization energies, for all elements in the periodic table. We obtained a huge data of PAPC for each of the several materials considered. The point at which two or more PAPC values cross one another is termed to be a region of conflicting order of ionization, where all the atoms absorb equal portion of the photon source at the same time. At this point, a greater fraction of the photon source is pumped into the material which could lead to an explosive response from the material. In fact, an unimaginable and unreported phenomenon (in physics) could occur, when two or more PAPCs cross, and the material is able to absorb more than that the photon source could provide, at this point. These resulting effects might be of immense materials engineering applications.

Structural and dynamical properties of liquid Al-Au alloys

NASA Astrophysics Data System (ADS)

Peng, H. L.; Voigtmann, Th.; Kolland, G.; Kobatake, H.; Brillo, J.

2015-11-01

We investigate temperature- and composition-dependent structural and dynamical properties of Al-Au melts. Experiments are performed to obtain accurate density and viscosity data. The system shows a strong negative excess volume, similar to other Al-based binary alloys. We develop a molecular-dynamics (MD) model of the melt based on the embedded-atom method (EAM), gauged against the available experimental liquid-state data. A rescaling of previous EAM potentials for solid-state Au and Al improves the quantitative agreement with experimental data in the melt. In the MD simulation, the admixture of Au to Al can be interpreted as causing a local compression of the less dense Al system, driven by less soft Au-Au interactions. This local compression provides a microscopic mechanism explaining the strong negative excess volume of the melt. We further discuss the concentration dependence of self- and interdiffusion and viscosity in the MD model. Al atoms are more mobile than Au, and their increased mobility is linked to a lower viscosity of the melt.

On the Difference Between Additive and Subtractive QM/MM Calculations

PubMed Central

Cao, Lili; Ryde, Ulf

2018-01-01

The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e., the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic, and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended. PMID:29666794

Number series of atoms, interatomic bonds and interface bonds defining zinc-blende nanocrystals as function of size, shape and surface orientation: Analytic tools to interpret solid state spectroscopy data

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

König, Dirk, E-mail: dirk.koenig@unsw.edu.au

2016-08-15

Semiconductor nanocrystals (NCs) experience stress and charge transfer by embedding materials or ligands and impurity atoms. In return, the environment of NCs experiences a NC stress response which may lead to matrix deformation and propagated strain. Up to now, there is no universal gauge to evaluate the stress impact on NCs and their response as a function of NC size d{sub NC}. I deduce geometrical number series as analytical tools to obtain the number of NC atoms N{sub NC}(d{sub NC}[i]), bonds between NC atoms N{sub bnd}(d{sub NC}[i]) and interface bonds N{sub IF}(d{sub NC}[i]) for seven high symmetry zinc-blende (zb) NCsmore » with low-index faceting: {001} cubes, {111} octahedra, {110} dodecahedra, {001}-{111} pyramids, {111} tetrahedra, {111}-{001} quatrodecahedra and {001}-{111} quadrodecahedra. The fundamental insights into NC structures revealed here allow for major advancements in data interpretation and understanding of zb- and diamond-lattice based nanomaterials. The analytical number series can serve as a standard procedure for stress evaluation in solid state spectroscopy due to their deterministic nature, easy use and general applicability over a wide range of spectroscopy methods as well as NC sizes, forms and materials.« less

On the difference between additive and subtractive QM/MM calculations

NASA Astrophysics Data System (ADS)

Cao, Lili; Ryde, Ulf

2018-04-01

The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e. the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended.

Plasmonic properties of Ag nanoparticles embedded in GeO2-SiO2 matrix by atom beam sputtering.

PubMed

Mohapatra, Satyabrata

2016-02-07

Nanocomposite thin films containing Ag nanoparticles embedded in the GeO2-SiO2 matrix were synthesized by the atom beam co-sputtering technique. The structural, optical and plasmonic properties and the chemical composition of the nanocomposite thin films were studied by transmission electron microscopy (TEM) with energy dispersive X-ray spectroscopy (EDX), UV-visible absorption spectroscopy and X-ray photoelectron spectroscopy (XPS). UV-visible absorption studies on Ag-SiO2 nanocomposites revealed the presence of a strong localized surface plasmon resonance (LSPR) peak characteristic of Ag nanoparticles at 413 nm, which showed a blue shift of 26 nm (413 to 387 nm) along with a significant broadening and drastic decrease in intensity with the incorporation of 16 at% of Ge into the SiO2 matrix. TEM studies on Ag-GeO2-SiO2 nanocomposite thin films confirmed the presence of Ag nanoparticles with an average size of 3.8 nm in addition to their aggregates with an average size of 16.2 nm. Thermal annealing in air resulted in strong enhancement in the intensity of the LSPR peak, which showed a regular red shift of 51 nm (from 387 to 438 nm) with the increase in annealing temperature up to 500 °C. XPS studies showed that annealing in air resulted in oxidation of excess Ge atoms in the nanocomposite into GeO2. Our work demonstrates the possibility of controllably tuning the LSPR of Ag nanoparticles embedded in the GeO2-SiO2 matrix by single-step thermal annealing, which is interesting for optical applications.

The shear instability energy: a new parameter for materials design?

NASA Astrophysics Data System (ADS)

Kanani, M.; Hartmaier, A.; Janisch, R.

2017-10-01

Reliable and predictive relationships between fundamental microstructural material properties and observable macroscopic mechanical behaviour are needed for the successful design of new materials. In this study we establish a link between physical properties that are defined on the atomic level and the deformation mechanisms of slip planes and interfaces that govern the mechanical behaviour of a metallic material. To accomplish this, the shear instability energy Γ is introduced, which can be determined via quantum mechanical ab initio calculations or other atomistic methods. The concept is based on a multilayer generalised stacking fault energy calculation and can be applied to distinguish the different shear deformation mechanisms occurring at TiAl interfaces during finite-temperature molecular dynamics simulations. We use the new parameter Γ to construct a deformation mechanism map for different interfaces occurring in this intermetallic. Furthermore, Γ can be used to convert the results of ab initio density functional theory calculations into those obtained with an embedded atom method type potential for TiAl. We propose to include this new physical parameter into material databases to apply it for the design of materials and microstructures, which so far mainly relies on single-crystal values for the unstable and stable stacking fault energy.

New insights on ion track morphology in pyrochlores by aberration corrected scanning transmission electron microscopy

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

Sachan, Ritesh; Zhang, Yanwen; Ou, Xin

Here we demonstrate the enhanced imaging capabilities of an aberration corrected scanning transmission electron microscope to advance the understanding of ion track structure in pyrochlore structured materials (i.e., Gd 2Ti 2O 7 and Gd 2TiZrO 7). Track formation occurs due to the inelastic transfer of energy from incident ions to electrons, and atomic-level details of track morphology as a function of energy-loss are revealed in the present work. A comparison of imaging details obtained by varying collection angles of detectors is discussed in the present work. A quantitative analysis of phase identification using high-angle annular dark field imaging is performedmore » on the ion tracks. Finally, a novel 3-dimensional track reconstruction method is provided that is based on depth dependent imaging of the ion tracks. The technique is used in extracting the atomic-level details of nanoscale features, such as the disordered ion tracks, which are embedded in relatively thicker matrix. Another relevance of the method is shown by measuring the tilt of the ion tracks relative to the electron beam incidence that helps in knowing the structure and geometry of ion tracks quantitatively.« less

New insights on ion track morphology in pyrochlores by aberration corrected scanning transmission electron microscopy

DOE PAGES

Sachan, Ritesh; Zhang, Yanwen; Ou, Xin; ...

2016-12-13

Here we demonstrate the enhanced imaging capabilities of an aberration corrected scanning transmission electron microscope to advance the understanding of ion track structure in pyrochlore structured materials (i.e., Gd 2Ti 2O 7 and Gd 2TiZrO 7). Track formation occurs due to the inelastic transfer of energy from incident ions to electrons, and atomic-level details of track morphology as a function of energy-loss are revealed in the present work. A comparison of imaging details obtained by varying collection angles of detectors is discussed in the present work. A quantitative analysis of phase identification using high-angle annular dark field imaging is performedmore » on the ion tracks. Finally, a novel 3-dimensional track reconstruction method is provided that is based on depth dependent imaging of the ion tracks. The technique is used in extracting the atomic-level details of nanoscale features, such as the disordered ion tracks, which are embedded in relatively thicker matrix. Another relevance of the method is shown by measuring the tilt of the ion tracks relative to the electron beam incidence that helps in knowing the structure and geometry of ion tracks quantitatively.« less

Hydrogen-vacancy-dislocation interactions in α-Fe

NASA Astrophysics Data System (ADS)

Tehranchi, A.; Zhang, X.; Lu, G.; Curtin, W. A.

2017-02-01

Atomistic simulations of the interactions between dislocations, hydrogen atoms, and vacancies are studied to assess the viability of a recently proposed mechanism for the formation of nanoscale voids in Fe-based steels in the presence of hydrogen. Quantum-mechanics/molecular-mechanics method calculations confirm molecular statics simulations based on embedded atom method (EAM) potential showing that individual vacancies on the compressive side of an edge dislocation can be transported with the dislocation as it glides. Molecular dynamics simulations based on EAM potential then show, however, that vacancy clusters in the glide plane of an approaching dislocation are annihilated or reduced in size by the creation of a double-jog/climb process that is driven by the huge reduction in energy accompanying vacancy annihilation. The effectiveness of annihilation/reduction processes is not reduced by the presence of hydrogen in the vacancy clusters because typical V-H cluster binding energies are much lower than the vacancy formation energy, except at very high hydrogen content in the cluster. Analysis of a range of configurations indicates that hydrogen plays no special role in stabilizing nanovoids against jog formation processes that shrink voids. Experimental observations of nanovoids on the fracture surfaces of steels must be due to as-yet undetermined processes.

Capturing Nature's Diversity

PubMed Central

Pascolutti, Mauro; Campitelli, Marc; Nguyen, Bao; Pham, Ngoc; Gorse, Alain-Dominique; Quinn, Ronald J.

2015-01-01

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products. PMID:25902039

Molecular dynamics study of the melting of a supported 887-atom Pd decahedron.

PubMed

Schebarchov, D; Hendy, S C; Polak, W

2009-04-08

We employ classical molecular dynamics simulations to investigate the melting behaviour of a decahedral Pd(887) cluster on a single layer of graphite (graphene). The interaction between Pd atoms is modelled with an embedded-atom potential, while the adhesion of Pd atoms to the substrate is approximated with a Lennard-Jones potential. We find that the decahedral structure persists at temperatures close to the melting point, but that just below the melting transition, the cluster accommodates to the substrate by means of complete melting and then recrystallization into an fcc structure. These structural changes are in qualitative agreement with recently proposed models, and they verify the existence of an energy barrier preventing softly deposited clusters from 'wetting' the substrate at temperatures below the melting point.

Suppressing molecular motions for enhanced room-temperature phosphorescence of metal-free organic materials

PubMed Central

Kwon, Min Sang; Yu, Youngchang; Coburn, Caleb; Phillips, Andrew W.; Chung, Kyeongwoon; Shanker, Apoorv; Jung, Jaehun; Kim, Gunho; Pipe, Kevin; Forrest, Stephen R.; Youk, Ji Ho; Gierschner, Johannes; Kim, Jinsang

2015-01-01

Metal-free organic phosphorescent materials are attractive alternatives to the predominantly used organometallic phosphors but are generally dimmer and are relatively rare, as, without heavy-metal atoms, spin–orbit coupling is less efficient and phosphorescence usually cannot compete with radiationless relaxation processes. Here we present a general design rule and a method to effectively reduce radiationless transitions and hence greatly enhance phosphorescence efficiency of metal-free organic materials in a variety of amorphous polymer matrices, based on the restriction of molecular motions in the proximity of embedded phosphors. Covalent cross-linking between phosphors and polymer matrices via Diels–Alder click chemistry is devised as a method. A sharp increase in phosphorescence quantum efficiency is observed in a variety of polymer matrices with this method, which is ca. two to five times higher than that of phosphor-doped polymer systems having no such covalent linkage. PMID:26626796

Computational Modeling and Experimental Characterization of Martensitic Transformations in Nicoal for Self-Sensing Materials

NASA Technical Reports Server (NTRS)

Wallace, T. A.; Yamakov, V. I.; Hochhalter, J. D.; Leser, W. P.; Warner, J. E.; Newman, J. A.; Purja Pun, G. P.; Mishin, Y.

2015-01-01

Fundamental changes to aero-vehicle management require the utilization of automated health monitoring of vehicle structural components. A novel method is the use of self-sensing materials, which contain embedded sensory particles (SP). SPs are micron-sized pieces of shape-memory alloy that undergo transformation when the local strain reaches a prescribed threshold. The transformation is a result of a spontaneous rearrangement of the atoms in the crystal lattice under intensified stress near damaged locations, generating acoustic waves of a specific spectrum that can be detected by a suitably placed sensor. The sensitivity of the method depends on the strength of the emitted signal and its propagation through the material. To study the transition behavior of the sensory particle inside a metal matrix under load, a simulation approach based on a coupled atomistic-continuum model is used. The simulation results indicate a strong dependence of the particle's pseudoelastic response on its crystallographic orientation with respect to the loading direction and suggest possible ways of optimizing particle sensitivity. The technology of embedded sensory particles will serve as the key element in an autonomous structural health monitoring system that will constantly monitor for damage initiation in service, which will enable quick detection of unforeseen damage initiation in real-time and during onground inspections.

Supporting Students' Knowledge Integration with Technology-Enhanced Inquiry Curricula

ERIC Educational Resources Information Center

Chiu, Jennifer Lopseen

2010-01-01

Dynamic visualizations of scientific phenomena have the potential to transform how students learn and understand science. Dynamic visualizations enable interaction and experimentation with unobservable atomic-level phenomena. A series of studies clarify the conditions under which embedding dynamic visualizations in technology-enhanced inquiry…

Evaluation of optical and electronic properties of silicon nano-agglomerates embedded in SRO: applying density functional theory

PubMed Central

2014-01-01

In systems in atomic scale and nanoscale such as clusters or agglomerates constituted by particles from a few to less than 100 atoms, quantum confinement effects are very important. Their optical and electronic properties are often dependent on the size of the systems and the way in which the atoms in these clusters are bonded. Generally, these nanostructures display optical and electronic properties significantly different to those found in corresponding bulk materials. Silicon agglomerates embedded in silicon rich oxide (SRO) films have optical properties, which have been reported to be directly dependent on silicon nanocrystal size. Furthermore, the room temperature photoluminescence (PL) of SRO has repeatedly generated a huge interest due to its possible applications in optoelectronic devices. However, a plausible emission mechanism has not been widely accepted in the scientific community. In this work, we present a short review about the experimental results on silicon nanoclusters in SRO considering different techniques of growth. We focus mainly on their size, Raman spectra, and photoluminescence spectra. With this as background, we employed the density functional theory with a functional B3LYP and a basis set 6-31G* to calculate the optical and electronic properties of clusters of silicon (constituted by 15 to 20 silicon atoms). With the theoretical calculation of the structural and optical properties of silicon clusters, it is possible to evaluate the contribution of silicon agglomerates in the luminescent emission mechanism, experimentally found in thin SRO films. PMID:25276105

Laser-material interaction during atom probe tomography of oxides with embedded metal nanoparticles

DOE PAGES

Shinde, D.; Arnoldi, L.; Devaraj, A.; ...

2016-10-28

Oxide-supported metal nano-particles are of great interest in catalysis but also in the development of new large-spectrum-absorption materials. The design of such nano materials requires three-dimensional characterization with a high spatial resolution and elemental selectivity. The laser assisted Atom Probe Tomography (La-APT) presents both these capacities if an accurate understanding of laser-material interaction is developed. In this paper, we focus on the fundamental physics of field evaporation as a function of sample geometry, laser power, and DC electric field for Au nanoparticles embedded in MgO. By understanding the laser-material interaction through experiments and a theoretical model of heat diffusion insidemore » the sample after the interaction with laser pulse, we point out the physical origin of the noise and determine the conditions to reduce it by more than one order of magnitude, improving the sensitivity of the La-APT for metal-dielectric composites. Published by AIP Publishing.« less

First-principles calculations of Ti and O NMR chemical shift tensors in ferroelectric perovskites

NASA Astrophysics Data System (ADS)

Pechkis, Daniel; Walter, Eric; Krakauer, Henry

2011-03-01

Complementary chemical shift calculations were carried out with embedded clusters, using quantum chemistry methods, and with periodic boundary conditions, using the GIPAW approach within the Quantum Espresso package. Compared to oxygen chemical shifts, δ̂ (O), cluster calculations for δ̂ (Ti) were found to be more sensitive to size effects, termination, and choice of gaussian-type atomic basis set, while GIPAW results were found to be more sensitive to the pseudopotential construction. The two approaches complemented each other in optimizing these factors. We show that the two approaches yield comparable chemical shifts for suitably converged simulations, and results are compared with available experimental measurements. Supported by ONR.

Simulation of uniaxial deformation of hexagonal crystals (Mg, Be)

NASA Astrophysics Data System (ADS)

Vlasova, A. M.; Kesarev, A. G.

2017-12-01

Molecular dynamics (MD) simulations were performed for the nanocompression loading of nanocrystalline magnesium and beryllium modeled by an interatomic potential of the embedded atom method (EAM). It is shown that the main deformation modes are prismatic slip and twinning for magnesium, and only prismatic slip for beryllium. The formation of stable configurations of dislocation grids in magnesium and beryllium was observed. Dislocation networks are formed in the habit plane of the twin in a magnesium nanocrystall. Some dislocation reactions are suggested to explain the appearance of such networks. Shockley partial dislocations in a beryllium nanocrystall form grids in the slip plane. A strong anisotropy between slip systems was observed, which is in agreement with experimental data.

Order-disorder effects on the elastic properties of CuMPt6 (M=Cr and Co) compounds

NASA Astrophysics Data System (ADS)

Huang, Shuo; Li, Rui-Zi; Qi, San-Tao; Chen, Bao; Shen, Jiang

2014-04-01

The elastic properties of CuMPt6 (M=Cr and Co) in disordered face-centered cubic (fcc) structure and ordered Cu3Au-type structure are studied with lattice inversion embedded-atom method. The calculated lattice constant and Debye temperature agree quite well with the comparable experimental data. The obtained formation enthalpy demonstrates that the Cu3Au-type structure is energetically more favorable. Numerical estimates of the elastic constants, bulk/shear modulus, Young's modulus, Poisson's ratio, elastic anisotropy, and Debye temperature for both compounds are performed, and the results suggest that the disordered fcc structure is much softer than the ordered Cu3Au-type structure.

Interatomic Coulombic Decay Mediated by Ultrafast Superexchange Energy Transfer.

PubMed

Miteva, Tsveta; Kazandjian, Sévan; Kolorenč, Přemysl; Votavová, Petra; Sisourat, Nicolas

2017-08-25

Inner-valence ionized states of atoms and molecules live shorter if these species are embedded in an environment due to the possibility for ultrafast deexcitation known as interatomic Coulombic decay (ICD). In this Letter we show that the lifetime of these ICD active states decreases further when a bridge atom is in proximity to the two interacting monomers. This novel mechanism, termed superexchange ICD, is an electronic correlation effect driven by the efficient energy transfer via virtual states of the bridge atom. The superexchange ICD is discussed in detail on the example of the NeHeNe trimer. We demonstrate that the decay width of the Ne^{+}(2s^{-1})  ^{2}Σ_{g}^{+} resonance increases 6 times in the presence of the He atom at a distance of 4 Å between the two Ne atoms. Using a simple model, we provide a qualitative explanation of the superexchange ICD and we derive analytical expressions for the dependence of the decay width on the distance between the neon atoms.

Steady-State Solutions Originating from an Enhanced Nonlinear Feedback in a Hybrid Opto-mechanical System

NASA Astrophysics Data System (ADS)

Fan, Qiu-Bo; Wang, Yi-Ru; Chen, Jin; Pan, Yue-Wu; Han, Bai-Ping; Fu, Chang-Bao; Sun, Yan

2017-06-01

The steady-state properties of a hybrid system are investigated in this paper. Many cold atoms in the four-level tripod configuration are confined in an optical cavity with a movable end mirror. The confined cold atoms are driven with two external classical fields and an internal cavity field. The internal cavity field is excited by an external driving field and shows a radiation pressure upon the movable end mirror. The coupling of atom-light and opto-mechanical interactions is enhanced by embedding a four-level atomic system in a typical opto-mechanical cavity. And an enhanced nonlinear feedback mechanism is offered by the enhanced coupling, which permits the observation of five and three steady-state solutions for relevant variables near two-photon resonance. The enhanced nonlinear feedback mechanism also allows us to observe the obvious difference in the double-EIT phenomenon between the atom-assisted opto-mechanical system and usual atom-field system.

Polarization-dependent photon switch in a one-dimensional coupled-resonator waveguide.

PubMed

Zhang, Zhe-Yong; Dong, Yu-Li; Zhang, Sheng-Li; Zhu, Shi-Qun

2013-09-09

Polarization-dependent photon switch is one of the most important ingredients in building future large-scale all-optical quantum network. We present a scheme for a single-photon switch in a one-dimensional coupled-resonator waveguide, where N(a) Λ-type three-level atoms are individually embedded in each of the resonator. By tuning the interaction between atom and field, we show that an initial incident photon with a certain polarization can be transformed into its orthogonal polarization state. Finally, we use the fidelity as a figure of merit and numerically evaluate the performance of our photon switch scheme in varieties of system parameters, such as number of atoms, energy detuning and dipole couplings.

Structural properties and diffusion processes of the Cu 3Au (0 0 1) surface

NASA Astrophysics Data System (ADS)

Wang, Fang; Zhang, Jian-Min; Zhang, Yan; Ji, Vincent

2010-09-01

The surface relaxation and surface energy of both the mixed AuCu and pure Cu terminated Cu 3Au (0 0 1) surfaces are simulated and calculated by using the modified analytical embedded-atom method. We find that the mixed AuCu termination is energetically preferred over the pure Cu termination thereby the mono-vacancy diffusion is also investigated in the topmost few layers of the mixed AuCu terminated Cu 3Au (0 0 1) surface. In the mixed AuCu terminated surface the relaxed Au atoms are raised above Cu atoms for 0.13 Å in the topmost layer. All the surface atoms displace outwards, this effect occurs in the first three layers and changes the first two inter-layer spacing. For mono-vacancy migration in the first layer, the migration energies of Au and Cu mono-vacancy via two-type in-plane displace: the nearest neighbor jump (NNJ) and the second nearest neighbor jump (2NNJ), are calculated and the results show that the NNJ requires a much lower energy than 2NNJ. For the evolution of the energy requirements for successive nearest neighbor jumps (SNNJ) along three different paths: circularity, zigzag and beeline, we find that the circularity path is preferred over the other two paths due to its minimum energy barriers and final energies. In the second layer, the NN jumps in intra- and inter-layer of the Cu mono-vacancy are investigated. The calculated energy barriers and final energies show that the vacancy prefer jump up to a proximate Cu site. This replacement between the Cu vacancy in the second layer and Cu atom in the first layer is remunerative for the Au atoms enrichment in the topmost layer.

Ca-Embedded C2N: an efficient adsorbent for CO2 capture.

PubMed

Liu, Yuzhen; Meng, Zhaoshun; Guo, Xiaojian; Xu, Genjian; Rao, Dewei; Wang, Yuhui; Deng, Kaiming; Lu, Ruifeng

2017-10-25

Carbon dioxide as a greenhouse gas causes severe impacts on the environment, whereas it is also a necessary chemical feedstock that can be converted into carbon-based fuels via electrochemical reduction. To efficiently and reversibly capture CO 2 , it is important to find novel materials for a good balance between adsorption and desorption. In this study, we performed first-principles calculations and grand canonical Monte Carlo (GCMC) simulations, to systematically study metal-embedded carbon nitride (C 2 N) nanosheets for CO 2 capture. Our first-principles results indicated that Ca atoms can be uniformly trapped in the cavity center of C 2 N structure, while the transition metals (Sc, Ti, V, Cr, Mn, Fe, Co) are favorably embedded in the sites off the center of the cavity. The determined maximum number of CO 2 molecules with strong physisorption showed that Ca-embedded C 2 N monolayer is the most promising CO 2 adsorbent among all considered metal-embedded materials. Moreover, GCMC simulations revealed that at room temperature the gravimetric density for CO 2 adsorbed on Ca-embedded C 2 N reached 50 wt% at 30 bar and 23 wt% at 1 bar, higher than other layered materials, thus providing a satisfactory system for the CO 2 capture and utilization.

Dust, ice and gas in time (DIGIT): Herschel and Spitzer spectro-imaging of SMM3 and SMM4 in Serpens

NASA Astrophysics Data System (ADS)

Dionatos, O.; Jørgensen, J. K.; Green, J. D.; Herczeg, G. J.; Evans, N. J.; Kristensen, L. E.; Lindberg, J. E.; van Dishoeck, E. F.

2013-10-01

Context. Mid- and far-infrared observations of the environment around embedded protostars reveal a plethora of high excitation molecular and atomic emission lines. Different mechanisms for the origin of these lines have been proposed, including shocks induced by protostellar jets and radiation or heating by the embedded protostar of its immediate surroundings. Aims: By studying of the most important molecular and atomic coolants, we aim at constraining the physical conditions around the embedded protostars SMM3 and SMM4 in the Serpens molecular cloud core and measuring the CO/H2 ratio in warm gas. Methods: Spectro-imaging observations from the Spitzer Infrared Spectrograph (IRS) and the Herschel Photodetector Array Camera and Spectrometer (PACS) provide an almost complete wavelength coverage between 5 and 200 μm. Within this range, emission from all major molecular (H2, CO, H2O and OH) and many atomic ([OI], [CII], [FeII], [SiII] and [SI]) coolants of excited gas are detected. Emission line maps reveal the morphology of the observed emission and indicate associations between the different species. The excitation conditions for molecular species are assessed through rotational diagrams. Emission lines from major coolants are compared to the results of steady-state C- and J-type shock models. Results: Line emission tends to peak at distances of ~10-20″ from the protostellar sources with all but [CII] peaking at the positions of outflow shocks seen in near-IR and sub-millimeter interferometric observations. The [CII] emission pattern suggests that it is most likely excited from energetic UV radiation originating from the nearby flat-spectrum source SMM6. Excitation analysis indicates that H2 and CO originate in gas at two distinct rotational temperatures of ~300 K and 1000 K, while the excitation temperature for H2O and OH is ~100-200 K. The morphological and physical association between CO and H2 suggests a common excitation mechanism, which allows direct comparisons between the two molecules. The CO/H2 abundance ratio varies from ~10-5 in the warmer gas up to ~10-4 in the hotter regions. Shock models indicate that C-shocks can account for the observed line intensities if a beam filling factor and a temperature stratification in the shock front are considered. C-type shocks can best explain the emission from H2O. The existence of J-shocks is suggested by the strong atomic/ionic (except for [CII]) emission and a number of line ratio diagnostics. Dissociative shocks can account for the CO and H2 emission in a single excitation temperature structure. Conclusions: The bulk of cooling from molecular and atomic lines is associated with gas excited in outflow shocks. The strong association between H2 and CO constrain their abundance ratio in warm gas. Both C- and J-type shocks can account for the observed molecular emission; however, J-shocks are strongly suggested by the atomic emission and provide simpler and more homogeneous solutions for CO and H2. The variations in the CO/H2 abundance ratio for gas at different temperatures can be interpreted by their reformation rates in dissociative J-type shocks, or the influence of both C and J shocks. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.Appendices A-C are available in electronic form at http://www.aanda.org

Atomic Force Microscopy (AFM) for In-Situ Biofilm Surface Characterization during Free Chlorine and Monochloramine Exposure

EPA Science Inventory

Drinking water distribution system biofilm are attached to pipe walls and found in sediments. These biofilms are complex and contain a variety of microorganisms embedded in a matrix with extracellular polymeric substances (EPS), providing protection from disinfection. Without pro...

Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys

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

Zhang, Hao; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4; Zhong, Cheng

2015-04-28

We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by “dynamic heterogeneity” in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔG{sub a} with temperature of both the Cumore » and Zr diffusion coefficients D, and the alpha structural relaxation time τ{sub α} can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract “cooperatively rearranging regions” of AG. We also find coexisting clusters of relatively “immobile” atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of “mobile” atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized (“immobile”) and wandering (“mobile”) particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.« less

A basin-hopping Monte Carlo investigation of the structural and energetic properties of 55- and 561-atom bimetallic nanoclusters: the examples of the ZrCu, ZrAl, and CuAl systems.

PubMed

De Souza, Douglas G; Cezar, Henrique M; Rondina, Gustavo G; de Oliveira, Marcelo F; Da Silva, Juarez L F

2016-05-05

We report a basin-hopping Monte Carlo investigation within the embedded-atom method of the structural and energetic properties of bimetallic ZrCu, ZrAl, and CuAl nanoclusters with 55 and 561 atoms. We found that unary Zr55, Zr561, Cu55, Cu561, Al55, and Al561 systems adopt the well known compact icosahedron (ICO) structure. The excess energy is negative for all systems and compositions, which indicates an energetic preference for the mixing of both chemical species. The ICO structure is preserved if a few atoms of the host system are replaced by different species, however, the composition limit in which the ICO structure is preserved depends on both the host and new chemical species. Using several structural analyses, three classes of structures, namely ideal ICO, nearly ICO, and distorted ICO structures, were identified. As the amounts of both chemical species change towards a more balanced composition, configurations far from the ICO structure arise and the dominant structures are nearly spherical, which indicates a strong minimization of the surface energy by decreasing the number of atoms with lower coordination on the surface. The average bond lengths follow Vegard's law almost exactly for ZrCu and ZrAl, however, this is not the case for CuAl. Furthermore, the radial distribution allowed us to identify the presence of an onion-like behavior in the surface of the 561-atom CuAl nanocluster with the Al atoms located in the outermost surface shell, which can be explained by the lower surface energies of the Al surfaces compared with the Cu surfaces. In ZrCu and ZrAl the radial distribution indicates a nearly homogeneous distribution for the chemical species, however, with a slightly higher concentration of Al atoms on the ZrAl surface, which can also be explained by the lower surface energy.

Direct observation of nanowire growth and decomposition.

PubMed

Rackauskas, Simas; Shandakov, Sergey D; Jiang, Hua; Wagner, Jakob B; Nasibulin, Albert G

2017-09-26

Fundamental concepts of the crystal formation suggest that the growth and decomposition are determined by simultaneous embedding and removal of the atoms. Apparently, by changing the crystal formation conditions one can switch the regimes from the growth to decomposition. To the best of our knowledge, so far this has been only postulated, but never observed at the atomic level. By means of in situ environmental transmission electron microscopy we monitored and examined the atomic layer transformation at the conditions of the crystal growth and its decomposition using CuO nanowires selected as a model object. The atomic layer growth/decomposition was studied by varying an O 2 partial pressure. Three distinct regimes of the atomic layer evolution were experimentally observed: growth, transition and decomposition. The transition regime, at which atomic layer growth/decomposition switch takes place, is characterised by random nucleation of the atomic layers on the growing {111} surface. The decomposition starts on the side of the nanowire by removing the atomic layers without altering the overall crystal structure, which besides the fundamental importance offers new possibilities for the nanowire manipulation. Understanding of the crystal growth kinetics and nucleation at the atomic level is essential for the precise control of 1D crystal formation.

CoMD Implementation Suite in Emerging Programming Models

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

Haque, Riyaz; Reeve, Sam; Juallmes, Luc

CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended tomore » support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.« less

Hetero-diffusion of Au epitaxy on stepped Ag(110) surface: Study of the jump rate and diffusion coefficient

NASA Astrophysics Data System (ADS)

Benlattar, M.; El koraychy, E.; Kotri, A.; Mazroui, M.

2017-12-01

We have used molecular dynamics simulations combined with an interatomic potential derived from the embedded atom method, to investigate the hetero-diffusion of Au adatom near a stepped Ag(110) surface with the height of one monoatomic layer. The activation energies for different diffusion processes, which occur on the terrace and near the step edge, are calculated both by molecular statics and molecular dynamics simulations. Static energies are found by the drag method, whereas the dynamic barriers are computed at high temperature from the Arrhenius plots. Our numerical results reveal that the jump process requires very high activation energy compared to the exchange process either on the terrace or near the step edge. In this work, other processes, such as upward and downward diffusion at step edges, have also been discussed.

Embedded arrays of vertically aligned carbon nanotube carpets and methods for making them

DOEpatents

Kim, Myung Jong; Nicholas, Nolan Walker; Kittrell, W. Carter; Schmidt, Howard K.

2015-06-30

According to some embodiments, the present invention provides a system and method for supporting a carbon nanotube array that involve an entangled carbon nanotube mat integral with the array, where the mat is embedded in an embedding material. The embedding material may be depositable on a carbon nanotube. A depositable material may be metallic or nonmetallic. The embedding material may be an adhesive material. The adhesive material may optionally be mixed with a metal powder. The embedding material may be supported by a substrate or self-supportive. The embedding material may be conductive or nonconductive. The system and method provide superior mechanical and, when applicable, electrical, contact between the carbon nanotubes in the array and the embedding material. The optional use of a conductive material for the embedding material provides a mechanism useful for integration of carbon nanotube arrays into electronic devices.

Diffraction peak profiles of surface relaxed spherical nanocrystals

NASA Astrophysics Data System (ADS)

Perez-Demydenko, C.; Scardi, P.

2017-09-01

A model is proposed for surface relaxation of spherical nanocrystals. Besides reproducing the primary effect of changing the average unit cell parameter, the model accounts for the inhomogeneous atomic displacement caused by surface relaxation and its effect on the diffraction line profiles. Based on three parameters with clear physical meanings - extension of the sub-coordination effect, maximum radial displacement due to sub-coordination, and effective hydrostatic pressure - the model also considers elastic anisotropy and provides parametric expressions of the diffraction line profiles directly applicable in data analysis. The model was tested on spherical nanocrystals of several fcc metals, matching atomic positions with those provided by Molecular Dynamics (MD) simulations based on embedded atom potentials. Agreement was also verified between powder diffraction patterns generated by the Debye scattering equation, using atomic positions from MD and the proposed model.

The Path Resistance Method for Bounding the Smallest Nontrivial Eigenvalue of a Laplacian

NASA Technical Reports Server (NTRS)

Guattery, Stephen; Leighton, Tom; Miller, Gary L.

1997-01-01

We introduce the path resistance method for lower bounds on the smallest nontrivial eigenvalue of the Laplacian matrix of a graph. The method is based on viewing the graph in terms of electrical circuits; it uses clique embeddings to produce lower bounds on lambda(sub 2) and star embeddings to produce lower bounds on the smallest Rayleigh quotient when there is a zero Dirichlet boundary condition. The method assigns priorities to the paths in the embedding; we show that, for an unweighted tree T, using uniform priorities for a clique embedding produces a lower bound on lambda(sub 2) that is off by at most an 0(log diameter(T)) factor. We show that the best bounds this method can produce for clique embeddings are the same as for a related method that uses clique embeddings and edge lengths to produce bounds.

Exact density functional and wave function embedding schemes based on orbital localization

NASA Astrophysics Data System (ADS)

Hégely, Bence; Nagy, Péter R.; Ferenczy, György G.; Kállay, Mihály

2016-08-01

Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

Converging Institutions: Shaping Relationships between Nanotechnologies, Economy, and Society

ERIC Educational Resources Information Center

Ott, Ingrid; Papilloud, Christian

2007-01-01

Nanotechnologies are technologies applied to a molecular level, which can be embedded in materials including human cells and atoms of mineral, chemical, or physical substrates. Nanotechnologies have been used in attempts to foster interactions between a multitude of products, production processes, and social actors. Just like bio, info, and…

Reasoning with Atomic-Scale Molecular Dynamic Models

ERIC Educational Resources Information Center

Pallant, Amy; Tinker, Robert F.

2004-01-01

The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

Accuracy-energy configurable sensor processor and IoT device for long-term activity monitoring in rare-event sensing applications.

PubMed

Park, Daejin; Cho, Jeonghun

2014-01-01

A specially designed sensor processor used as a main processor in IoT (internet-of-thing) device for the rare-event sensing applications is proposed. The IoT device including the proposed sensor processor performs the event-driven sensor data processing based on an accuracy-energy configurable event-quantization in architectural level. The received sensor signal is converted into a sequence of atomic events, which is extracted by the signal-to-atomic-event generator (AEG). Using an event signal processing unit (EPU) as an accelerator, the extracted atomic events are analyzed to build the final event. Instead of the sampled raw data transmission via internet, the proposed method delays the communication with a host system until a semantic pattern of the signal is identified as a final event. The proposed processor is implemented on a single chip, which is tightly coupled in bus connection level with a microcontroller using a 0.18 μm CMOS embedded-flash process. For experimental results, we evaluated the proposed sensor processor by using an IR- (infrared radio-) based signal reflection and sensor signal acquisition system. We successfully demonstrated that the expected power consumption is in the range of 20% to 50% compared to the result of the basement in case of allowing 10% accuracy error.

Energetics and structural properties of twist grain boundaries in Cu

NASA Technical Reports Server (NTRS)

Karimi, Majid

1992-01-01

Structural and energetics properties of atoms near a grain boundary are of great importance from theoretical and experimental standpoints. From various experimental work it is concluded that diffusion at low temperatures at polycrystalline materials take place near grain boundary. Experimental and theoretical results also indicate changes of up to 70 percent in physical properties near a grain boundary. The Embedded Atom Method (EAM) calculations on structural properties of Au twist grain boundaries are in quite good agreement with their experimental counterparts. The EAM is believed to predict reliable values for the single vacancy formation energy as well as migration energy. However, it is not clear whether the EAM functions which are fitted to the bulk properties of a perfect crystalline solid can produce reliable results on grain boundaries. One of the objectives of this work is to construct the EAM functions for Cu and use them in conjunction with the molecular static simulation to study structures and energetics of atoms near twist grain boundaries in Cu. This provides tests of the EAM functions near a grain boundary. In particular, we determine structure, single vacancy formation energy, migration energy, single vacancy activation energy, and interlayer spacing as a function of distance from grain boundary. Our results are compared with the available experimental and theoretical results from grain boundaries and bulk.

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

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

Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascademore » production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.« less

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

DOE PAGES

Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.

2015-06-03

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascademore » production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.« less

Three-dimensional atomic mapping of hydrogenated polymorphous silicon solar cells

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

Chen, Wanghua, E-mail: wanghua.chen@polytechnique.edu; Roca i Cabarrocas, Pere; Pareige, Philippe

Hydrogenated polymorphous silicon (pm-Si:H) is a nanostructured material consisting of silicon nanocrystals embedded in an amorphous silicon matrix. Its use as the intrinsic layer in thin film p-i-n solar cells has led to good cell properties in terms of stability and efficiency. Here, we have been able to assess directly the concentration and distribution of nanocrystals and impurities (dopants) in p-i-n solar cells, by using femtosecond laser-assisted atom probe tomography (APT). An effective sample preparation method for APT characterization is developed. Based on the difference in atomic density between hydrogenated amorphous and crystalline silicon, we are able to distinguish themore » nanocrystals from the amorphous matrix by using APT. Moreover, thanks to the three-dimensional reconstruction, we demonstrate that Si nanocrystals are homogeneously distributed in the entire intrinsic layer of the solar cell. The influence of the process pressure on the incorporation of nanocrystals and their distribution is also investigated. Thanks to APT we could determine crystalline fractions as low as 4.2% in the pm-Si:H films, which is very difficult to determine by standard techniques, such as X-ray diffraction, Raman spectroscopy, and spectroscopic ellipsometry. Moreover, we also demonstrate a sharp p/i interface in our solar cells.« less

Many-body expansion of the Fock matrix in the fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Fedorov, Dmitri G.; Kitaura, Kazuo

2017-09-01

A many-body expansion of the Fock matrix in the fragment molecular orbital method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic orbital basis and compared to the expansion in the basis of fragment molecular orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon. The physical nature of metallicity is discussed, and it is shown what kinds of metallic systems can be treated by fragment-based methods. The density of states is calculated for a fully closed and a partially open nano-ring of boron nitride with a diameter of 105 nm.

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

Shockwave-Induced Plasticity Via Large-Scale Nonequilibrium Molecular Dynamics

NASA Astrophysics Data System (ADS)

Holian, Brad Lee

1997-07-01

In nonequilibrium molecular-dynamics (MD) simulations of shock waves in single crystals, carried out in 1979 at Los Alamos,(B.L. Holian and G.K. Straub, Phys. Rev. Lett. 43), 1598 (1979). we discovered that, above a threshold strength, strongly shocked crystals deform in a very simple way. Rather than experiencing massive deformation, a simple slippage occurs at the shock front, relieving the peak shear stress, and leaving behind a stacking fault. We realized, of course, that real materials could yield at much lower thresholds, and speculated then that pre-existing defects could nucleate plastic flow at lower shock strengths than those characteristic of pure single crystals. (Historical note: at about the same time as our earliest dynamical shockwave simulations, Mogilevsky, working independently in the Soviet Union, carried out relaxation MD calculations under uniaxial strain, and observed spontaneous production of dislocations.(M.A. Mogilevsky, in Shock Waves and High Strain Rate Phenomena in Metals) (Plenum, New York, 1981), p.531.) Further Los Alamos calculations, carried out nearly a decade later in five-times larger systems (up to 10,000 atoms), confirmed this observation and quantified the threshold strength, namely the yield strength of the perfect crystal.(B.L. Holian, Phys. Rev. A 37), 2562 (1988); for a review, see B.L. Holian, Shock Waves 5, 149 (1995). Subsequently, Zaretskii and co-workers,(E.B. Zaretskii, G.I. Kanel, P.A. Mogilevskii, and V.E. Fortov, Sov. Phys. Dokl. 36), 76 (1991). using x-ray diffraction of shocked single crystals, confirmed our MD observations of stacking faults produced by shockwave passage. With the advent of massively parallel computers, we have recently studied systems with over six-times larger cross-sectional area and four-times longer distance of run to the steady state (approximately 270,000 atoms). We have seen that the increased cross-section allows the system to slip along both available forward slip systems, in different places along the now non-planar shock front, though only one stacking fault survives. This leads us to attempt simulations with even larger cross-sectional areas, and with pre-existing defects embedded in the sample, such as those we will report on here (36-times larger cross-sectional area: 10 million atoms). We report on shock waves in fcc copper, where the atoms interact via an EAM (embedded-atom-method) many-body potential, as well as pair-potential materials.(B.L. Holian, P.S. Lomdahl, S.J. Zhou, D.M. Beazley, and A.F. Voter, (1997, unpublished).)

Embedded WENO: A design strategy to improve existing WENO schemes

NASA Astrophysics Data System (ADS)

van Lith, Bart S.; ten Thije Boonkkamp, Jan H. M.; IJzerman, Wilbert L.

2017-02-01

Embedded WENO methods utilise all adjacent smooth substencils to construct a desirable interpolation. Conventional WENO schemes under-use this possibility close to large gradients or discontinuities. We develop a general approach for constructing embedded versions of existing WENO schemes. Embedded methods based on the WENO schemes of Jiang and Shu [1] and on the WENO-Z scheme of Borges et al. [2] are explicitly constructed. Several possible choices are presented that result in either better spectral properties or a higher order of convergence for sufficiently smooth solutions. However, these improvements carry over to discontinuous solutions. The embedded methods are demonstrated to be indeed improvements over their standard counterparts by several numerical examples. All the embedded methods presented have no added computational effort compared to their standard counterparts.

Atomic-scale dynamics of a model glass-forming metallic liquid: Dynamical crossover, dynamical decoupling, and dynamical clustering

DOE PAGES

Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang

2015-04-01

The phase behavior of multi-component metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamic aspects of such a model ternary metallic liquid Cu 40Zr 51Al 9 using molecular dynamics simulation with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (diffusion coefficient, relaxation times, and shear viscosity) bordered at T x ~1300K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs in the equilibrium liquid state well above the melting temperature of the system (T m ~ 900K),more » and the crossover temperature is roughly twice of the glass-transition temperature (T g). Below T x, we found the elemental dynamics decoupled and the Stokes-Einstein relation broke down, indicating the onset of heterogeneous spatially correlated dynamics in the system mediated by dynamic communications among local configurational excitations. To directly characterize and visualize the correlated dynamics, we employed a non-parametric, unsupervised machine learning technique and identified dynamical clusters of atoms with similar atomic mobility. The revealed average dynamical cluster size shows an accelerated increase below T x and mimics the trend observed in other ensemble averaged quantities that are commonly used to quantify the spatially heterogeneous dynamics such as the non-Gaussian parameter and the four-point correlation function.« less

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

Hégely, Bence; Nagy, Péter R.; Kállay, Mihály, E-mail: kallay@mail.bme.hu

Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up themore » system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.« less

RESLanjut: The learning media for improve students understanding in embedded systems

NASA Astrophysics Data System (ADS)

Indrianto, Susanti, Meilia Nur Indah; Karina, Djunaidi

2017-08-01

The use of network in embedded system can be done with many kinds of network, with the use of mobile phones, bluetooths, modems, ethernet cards, wireless technology and so on. Using network in embedded system could help people to do remote controlling. On previous research, researchers found that many students have the ability to comprehend the basic concept of embedded system. They could also make embedded system tools but without network integration. And for that, a development is needed for the embedded system module. The embedded system practicum module design needs a prototype method in order to achieve the desired goal. The prototype method is often used in the real world. Or even, a prototype method is a part of products that consist of logic expression or external physical interface. The embedded system practicum module is meant to increase student comprehension of embedded system course, and also to encourage students to innovate on technology based tools. It is also meant to help teachers to teach the embedded system concept on the course. The student comprehension is hoped to increase with the use of practicum course.

Entanglement measures in embedding quantum simulators with nuclear spins

NASA Astrophysics Data System (ADS)

Xin, Tao; Pedernales, Julen S.; Solano, Enrique; Long, Gui-Lu

2018-02-01

We implement an embedding quantum simulator (EQS) in nuclear spin systems. The experiment consists of a simulator of up to three qubits, plus a single ancillary qubit, where we are able to efficiently measure the concurrence and the three-tangle of two-qubit and three-qubit systems as they undergo entangling dynamics. The EQS framework allows us to drastically reduce the number of measurements needed for this task, which otherwise would require full-state reconstruction of the qubit system. Our simulator is built of the nuclear spins of four 13C atoms in a molecule of trans-crotonic acid manipulated with NMR techniques.

Combined electron beam imaging and ab initio modeling of T1 precipitates in Al-Li-Cu alloys

NASA Astrophysics Data System (ADS)

Dwyer, C.; Weyland, M.; Chang, L. Y.; Muddle, B. C.

2011-05-01

Among the many considerable challenges faced in developing a rational basis for advanced alloy design, establishing accurate atomistic models is one of the most fundamental. Here we demonstrate how advanced imaging techniques in a double-aberration-corrected transmission electron microscope, combined with ab initio modeling, have been used to determine the atomic structure of embedded 1 nm thick T1 precipitates in precipitation-hardened Al-Li-Cu aerospace alloys. The results provide an accurate determination of the controversial T1 structure, and demonstrate how next-generation techniques permit the characterization of embedded nanostructures in alloys and other nanostructured materials.

Observation of correlated electronic decay in expanding clusters triggered by near-infrared fields

PubMed Central

Schütte, B.; Arbeiter, M.; Fennel, T.; Jabbari, G.; Kuleff, A.I.; Vrakking, M.J.J.; Rouzée, A.

2015-01-01

When an excited atom is embedded into an environment, novel relaxation pathways can emerge that are absent for isolated atoms. A well-known example is interatomic Coulombic decay, where an excited atom relaxes by transferring its excess energy to another atom in the environment, leading to its ionization. Such processes have been observed in clusters ionized by extreme-ultraviolet and X-ray lasers. Here, we report on a correlated electronic decay process that occurs following nanoplasma formation and Rydberg atom generation in the ionization of clusters by intense, non-resonant infrared laser fields. Relaxation of the Rydberg states and transfer of the available electronic energy to adjacent electrons in Rydberg states or quasifree electrons in the expanding nanoplasma leaves a distinct signature in the electron kinetic energy spectrum. These so far unobserved electron-correlation-driven energy transfer processes may play a significant role in the response of any nano-scale system to intense laser light. PMID:26469997

Electrochemistry at Edge of Single Graphene Layer in a Nanopore

PubMed Central

Banerjee, Shouvik; Shim, Jiwook; Rivera, Jose; Jin, Xiaozhong; Estrada, David; Solovyeva, Vita; You, Xiuque; Pak, James; Pop, Eric; Aluru, Narayana; Bashir, Rashid

2013-01-01

We study the electrochemistry of single layer graphene edges using a nanopore-based structure consisting of stacked graphene and Al2O3 dielectric layers. Nanopores, with diameters ranging from 5 to 20 nm, are formed by an electron beam sculpting process on the stacked layers. This leads to unique edge structure which, along with the atomically thin nature of the embedded graphene electrode, demonstrates electrochemical current densities as high as 1.2 × 104 A/cm2. The graphene edge embedded structure offers a unique capability to study the electrochemical exchange at an individual graphene edge, isolated from the basal plane electrochemical activity. We also report ionic current modulation in the nanopore by biasing the embedded graphene terminal with respect to the electrodes in the fluid. The high electrochemical specific current density for a graphene nanopore-based device can have many applications in sensitive chemical and biological sensing, and energy storage devices. PMID:23249127

Medium-induced change of the optical response of metal clusters in rare-gas matrices

NASA Astrophysics Data System (ADS)

Xuan, Fengyuan; Guet, Claude

2017-10-01

Interaction with the surrounding medium modifies the optical response of embedded metal clusters. For clusters from about ten to a few hundreds of silver atoms, embedded in rare-gas matrices, we study the environment effect within the matrix random phase approximation with exact exchange (RPAE) quantum approach, which has proved successful for free silver clusters. The polarizable surrounding medium screens the residual two-body RPAE interaction, adds a polarization term to the one-body potential, and shifts the vacuum energy of the active delocalized valence electrons. Within this model, we calculate the dipole oscillator strength distribution for Ag clusters embedded in helium droplets, neon, argon, krypton, and xenon matrices. The main contribution to the dipole surface plasmon red shift originates from the rare-gas polarization screening of the two-body interaction. The large size limit of the dipole surface plasmon agrees well with the classical prediction.

Implementation of a quantum metamaterial using superconducting qubits.

PubMed

Macha, Pascal; Oelsner, Gregor; Reiner, Jan-Michael; Marthaler, Michael; André, Stephan; Schön, Gerd; Hübner, Uwe; Meyer, Hans-Georg; Il'ichev, Evgeni; Ustinov, Alexey V

2014-10-14

The key issue for the implementation of a metamaterial is to demonstrate the existence of collective modes corresponding to coherent oscillations of the meta-atoms. Atoms of natural materials interact with electromagnetic fields as quantum two-level systems. Artificial quantum two-level systems can be made, for example, using superconducting nonlinear resonators cooled down to their ground state. Here we perform an experiment in which 20 of these quantum meta-atoms, so-called flux qubits, are embedded into a microwave resonator. We observe the dispersive shift of the resonator frequency imposed by the qubit metamaterial and the collective resonant coupling of eight qubits. The realized prototype represents a mesoscopic limit of naturally occurring spin ensembles and as such we demonstrate the AC-Zeeman shift of a resonant qubit ensemble. The studied system constitutes the implementation of a basic quantum metamaterial in the sense that many artificial atoms are coupled collectively to the quantized mode of a photon field.

Features of structural changes in the near-surface aluminum layer under various schemes of ion implantation

NASA Astrophysics Data System (ADS)

Kryzhevich, Dmitrij S.; Zolnikov, Konstantin P.; Korchuganov, Aleksandr V.

2017-10-01

The molecular dynamics simulation of structural rearrangements in the surface layer of aluminum samples under ion implantation of various intensities was carried out. The features of the internal structure and the crystallographic orientation of the irradiated crystallite were taken into account. To describe the interatomic interaction many-body potentials obtained in the framework of the embedded atom method were used. Irradiation of the {100} surface results in much less number of formed defects than irradiation of the {110} and {111} ones. When irradiating surfaces with beams of relatively low energy grains remain unchanged in the surface region and the formation of stacking faults was not observed. At a high intensity of irradiation, the near-surface layer of the crystallite melts. In the absence of heat removal, the centers of crystallization become grains lying on the boundary of the solid and liquid phases. Those grains increase due to the adjustment of the atoms of the liquid phase to their lattice. As a result, the grain size in the near-surface region increases.

Understanding homogeneous nucleation in solidification of aluminum by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mahata, Avik; Asle Zaeem, Mohsen; Baskes, Michael I.

2018-02-01

Homogeneous nucleation from aluminum (Al) melt was investigated by million-atom molecular dynamics simulations utilizing the second nearest neighbor modified embedded atom method potentials. The natural spontaneous homogenous nucleation from the Al melt was produced without any influence of pressure, free surface effects and impurities. Initially isothermal crystal nucleation from undercooled melt was studied at different constant temperatures, and later superheated Al melt was quenched with different cooling rates. The crystal structure of nuclei, critical nucleus size, critical temperature for homogenous nucleation, induction time, and nucleation rate were determined. The quenching simulations clearly revealed three temperature regimes: sub-critical nucleation, super-critical nucleation, and solid-state grain growth regimes. The main crystalline phase was identified as face-centered cubic, but a hexagonal close-packed (hcp) and an amorphous solid phase were also detected. The hcp phase was created due to the formation of stacking faults during solidification of Al melt. By slowing down the cooling rate, the volume fraction of hcp and amorphous phases decreased. After the box was completely solid, grain growth was simulated and the grain growth exponent was determined for different annealing temperatures.

Synthesis and characterization of the NiFe2O4@TEOS-TPS@Ag nanocomposite and investigation of its antibacterial activity

NASA Astrophysics Data System (ADS)

Allafchian, Ali R.; Jalali, S. A. H.; Amiri, R.; Shahabadi, Sh.

2016-11-01

In this study, the NiFe2O4 was embedded in (3-mercaptopropyl) trimethoxysilane (TPS) and tetraethyl orthosilicate (TEOS) using the sol-gel method. These compounds were used as the support of Ag nanoparticles (Ag NPs). The NiFe2O4@TEOS-TPS@Ag nanocomposites were obtained with the development of bonding between the silver atoms of Ag NPs and the sulfur atoms of TPS molecule. Field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FT-IR) were used for the characterization of the Ag nanocomposites. Also, the magnetic properties of these nanocomposites were studied by using a vibrating sample magnetometer (VSM) technique. The disk diffusion, minimum inhibition concentration (MIC) and minimum bactericidal concentrations (MBC) tests were used for the investigation of the antibacterial effect of this nanocomposite against bacterial strains. The synthesized nanocomposite presented high reusability and good antibacterial activity against gram-positive and gram-negative bacteria. Remarkably, this nanocomposite could be easily removed from the disinfected media by magnetic decantation.

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.

Ligand-surface interactions and surface oxidation of colloidal PbSe quantum dots revealed by thin-film positron annihilation methods

NASA Astrophysics Data System (ADS)

Shi, Wenqin; Eijt, Stephan W. H.; Suchand Sandeep, C. S.; Siebbeles, Laurens D. A.; Houtepen, Arjan J.; Kinge, Sachin; Brück, Ekkes; Barbiellini, Bernardo; Bansil, Arun

2016-02-01

Positron Two Dimensional Angular Correlation of Annihilation Radiation (2D-ACAR) measurements reveal modifications of the electronic structure and composition at the surfaces of PbSe quantum dots (QDs), deposited as thin films, produced by various ligands containing either oxygen or nitrogen atoms. In particular, the 2D-ACAR measurements on thin films of colloidal PbSe QDs capped with oleic acid ligands yield an increased intensity in the electron momentum density (EMD) at high momenta compared to PbSe quantum dots capped with oleylamine. Moreover, the EMD of PbSe QDs is strongly affected by the small ethylenediamine ligands, since these molecules lead to small distances between QDs and favor neck formation between near neighbor QDs, inducing electronic coupling between neighboring QDs. The high sensitivity to the presence of oxygen atoms at the surface can be also exploited to monitor the surface oxidation of PbSe QDs upon exposure to air. Our study clearly demonstrates that positron annihilation spectroscopy applied to thin films can probe surface transformations of colloidal semiconductor QDs embedded in functional layers.

Modeling of point defects and rare gas incorporation in uranium mono-carbide

NASA Astrophysics Data System (ADS)

Chartier, A.; Van Brutzel, L.

2007-02-01

An embedded atom method (EAM) potential has been established for uranium mono-carbide. This EAM potential was fitted on structural properties of metallic uranium and uranium mono-carbide. The formation energies of point defects, as well as activation energies for self migration, have been evaluated in order to cross-check the suitability of the potential. Assuming that the carbon vacancies are the main defects in uranium mono-carbide compounds, the migration paths and energies are consistent with experimental data selected by Catlow[C.R.A. Catlow, J. Nucl. Mater. 60 (1976) 151]. The insertion and migration energies for He, Kr and Xe have also been evaluated with available inter-atomic potentials [H.H. Andersen, P. Sigmund, Nucl. Instr. and Meth. B 38 (1965) 238]. Results show that the most stable defect configuration for rare gases is within uranium vacancies. The migration energy of an interstitial Xe is 0.5 eV, in agreement with the experimental value of 0.5 eV [Hj. Matzke, Science of advanced LMFBR fuels, Solid State Physics, Chemistry and Technology of Carbides, Nitrides and Carbonitrides of Uranium and Plutonium, North-Holland, 1986].

A possible oriented attachment growth mechanism for silver nanowire formation

DOE PAGES

Murph, Simona E. Hunyadi; Murphy, Catherine J.; Leach, Austin; ...

2015-04-06

Electron microscopy studies suggest that silver nanowires prepared by an approach reported earlier by us (Caswell, K. K., Bender, C. M., Murphy, C. J. Nano Lett.,2003, 3, 667–669) form through a coarsening process via an oriented attachment mechanism. Initially, silver nucleation centers were produced by chemical reduction of silver ions in boiling water, with sodium citrate and sodium hydroxide as additives in solution. These nucleation centers, with a twinned crystallographic orientation, ultimately merge into fully grown silver nanowires. This is a completely different mechanism from the seed-mediated growth approach, which has also been used to produce silver nanowires. Furthermore, companionmore » molecular dynamics performed with the embedded atom method are in agreement with our experimental data.« less

A possible oriented attachment growth mechanism for silver nanowire formation

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

Murph, Simona E. Hunyadi; Murphy, Catherine J.; Leach, Austin

Electron microscopy studies suggest that silver nanowires prepared by an approach reported earlier by us (Caswell, K. K., Bender, C. M., Murphy, C. J. Nano Lett.,2003, 3, 667–669) form through a coarsening process via an oriented attachment mechanism. Initially, silver nucleation centers were produced by chemical reduction of silver ions in boiling water, with sodium citrate and sodium hydroxide as additives in solution. These nucleation centers, with a twinned crystallographic orientation, ultimately merge into fully grown silver nanowires. This is a completely different mechanism from the seed-mediated growth approach, which has also been used to produce silver nanowires. Furthermore, companionmore » molecular dynamics performed with the embedded atom method are in agreement with our experimental data.« less

The parametric resonance—from LEGO Mindstorms to cold atoms

NASA Astrophysics Data System (ADS)

Kawalec, Tomasz; Sierant, Aleksandra

2017-07-01

We show an experimental setup based on a popular LEGO Mindstorms set, allowing us to both observe and investigate the parametric resonance phenomenon. The presented method is simple but covers a variety of student activities like embedded software development, conducting measurements, data collection and analysis. It may be used during science shows, as part of student projects and to illustrate the parametric resonance in mechanics or even quantum physics, during lectures or classes. The parametrically driven LEGO pendulum gains energy in a spectacular way, increasing its amplitude from 10° to about 100° within a few tens of seconds. We provide also a short description of a wireless absolute orientation sensor that may be used in quantitative analysis of driven or free pendulum movement.

Design of the magnetic homonuclear bonds boron nitride nanosheets using DFT methods.

PubMed

Anota, E Chigo; Hernández, A Bautista; Morales, A Escobedo; Castro, M

2017-06-01

Design and characterization of the structural, electronic, and magnetic properties of armchair boron-nitride, BN (B 27 N 27 H 18 ), nanosheets were performed by means of density functional theory all-electron calculations. The HSEh1PBE-GGA method together with 6-31G(d) basis sets were used. Non-stoichiometric B 30 N 24 H 18 and B 24 N 30 H 18 compositions: rich in boron or nitrogen atoms, forming homonuclear B or N bonds, respectively, were chosen. The obtained results reveal that these BN nanosheets reach structural stability in the anionic form, where semiconductor and magnetic behaviors are promoted. Effectively, the HOMO-LUMO gap is of 2.03 and 2.39eV, respectively and the magnetic moments are of 1.0 magneton bohrs, coming from the boron atoms in both systems. The rich in boron nanosheets present high-polarity, either in the gas phase or embedded in aqueous mediums like water, as well as low chemical reactivity, signifying potential applicability in the transportation of pharmaceutical species in biological mediums. These systems are also promising for the design of electronic devices, because they possess low-work functions, mainly arising from the homonuclear boron or nitrogen bond formation. Copyright © 2017 Elsevier Inc. All rights reserved.

Detecting the Curvature of de Sitter Universe with Two Entangled Atoms

NASA Astrophysics Data System (ADS)

Tian, Zehua; Wang, Jieci; Jing, Jiliang; Dragan, Andrzej

2016-10-01

Casimir-Polder interaction arises from the vacuum fluctuations of quantum field that depend on spacetime curvature and thus is spacetime-dependent. Here we show how to use the resonance Casimir-Polder interaction (RCPI) between two entangled atoms to detect spacetime curvature. We find that the RCPI of two static entangled atoms in the de Sitter-invariant vacuum depends on the de Sitter spacetime curvature relevant to the temperature felt by the static observer. It is characterized by a 1/L2 power law decay when beyond a characteristic length scale associated to the breakdown of a local inertial description of the two-atom system. However, the RCPI of the same setup embedded in a thermal bath in the Minkowski universe is temperature-independent and is always characterized by a 1/L power law decay. Therefore, although a single static atom in the de Sitter-invariant vacuum responds as if it were bathed in thermal radiation in a Minkowski universe, using the distinct difference between RCPI of two entangled atoms one can in principle distinguish these two universes.

Detecting the Curvature of de Sitter Universe with Two Entangled Atoms.

PubMed

Tian, Zehua; Wang, Jieci; Jing, Jiliang; Dragan, Andrzej

2016-10-12

Casimir-Polder interaction arises from the vacuum fluctuations of quantum field that depend on spacetime curvature and thus is spacetime-dependent. Here we show how to use the resonance Casimir-Polder interaction (RCPI) between two entangled atoms to detect spacetime curvature. We find that the RCPI of two static entangled atoms in the de Sitter-invariant vacuum depends on the de Sitter spacetime curvature relevant to the temperature felt by the static observer. It is characterized by a 1/L 2 power law decay when beyond a characteristic length scale associated to the breakdown of a local inertial description of the two-atom system. However, the RCPI of the same setup embedded in a thermal bath in the Minkowski universe is temperature-independent and is always characterized by a 1/L power law decay. Therefore, although a single static atom in the de Sitter-invariant vacuum responds as if it were bathed in thermal radiation in a Minkowski universe, using the distinct difference between RCPI of two entangled atoms one can in principle distinguish these two universes.

Detecting the Curvature of de Sitter Universe with Two Entangled Atoms

PubMed Central

Tian, Zehua; Wang, Jieci; Jing, Jiliang; Dragan, Andrzej

2016-01-01

Casimir-Polder interaction arises from the vacuum fluctuations of quantum field that depend on spacetime curvature and thus is spacetime-dependent. Here we show how to use the resonance Casimir-Polder interaction (RCPI) between two entangled atoms to detect spacetime curvature. We find that the RCPI of two static entangled atoms in the de Sitter-invariant vacuum depends on the de Sitter spacetime curvature relevant to the temperature felt by the static observer. It is characterized by a 1/L2 power law decay when beyond a characteristic length scale associated to the breakdown of a local inertial description of the two-atom system. However, the RCPI of the same setup embedded in a thermal bath in the Minkowski universe is temperature-independent and is always characterized by a 1/L power law decay. Therefore, although a single static atom in the de Sitter-invariant vacuum responds as if it were bathed in thermal radiation in a Minkowski universe, using the distinct difference between RCPI of two entangled atoms one can in principle distinguish these two universes. PMID:27731419

Structural predictions for Correlated Electron Materials Using the Functional Dynamical Mean Field Theory Approach

NASA Astrophysics Data System (ADS)

Haule, Kristjan

2018-04-01

The Dynamical Mean Field Theory (DMFT) in combination with the band structure methods has been able to address reach physics of correlated materials, such as the fluctuating local moments, spin and orbital fluctuations, atomic multiplet physics and band formation on equal footing. Recently it is getting increasingly recognized that more predictive ab-initio theory of correlated systems needs to also address the feedback effect of the correlated electronic structure on the ionic positions, as the metal-insulator transition is almost always accompanied with considerable structural distortions. We will review recently developed extension of merger between the Density Functional Theory (DFT) and DMFT method, dubbed DFT+ embedded DMFT (DFT+eDMFT), whichsuccessfully addresses this challenge. It is based on the stationary Luttinger-Ward functional to minimize the numerical error, it subtracts the exact double-counting of DFT and DMFT, and implements self-consistent forces on all atoms in the unit cell. In a few examples, we will also show how the method elucidated the important feedback effect of correlations on crystal structure in rare earth nickelates to explain the mechanism of the metal-insulator transition. The method showed that such feedback effect is also essential to understand the dynamic stability of the high-temperature body-centered cubic phase of elemental iron, and in particular it predicted strong enhancement of the electron-phonon coupling over DFT values in FeSe, which was very recently verified by pioneering time-domain experiment.

Oriented Polar Molecules in a Solid Inert-Gas Matrix: A Proposed Method for Measuring the Electric Dipole Moment of the Electron

NASA Astrophysics Data System (ADS)

Vutha, A.; Horbatsch, M.; Hessels, E.

2018-01-01

We propose a very sensitive method for measuring the electric dipole moment of the electron using polar molecules embedded in a cryogenic solid matrix of inert-gas atoms. The polar molecules can be oriented in the $\\hat{\\rm{z}}$ direction by an applied electric field, as has recently been demonstrated by Park, et al. [Angewandte Chemie {\\bf 129}, 1066 (2017)]. The trapped molecules are prepared into a state which has its electron spin perpendicular to $\\hat{\\rm{z}}$, and a magnetic field along $\\hat{\\rm{z}}$ causes precession of this spin. An electron electric dipole moment $d_e$ would affect this precession due to the up to 100~GV/cm effective electric field produced by the polar molecule. The large number of polar molecules that can be embedded in a matrix, along with the expected long coherence times for the precession, allows for the possibility of measuring $d_e$ to an accuracy that surpasses current measurements by many orders of magnitude. Because the matrix can inhibit molecular rotations and lock the orientation of the polar molecules, it may not be necessary to have an electric field present during the precession. The proposed technique can be applied using a variety of polar molecules and inert gases, which, along with other experimental variables, should allow for careful study of systematic uncertainties in the measurement.

An embedded formula of the Chebyshev collocation method for stiff problems

NASA Astrophysics Data System (ADS)

Piao, Xiangfan; Bu, Sunyoung; Kim, Dojin; Kim, Philsu

2017-12-01

In this study, we have developed an embedded formula of the Chebyshev collocation method for stiff problems, based on the zeros of the generalized Chebyshev polynomials. A new strategy for the embedded formula, using a pair of methods to estimate the local truncation error, as performed in traditional embedded Runge-Kutta schemes, is proposed. The method is performed in such a way that not only the stability region of the embedded formula can be widened, but by allowing the usage of larger time step sizes, the total computational costs can also be reduced. In terms of concrete convergence and stability analysis, the constructed algorithm turns out to have an 8th order convergence and it exhibits A-stability. Through several numerical experimental results, we have demonstrated that the proposed method is numerically more efficient, compared to several existing implicit methods.

Computer simulation of metal wire explosion under high rate heating

NASA Astrophysics Data System (ADS)

Zolnikov, K. P.; Kryzhevich, D. S.; Korchuganov, A. V.

2017-05-01

Synchronous electric explosion of metal wires and synthesis of bicomponent nanoparticles were investigated on the base of molecular dynamics method. Copper and nickel nanosized crystallites of cylindrical shape were chosen as conductors for explosion. The embedded atom approximation was used for calculation of the interatomic interactions. The agglomeration process after explosion metal wires was the main mechanism for particle synthesis. The distribution of chemical elements was non-uniform over the cross section of the bicomponent particles. The copper concentration in the surface region was higher than in the bulk of the synthesized particle. By varying the loading parameters (heating temperature, the distance between the wires) one can control the size and internal structure of the synthesized bicomponent nanoparticles. The obtained results showed that the method of molecular dynamics can be effectively used to determine the optimal technological mode of nanoparticle synthesis on the base of electric explosion of metal wires.

Surface tension of undercooled liquid cobalt

NASA Astrophysics Data System (ADS)

Yao, W. J.; Han, X. J.; Chen, M.; Wei, B.; Guo, Z. Y.

2002-08-01

This paper provides the results on experimentally measured and numerically predicted surface tensions of undercooled liquid cobalt. The experiments were performed by using the oscillation drop technique combined with electromagnetic levitation. The simulations are carried out with the Monte Carlo (MC) method, where the surface tension is predicted through calculations of the work of cohesion, and the interatomic interaction is described with an embedded-atom method. The maximum undercooling of the liquid cobalt is reached at 231 K (0.13Tm) in the experiment and 268 K (0.17Tm) in the simulation. The surface tension and its relationship with temperature obtained in the experiment and simulation are σexp = 1.93 - 0.000 33 (T - T m) N m-1 and σcal = 2.26 - 0.000 32 (T - T m) N m-1 respectively. The temperature dependence of the surface tension calculated from the MC simulation is in reasonable agreement with that measured in the experiment.

Nonlinear vs. linear biasing in Trp-cage folding simulations

NASA Astrophysics Data System (ADS)

Spiwok, Vojtěch; Oborský, Pavel; Pazúriková, Jana; Křenek, Aleš; Králová, Blanka

2015-03-01

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

Nonlinear vs. linear biasing in Trp-cage folding simulations.

PubMed

Spiwok, Vojtěch; Oborský, Pavel; Pazúriková, Jana; Křenek, Aleš; Králová, Blanka

2015-03-21

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

Embedding of multidimensional time-dependent observations.

PubMed

Barnard, J P; Aldrich, C; Gerber, M

2001-10-01

A method is proposed to reconstruct dynamic attractors by embedding of multivariate observations of dynamic nonlinear processes. The Takens embedding theory is combined with independent component analysis to transform the embedding into a vector space of linearly independent vectors (phase variables). The method is successfully tested against prediction of the unembedded state vector in two case studies of simulated chaotic processes.

Embedding of multidimensional time-dependent observations

NASA Astrophysics Data System (ADS)

Barnard, Jakobus P.; Aldrich, Chris; Gerber, Marius

2001-10-01

A method is proposed to reconstruct dynamic attractors by embedding of multivariate observations of dynamic nonlinear processes. The Takens embedding theory is combined with independent component analysis to transform the embedding into a vector space of linearly independent vectors (phase variables). The method is successfully tested against prediction of the unembedded state vector in two case studies of simulated chaotic processes.

Single-Photon Routing for a L-Shaped Channel

NASA Astrophysics Data System (ADS)

Yang, Xiong; Hou, Jiao-Jiao; Wu, Chun

2018-02-01

We have investigated the transport properties of a single photon scattered by a two-level atom embedded in a L-shaped waveguide, which is made of two one-dimensional (1D) semi-infinite coupled-resonator waveguides (CRWs). Single photons can be directed from one CRW to the other due to spontaneous emission of the atom. The result shows that the spontaneous emission of the TLS still routes single photon from one CRW to the other; the boundary existing makes the probability of finding single photon in a CRW could reach one. Our the scheme is helpful to construct a ring quantum networks.

Joining of graphene flakes by low energy N ion beam irradiation

NASA Astrophysics Data System (ADS)

Wu, Xin; Zhao, Haiyan; Pei, Jiayun; Yan, Dong

2017-03-01

An approach utilizing low energy N ion beam irradiation is applied in joining two monolayer graphene flakes. Raman spectrometry and atomic force microscopy show the joining signal under 40 eV and 1 × 1014 cm-2 N ion irradiation. Molecular dynamics simulations demonstrate that the joining phenomenon is attributed to the punch-down effect and the subsequent chemical bond generation between the two sheets. The generated chemical bonds are made up of inserted ions (embedded joining) and knocked-out carbon atoms (saturation joining). The electronic transport properties of the joint are also calculated for its applications.

Nanoscale Subsurface Imaging via Resonant Difference-Frequency Atomic Force Ultrasonic Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, Sean A.; Cantrell, John H.; Lilehei, Peter T.

2007-01-01

A novel scanning probe microscope methodology has been developed that employs an ultrasonic wave launched from the bottom of a sample while the cantilever of an atomic force microscope, driven at a frequency differing from the ultrasonic frequency by the fundamental resonance frequency of the cantilever, engages the sample top surface. The nonlinear mixing of the oscillating cantilever and the ultrasonic wave in the region defined by the cantilever tip-sample surface interaction force generates difference-frequency oscillations at the cantilever fundamental resonance. The resonance-enhanced difference-frequency signals are used to create images of embedded nanoscale features.

A Student Experiment Method for Learning the Basics of Embedded Software Technologies Including Hardware/Software Co-design

NASA Astrophysics Data System (ADS)

Kambe, Hidetoshi; Mitsui, Hiroyasu; Endo, Satoshi; Koizumi, Hisao

The applications of embedded system technologies have spread widely in various products, such as home appliances, cellular phones, automobiles, industrial machines and so on. Due to intensified competition, embedded software has expanded its role in realizing sophisticated functions, and new development methods like a hardware/software (HW/SW) co-design for uniting HW and SW development have been researched. The shortfall of embedded SW engineers was estimated to be approximately 99,000 in the year 2006, in Japan. Embedded SW engineers should understand HW technologies and system architecture design as well as SW technologies. However, a few universities offer this kind of education systematically. We propose a student experiment method for learning the basics of embedded system development, which includes a set of experiments for developing embedded SW, developing embedded HW and experiencing HW/SW co-design. The co-design experiment helps students learn about the basics of embedded system architecture design and the flow of designing actual HW and SW modules. We developed these experiments and evaluated them.

Multibillion-atom Molecular Dynamics Simulations of Plasticity, Spall, and Ejecta

NASA Astrophysics Data System (ADS)

Germann, Timothy C.

2007-06-01

Modern supercomputing platforms, such as the IBM BlueGene/L at Lawrence Livermore National Laboratory and the Roadrunner hybrid supercomputer being built at Los Alamos National Laboratory, are enabling large-scale classical molecular dynamics simulations of phenomena that were unthinkable just a few years ago. Using either the embedded atom method (EAM) description of simple (close-packed) metals, or modified EAM (MEAM) models of more complex solids and alloys with mixed covalent and metallic character, simulations containing billions to trillions of atoms are now practical, reaching volumes in excess of a cubic micron. In order to obtain any new physical insights, however, it is equally important that the analysis of such systems be tractable. This is in fact possible, in large part due to our highly efficient parallel visualization code, which enables the rendering of atomic spheres, Eulerian cells, and other geometric objects in a matter of minutes, even for tens of thousands of processors and billions of atoms. After briefly describing the BlueGene/L and Roadrunner architectures, and the code optimization strategies that were employed, results obtained thus far on BlueGene/L will be reviewed, including: (1) shock compression and release of a defective EAM Cu sample, illustrating the plastic deformation accompanying void collapse as well as the subsequent void growth and linkup upon release; (2) solid-solid martensitic phase transition in shock-compressed MEAM Ga; and (3) Rayleigh-Taylor fluid instability modeled using large-scale direct simulation Monte Carlo (DSMC) simulations. I will also describe our initial experiences utilizing Cell Broadband Engine processors (developed for the Sony PlayStation 3), and planned simulation studies of ejecta and spall failure in polycrystalline metals that will be carried out when the full Petaflop Opteron/Cell Roadrunner supercomputer is assembled in mid-2008.

Fusion of multichannel local and global structural cues for photo aesthetics evaluation.

PubMed

Luming Zhang; Yue Gao; Zimmermann, Roger; Qi Tian; Xuelong Li

2014-03-01

Photo aesthetic quality evaluation is a fundamental yet under addressed task in computer vision and image processing fields. Conventional approaches are frustrated by the following two drawbacks. First, both the local and global spatial arrangements of image regions play an important role in photo aesthetics. However, existing rules, e.g., visual balance, heuristically define which spatial distribution among the salient regions of a photo is aesthetically pleasing. Second, it is difficult to adjust visual cues from multiple channels automatically in photo aesthetics assessment. To solve these problems, we propose a new photo aesthetics evaluation framework, focusing on learning the image descriptors that characterize local and global structural aesthetics from multiple visual channels. In particular, to describe the spatial structure of the image local regions, we construct graphlets small-sized connected graphs by connecting spatially adjacent atomic regions. Since spatially adjacent graphlets distribute closely in their feature space, we project them onto a manifold and subsequently propose an embedding algorithm. The embedding algorithm encodes the photo global spatial layout into graphlets. Simultaneously, the importance of graphlets from multiple visual channels are dynamically adjusted. Finally, these post-embedding graphlets are integrated for photo aesthetics evaluation using a probabilistic model. Experimental results show that: 1) the visualized graphlets explicitly capture the aesthetically arranged atomic regions; 2) the proposed approach generalizes and improves four prominent aesthetic rules; and 3) our approach significantly outperforms state-of-the-art algorithms in photo aesthetics prediction.

Co-sputter deposited nickel-copper bimetallic nanoalloy embedded carbon films for electrocatalytic biomarker detection

NASA Astrophysics Data System (ADS)

Shiba, Shunsuke; Kato, Dai; Kamata, Tomoyuki; Niwa, Osamu

2016-06-01

We report the fabrication of a nickel (Ni)-copper (Cu) bimetallic nanoalloy (~3 nm) embedded carbon film electrode with the unbalanced magnetron (UBM) co-sputtering technique, which requires only a one-step process at room temperature. Most of each nanoalloy body was firmly embedded in a chemically stable carbon matrix with an atomically flat surface (Ra: 0.21 nm), suppressing the aggregation and/or detachment of the nanoalloy from the electrode surface. The nanoalloy size and composition can be controlled simply by individually controlling the target powers of carbon, Ni and Cu, which also makes it possible to localize the nanoalloys near the electrode surface. This electrode exhibited excellent electrocatalytic activity for d-mannitol, which should be detected with a low detection limit in urine samples for the diagnosis of severe intestinal diseases. With a Ni/Cu ratio of around 64/36, the electrocatalytic current per metal area was 3.4 times larger than that of an alloy film electrode with a similar composition (~70/30). This improved electrocatalytic activity realized higher stability (n = 60, relative standard deviation (RSD): 4.6%) than the alloy film (RSD: 32.2%) as demonstrated by continuous measurements of d-mannitol.We report the fabrication of a nickel (Ni)-copper (Cu) bimetallic nanoalloy (~3 nm) embedded carbon film electrode with the unbalanced magnetron (UBM) co-sputtering technique, which requires only a one-step process at room temperature. Most of each nanoalloy body was firmly embedded in a chemically stable carbon matrix with an atomically flat surface (Ra: 0.21 nm), suppressing the aggregation and/or detachment of the nanoalloy from the electrode surface. The nanoalloy size and composition can be controlled simply by individually controlling the target powers of carbon, Ni and Cu, which also makes it possible to localize the nanoalloys near the electrode surface. This electrode exhibited excellent electrocatalytic activity for d-mannitol, which should be detected with a low detection limit in urine samples for the diagnosis of severe intestinal diseases. With a Ni/Cu ratio of around 64/36, the electrocatalytic current per metal area was 3.4 times larger than that of an alloy film electrode with a similar composition (~70/30). This improved electrocatalytic activity realized higher stability (n = 60, relative standard deviation (RSD): 4.6%) than the alloy film (RSD: 32.2%) as demonstrated by continuous measurements of d-mannitol. Electronic supplementary information (ESI) available: The concept of UBM co-sputtering for fabricating nanoalloy embedded carbon films. HRTEM images of the NiNP and Ni32Cu68 nanoalloy embedded carbon films. The experimental conditions for sputter deposition, HRTEM, HAADF-STEM, STEM-EDS measurements and continuous flow injection analysis. XPS analysis of the nanoalloy embedded carbon film. Repeated CVs of both the nanoalloy embedded carbon film and the alloy film. Amperometric detection of d-mannitol in the presence of chloride ions. See DOI: 10.1039/c6nr02287a

The data embedding method

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

Sandford, M.T. II; Bradley, J.N.; Handel, T.G.

Data embedding is a new steganographic method for combining digital information sets. This paper describes the data embedding method and gives examples of its application using software written in the C-programming language. Sandford and Handel produced a computer program (BMPEMBED, Ver. 1.51 written for IBM PC/AT or compatible, MS/DOS Ver. 3.3 or later) that implements data embedding in an application for digital imagery. Information is embedded into, and extracted from, Truecolor or color-pallet images in Microsoft{reg_sign} bitmap (.BMP) format. Hiding data in the noise component of a host, by means of an algorithm that modifies or replaces the noise bits,more » is termed {open_quote}steganography.{close_quote} Data embedding differs markedly from conventional steganography, because it uses the noise component of the host to insert information with few or no modifications to the host data values or their statistical properties. Consequently, the entropy of the host data is affected little by using data embedding to add information. The data embedding method applies to host data compressed with transform, or {open_quote}lossy{close_quote} compression algorithms, as for example ones based on discrete cosine transform and wavelet functions. Analysis of the host noise generates a key required for embedding and extracting the auxiliary data from the combined data. The key is stored easily in the combined data. Images without the key cannot be processed to extract the embedded information. To provide security for the embedded data, one can remove the key from the combined data and manage it separately. The image key can be encrypted and stored in the combined data or transmitted separately as a ciphertext much smaller in size than the embedded data. The key size is typically ten to one-hundred bytes, and it is in data an analysis algorithm.« less

Data embedding method

NASA Astrophysics Data System (ADS)

Sandford, Maxwell T., II; Bradley, Jonathan N.; Handel, Theodore G.

1996-01-01

Data embedding is a new steganographic method for combining digital information sets. This paper describes the data embedding method and gives examples of its application using software written in the C-programming language. Sandford and Handel produced a computer program (BMPEMBED, Ver. 1.51 written for IBM PC/AT or compatible, MS/DOS Ver. 3.3 or later) that implements data embedding in an application for digital imagery. Information is embedded into, and extracted from, Truecolor or color-pallet images in MicrosoftTM bitmap (BMP) format. Hiding data in the noise component of a host, by means of an algorithm that modifies or replaces the noise bits, is termed `steganography.' Data embedding differs markedly from conventional steganography, because it uses the noise component of the host to insert information with few or no modifications to the host data values or their statistical properties. Consequently, the entropy of the host data is affected little by using data embedding to add information. The data embedding method applies to host data compressed with transform, or `lossy' compression algorithms, as for example ones based on discrete cosine transform and wavelet functions. Analysis of the host noise generates a key required for embedding and extracting the auxiliary data from the combined data. The key is stored easily in the combined data. Images without the key cannot be processed to extract the embedded information. To provide security for the embedded data, one can remove the key from the combined data and manage it separately. The image key can be encrypted and stored in the combined data or transmitted separately as a ciphertext much smaller in size than the embedded data. The key size is typically ten to one-hundred bytes, and it is derived from the original host data by an analysis algorithm.

Atomic Force Microscopy Studies of Functional and Dysfunctional Pulmonary Surfactant Films. I. Micro- and Nanostructures of Functional Pulmonary Surfactant Films and the Effect of SP-A

PubMed Central

Zuo, Yi Y.; Keating, Eleonora; Zhao, Lin; Tadayyon, Seyed M.; Veldhuizen, Ruud A. W.; Petersen, Nils O.; Possmayer, Fred

2008-01-01

Monolayers of a functional pulmonary surfactant (PS) can reach very low surface tensions well below their equilibrium value. The mechanism by which PS monolayers reach such low surface tensions and maintain film stability remains unknown. As shown previously by fluorescence microscopy, phospholipid phase transition and separation seem to be important for the normal biophysical properties of PS. This work studied phospholipid phase transitions and separations in monolayers of bovine lipid extract surfactant using atomic force microscopy. Atomic force microscopy showed phospholipid phase separation on film compression and a monolayer-to-multilayer transition at surface pressure 40–50 mN/m. The tilted-condensed phase consisted of domains not only on the micrometer scale, as detected previously by fluorescence microscopy, but also on the nanometer scale, which is below the resolution limits of conventional optical methods. The nanodomains were embedded uniformly within the liquid-expanded phase. On compression, the microdomains broke up into nanodomains, thereby appearing to contribute to tilted-condensed and liquid-expanded phase remixing. Addition of surfactant protein A altered primarily the nanodomains and promoted the formation of multilayers. We conclude that the nanodomains play a predominant role in affecting the biophysical properties of PS monolayers and the monolayer-to-multilayer transition. PMID:18212010

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

Hu, Shenyang; Setyawan, Wahyu; Joshi, Vineet V.

Xe gas bubble superlattice formation is observed in irradiated uranium–10 wt% molybdenum (U10Mo) fuels. However, the thermodynamic properties of the bubbles (the relationship among bubble size, equilibrium Xe concentration, and bubble pressure) and the mechanisms of bubble growth and superlattice formation are not well known. In this work, molecular dynamics is used to study these properties and mechanisms. The results provide important inputs for quantitative mesoscale models of gas bubble evolution and fuel performance. In the molecular dynamics simulations, the embedded-atom method (EAM) potential of U10Mo-Xe (Smirnova et al. 2013) is employed. Initial gas bubbles with low Xe concentration aremore » generated in a U10Mo single crystal. Then Xe atom atoms are continuously added into the bubbles, and the evolution of pressure and dislocation emission around the bubbles is analyzed. The relationship between pressure, equilibrium Xe concentration, and radius of the bubbles is established. It was found that the gas bubble growth is accompanied by partial dislocation emission, which results in a star-shaped dislocation structure and an anisotropic stress field. The emitted partial dislocations have a Burgers vector along the <111> direction and a slip plane of (11-2). Dislocation loop punch-out was not observed. A tensile stress was found along <110> directions around the bubble, favoring the nucleation and formation of a face-centered cubic bubble superlattice in body-centered cubic U10Mo fuels.« less

Influence of string-like cooperative atomic motion on surface diffusion in the (110) interfacial region of crystalline Ni

PubMed Central

Zhang, Hao; Yang, Ying; Douglas, Jack F.

2015-01-01

Although we often think about crystalline materials in terms of highly organized arrays of atoms, molecules, or even colloidal particles, many of the important properties of this diverse class of materials relating to their catalytic behavior, thermodynamic stability, and mechanical properties derive from the dynamics and thermodynamics of their interfacial regions, which we find they have a dynamics more like glass-forming (GF) liquids than crystals at elevated temperatures. This is a general problem arising in any attempt to model the properties of naturally occurring crystalline materials since many aspects of the dynamics of glass-forming liquids remain mysterious. We examine the nature of this phenomenon in the “simple” case of the (110) interface of crystalline Ni, based on a standard embedded-atom model potential, and we then quantify the collective dynamics in this interfacial region using newly developed methods for characterizing the cooperative dynamics of glass-forming liquids. As in our former studies of the interfacial dynamics of grain-boundaries and the interfacial dynamics of crystalline Ni nanoparticles (NPs), we find that the interface of bulk crystalline Ni exhibits all the characteristics of glass-forming materials, even at temperatures well below the equilibrium crystal melting temperature, Tm. This perspective offers a new approach to modeling and engineering the properties of crystalline materials. PMID:25725748

Accuracy-Energy Configurable Sensor Processor and IoT Device for Long-Term Activity Monitoring in Rare-Event Sensing Applications

PubMed Central

2014-01-01

A specially designed sensor processor used as a main processor in IoT (internet-of-thing) device for the rare-event sensing applications is proposed. The IoT device including the proposed sensor processor performs the event-driven sensor data processing based on an accuracy-energy configurable event-quantization in architectural level. The received sensor signal is converted into a sequence of atomic events, which is extracted by the signal-to-atomic-event generator (AEG). Using an event signal processing unit (EPU) as an accelerator, the extracted atomic events are analyzed to build the final event. Instead of the sampled raw data transmission via internet, the proposed method delays the communication with a host system until a semantic pattern of the signal is identified as a final event. The proposed processor is implemented on a single chip, which is tightly coupled in bus connection level with a microcontroller using a 0.18 μm CMOS embedded-flash process. For experimental results, we evaluated the proposed sensor processor by using an IR- (infrared radio-) based signal reflection and sensor signal acquisition system. We successfully demonstrated that the expected power consumption is in the range of 20% to 50% compared to the result of the basement in case of allowing 10% accuracy error. PMID:25580458

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Discriminative graph embedding for label propagation.

PubMed

Nguyen, Canh Hao; Mamitsuka, Hiroshi

2011-09-01

In many applications, the available information is encoded in graph structures. This is a common problem in biological networks, social networks, web communities and document citations. We investigate the problem of classifying nodes' labels on a similarity graph given only a graph structure on the nodes. Conventional machine learning methods usually require data to reside in some Euclidean spaces or to have a kernel representation. Applying these methods to nodes on graphs would require embedding the graphs into these spaces. By embedding and then learning the nodes on graphs, most methods are either flexible with different learning objectives or efficient enough for large scale applications. We propose a method to embed a graph into a feature space for a discriminative purpose. Our idea is to include label information into the embedding process, making the space representation tailored to the task. We design embedding objective functions that the following learning formulations become spectral transforms. We then reformulate these spectral transforms into multiple kernel learning problems. Our method, while being tailored to the discriminative tasks, is efficient and can scale to massive data sets. We show the need of discriminative embedding on some simulations. Applying to biological network problems, our method is shown to outperform baselines.

Synthesis and Luminescence Properties of Transparent Nanocrystalline GdF3:Tb Glass-Ceramic Scintillator.

PubMed

Lee, Gyuhyon; Savage, Nicholas; Wagner, Brent; Zhang, Yuelan; Jacobs, Benjamin; Menkara, Hisham; Summers, Christopher; Kang, Zhitao

2014-03-01

Transparent glass-ceramic containing rare-earth doped halide nanocrystals exhibits enhanced luminescence performance. In this study, a glass-ceramic with Tb doped gadolinium fluoride nanocrystals embedded in an aluminosilicate glass matrix is investigated for X-ray imaging applications. The nanocrystalline glass-ceramic scintillator was prepared by a melt-quench method followed by an anneal. The GdF 3 :Tb nanocrystals precipitated within the oxide glass matrix during the processing and their luminescence and scintillation properties were investigated. In this nanocomposite scintillator system, the incorporation of high atomic number Gd compound into the glass matrix increases the X-ray stopping power of the glass scintillator, and effective energy transfer between Gd 3+ and Tb 3+ ions in the nanocrystals enhances the scintillation efficiency.

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

Patel, Sajan; Petty, Clayton W.; Krafcik, Karen Lee

Electrostatic modes of atomic force microscopy have shown to be non-destructive and relatively simple methods for imaging conductors embedded in insulating polymers. Here we use electrostatic force microscopy to image the dispersion of carbon nanotubes in a latex-based conductive composite, which brings forth features not observed in previously studied systems employing linear polymer films. A fixed-potential model of the probe-nanotube electrostatics is presented which in principle gives access to the conductive nanoparticle's depth and radius, and the polymer film dielectric constant. Comparing this model to the data results in nanotube depths that appear to be slightly above the film–air interface.more » Furthermore, this result suggests that water-mediated charge build-up at the film–air interface may be the source of electrostatic phase contrast in ambient conditions.« less

Molecular-dynamics study of solid-liquid interface migration in fcc metals

NASA Astrophysics Data System (ADS)

Mendelev, M. I.; Rahman, M. J.; Hoyt, J. J.; Asta, M.

2010-10-01

In order to establish a link between various structural and kinetic properties of metals and the crystal-melt interfacial mobility, free-solidification molecular-dynamics simulations have been performed for a total of nine embedded atom method interatomic potentials describing pure Al, Cu and Ni. To fully explore the space of materials properties three new potentials have been developed. The new potentials are based on a previous description of Al, but in each case the liquid structure, the melting point and/or the latent heat are varied considerably. The kinetic coefficient, μ, for all systems has been compared with several theoretical predictions. It is found that at temperatures close to the melting point the magnitude of μ correlates well with the value of the diffusion coefficient in the liquid.

Synthesis and Luminescence Properties of Transparent Nanocrystalline GdF3:Tb Glass-Ceramic Scintillator

PubMed Central

Lee, Gyuhyon; Savage, Nicholas; Wagner, Brent; Zhang, Yuelan; Jacobs, Benjamin; Menkara, Hisham; Summers, Christopher; Kang, Zhitao

2014-01-01

Transparent glass-ceramic containing rare-earth doped halide nanocrystals exhibits enhanced luminescence performance. In this study, a glass-ceramic with Tb doped gadolinium fluoride nanocrystals embedded in an aluminosilicate glass matrix is investigated for X-ray imaging applications. The nanocrystalline glass-ceramic scintillator was prepared by a melt-quench method followed by an anneal. The GdF3:Tb nanocrystals precipitated within the oxide glass matrix during the processing and their luminescence and scintillation properties were investigated. In this nanocomposite scintillator system, the incorporation of high atomic number Gd compound into the glass matrix increases the X-ray stopping power of the glass scintillator, and effective energy transfer between Gd3+ and Tb3+ ions in the nanocrystals enhances the scintillation efficiency. PMID:24610960

Atomic-level molybdenum oxide nanorings with full-spectrum absorption and photoresponsive properties.

PubMed

Yang, Yong; Yang, Yang; Chen, Shuangming; Lu, Qichen; Song, Li; Wei, Yen; Wang, Xun

2017-11-16

Superthin nanostructures, particularly with atomic-level thicknesses, typically display unique optical properties because of their exceptional light-matter interactions. Here, we report a facile strategy for the synthesis of sulfur-doped molybdenum oxide nanorings with an atomic-level size (thickness of 0.5 nm) and a tunable ring-in-ring architecture. These atomic-level nanorings displayed strong photo-absorption in both the visible and infrared-light ranges and acted as a photothermal agent. Under irradiation with an 808 nm laser with an intensity of 1 W/cm 2 , a composite of the nanorings embedded in polydimethylsiloxane showed an ultrafast photothermal effect, delivering a local temperature of up to 400 °C within 20 s, which to the best of our knowledge is the highest temperature by light irradiation reported to date. Meanwhile, the resulting nanorings were also employed as a photoinitiator to remotely induce a visible-light shape memory response, self-healing, reshaping performance and reversible actuation of dynamic three-dimensional structures. This study demonstrates an advancement towards controlling atomic-level-sized nanostructures and achieving greatly enhanced optical performances for optoelectronics.

Synthesis of nitrogen-containing carbon by solution plasma in aniline with high-repetition frequency discharges

NASA Astrophysics Data System (ADS)

Hyun, Koangyong; Ueno, Tomonaga; Saito, Nagahiro

2016-01-01

Nitrogen-containing carbon nanoparticles were synthesized in aniline by solution plasma with high-repetition frequency discharges. We developed a bipolar pulsed power supply that can apply high-repetition frequencies ranging from 25 to 200 kHz. By utilizing high-repetition frequencies, conductive carbons were directly synthesized. The crystallinity was increased and H/C ratio of carbon was decreased. Furthermore, nitrogen atoms were simultaneously embedded in the carbon matrix. Due to the presence of nitrogen atoms, the conductivity and electrocatalytic activity of the samples were remarkably improved compared to that of a pure carbon matrix synthesized from a benzene precursor.

Multistep modeling of protein structure: application to bungarotoxin

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Shibata, M.; Rein, R.

1986-01-01

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

Choosing a therapy electron accelerator target.

PubMed

Hutcheon, R M; Schriber, S O; Funk, L W; Sherman, N K

1979-01-01

Angular distributions of photon depth dose produced by 25-MeV electrons incident on several fully stopping single-element targets (C, Al, Cu, Mo, Ta, Pb) and two composite layered targets (Ni-Al, W-Al) were studied. Depth-dose curves measured using TLD-700 (thermoluminescent dosimeter) chips embedded in lucite phantoms. Several useful therapy electron accelerator design curves were determined, including relative flattener thickness as a function of target atomic number, "effective" bremsstrahlung endpoint energy or beam "hardness" as a function of target atomic number and photon emission angle, and estimates of shielding thickness as a function of angle required to reduce the radiation outside the treatment cone to required levels.

Magnetism by embedding 3d transition metal atoms into germanene

NASA Astrophysics Data System (ADS)

Sharma, Durgesh Kumar; Kumar, Sudhir; Auluck, Sushil

2018-06-01

We have performed a series of first-principles calculations within the framework of density functional theory for germanene including mono vacancy (MV) and double vacancy (DV). Perdew–Burke–Ernzerhof generalized gradient approximation (GGA) in the form of exchange-correlation potential was used. Ten transition metals (TMs) i.e. Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu and Zn, have been embedded at MV and DV site for the purpose to introduce magnetism into germanene. We find TM embedded germanene is stable and the value of magnetic moment can be tune with the TM impurities. Further, carbon (C) or nitrogen (N) in the vicinity of MV has been considered to find its influence on stability and total magnetic moment. Present predictions indicate Mn impurity shows largest magnetic moment among considered ten TMs. The Heyd–Scuseria–Ernzerhof (HSE06) hybrid functional based calculations have been also carried out for Mn system only for shake of comparison standpoint. The GGA/HSE06 calculations show better stability of TM embedded germanene after doping of C or N in vicinity of TM. Our calculations may provide a promising approach to design germanene based spintronic devices.

Ion beam processing and characterization of advanced optical materials

NASA Astrophysics Data System (ADS)

Zhu, Jie

Ion beams have been extensively applied for materials modification and characterization. In this dissertation, I will focus on the applications of ion beams for advanced optical materials. The first part of my work addresses the effects of 1.0 MeV proton irradiation on photoluminescence (PL) properties of self-assembled InAs QDs. Compared to the QDs grown in a GaAs thin film, the QDs embedded in an AlAs/GaAs superlattice structure exhibits much higher photoluminescence degradation resistance to proton irradiation. Proton irradiation combined with thermal annealing results in significant blueshifts in PL spectra of QDs embedded in GaAs, suggesting enhanced atomic intermixing in the QD systems due to point defects introduced by ion irradiation. In the second part of my work, ion channeling combined with Rutherford backscattering is applied to investigate In-Ga atomic intermixing processes in the proton irradiated InAs QD system. Ion channeling along the growth (<100>) direction shows evidence of In atoms with small displacement from the atomic row, which gives direct signature of QD lattice structures, allowing us to monitor atomic intermixing between In and Ga. Based on the channeling data, a model for In-Ga atomic intermixing in InAs/GaAs QD system is proposed, in which In-Ga atomic intermixing can take place along both the growth direction and the lateral direction in the QD layer. The third part of my dissertation is the elemental mapping of silica-based optical cross section using micron-ion-beam imaging techniques. This work is intended to examine the thermal stability of Ge-doped fiber cores in high-temperature environments. Our measurements show that Ge completely diffuses out of the core region following thermal annealing at 1000°C. This indicates that silica-based optical fibers cannot be used for applications at extreme high temperatures. The final part is the study of the effects of various wet treatment on GaN surface, which is a necessary step during the GaN device fabrication. In our work, the HCL treatment has reduced the Ga concentration on the surface for N type GaN. However, for samples with lower concentration of Si doping or P type GaN samples, this effect does not occur.

Magnetic properties of single-phase MnBi grown from MnBi{sub 49} melt

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

Xiao, X. F.; Si, P. Z., E-mail: pzsi@cjlu.edu.cn; Feng, H.

2014-05-07

The single-phase NiAs-type MnBi, embedded in Bi matrix, was grown from homogeneous MnBi{sub 49} melt at low temperatures to prevent the formation of Mn{sub 1.08}Bi. An abrupt magnetization change was observed at ∼240 K. The origin of this change was ascribed to the movement of the Mn atoms between the regular sites and the interstitial sites in the MnBi lattices. The splitting of the x-ray photoelectron lines of MnBi indicates the presence of two binding states of Mn atoms, one of which was ascribed to interstitial Mn atoms. A large coercivity up to 1.79 T at 400 K was observed in the as-grownmore » bulk isotropic MnBi alloys.« less

First-Principles Study of Mo Segregation in MoNi(111): Effects of Chemisorbed Atomic Oxygen

PubMed Central

Yu, Yanlin; Xiao, Wei; Wang, Jianwei; Wang, Ligen

2015-01-01

Segregation at metal alloy surfaces is an important issue because many electrochemical and catalytic properties are directly correlated to the surface composition. We have performed density functional theory calculations for Mo segregation in MoNi(111) in the presence of chemisorbed atomic oxygen. In particular, the coverage dependence and possible adsorption-induced segregation phenomena are addressed by investigating segregation energies of the Mo atom in MoNi(111). The theoretical calculated results show that the Mo atom prefers to be embedded in the bulk for the clean MoNi(111), while it segregates to the top-most layer when the oxygen coverage is thicker than 1/9 monolayer (ML). Furthermore, we analyze the densities of states for the clean and oxygen-chemisorbed MoNi(111), and see a strong covalent bonding between Mo d-band states and O p-states. The present study provides valuable insight for exploring practical applications of Ni-based alloys as hydrogen evolution electrodes. PMID:28787811

Cohesive Relations for Surface Atoms in the Iron-Technetium Binary System

DOE PAGES

Taylor, Christopher D.

2011-01-01

Iron-technetium alloys are of relevance to the development of waste forms for disposition of radioactive technetium-99 obtained from spent nuclear fuel. Corrosion of candidate waste forms is a function of the local cohesive energy () of surface atoms. A theoretical model for calculating is developed. Density functional theory was used to construct a modified embedded atom (MEAM) potential for iron-technetium. Materials properties determined for the iron-technetium system were in good agreement with the literature. To explore the relationship between local structure and corrosion, MEAM simulations were performed on representative iron-technetium alloys and intermetallics. Technetium-rich phases have lower , suggesting thatmore » these phases will be more noble than iron-rich ones. Quantitative estimates of based on numbers of nearest neighbors alone can lead to errors up to 0.5 eV. Consequently, atomistic corrosion simulations for alloy systems should utilize physics-based models that consider not only neighbor counts, but also local compositions and atomic arrangements.« less

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

Many-body physics in two-component Bose–Einstein condensates in a cavity: fragmented superradiance and polarization

NASA Astrophysics Data System (ADS)

Lode, Axel U. J.; Diorico, Fritz S.; Wu, RuGway; Molignini, Paolo; Papariello, Luca; Lin, Rui; Lévêque, Camille; Exl, Lukas; Tsatsos, Marios C.; Chitra, R.; Mauser, Norbert J.

2018-05-01

We consider laser-pumped one-dimensional two-component bosons in a parabolic trap embedded in a high-finesse optical cavity. Above a threshold pump power, the photons that populate the cavity modify the effective atom trap and mediate a coupling between the two components of the Bose–Einstein condensate. We calculate the ground state of the laser-pumped system and find different stages of self-organization depending on the power of the laser. The modified potential and the laser-mediated coupling between the atomic components give rise to rich many-body physics: an increase of the pump power triggers a self-organization of the atoms while an even larger pump power causes correlations between the self-organized atoms—the BEC becomes fragmented and the reduced density matrix acquires multiple macroscopic eigenvalues. In this fragmented superradiant state, the atoms can no longer be described as two-level systems and the mapping of the system to the Dicke model breaks down.

SEM and AFM Studies of Two-Phase Magnetic Alkali Borosilicate Glasses

PubMed Central

Tomkovich, M.; Nacke, B.; Filimonov, A.; Alekseeva, O.; Vanina, P.; Nizhankovskii, V.

2017-01-01

The morphology and composition of four types of two-phase alkali borosilicate glasses with magnetic atoms prepared by inductive melting have been studied. The results of scanning electron microscopy point to uniform distribution of Na, Si, and O atoms in these samples while magnetic iron atoms form ball-shaped agglomerates. The magnetic properties of these agglomerates have been confirmed by magnetic force microscopy. Atomic force microscopy had shown that in these samples two different morphological structures, drop-like and dendrite net, are formed. The formation of dendrite-like structure is a necessary condition for production of porous magnetic glasses. The obtained results allow us to optimize the melting and heat treatment processes leading to production of porous alkali borosilicate glasses with magnetic properties. The first results for nanocomposite materials on the basis of magnetic glasses containing the embedded ferroelectrics KH2PO4 demonstrate the effect of applied magnetic field on the ferroelectric phase transition. PMID:28428976

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

PubMed

Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

2015-04-14

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

'No one to trust': the cultural embedding of atomism in financial markets.

PubMed

Ailon, Galit

2018-05-13

The paper ethnographically explores the cultural embedding of atomistic indifference in online, global financial markets: arenas that have been digitally designed according to economic ideals and that demand an extreme form of relational and social dissociation from the partners to exchange and from those affected by the transactions. Its case-study is lay financial-trading in Israel, a country undergoing extensive neoliberalization. The study shows that dissociation is embedded in an economic culture marked by constant, multi-sited declarations that economic-Others are cold, uncaring and manipulative. It takes shape as traders convert the distrust towards Others into distrust towards portions of the Self that represent links to these Others, namely their own social-psychology and social concern. Acting atomistically and selfishly in the market thus entails considerable reflexive work. The paper contributes to an ongoing debate on the moral and cultural embeddedness of markets in general and of the expanding financial markets in particular. © London School of Economics and Political Science 2018.

Adaptive Multi-Sensor Interrogation of Targets Embedded in Complex Environments

DTIC Science & Technology

2010-06-09

to efficient refinement of data from distributed networked sensor systems for interpretation by both machines and humans in a low latency and...of a DP draw: Tk^HIltiU-^). Vk*& Beta{l,a), d’k ~ d" H. (19) where 5g - is a point measure concentrated at 9*k (each 9*k is termed an atom

Atomic Layer Deposited Oxide-Based Nanocomposite Structures with Embedded CoPtx Nanocrystals for Resistive Random Access Memory Applications.

PubMed

Wang, Lai-Guo; Cao, Zheng-Yi; Qian, Xu; Zhu, Lin; Cui, Da-Peng; Li, Ai-Dong; Wu, Di

2017-02-22

Al 2 O 3 - or HfO 2 -based nanocomposite structures with embedded CoPt x nanocrystals (NCs) on TiN-coated Si substrates have been prepared by combination of thermal atomic layer deposition (ALD) and plasma-enhanced ALD for resistive random access memory (RRAM) applications. The impact of CoPt x NCs and their average size/density on the resistive switching properties has been explored. Compared to the control sample without CoPt x NCs, ALD-derived Pt/oxide/100 cycle-CoPt x NCs/TiN/SiO 2 /Si exhibits a typical bipolar, reliable, and reproducible resistive switching behavior, such as sharp distribution of RRAM parameters, smaller set/reset voltages, stable resistance ratio (≥10 2 ) of OFF/ON states, better switching endurance up to 10 4 cycles, and longer data retention over 10 5 s. The possible resistive switching mechanism based on nanocomposite structures of oxide/CoPt x NCs has been proposed. The dominant conduction mechanisms in low- and high-resistance states of oxide-based device units with embedded CoPt x NCs are Ohmic behavior and space-charge-limited current, respectively. The insertion of CoPt x NCs can effectively improve the formation of conducting filaments due to the CoPt x NC-enhanced electric field intensity. Besides excellent resistive switching performances, the nanocomposite structures also simultaneously present ferromagnetic property. This work provides a flexible pathway by combining PEALD and TALD compatible with state-of-the-art Si-based technology for multifunctional electronic devices applications containing RRAM.

Improved Secret Image Sharing Scheme in Embedding Capacity without Underflow and Overflow.

PubMed

Pang, Liaojun; Miao, Deyu; Li, Huixian; Wang, Qiong

2015-01-01

Computational secret image sharing (CSIS) is an effective way to protect a secret image during its transmission and storage, and thus it has attracted lots of attentions since its appearance. Nowadays, it has become a hot topic for researchers to improve the embedding capacity and eliminate the underflow and overflow situations, which is embarrassing and difficult to deal with. The scheme, which has the highest embedding capacity among the existing schemes, has the underflow and overflow problems. Although the underflow and overflow situations have been well dealt with by different methods, the embedding capacities of these methods are reduced more or less. Motivated by these concerns, we propose a novel scheme, in which we take the differential coding, Huffman coding, and data converting to compress the secret image before embedding it to further improve the embedding capacity, and the pixel mapping matrix embedding method with a newly designed matrix is used to embed secret image data into the cover image to avoid the underflow and overflow situations. Experiment results show that our scheme can improve the embedding capacity further and eliminate the underflow and overflow situations at the same time.

Improved Secret Image Sharing Scheme in Embedding Capacity without Underflow and Overflow

PubMed Central

Pang, Liaojun; Miao, Deyu; Li, Huixian; Wang, Qiong

2015-01-01

Computational secret image sharing (CSIS) is an effective way to protect a secret image during its transmission and storage, and thus it has attracted lots of attentions since its appearance. Nowadays, it has become a hot topic for researchers to improve the embedding capacity and eliminate the underflow and overflow situations, which is embarrassing and difficult to deal with. The scheme, which has the highest embedding capacity among the existing schemes, has the underflow and overflow problems. Although the underflow and overflow situations have been well dealt with by different methods, the embedding capacities of these methods are reduced more or less. Motivated by these concerns, we propose a novel scheme, in which we take the differential coding, Huffman coding, and data converting to compress the secret image before embedding it to further improve the embedding capacity, and the pixel mapping matrix embedding method with a newly designed matrix is used to embed secret image data into the cover image to avoid the underflow and overflow situations. Experiment results show that our scheme can improve the embedding capacity further and eliminate the underflow and overflow situations at the same time. PMID:26351657

Nanocomposite TiN films with embedded MoS2 inorganic fullerenes produced by combining supersonic cluster beam deposition with cathodic arc reactive evaporation

NASA Astrophysics Data System (ADS)

Piazzoni, C.; Blomqvist, M.; Podestà, A.; Bardizza, G.; Bonati, M.; Piseri, P.; Milani, P.; Davies, C.; Hatto, P.; Ducati, C.; Sedláčková, K.; Radnóczi, G.

2008-01-01

We report the production and characterization of nanocomposite thin films consisting of a titanium nitride matrix with embedded molybdenum disulphide fullerene-like nanoparticles. This was achieved by combining a cluster source generating a pulsed supersonic beam of MoS2 clusters with an industrial cathodic arc reactive evaporation apparatus used for TiN deposition. Cluster-assembled films show the presence of MoS2 nanocages and nanostructures and the survival of such structures dispersed in the TiN matrix in the co-deposited samples. Nanotribological characterization by atomic force microscopy shows that the presence of MoS2 nanoparticles even in very low concentration modifies the behaviour of the TiN matrix.

Strain-Rate Dependence of Deformation-Twinning in Tantalum

NASA Astrophysics Data System (ADS)

Abeywardhana, Jayalath; Germann, Tim; Ravelo, Ramon

2017-06-01

Large-Scale molecular dynamics (MD) simulations are used to model quasi-isentropic compression and expansion (QIC) in tantalum crystals varying the rate of deformation between the range 108 -1012s-1 and compressive pressures up to 100 GPa. The atomic interactions were modeled employing an embedded-atom method (EAM) potential of Ta. Isentropic expansion was done employing samples initially compressed to pressures of 60 and 100 GPa followed by uniaxial and quasi-isentropically expansion to zero pressure. The effect of initial dislocation density on twinning was also examined by varying the initial defect density of the Ta samples (1010 -1012cm-2). At these high-strain rates, a threshold in strain-rate on deformation twining is observed. Under expansion or compression, deformation twinning increases with strain rate for strain-rates >109s-1 . Below this value, small fraction of twins nucleates but anneal out with time. Samples with lower fraction of twins equilibrate to defect states containing higher screw dislocation densities from those with initially higher twinning fractions. This work was supported by the Department of Energy under contract DE-AC52-06NA25396 and by the Air Force Office of Scientific Research under AFOSR Award No. FA9550-12-1-0476.

CoFe2O4-TiO2 and CoFe2O4-ZnO thin film nanostructures elaborated from colloidal chemistry and atomic layer deposition.

PubMed

Clavel, Guylhaine; Marichy, Catherine; Willinger, Marc-Georg; Ravaine, Serge; Zitoun, David; Pinna, Nicola

2010-12-07

CoFe(2)O(4)-TiO(2) and CoFe(2)O(4)-ZnO nanoparticles/film composites were prepared from directed assembly of colloidal CoFe(2)O(4) in a Langmuir-Blodgett monolayer and atomic layer deposition (ALD) of an oxide (TiO(2) or ZnO). The combination of these two methods permits the use of well-defined nanoparticles from colloidal chemistry, their assembly on a large scale, and the control over the interface between a ferrimagnetic material (CoFe(2)O(4)) and a semiconductor (TiO(2) or ZnO). Using this approach, architectures can be assembled with a precise control from the Angstrom scale (ALD) to the micrometer scale (Langmuir-Blodgett film). The resulting heterostructures present well-calibrated thicknesses. Electron microscopy and magnetic measurement studies give evidence that the size of the nanoparticles and their intrinsic magnetic properties are not altered by the various steps involved in the synthesis process. Therefore, the approach is suitable to obtain a layered composite with a quasi-monodisperse layer of ferrimagnetic nanoparticles embedded in an ultrathin film of semiconducting material.

Improved prediction of heat of mixing and segregation in metallic alloys using tunable mixing rule for embedded atom method

NASA Astrophysics Data System (ADS)

Divi, Srikanth; Agrahari, Gargi; Ranjan Kadulkar, Sanket; Kumar, Sanjeet; Chatterjee, Abhijit

2017-12-01

Capturing segregation behavior in metal alloy nanoparticles accurately using computer simulations is contingent upon the availability of high-fidelity interatomic potentials. The embedded atom method (EAM) potential is a widely trusted interatomic potential form used with pure metals and their alloys. When limited experimental data is available, the A-B EAM cross-interaction potential for metal alloys AxB 1-x are often constructed from pure metal A and B potentials by employing a pre-defined ‘mixing rule’ without any adjustable parameters. While this approach is convenient, we show that for AuPt, NiPt, AgAu, AgPd, AuNi, NiPd, PtPd and AuPd such mixing rules may not even yield the correct alloy properties, e.g., heats of mixing, that are closely related to the segregation behavior. A general theoretical formulation based on scaling invariance arguments is introduced that addresses this issue by tuning the mixing rule to better describe alloy properties. Starting with an existing pure metal EAM potential that is used extensively in literature, we find that the mixing rule fitted to heats of mixing for metal solutions usually provides good estimates of segregation energies, lattice parameters and cohesive energy, as well as equilibrium distribution of metals within a nanoparticle using Monte Carlo simulations. While the tunable mixing rule generally performs better than non-adjustable mixing rules, the use of the tunable mixing rule may still require some caution. For e.g., in Pt-Ni system we find that the segregation behavior can deviate from the experimentally observed one at Ni-rich compositions. Despite this the overall results suggest that the same approach may be useful for developing improved cross-potentials with other existing pure metal EAM potentials as well. As a further test of our approach, mixing rule estimated from binary data is used to calculate heat of mixing in AuPdPt, AuNiPd, AuPtNi, AgAuPd and NiPtPd. Excellent agreement with experiments is observed for AuPdPt.

Generation of Controlled Analog Emissions from Embedded Devices using Software Stress Methods

DTIC Science & Technology

2017-03-01

Generation of Controlled Analog Emissions from Embedded Devices using Software Stress Methods Oren Sternberg, Jonathan H. Nelson, Israel Perez...Abstract: In this paper, we present a new method that uses software diagnostic tools to study the generation of induced spurious physical emissions from...types of attacks warrants an understanding of unwanted signal generation. We examine this connection by observing the emission profile of an embedded

Mechanical properties of metastatic breast cancer cells invading into collagen I matrices

NASA Astrophysics Data System (ADS)

Ros, Robert

2014-03-01

Mechanical interactions between cells and the extracellular matrix (ECM) are critical to the metastasis of cancer cells. To investigate the mechanical interplay between the cells and ECM during invasion, we created thin bovine collagen I hydrogels ranging from 0.1-5 kPa in Young's modulus that were seeded with highly metastatic MDA-MB-231 breast cancer cells. Significant population fractions invaded the matrices either partially or fully within 24 h. We then combined confocal fluorescence microscopy and indentation with an atomic force microscope to determine the Young's moduli of individual embedded cells and the pericellular matrix using novel analysis methods for heterogeneous samples. In partially embedded cells, we observe a statistically significant correlation between the degree of invasion and the Young's modulus, which was up to an order of magnitude greater than that of the same cells measured in 2D. ROCK inhibition returned the cells' Young's moduli to values similar to 2D and diminished but did not abrogate invasion. This provides evidence that Rho/ROCK-dependent acto-myosin contractility is employed for matrix reorganization during initial invasion, and suggests the observed cell stiffening is due to an attendant increase in actin stress fibers. This work was supported by the National Cancer Institute under the grant U54 CA143862.

Size-controlled growth and antibacterial mechanism for Cu:C nanocomposite thin films.

PubMed

Javid, Amjed; Kumar, Manish; Yoon, Seokyoung; Lee, Jung Heon; Han, Jeon Geon

2016-12-21

The interdependence of 'size' and 'volume-fraction' hinders the identification of their individual role in the interface properties of metal nanoparticles (NPs) embedded in a matrix. Here, the case of Cu NPs embedded in a C matrix is presented for their profound antibacterial activity. Cu:C nanocomposite thin films with fixed Cu content (≈12 atomic%) are prepared using a plasma process where plasma energy controls the size of Cu NPs (from 9 nm to 16 nm). An inverse relationship between the size-effect on antibacterial activity against Escherichia coli and Staphylococcus aureus bacteria is established through the real time monitoring of an aliquot by inductively coupled plasma mass spectrometry, which confirmed the inverse relationship of Cu ion release from the nanocomposite with varied Cu NP sizes. It was found that enhancing the total power density increases the plasma density as well as effective kinetic energy of the plasma species, which in turn creates a large number of nucleation sites and restricts the island kind of growth of Cu NPs. The mechanism of NP size-control is illustrated on the basis of ion density and nucleation and the growth regime of plasma species. This physical approach to NP size reduction anticipates a contamination-free competitive recipe of size-control to capping based chemical methods.

Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP Synthases.

PubMed

Zhou, Wenchang; Leone, Vanessa; Krah, Alexander; Faraldo-Gómez, José D

2017-04-20

Recent years have witnessed a renewed interest in the ATP synthase as a drug target against human pathogens. Indeed, clinical, biochemical, and structural data indicate that hydrophobic inhibitors targeting the membrane-embedded proton-binding sites of the c-subunit ring could serve as last-resort antibiotics against multidrug resistant strains. However, because inhibition of the mitochondrial ATP synthase in humans is lethal, it is essential that these inhibitors be not only potent but also highly selective for the bacterial enzyme. To this end, a detailed understanding of the structure of this protein target is arguably instrumental. Here, we use computational methods to predict the atomic structures of the proton-binding sites in two prototypical c-rings: that of the ATP synthase from Saccharomyces cerevisiae, which is a model system for mitochondrial enzymes, and that from Escherichia coli, which can be pathogenic for humans. Our study reveals the structure of these binding sites loaded with protons and in the context of the membrane, that is, in the state that would mediate the recognition of a potential inhibitor. Both structures reflect a mode of proton coordination unlike those previously observed in other c-ring structures, whether experimental or modeled.

Modular error embedding

DOEpatents

Sandford, II, Maxwell T.; Handel, Theodore G.; Ettinger, J. Mark

1999-01-01

A method of embedding auxiliary information into the digital representation of host data containing noise in the low-order bits. The method applies to digital data representing analog signals, for example digital images. The method reduces the error introduced by other methods that replace the low-order bits with auxiliary information. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user through use of a digital key. The modular error embedding method includes a process to permute the order in which the host data values are processed. The method doubles the amount of auxiliary information that can be added to host data values, in comparison with bit-replacement methods for high bit-rate coding. The invention preserves human perception of the meaning and content of the host data, permitting the addition of auxiliary data in the amount of 50% or greater of the original host data.

Audio Watermark Embedding Technique Applying Auditory Stream Segregation: "G-encoder Mark" Able to Be Extracted by Mobile Phone

NASA Astrophysics Data System (ADS)

Modegi, Toshio

We are developing audio watermarking techniques which enable extraction of embedded data by cell phones. For that we have to embed data onto frequency ranges, where our auditory response is prominent, therefore data embedding will cause much auditory noises. Previously we have proposed applying a two-channel stereo play-back feature, where noises generated by a data embedded left-channel signal will be reduced by the other right-channel signal. However, this proposal has practical problems of restricting extracting terminal location. In this paper, we propose synthesizing the noise reducing right-channel signal with the left-signal and reduces noises completely by generating an auditory stream segregation phenomenon to users. This newly proposed makes the noise reducing right-channel signal unnecessary and supports monaural play-back operations. Moreover, we propose a wide-band embedding method causing dual auditory stream segregation phenomena, which enables data embedding on whole public phone frequency ranges and stable extractions with 3-G mobile phones. From these proposals, extraction precisions become higher than those by the previously proposed method whereas the quality damages of embedded signals become smaller. In this paper we present an abstract of our newly proposed method and experimental results comparing with those by the previously proposed method.

Embedding beyond electrostatics-The role of wave function confinement.

PubMed

Nåbo, Lina J; Olsen, Jógvan Magnus Haugaard; Holmgaard List, Nanna; Solanko, Lukasz M; Wüstner, Daniel; Kongsted, Jacob

2016-09-14

We study excited states of cholesterol in solution and show that, in this specific case, solute wave-function confinement is the main effect of the solvent. This is rationalized on the basis of the polarizable density embedding scheme, which in addition to polarizable embedding includes non-electrostatic repulsion that effectively confines the solute wave function to its cavity. We illustrate how the inclusion of non-electrostatic repulsion results in a successful identification of the intense π → π(∗) transition, which was not possible using an embedding method that only includes electrostatics. This underlines the importance of non-electrostatic repulsion in quantum-mechanical embedding-based methods.

Lossless Data Embedding—New Paradigm in Digital Watermarking

NASA Astrophysics Data System (ADS)

Fridrich, Jessica; Goljan, Miroslav; Du, Rui

2002-12-01

One common drawback of virtually all current data embedding methods is the fact that the original image is inevitably distorted due to data embedding itself. This distortion typically cannot be removed completely due to quantization, bit-replacement, or truncation at the grayscales 0 and 255. Although the distortion is often quite small and perceptual models are used to minimize its visibility, the distortion may not be acceptable for medical imagery (for legal reasons) or for military images inspected under nonstandard viewing conditions (after enhancement or extreme zoom). In this paper, we introduce a new paradigm for data embedding in images (lossless data embedding) that has the property that the distortion due to embedding can be completely removed from the watermarked image after the embedded data has been extracted. We present lossless embedding methods for the uncompressed formats (BMP, TIFF) and for the JPEG format. We also show how the concept of lossless data embedding can be used as a powerful tool to achieve a variety of nontrivial tasks, including lossless authentication using fragile watermarks, steganalysis of LSB embedding, and distortion-free robust watermarking.

Non-integer expansion embedding techniques for reversible image watermarking

NASA Astrophysics Data System (ADS)

Xiang, Shijun; Wang, Yi

2015-12-01

This work aims at reducing the embedding distortion of prediction-error expansion (PE)-based reversible watermarking. In the classical PE embedding method proposed by Thodi and Rodriguez, the predicted value is rounded to integer number for integer prediction-error expansion (IPE) embedding. The rounding operation makes a constraint on a predictor's performance. In this paper, we propose a non-integer PE (NIPE) embedding approach, which can proceed non-integer prediction errors for embedding data into an audio or image file by only expanding integer element of a prediction error while keeping its fractional element unchanged. The advantage of the NIPE embedding technique is that the NIPE technique can really bring a predictor into full play by estimating a sample/pixel in a noncausal way in a single pass since there is no rounding operation. A new noncausal image prediction method to estimate a pixel with four immediate pixels in a single pass is included in the proposed scheme. The proposed noncausal image predictor can provide better performance than Sachnev et al.'s noncausal double-set prediction method (where data prediction in two passes brings a distortion problem due to the fact that half of the pixels were predicted with the watermarked pixels). In comparison with existing several state-of-the-art works, experimental results have shown that the NIPE technique with the new noncausal prediction strategy can reduce the embedding distortion for the same embedding payload.

A Spiral Step-by-Step Educational Method for Cultivating Competent Embedded System Engineers to Meet Industry Demands

ERIC Educational Resources Information Center

Jing,Lei; Cheng, Zixue; Wang, Junbo; Zhou, Yinghui

2011-01-01

Embedded system technologies are undergoing dramatic change. Competent embedded system engineers are becoming a scarce resource in the industry. Given this, universities should revise their specialist education to meet industry demands. In this paper, a spirally tight-coupled step-by-step educational method, based on an analysis of industry…

Rich interfacial chemistry and properties of carbon-doped hexagonal boron nitride nanosheets revealed by electronic structure calculations

NASA Astrophysics Data System (ADS)

Xie, Wei; Tamura, Takahiro; Yanase, Takashi; Nagahama, Taro; Shimada, Toshihiro

2018-04-01

The effect of C doping to hexagonal boron nitride (h-BN) to its electronic structure is examined by first principles calculations using the association from π-electron systems of organic molecules embedded in a two-dimensional insulator. In a monolayered carbon-doped structure, odd-number doping with carbon atoms confers metallic properties with different work functions. Various electronic interactions occur between two layers with odd-number carbon substitution. A direct sp3 covalent chemical bond is formed when C replaces adjacent B and N in different layers. A charge transfer complex between layers is found when C replaces B and N in the next-neighboring region, which results in narrower band gaps (e.g., 0.37 eV). Direct bonding between C and B atoms is found when two C atoms in different layers are at a certain distance.

The adsorption properties of CHx species on metal modified graphene

NASA Astrophysics Data System (ADS)

Tang, Yanan; Shen, Zigang; Chen, Weiguang; Zhu, Dalei; Chai, Huadou; Zhao, Mingyu

2018-05-01

The adsorption geometries of CHx species (x = 0, 1, 2, 3 and 4) on the metal embedded graphene (M-graphene) substrates and the change in electronic structure and magnetic property of systems are analyzed using the first-principles calculations. The calculated results show that the doped metal atoms can provide transferred electrons to neighboring carbon atoms at defective site and thus exhibit positive charges, as well as turning the adsorption sensing of M-graphene for detecting CHx species. Compared with the adsorbed CH3, the adsorption of C, CH and CH2 species exhibit more stability ( >3.0 eV) on M-graphene. Besides, more stable C atom on M-graphene can effectively turn the magnetic property of systems as compared with other species. This result provides a useful reference for fabricating the functional metal-graphene complex as gas sensors and catalytic materials.

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

Dutta, S.; Saha, J. K.; Chandra, R.

The Rayleigh-Ritz variational technique with a Hylleraas basis set is being tested for the first time to estimate the structural modifications of a lithium atom embedded in a weakly coupled plasma environment. The Debye-Huckel potential is used to mimic the weakly coupled plasma environment. The wave functions for both the helium-like lithium ion and the lithium atom are expanded in the explicitly correlated Hylleraas type basis set which fully takes care of the electron-electron correlation effect. Due to the continuum lowering under plasma environment, the ionization potential of the system gradually decreases leading to the destabilization of the atom. Themore » excited states destabilize at a lower value of the plasma density. The estimated ionization potential agrees fairly well with the few available theoretical estimates. The variation of one and two particle moments, dielectric susceptibility and magnetic shielding constant, with respect to plasma density is also been discussed in detail.« less

Critical Landau Velocity in Helium Nanodroplets

NASA Astrophysics Data System (ADS)

Brauer, Nils B.; Smolarek, Szymon; Loginov, Evgeniy; Mateo, David; Hernando, Alberto; Pi, Marti; Barranco, Manuel; Buma, Wybren J.; Drabbels, Marcel

2013-10-01

The best-known property of superfluid helium is the vanishing viscosity that objects experience while moving through the liquid with speeds below the so-called critical Landau velocity. This critical velocity is generally considered a macroscopic property as it is related to the collective excitations of the helium atoms in the liquid. In the present work we determine to what extent this concept can still be applied to nanometer-scale, finite size helium systems. To this end, atoms and molecules embedded in helium nanodroplets of various sizes are accelerated out of the droplets by means of optical excitation, and the speed distributions of the ejected particles are determined. The measurements reveal the existence of a critical velocity in these systems, even for nanodroplets consisting of only a thousand helium atoms. Accompanying theoretical simulations based on a time-dependent density functional description of the helium confirm and further elucidate this experimental finding.

Intrinsic cavity QED and emergent quasinormal modes for a single photon

NASA Astrophysics Data System (ADS)

Dong, H.; Gong, Z. R.; Ian, H.; Zhou, Lan; Sun, C. P.

2009-06-01

We propose a special cavity design that is constructed by terminating a one-dimensional waveguide with a perfect mirror at one end and doping a two-level atom at the other. We show that this atom plays the intrinsic role of a semitransparent mirror for single-photon transports such that quasinormal modes emerge spontaneously in the cavity system. This atomic mirror has its reflection coefficient tunable through its level spacing and its coupling to the cavity field, for which the cavity system can be regarded as a two-end resonator with a continuously tunable leakage. The overall investigation predicts the existence of quasibound states in the waveguide continuum. Solid-state implementations based on a dc-superconducting quantum interference device circuit and a defected line resonator embedded in a photonic crystal are illustrated to show the experimental accessibility of the generic model.

Microscopic Modeling of Tribological Phenomena

DTIC Science & Technology

1990-02-28

37,4132 (1988). cohesive energy and lattice constant of nickel (t, -3.54 X 10- 󈧑 erg, ’This interface orientation was chosen in view ofour previous...such as lattice constants, heats of sublimation, elastic constants, vacancy-formation energies and heats of solution (47]. Following equilibration of...of the tip and 10 substrate materials to optimize their embedding energies (which are density dependent, deriving froam the tails of the atomic

Nonlinear vs. linear biasing in Trp-cage folding simulations

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

Spiwok, Vojtěch, E-mail: spiwokv@vscht.cz; Oborský, Pavel; Králová, Blanka

2015-03-21

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energymore » minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.« less

Application of RT-PCR in formalin-fixed and paraffin-embedded lung cancer tissues.

PubMed

Zhang, Fan; Wang, Zhuo-min; Liu, Hong-yu; Bai, Yun; Wei, Sen; Li, Ying; Wang, Min; Chen, Jun; Zhou, Qing-hua

2010-01-01

To analyze gene expression in formalin-fixed, paraffin-embedded lung cancer tissues using modified method. Total RNA from frozen tissues was extracted using TRIZOL reagent. RNA was extracted from formalin-fixed, paraffin-embedded tissues by digestion with proteinase K before the acid-phenol:chloroform extraction and carrier precipitation. We modified this method by using a higher concentration of proteinase K and a longer digestion time, optimized to 16 hours. RT-PCR and real-time RT-PCR were used to check reproducibility and the concordance between frozen and paraffin-embedded samples. The results showed that the RNA extracted from the paraffin-embedded lung tissues had high quality with the most fragment length between 28S and 18S bands (about 1000 to 2000 bases). The housekeeping gene GUSB exhibited low variation of expression in frozen and paraffin-embedded lung tissues, whereas PGK1 had the lowest variation in lymphoma tissues. Furthermore, real-time PCR analysis of the expression of known prognostic genes in non-small cell lung carcinoma (NSCLC) demonstrated an extremely high correlation (r>0.880) between the paired frozen and formalin-fixed, paraffin-embedded specimens. This improved method of RNA extraction is suitable for real-time quantitative RT-PCR, and may be used for global gene expression profiling of paraffin-embedded tissues.

Engineering giant magnetic anisotropy in single-molecule magnets by dimerizing heavy transition-metal atoms

NASA Astrophysics Data System (ADS)

Qu, Jiaxing; Hu, Jun

2018-05-01

The search for single-molecule magnets with large magnetic anisotropy energy (MAE) is essential for the development of molecular spintronics devices for use at room temperature. Through systematic first-principles calculations, we found that an Os–Os or Ir–Ir dimer embedded in the (5,5‧-Br2-salophen) molecule gives rise to a large MAE of 41.6 or 51.4 meV, respectively, which is large enough to hold the spin orientation at room temperature. Analysis of the electronic structures reveals that the top Os and Ir atoms play the most important part in the total spin moments and large MAEs of the molecules.

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

Kuraptsev, A. S., E-mail: aleksej-kurapcev@yandex.ru; Sokolov, I. M.

We develop a consistent quantum theory of the collective effects that take place when electromagnetic radiation interacts with a dense ensemble of impurity centers embedded in a transparent dielectric and placed in a Fabry–Perot cavity. We have calculated the spontaneous decay dynamics of an excited impurity atom as a specific example of applying the developed general theory. We analyze the dependence of the decay rate on the density of impurity centers and the sample sizes as well as on the characteristic level shifts of impurity atoms caused by the internal fields of the dielectric. We show that a cavity canmore » affect significantly the pattern of collective processes, in particular, the lifetimes of collective states.« less

Electron momentum densities in disordered muffin-tin alloys

NASA Astrophysics Data System (ADS)

Bansil, A.; Rao, R. S.; Mijnarends, P. E.; Schwartz, L.

1981-04-01

The application of average t-matrix (ATA) and coherent potential (CPA) approximations to the calculation of average electron momentum density ρ(p-->) in random muffin-tin alloys AxB1-x is considered. The necessary equations for the general matrix elements of the operators describing scattering by the CPA atom and also by an A or B atom embedded in the effective medium are derived. Various versions of the ATA for ρ(p-->) are discussed. Several ρ(p-->) curves calculated on the basis of the CPA and ATA in CuxNi1-x are presented. These results are used to delineate the effects on ρ(p-->) of self-consistency in the treatment of disorder.

Toward improving CO2 dissociation and conversion to methanol via CO-hydrogenation on Cu(100) surface by introducing embedded Co nanoclusters as promoters: A DFT study

NASA Astrophysics Data System (ADS)

Qiu, Mei; Tao, Huilin; Li, Yali; Li, Yi; Ding, Kaining; Huang, Xin; Chen, Wenkai; Zhang, Yongfan

2018-01-01

The dissociation and hydrogenation of CO2 on Cu(100) surfaces that are modified by introducing Co nanoclusters with different size into the top layer have been investigated using density functional theory method. Our results show that on all surfaces the Co atoms are the sites for the adsorption of CO2, and in the early stage of introducing Co dopant, the chemisorption behavior of CO2 is sensitive to the amount of Co atom. According to the predicted pathways for the dissociation of CO2 to CO, it is interesting that the energy barrier decreases first and then increases as more Co atoms are dispersed on the surface, forming a ;V; shape. The minimum energy barrier of CO2 decomposition is predicted on the Cu(100) surface that contains four Co atoms aggregated together on the top layer, namely Co4/Cu(100) bimetallic surface. The most favorable reaction pathway for the hydrogenation of CO to methanol on such surface is further determined, which follows the sequence of CO* → HCO* → H2CO* → H3CO* → H3COH*, and the rate-limiting step is the hydrogenation of H3CO species with an activation barrier of 106.4 kJ/mol. It is noted that with respect to the pure Cu(100), since more stronger Cosbnd O adsorption bonds are formed on the Co-modified surface, the stability of formaldehyde intermediate is significantly enhanced. Correspondingly, the introducing of Co4 cluster tends to improve the productivity and selectivity towards methanol synthesis on Cu(100) surface.

Diffusion on Cu surfaces

NASA Technical Reports Server (NTRS)

Karimi, Majid

1993-01-01

Understanding surface diffusion is essential in understanding surface phenomena, such as crystal growth, thin film growth, corrosion, physisorption, and chemisorption. Because of its importance, various experimental and theoretical efforts have been directed to understand this phenomena. The Field Ion Microscope (FIM) has been the major experimental tool for studying surface diffusion. FIM have been employed by various research groups to study surface diffusion of adatoms. Because of limitations of the FIM, such studies are only limited to a few surfaces: nickel, platinum, aluminum, iridium, tungsten, and rhodium. From the theoretical standpoint, various atomistic simulations are performed to study surface diffusion. In most of these calculations the Embedded Atom Method (EAM) along with the molecular static (MS) simulation are utilized. The EAM is a semi-empirical approach for modeling the interatomic interactions. The MS simulation is a technique for minimizing the total energy of a system of particles with respect to the positions of its particles. One of the objectives of this work is to develop the EAM functions for Cu and use them in conjunction with the molecular static (MS) simulation to study diffusion of a Cu atom on a perfect as well as stepped Cu(100) surfaces. This will provide a test of the validity of the EAM functions on Cu(100) surface and near the stepped environments. In particular, we construct a terrace-ledge-kink (TLK) model and calculate the migration energies of an atom on a terrace, near a ledge site, near a kink site, and going over a descending step. We have also calculated formation energies of an atom on the bare surface, a vacancy in the surface, a stepped surface, and a stepped-kink surface. Our results are compared with the available experimental and theoretical results.

Dislocation and Structural Studies at Metal-Metallic Glass Interface at Low Temperature

NASA Astrophysics Data System (ADS)

Gupta, Pradeep; Yedla, Natraj

2017-12-01

In this paper, molecular dynamics (MD) simulation deformation studies on the Al (metal)-Cu50Zr50 (metallic glass) model interface is carried out based on cohesive zone model. The interface is subjected to mode-I loading at a strain rate of 109 s-1 and temperature of 100 K. The dislocations reactions and evolution of dislocation densities during the deformation have been investigated. Atomic interactions between Al, Cu and Zr atoms are modeled using EAM (embedded atom method) potential, and a timestep of 0.002 ps is used for performing the MD simulations. A circular crack and rectangular notch are introduced at the interface to investigate the effect on the deformation behavior and fracture. Further, scale size effect is also investigated. The structural changes and evolution of dislocation density are also examined. It is found that the dominant deformation mechanism is by Shockley partial dislocation nucleation. Amorphization is observed in the Al regions close to the interface and occurs at a lower strain in the presence of a crack. The total dislocation density is found to be maximum after the first yield in both the perfect and defect interface models and is highest in the case of perfect interface with a density of 6.31 × 1017 m-2. In the perfect and circular crack defect interface models, it is observed that the fraction of Shockley partial dislocation density decreases, whereas that of strain rod dislocations increases with increase in strain.

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

NASA Astrophysics Data System (ADS)

Samolyuk, G. D.; Osetsky, Y. N.; Stoller, R. E.

2015-10-01

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascade production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (∼0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential. The Gao-Weber potential appears to give a more realistic description of cascade dynamics in SiC, but still has some shortcomings when the defect migration barriers are compared to the ab initio results.

Electron correlation by polarization of interacting densities

NASA Astrophysics Data System (ADS)

Whitten, Jerry L.

2017-02-01

Coulomb interactions that occur in electronic structure calculations are correlated by allowing basis function components of the interacting densities to polarize dynamically, thereby reducing the magnitude of the interaction. Exchange integrals of molecular orbitals are not correlated. The modified Coulomb interactions are used in single-determinant or configuration interaction calculations. The objective is to account for dynamical correlation effects without explicitly introducing higher spherical harmonic functions into the molecular orbital basis. Molecular orbital densities are decomposed into a distribution of spherical components that conserve the charge and each of the interacting components is considered as a two-electron wavefunction embedded in the system acted on by an average field Hamiltonian plus r12-1. A method of avoiding redundancy is described. Applications to atoms, negative ions, and molecules representing different types of bonding and spin states are discussed.

Imaging latex–carbon nanotube composites by subsurface electrostatic force microscopy

DOE PAGES

Patel, Sajan; Petty, Clayton W.; Krafcik, Karen Lee; ...

2016-09-08

Electrostatic modes of atomic force microscopy have shown to be non-destructive and relatively simple methods for imaging conductors embedded in insulating polymers. Here we use electrostatic force microscopy to image the dispersion of carbon nanotubes in a latex-based conductive composite, which brings forth features not observed in previously studied systems employing linear polymer films. A fixed-potential model of the probe-nanotube electrostatics is presented which in principle gives access to the conductive nanoparticle's depth and radius, and the polymer film dielectric constant. Comparing this model to the data results in nanotube depths that appear to be slightly above the film–air interface.more » Furthermore, this result suggests that water-mediated charge build-up at the film–air interface may be the source of electrostatic phase contrast in ambient conditions.« less

Self-Cleaning Anticondensing Glass via Supersonic Spraying of Silver Nanowires, Silica, and Polystyrene Nanoparticles.

PubMed

Lee, Jong-Gun; An, Seongpil; Kim, Tae-Gun; Kim, Min-Woo; Jo, Hong-Seok; Swihart, Mark T; Yarin, Alexander L; Yoon, Sam S

2017-10-11

We have sequentially deposited layers of silver nanowires (AgNWs), silicon dioxide (SiO 2 ) nanoparticles, and polystyrene (PS) nanoparticles on uncoated glass by a rapid low-cost supersonic spraying method to create antifrosting, anticondensation, and self-cleaning glass. The conductive silver nanowire network embedded in the coating allows electrical heating of the glass surface. Supersonic spraying is a single-step coating technique that does not require vacuum. The fabricated multifunctional glass was characterized by X-ray diffraction analysis (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), ultraviolet-visible spectroscopy, and transmission electron microscopy (TEM). The thermal insulation and antifrosting performance were demonstrated using infrared thermal imaging. The reliability of the electrical heating function was tested through extensive cycling. This transparent multifunctional coating holds great promise for use in various smart window designs.

Sparse representation of electrodermal activity with knowledge-driven dictionaries.

PubMed

Chaspari, Theodora; Tsiartas, Andreas; Stein, Leah I; Cermak, Sharon A; Narayanan, Shrikanth S

2015-03-01

Biometric sensors and portable devices are being increasingly embedded into our everyday life, creating the need for robust physiological models that efficiently represent, analyze, and interpret the acquired signals. We propose a knowledge-driven method to represent electrodermal activity (EDA), a psychophysiological signal linked to stress, affect, and cognitive processing. We build EDA-specific dictionaries that accurately model both the slow varying tonic part and the signal fluctuations, called skin conductance responses (SCR), and use greedy sparse representation techniques to decompose the signal into a small number of atoms from the dictionary. Quantitative evaluation of our method considers signal reconstruction, compression rate, and information retrieval measures, that capture the ability of the model to incorporate the main signal characteristics, such as SCR occurrences. Compared to previous studies fitting a predetermined structure to the signal, results indicate that our approach provides benefits across all aforementioned criteria. This paper demonstrates the ability of appropriate dictionaries along with sparse decomposition methods to reliably represent EDA signals and provides a foundation for automatic measurement of SCR characteristics and the extraction of meaningful EDA features.

Prospects of Optical Single Atom Detection in Noble Gas Solids for Measurements of Rare Nuclear Reactions

NASA Astrophysics Data System (ADS)

Singh, Jaideep; Bailey, Kevin G.; Lu, Zheng-Tian; Mueller, Peter; O'Connor, Thomas P.; Xu, Chen-Yu; Tang, Xiaodong

2013-04-01

Optical detection of single atoms captured in solid noble gas matrices provides an alternative technique to study rare nuclear reactions relevant to nuclear astrophysics. I will describe the prospects of applying this approach for cross section measurements of the ^22Ne,,),25Mg reaction, which is the crucial neutron source for the weak s process inside of massive stars. Noble gas solids are a promising medium for the capture, detection, and manipulation of atoms and nuclear spins. They provide stable and chemically inert confinement for a wide variety of guest species. Because noble gas solids are transparent at optical wavelengths, the guest atoms can be probed using lasers. We have observed that ytterbium in solid neon exhibits intersystem crossing (ISC) which results in a strong green fluorescence (546 nm) under excitation with blue light (389 nm). Several groups have observed ISC in many other guest-host pairs, notably magnesium in krypton. Because of the large wavelength separation of the excitation light and fluorescence light, optical detection of individual embedded guest atoms is feasible. This work is supported by DOE, Office of Nuclear Physics, under contract DE-AC02-06CH11357.

Electronic components embedded in a single graphene nanoribbon.

PubMed

Jacobse, P H; Kimouche, A; Gebraad, T; Ervasti, M M; Thijssen, J M; Liljeroth, P; Swart, I

2017-07-25

The use of graphene in electronic devices requires a band gap, which can be achieved by creating nanostructures such as graphene nanoribbons. A wide variety of atomically precise graphene nanoribbons can be prepared through on-surface synthesis, bringing the concept of graphene nanoribbon electronics closer to reality. For future applications it is beneficial to integrate contacts and more functionality directly into single ribbons by using heterostructures. Here, we use the on-surface synthesis approach to fabricate a metal-semiconductor junction and a tunnel barrier in a single graphene nanoribbon consisting of 5- and 7-atom wide segments. We characterize the atomic scale geometry and electronic structure by combined atomic force microscopy, scanning tunneling microscopy, and conductance measurements complemented by density functional theory and transport calculations. These junctions are relevant for developing contacts in all-graphene nanoribbon devices and creating diodes and transistors, and act as a first step toward complete electronic devices built into a single graphene nanoribbon.Adding functional electronic components to graphene nanoribbons requires precise control over their atomic structure. Here, the authors use a bottom-up approach to build a metal-semiconductor junction and a tunnel barrier directly into a single graphene nanoribbon, an exciting development for graphene-based electronic devices.

A novel sample preparation method to avoid influence of embedding medium during nano-indentation

NASA Astrophysics Data System (ADS)

Meng, Yujie; Wang, Siqun; Cai, Zhiyong; Young, Timothy M.; Du, Guanben; Li, Yanjun

2013-02-01

The effect of the embedding medium on the nano-indentation measurements of lignocellulosic materials was investigated experimentally using nano-indentation. Both the reduced elastic modulus and the hardness of non-embedded cell walls were found to be lower than those of the embedded samples, proving that the embedding medium used for specimen preparation on cellulosic material during nano-indentation can modify cell-wall properties. This leads to structural and chemical changes in the cell-wall constituents, changes that may significantly alter the material properties. Further investigation was carried out to detect the influence of different vacuum times on the cell-wall mechanical properties during the embedding procedure. Interpretation of the statistical analysis revealed no linear relationships between vacuum time and the mechanical properties of cell walls. The quantitative measurements confirm that low-viscosity resin has a rapid penetration rate early in the curing process. Finally, a novel sample preparation method aimed at preventing resin diffusion into lignocellulosic cell walls was developed using a plastic film to wrap the sample before embedding. This method proved to be accessible and straightforward for many kinds of lignocellulosic material, but is especially suitable for small, soft samples.

A testbed for optimizing electrodes embedded in the skull or in artificial skull replacement pieces used after injury

PubMed Central

Jiang, JingLe; Marathe, Amar R.; Keene, Jennifer C.; Taylor, Dawn M.

2016-01-01

Background Custom-fitted skull replacement pieces are often used after a head injury or surgery to replace damaged bone. Chronic brain recordings are beneficial after injury/surgery for monitoring brain health and seizure development. Embedding electrodes directly in these artificial skull replacement pieces would be a novel, low-risk way to perform chronic brain monitoring in these patients. Similarly, embedding electrodes directly in healthy skull would be a viable minimally-invasive option for many other neuroscience and neurotechnology applications requiring chronic brain recordings. New Method We demonstrate a preclinical testbed that can be used for refining electrode designs embedded in artificial skull replacement pieces or for embedding directly into the skull itself. Options are explored to increase the surface area of the contacts without increasing recording contact diameter to maximize recording resolution. Results Embedding electrodes in real or artificial skull allows one to lower electrode impedance without increasing the recording contact diameter by making use of conductive channels that extend into the skull. The higher density of small contacts embedded in the artificial skull in this testbed enables one to optimize electrode spacing for use in real bone. Comparison with Existing Methods For brain monitoring applications, skull-embedded electrodes fill a gap between electroencephalograms recorded on the scalp surface and the more invasive epidural or subdural electrode sheets. Conclusions Embedding electrodes into the skull or in skull replacement pieces may provide a safe, convenient, minimally-invasive alternative for chronic brain monitoring. The manufacturing methods described here will facilitate further testing of skull-embedded electrodes in animal models. PMID:27979758

ADAPTIVE METHODS FOR STOCHASTIC DIFFERENTIAL EQUATIONS VIA NATURAL EMBEDDINGS AND REJECTION SAMPLING WITH MEMORY.

PubMed

Rackauckas, Christopher; Nie, Qing

2017-01-01

Adaptive time-stepping with high-order embedded Runge-Kutta pairs and rejection sampling provides efficient approaches for solving differential equations. While many such methods exist for solving deterministic systems, little progress has been made for stochastic variants. One challenge in developing adaptive methods for stochastic differential equations (SDEs) is the construction of embedded schemes with direct error estimates. We present a new class of embedded stochastic Runge-Kutta (SRK) methods with strong order 1.5 which have a natural embedding of strong order 1.0 methods. This allows for the derivation of an error estimate which requires no additional function evaluations. Next we derive a general method to reject the time steps without losing information about the future Brownian path termed Rejection Sampling with Memory (RSwM). This method utilizes a stack data structure to do rejection sampling, costing only a few floating point calculations. We show numerically that the methods generate statistically-correct and tolerance-controlled solutions. Lastly, we show that this form of adaptivity can be applied to systems of equations, and demonstrate that it solves a stiff biological model 12.28x faster than common fixed timestep algorithms. Our approach only requires the solution to a bridging problem and thus lends itself to natural generalizations beyond SDEs.

ADAPTIVE METHODS FOR STOCHASTIC DIFFERENTIAL EQUATIONS VIA NATURAL EMBEDDINGS AND REJECTION SAMPLING WITH MEMORY

PubMed Central

Rackauckas, Christopher

2017-01-01

Adaptive time-stepping with high-order embedded Runge-Kutta pairs and rejection sampling provides efficient approaches for solving differential equations. While many such methods exist for solving deterministic systems, little progress has been made for stochastic variants. One challenge in developing adaptive methods for stochastic differential equations (SDEs) is the construction of embedded schemes with direct error estimates. We present a new class of embedded stochastic Runge-Kutta (SRK) methods with strong order 1.5 which have a natural embedding of strong order 1.0 methods. This allows for the derivation of an error estimate which requires no additional function evaluations. Next we derive a general method to reject the time steps without losing information about the future Brownian path termed Rejection Sampling with Memory (RSwM). This method utilizes a stack data structure to do rejection sampling, costing only a few floating point calculations. We show numerically that the methods generate statistically-correct and tolerance-controlled solutions. Lastly, we show that this form of adaptivity can be applied to systems of equations, and demonstrate that it solves a stiff biological model 12.28x faster than common fixed timestep algorithms. Our approach only requires the solution to a bridging problem and thus lends itself to natural generalizations beyond SDEs. PMID:29527134

Steganographic embedding in containers-images

NASA Astrophysics Data System (ADS)

Nikishova, A. V.; Omelchenko, T. A.; Makedonskij, S. A.

2018-05-01

Steganography is one of the approaches to ensuring the protection of information transmitted over the network. But a steganographic method should vary depending on a used container. According to statistics, the most widely used containers are images and the most common image format is JPEG. Authors propose a method of data embedding into a frequency area of images in format JPEG 2000. It is proposed to use the method of Benham-Memon- Yeo-Yeung, in which instead of discrete cosine transform, discrete wavelet transform is used. Two requirements for images are formulated. Structure similarity is chosen to obtain quality assessment of data embedding. Experiments confirm that requirements satisfaction allows achieving high quality assessment of data embedding.

Single Atomic Iron Catalysts for Oxygen Reduction in Acidic Media: Particle Size Control and Thermal Activation

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

Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu

It remains a grand challenge to replace platinum group metal (PGM) catalysts with earth-abundant materials for the oxygen reduction reaction (ORR) in acidic media, which is crucial for large-scale deployment of proton exchange membrane fuel cells (PEMFCs). Here, we report a high-performance atomic Fe catalyst derived from chemically Fe-doped zeolitic imidazolate frameworks (ZIFs) by directly bonding Fe ions to imidazolate ligands within 3D frameworks. Although the ZIF was identified as a promising precursor, the new synthetic chemistry enables the creation of well-dispersed atomic Fe sites embedded into porous carbon without the formation of aggregates. The size of catalyst particles ismore » tunable through synthesizing Fe-doped ZIF nanocrystal precursors in a wide range from 20 to 1000 nm followed by one-step thermal activation. Similar to Pt nanoparticles, the unique size control without altering chemical properties afforded by this approach is able to increase the number of PGM-free active sites. The best ORR activity is measured with the catalyst at a size of 50 nm. Further size reduction to 20 nm leads to significant particle agglomeration, thus decreasing the activity. Using the homogeneous atomic Fe model catalysts, we elucidated the active site formation process through correlating measured ORR activity with the change of chemical bonds in precursors during thermal activation up to 1100 °C. The critical temperature to form active sites is 800 °C, which is associated with a new Fe species with a reduced oxidation number (from Fe3+ to Fe2+) likely bonded with pyridinic N (FeN4) embedded into the carbon planes. Further increasing the temperature leads to continuously enhanced activity, linked to the rise of graphitic N and Fe–N species. The new atomic Fe catalyst has achieved respectable ORR activity in challenging acidic media (0.5 M H2SO4), showing a half-wave potential of 0.85 V vs RHE and leaving only a 30 mV gap with Pt/C (60 μgPt/cm2). Enhanced stability is attained with the same catalyst, which loses only 20 mV after 10 000 potential cycles (0.6–1.0 V) in O2 saturated acid. The high-performance atomic Fe PGM-free catalyst holds great promise as a replacement for Pt in future PEMFCs.« less

Single Atomic Iron Catalysts for Oxygen Reduction in Acidic Media: Particle Size Control and Thermal Activation

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

Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu

It remains a grand challenge to replace platinum group metal (PGM) catalysts with earth-abundant materials for the oxygen reduction reaction (ORR) in acidic media, which is crucial for large-scale deployment of proton exchange membrane fuel cells (PEMFCs). We report a high-performance atomic Fe catalyst derived from chemically Fe-doped zeolitic imidazolate frameworks (ZIFs) by directly bonding Fe ions to imidazolate ligands within 3D frameworks. Although the ZIF was identified as a promising precursor, the new synthetic chemistry enables the creation of well-dispersed atomic Fe sites embedded into porous carbon without the formation of aggregates. The size of catalyst particles is tunablemore » through synthesizing Fe-doped ZIF nanocrystal precursors in a wide range from 20 to 1000 nm followed by one-step thermal activation. Similar to Pt nanoparticles, the unique size control without altering chemical properties afforded by this approach is able to increase the number of PGM-free active sites. The best ORR activity is measured with the catalyst at a size of 50 nm. Further size reduction to 20 nm leads to significant particle agglomeration, thus decreasing the activity. In using the homogeneous atomic Fe model catalysts, we elucidated the active site formation process through correlating measured ORR activity with the change of chemical bonds in precursors during thermal activation up to 1100 °C. The critical temperature to form active sites is 800 °C, which is associated with a new Fe species with a reduced oxidation number (from Fe 3+ to Fe 2+) likely bonded with pyridinic N (FeN 4) embedded into the carbon planes. Further increasing the temperature leads to continuously enhanced activity, linked to the rise of graphitic N and Fe–N species. The new atomic Fe catalyst has achieved respectable ORR activity in challenging acidic media (0.5 M H 2SO 4), showing a half-wave potential of 0.85 V vs RHE and leaving only a 30 mV gap with Pt/C (60 μg Pt/cm 2). Finally, enhanced stability is attained with the same catalyst, which loses only 20 mV after 10 000 potential cycles (0.6–1.0 V) in O 2 saturated acid. The high-performance atomic Fe PGM-free catalyst holds great promise as a replacement for Pt in future PEMFCs.« less

Single Atomic Iron Catalysts for Oxygen Reduction in Acidic Media: Particle Size Control and Thermal Activation

DOE PAGES

Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu; ...

2017-09-13

It remains a grand challenge to replace platinum group metal (PGM) catalysts with earth-abundant materials for the oxygen reduction reaction (ORR) in acidic media, which is crucial for large-scale deployment of proton exchange membrane fuel cells (PEMFCs). We report a high-performance atomic Fe catalyst derived from chemically Fe-doped zeolitic imidazolate frameworks (ZIFs) by directly bonding Fe ions to imidazolate ligands within 3D frameworks. Although the ZIF was identified as a promising precursor, the new synthetic chemistry enables the creation of well-dispersed atomic Fe sites embedded into porous carbon without the formation of aggregates. The size of catalyst particles is tunablemore » through synthesizing Fe-doped ZIF nanocrystal precursors in a wide range from 20 to 1000 nm followed by one-step thermal activation. Similar to Pt nanoparticles, the unique size control without altering chemical properties afforded by this approach is able to increase the number of PGM-free active sites. The best ORR activity is measured with the catalyst at a size of 50 nm. Further size reduction to 20 nm leads to significant particle agglomeration, thus decreasing the activity. In using the homogeneous atomic Fe model catalysts, we elucidated the active site formation process through correlating measured ORR activity with the change of chemical bonds in precursors during thermal activation up to 1100 °C. The critical temperature to form active sites is 800 °C, which is associated with a new Fe species with a reduced oxidation number (from Fe 3+ to Fe 2+) likely bonded with pyridinic N (FeN 4) embedded into the carbon planes. Further increasing the temperature leads to continuously enhanced activity, linked to the rise of graphitic N and Fe–N species. The new atomic Fe catalyst has achieved respectable ORR activity in challenging acidic media (0.5 M H 2SO 4), showing a half-wave potential of 0.85 V vs RHE and leaving only a 30 mV gap with Pt/C (60 μg Pt/cm 2). Finally, enhanced stability is attained with the same catalyst, which loses only 20 mV after 10 000 potential cycles (0.6–1.0 V) in O 2 saturated acid. The high-performance atomic Fe PGM-free catalyst holds great promise as a replacement for Pt in future PEMFCs.« less

Carbon nanotube embedded PVDF membranes: Effect of solvent composition on the structural morphology for membrane distillation

NASA Astrophysics Data System (ADS)

Mapunda, Edgar C.; Mamba, Bhekie B.; Msagati, Titus A. M.

2017-08-01

Rapid population increase, growth in industrial and agricultural sectors and global climate change have added significant pressure on conventional freshwater resources. Tapping freshwater from non-conventional water sources such as desalination and wastewater recycling is considered as sustainable alternative to the fundamental challenges of water scarcity. However, affordable and sustainable technologies need to be applied for the communities to benefit from the treatment of non-conventional water source. Membrane distillation is a potential desalination technology which can be used sustainably for this purpose. In this work multi-walled carbon nanotube embedded polyvinylidene fluoride membranes for application in membrane distillation desalination were prepared via non-solvent induced phase separation method. The casting solution was prepared using mixed solvents (N, N-dimethylacetamide and triethyl phosphate) at varying ratios to study the effect of solvent composition on membrane morphological structures. Membrane morphological features were studied using a number of techniques including scanning electron microscope, atomic force microscope, SAXSpace tensile strength analysis, membrane thickness, porosity and contact angle measurements. It was revealed that membrane hydrophobicity, thickness, tensile strength and surface roughness were increasing as the composition of N, N-dimethylacetamide in the solvent was increasing with maximum values obtained between 40 and 60% N, N-dimethylacetamide. Internal morphological structures were changing from cellular structures to short finger-like and sponge-like pores and finally to large macro void type of pores when the amount of N, N-dimethylacetamide in the solvent was changed from low to high respectively. Multi-walled carbon nanotube embedded polyvinylidene fluoride membranes of desired morphological structures and physical properties can be synthesized by regulating the composition of solvents used to prepare the casting solution.

A family of four stages embedded explicit six-step methods with eliminated phase-lag and its derivatives for the numerical solution of the second order problems

NASA Astrophysics Data System (ADS)

Simos, T. E.

2017-11-01

A family of four stages high algebraic order embedded explicit six-step methods, for the numerical solution of second order initial or boundary-value problems with periodical and/or oscillating solutions, are studied in this paper. The free parameters of the new proposed methods are calculated solving the linear system of equations which is produced by requesting the vanishing of the phase-lag of the methods and the vanishing of the phase-lag's derivatives of the schemes. For the new obtained methods we investigate: • Its local truncation error (LTE) of the methods.• The asymptotic form of the LTE obtained using as model problem the radial Schrödinger equation.• The comparison of the asymptotic forms of LTEs for several methods of the same family. This comparison leads to conclusions on the efficiency of each method of the family.• The stability and the interval of periodicity of the obtained methods of the new family of embedded finite difference pairs.• The applications of the new obtained family of embedded finite difference pairs to the numerical solution of several second order problems like the radial Schrödinger equation, astronomical problems etc. The above applications lead to conclusion on the efficiency of the methods of the new family of embedded finite difference pairs.

Immunocytochemistry by electron spectroscopic imaging using a homogeneously boronated peptide.

PubMed

Kessels, M M; Qualmann, B; Klobasa, F; Sierralta, W D

1996-05-01

A linear all-L-oligopeptide containing five carboranyl amino acids (corresponding to 50 boron atoms) was synthesized and specifically attached to the free thiol group of monovalent antibody fragments F(ab)'. The boronated immunoreagent was used for the direct post-embedding detection of somatotrophic hormone in ultrathin sections of porcine pituitary embedded in Spurr resin. The specific boron-labelling of secretory vesicles in somatotrophs was detected by electron spectroscopic imaging and confirmed by conventional immunogold labelling run in parallel. In comparison with immunogold, boron-labelled F(ab)'-fragments showed higher tagging frequencies, as was expected; the small uncharged immunoreagents have an elongated shape and carry the antigen-combining structure and the detection tag at opposite ends, thus allowing for high spatial resolution in electron spectroscopic imaging.

Embedding and Chemical Reactivation of Green Fluorescent Protein in the Whole Mouse Brain for Optical Micro-Imaging

PubMed Central

Gang, Yadong; Zhou, Hongfu; Jia, Yao; Liu, Ling; Liu, Xiuli; Rao, Gong; Li, Longhui; Wang, Xiaojun; Lv, Xiaohua; Xiong, Hanqing; Yang, Zhongqin; Luo, Qingming; Gong, Hui; Zeng, Shaoqun

2017-01-01

Resin embedding has been widely applied to fixing biological tissues for sectioning and imaging, but has long been regarded as incompatible with green fluorescent protein (GFP) labeled sample because it reduces fluorescence. Recently, it has been reported that resin-embedded GFP-labeled brain tissue can be imaged with high resolution. In this protocol, we describe an optimized protocol for resin embedding and chemical reactivation of fluorescent protein labeled mouse brain, we have used mice as experiment model, but the protocol should be applied to other species. This method involves whole brain embedding and chemical reactivation of the fluorescent signal in resin-embedded tissue. The whole brain embedding process takes a total of 7 days. The duration of chemical reactivation is ~2 min for penetrating 4 μm below the surface in the resin-embedded brain. This protocol provides an efficient way to prepare fluorescent protein labeled sample for high-resolution optical imaging. This kind of sample was demonstrated to be imaged by various optical micro-imaging methods. Fine structures labeled with GFP across a whole brain can be detected. PMID:28352214

General synthesis and definitive structural identification of MN 4C 4 single-atom catalysts with tunable electrocatalytic activities

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

Fei, Huilong; Dong, Juncai; Feng, Yexin

Single-atom catalysts (SACs) have recently attracted broad research interest as they combine the merits of both homogeneous and heterogeneous catalysts. Rational design and synthesis of SACs are of immense significance but have so far been plagued by the lack of a definitive correlation between structure and catalytic properties. Here, we report a general approach to a series of monodispersed atomic transition metals (for example, Fe, Co, Ni) embedded in nitrogen-doped graphene with a common MNsub>4C 4 moiety, identified by systematic X-ray absorption fine structure analyses and direct transmission electron microscopy imaging. The unambiguous structure determination allows density functional theoretical predictionmore » of MNsub>4C 4 moieties as efficient oxygen evolution catalysts with activities following the trend Ni > Co > Fe, which is confirmed by electrochemical measurements. Determination of atomistic structure and its correlation with catalytic properties represents a critical step towards the rational design and synthesis of precious or nonprecious SACs with exceptional atom utilization efficiency and catalytic activities.« less

General synthesis and definitive structural identification of MN 4C 4 single-atom catalysts with tunable electrocatalytic activities

DOE PAGES

Fei, Huilong; Dong, Juncai; Feng, Yexin; ...

2018-01-08

Single-atom catalysts (SACs) have recently attracted broad research interest as they combine the merits of both homogeneous and heterogeneous catalysts. Rational design and synthesis of SACs are of immense significance but have so far been plagued by the lack of a definitive correlation between structure and catalytic properties. Here, we report a general approach to a series of monodispersed atomic transition metals (for example, Fe, Co, Ni) embedded in nitrogen-doped graphene with a common MNsub>4C 4 moiety, identified by systematic X-ray absorption fine structure analyses and direct transmission electron microscopy imaging. The unambiguous structure determination allows density functional theoretical predictionmore » of MNsub>4C 4 moieties as efficient oxygen evolution catalysts with activities following the trend Ni > Co > Fe, which is confirmed by electrochemical measurements. Determination of atomistic structure and its correlation with catalytic properties represents a critical step towards the rational design and synthesis of precious or nonprecious SACs with exceptional atom utilization efficiency and catalytic activities.« less

Diverse Power Iteration Embeddings and Its Applications

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

Huang H.; Yoo S.; Yu, D.

2014-12-14

Abstract—Spectral Embedding is one of the most effective dimension reduction algorithms in data mining. However, its computation complexity has to be mitigated in order to apply it for real-world large scale data analysis. Many researches have been focusing on developing approximate spectral embeddings which are more efficient, but meanwhile far less effective. This paper proposes Diverse Power Iteration Embeddings (DPIE), which not only retains the similar efficiency of power iteration methods but also produces a series of diverse and more effective embedding vectors. We test this novel method by applying it to various data mining applications (e.g. clustering, anomaly detectionmore » and feature selection) and evaluating their performance improvements. The experimental results show our proposed DPIE is more effective than popular spectral approximation methods, and obtains the similar quality of classic spectral embedding derived from eigen-decompositions. Moreover it is extremely fast on big data applications. For example in terms of clustering result, DPIE achieves as good as 95% of classic spectral clustering on the complex datasets but 4000+ times faster in limited memory environment.« less

Reputation Effects in Social Networks Do Not Promote Cooperation: An Experimental Test of the Raub & Weesie Model.

PubMed

Corten, Rense; Rosenkranz, Stephanie; Buskens, Vincent; Cook, Karen S

2016-01-01

Despite the popularity of the notion that social cohesion in the form of dense social networks promotes cooperation in Prisoner's Dilemmas through reputation, very little experimental evidence for this claim exists. We address this issue by testing hypotheses from one of the few rigorous game-theoretic models on this topic, the Raub & Weesie model, in two incentivized lab experiments. In the experiments, 156 subjects played repeated two-person PDs in groups of six. In the "atomized interactions" condition, subjects were only informed about the outcomes of their own interactions, while in the "embedded" condition, subjects were informed about the outcomes of all interactions in their group, allowing for reputation effects. The design of the experiments followed the specification of the RW model as closely as possible. For those aspects of the model that had to be modified to allow practical implementation in an experiment, we present additional analyses that show that these modifications do not affect the predictions. Contrary to expectations, we do not find that cooperation is higher in the embedded condition than in the atomized interaction. Instead, our results are consistent with an interpretation of the RW model that includes random noise, or with learning models of cooperation in networks.

Analysis of fcc metals fracture behaviour: Fracture behaviour of fcc metals: brittle/ductile behaviour criteria : with ab-initio, embedded atom and pseudopotential parameterization for Au, Ir and Al. analysis for Au, Ir and Al.

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.; Katsnelson, M. I.; Mryasov, Oleg N.; Freeman, A. J.; Trefilov, M. V.

1998-03-01

Theoretical analysis of the fracture behaviour of fcc Au, Ir and Al have been performed within various brittle/ductile criteria (BDC) with ab-initio, embedded atom (EAM), and pseudopotential parameterizations. We systematically examined several important aspects of the fracture behaviour: (i) dislocation structure, (ii) energetics of the cleavage decohesion and (iii) character of the interatomic interactions. Unit dislocation structures were analyzed within a two dimensional generalization of the Peierls-Nabarro model with restoring forces determined from ab-initio total energy calculations and found to be split with well defined highly mobile partials for all considered metals. We find from ab-initio and pseudopotential that in contrast with most of fcc metals, cleavage decohesion curve for Al appreciably differs from UBER relation. Finally, using ab-initio, EAM and pseudopotential parameterizations, we demonstrate that (i) Au (as a typical example of a ductile metal) is well described within existing BDC's, (ii) anomalous cleavage-like crack propagation of Ir is driven predominantly by it's high elastic modulus and (iii) Al is not described within BDC due to it's long-range interatomic interactions (and hence requires adjustments of the brittle/ductile criteria).

Composite targets in HiPIMS plasmas: Correlation of in-vacuum XPS characterization and optical plasma diagnostics

NASA Astrophysics Data System (ADS)

Layes, Vincent; Monje, Sascha; Corbella, Carles; Schulz-von der Gathen, Volker; von Keudell, Achim; de los Arcos, Teresa

2017-05-01

In-vacuum characterization of magnetron targets after High Power Impulse Magnetron Sputtering (HiPIMS) has been performed by X-ray photoelectron spectroscopy (XPS). Al-Cr composite targets (circular, 50 mm diameter) mounted in two different geometries were investigated: an Al target with a small Cr disk embedded at the racetrack position and a Cr target with a small Al disk embedded at the racetrack position. The HiPIMS discharge and the target surface composition were characterized in parallel for low, intermediate, and high power conditions, thus covering both the Ar-dominated and the metal-dominated HiPIMS regimes. The HiPIMS plasma was investigated using optical emission spectroscopy and fast imaging using a CCD camera; the spatially resolved XPS surface characterization was performed after in-vacuum transfer of the magnetron target to the XPS chamber. This parallel evaluation showed that (i) target redeposition of sputtered species was markedly more effective for Cr atoms than for Al atoms; (ii) oxidation at the target racetrack was observed even though the discharge ran in pure Ar gas without O2 admixture, the oxidation depended on the discharge power and target composition; and (iii) a bright emission spot fixed on top of the inserted Cr disk appeared for high power conditions.

Experimental study on cross-sensitivity of temperature and vibration of embedded fiber Bragg grating sensors

NASA Astrophysics Data System (ADS)

Chen, Tao; Ye, Meng-li; Liu, Shu-liang; Deng, Yan

2018-03-01

In view of the principle for occurrence of cross-sensitivity, a series of calibration experiments are carried out to solve the cross-sensitivity problem of embedded fiber Bragg gratings (FBGs) using the reference grating method. Moreover, an ultrasonic-vibration-assisted grinding (UVAG) model is established, and finite element analysis (FEA) is carried out under the monitoring environment of embedded temperature measurement system. In addition, the related temperature acquisition tests are set in accordance with requirements of the reference grating method. Finally, comparative analyses of the simulation and experimental results are performed, and it may be concluded that the reference grating method may be utilized to effectively solve the cross-sensitivity of embedded FBGs.

Feature Genes Selection Using Supervised Locally Linear Embedding and Correlation Coefficient for Microarray Classification

PubMed Central

Wang, Yun; Huang, Fangzhou

2018-01-01

The selection of feature genes with high recognition ability from the gene expression profiles has gained great significance in biology. However, most of the existing methods have a high time complexity and poor classification performance. Motivated by this, an effective feature selection method, called supervised locally linear embedding and Spearman's rank correlation coefficient (SLLE-SC2), is proposed which is based on the concept of locally linear embedding and correlation coefficient algorithms. Supervised locally linear embedding takes into account class label information and improves the classification performance. Furthermore, Spearman's rank correlation coefficient is used to remove the coexpression genes. The experiment results obtained on four public tumor microarray datasets illustrate that our method is valid and feasible. PMID:29666661

Feature Genes Selection Using Supervised Locally Linear Embedding and Correlation Coefficient for Microarray Classification.

PubMed

Xu, Jiucheng; Mu, Huiyu; Wang, Yun; Huang, Fangzhou

2018-01-01

The selection of feature genes with high recognition ability from the gene expression profiles has gained great significance in biology. However, most of the existing methods have a high time complexity and poor classification performance. Motivated by this, an effective feature selection method, called supervised locally linear embedding and Spearman's rank correlation coefficient (SLLE-SC 2 ), is proposed which is based on the concept of locally linear embedding and correlation coefficient algorithms. Supervised locally linear embedding takes into account class label information and improves the classification performance. Furthermore, Spearman's rank correlation coefficient is used to remove the coexpression genes. The experiment results obtained on four public tumor microarray datasets illustrate that our method is valid and feasible.

Data embedding

DOEpatents

Sandford, II, Maxwell T.; Handel, Theodore G.

1997-01-01

A method of embedding auxiliary information into a set of host data, such as a photograph, television signal, facsimile transmission, or identification card. All such host data contain intrinsic noise, allowing pixels in the host data which are nearly identical and which have values differing by less than the noise value to be manipulated and replaced with auxiliary data. As the embedding method does not change the elemental values of the host data, the auxiliary data do not noticeably affect the appearance or interpretation of the host data. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user.

Data embedding

DOEpatents

Sandford, M.T. II; Handel, T.G.

1997-08-19

A method is disclosed for embedding auxiliary information into a set of host data, such as a photograph, television signal, facsimile transmission, or identification card. All such host data contain intrinsic noise, allowing pixels in the host data which are nearly identical and which have values differing by less than the noise value to be manipulated and replaced with auxiliary data. As the embedding method does not change the elemental values of the host data, the auxiliary data do not noticeably affect the appearance or interpretation of the host data. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user. 19 figs.

Bridging the gap between structural bioinformatics and receptor research: the membrane-embedded, ligand-gated, P2X glycoprotein receptor.

PubMed

Mager, Peter P; Weber, Anje; Illes, Peter

2004-01-01

No details on P2X receptor architecture had been known at the atomic resolution level. Using comparative homology-based molecular modelling and threading, it was attempted to predict the three-dimensional structure of P2X receptors. This prediction could not be carried out, however, because important properties of the P2X family differ considerably from that of the potential template proteins. This paper reviews an alternative approach consisting of three research fields: bioinformatics, structural modelling, and a variety of the results of biological experiments. Starting point is the amino acid sequence. Using the sequential data, the first step is a secondary structure prediction. The resulting secondary structure is converted into a three-dimensional geometry. Then, the secondary and tertiary structures are optimized by using the quantum chemistry RHF/3-21G minimal basic set and the all-atom molecular mechanics AMBER96 force field. The fold of the membrane-embedded protein is simulated by a suitable dielectricum. The structure is refined using a conjugate gradient minimizer (Fletcher-Reeves modification of the Polak-Ribiere method). The results of the geometry optimization were checked by a Ramanchandran plot, rotamer analysis, all-atom contact dots, and the C(beta) deviation. As additional tools for the model building, multiple alignment analysis and comparative sequence-function analysis were used. The approach is exemplified on the membrane-embedded, ligand-gated P2X3 receptor subunit, a monovalent-bivalent cation channel-forming glycoprotein that is activated by extracellular adenosine 5'-triphosphate. From these results, a topology of the pore-forming motif of the P2X3 receptor subunit was proposed. It is believed that a fully functional P2X channel requires a precise coupling between (i) two distinct peptide modules, an extracellularly occurring ATP-binding module and a pore module that includes a long transmembrane and short intracellular part, (ii) an interaction surface with membranes, and (iii) hydrogen bonding forces of the residues and hydrated cations. Furthermore, this paper demonstrates the role of quantitative structure-activity relationships (QSARs) in P2X research (calcium ion permeability of the wild-type and after site-directed mutagenesis of the rat P2X2 receptor protein, KN-62 analogs as competitive antagonists of the human P2X7 receptor). EXPERIMENTAL PROOFS: The predictions are experimentally testable and may provide an additional interpretation of experimental observations published in literature. In particular, there is the good agreement of the geometry optimized P2X3 structure with experimentally proposed P2X receptor models obtained by neurophysiological, biochemical, pharmacological, and mutation experiments. Although the rat P2X3 receptor subunit is more complex (397 amino acids) than the KcsA protein (160 amino acids), the overall folds of the peptide backbone atoms are similar. To avoid semantic confusion, it should be noted that "prediction" is defined in a probabilistic sense. Matches to generic rules do not mean "this is true" but rather "this might be true". Only biological and chemical knowledge can determine whether or not these predictions are meaningful. Thus, the results from the computational tools are probabilistic predictions and subject to further experimental verification. The geometry optimized P2X3 receptor subunit is freely available for academic researchers on e-mail request (PDB format).

Evaluation of a Silver-Embedded Ceramic Tablet as a Primary and Secondary Point-of-Use Water Purification Technology in Limpopo Province, S. Africa

PubMed Central

Ehdaie, Beeta; Rento, Chloe T.; Son, Veronica; Turner, Sydney S.; Samie, Amidou; Dillingham, Rebecca A.

2017-01-01

The World Health Organization (WHO) recognizes point-of-use water treatment (PoUWT) technologies as effective means to improve water quality. This paper investigates long-term performance and social acceptance of a novel PoUWT technology, a silver-infused ceramic tablet, in Limpopo Province, South Africa. When placed in a water storage container, the silver-embedded ceramic tablet releases silver ions into water, thereby disinfecting microbial pathogens and leaving the water safe for human consumption. As a result of its simplicity and efficiency, the silver-embedded ceramic tablet can serve as a stand-alone PoUWT method and as a secondary PoUWT to improve exisitng PoUWT methods, such as ceramic water filters. In this paper, three PoUWT interventions were conducted to evaluate the silver-embedded ceramic tablet: (1) the silver-embedded ceramic tablet as a stand-alone PoUWT method, (2) ceramic water filters stand-alone, and (3) a filter-tablet combination. The filter-tablet combination evaluates the silver-embedded ceramic tablet as a secondary PoUWT method when placed in the lower reservoir of the ceramic water filter system to provide residual disinfection post-filtration. Samples were collected from 79 households over one year and analyzed for turbidity, total silver levels and coliform bacteria. Results show that the silver-embedded ceramic tablet effectively reduced total coliform bacteria (TC) and E. coli when used as a stand-alone PoUWT method and when used in combination with ceramic water filters. The silver-embedded ceramic tablet’s performance as a stand-alone PoUWT method was comparable to current inexpensive, single-use PoUWT methods, demonstrating 100% and 75% median reduction in E. coli and TC, respectively, after two months of use. Overall, the the filter-tablet combination performed the best of the three interventions, providing a 100% average percent reduction in E. coli over one year. User surveys were also conducted and indicated that the silver-embedded ceramic tablet was simple to use and culturally appropriate. Also, silver levels in all treated water samples remained below 20 μg/L, significantly lower than the drinking water standard of 100 μg/L, making it safe for consumption. Long-term data demonstrates that the silver-embedded ceramic tablet has beneficial effects even after one year of use. This study demonstrates that the silver-embedded ceramic tablet can effectively improve water quality when used alone, or with ceramic water filters, to reduce rates of recontamination. Therefore, the tablet has the potential to provide a low-cost means to purify water in resource-limited settings. PMID:28095435

Evaluation of a Silver-Embedded Ceramic Tablet as a Primary and Secondary Point-of-Use Water Purification Technology in Limpopo Province, S. Africa.

PubMed

Ehdaie, Beeta; Rento, Chloe T; Son, Veronica; Turner, Sydney S; Samie, Amidou; Dillingham, Rebecca A; Smith, James A

2017-01-01

The World Health Organization (WHO) recognizes point-of-use water treatment (PoUWT) technologies as effective means to improve water quality. This paper investigates long-term performance and social acceptance of a novel PoUWT technology, a silver-infused ceramic tablet, in Limpopo Province, South Africa. When placed in a water storage container, the silver-embedded ceramic tablet releases silver ions into water, thereby disinfecting microbial pathogens and leaving the water safe for human consumption. As a result of its simplicity and efficiency, the silver-embedded ceramic tablet can serve as a stand-alone PoUWT method and as a secondary PoUWT to improve exisitng PoUWT methods, such as ceramic water filters. In this paper, three PoUWT interventions were conducted to evaluate the silver-embedded ceramic tablet: (1) the silver-embedded ceramic tablet as a stand-alone PoUWT method, (2) ceramic water filters stand-alone, and (3) a filter-tablet combination. The filter-tablet combination evaluates the silver-embedded ceramic tablet as a secondary PoUWT method when placed in the lower reservoir of the ceramic water filter system to provide residual disinfection post-filtration. Samples were collected from 79 households over one year and analyzed for turbidity, total silver levels and coliform bacteria. Results show that the silver-embedded ceramic tablet effectively reduced total coliform bacteria (TC) and E. coli when used as a stand-alone PoUWT method and when used in combination with ceramic water filters. The silver-embedded ceramic tablet's performance as a stand-alone PoUWT method was comparable to current inexpensive, single-use PoUWT methods, demonstrating 100% and 75% median reduction in E. coli and TC, respectively, after two months of use. Overall, the the filter-tablet combination performed the best of the three interventions, providing a 100% average percent reduction in E. coli over one year. User surveys were also conducted and indicated that the silver-embedded ceramic tablet was simple to use and culturally appropriate. Also, silver levels in all treated water samples remained below 20 μg/L, significantly lower than the drinking water standard of 100 μg/L, making it safe for consumption. Long-term data demonstrates that the silver-embedded ceramic tablet has beneficial effects even after one year of use. This study demonstrates that the silver-embedded ceramic tablet can effectively improve water quality when used alone, or with ceramic water filters, to reduce rates of recontamination. Therefore, the tablet has the potential to provide a low-cost means to purify water in resource-limited settings.

Quality Scalability Aware Watermarking for Visual Content.

PubMed

Bhowmik, Deepayan; Abhayaratne, Charith

2016-11-01

Scalable coding-based content adaptation poses serious challenges to traditional watermarking algorithms, which do not consider the scalable coding structure and hence cannot guarantee correct watermark extraction in media consumption chain. In this paper, we propose a novel concept of scalable blind watermarking that ensures more robust watermark extraction at various compression ratios while not effecting the visual quality of host media. The proposed algorithm generates scalable and robust watermarked image code-stream that allows the user to constrain embedding distortion for target content adaptations. The watermarked image code-stream consists of hierarchically nested joint distortion-robustness coding atoms. The code-stream is generated by proposing a new wavelet domain blind watermarking algorithm guided by a quantization based binary tree. The code-stream can be truncated at any distortion-robustness atom to generate the watermarked image with the desired distortion-robustness requirements. A blind extractor is capable of extracting watermark data from the watermarked images. The algorithm is further extended to incorporate a bit-plane discarding-based quantization model used in scalable coding-based content adaptation, e.g., JPEG2000. This improves the robustness against quality scalability of JPEG2000 compression. The simulation results verify the feasibility of the proposed concept, its applications, and its improved robustness against quality scalable content adaptation. Our proposed algorithm also outperforms existing methods showing 35% improvement. In terms of robustness to quality scalable video content adaptation using Motion JPEG2000 and wavelet-based scalable video coding, the proposed method shows major improvement for video watermarking.

Equilibrium composition of interphase boundaries

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

Wynblatt, P.

1990-01-01

Two modeling approaches have been used to investigate segregation effects at interphase boundaries. The first approach is based on the nearest neighbor bond model, used in conjunction with the regular solution approximation, and is an extension of an earlier framework developed to address segregation phenomena at free surfaces. In order to model a semicoherent interphase boundary, we have employed a second modeling approach, based on Monte Carol simulation, in conjunction with the embedded atom method (EAM). The EAM is a powerful new method for describing interatomic interactions in metallic systems. It includes certain many-body interactions that depend on the localmore » environment of an atom. The Monte Carol approach has been applied to semicoherent interphase boundaries in Cu-Ag-Au alloys dilute in Au. These alloys consist of coexisting Cu-rich and Ag-rich phases, which differ in lattice constant by about 12%, such that good matching across in interface occurs when nine structural units of the Cu-rich phase are opposed to eight structural units of the Ag-rich phase. Thus far, interfaces with two different orientations have been studied: {l brace}001{r brace}-Cu//{l brace}001{r brace}-Ag, {l angle}110{r angle}-Cu//{l angle}110{r angle}-Ag; and {l brace}111{r brace}-Cu//{l brace}111{r brace}-Ag, {l angle}110{r angle}-Cu//{l angle}110{r angle}-Ag. These two interfaces will be referred to as the (001) and (111) interphase boundaries, for short. 18 refs.« less

Spontaneous emission from radiative chiral nematic liquid crystals at the photonic band-gap edge: an investigation into the role of the density of photon states near resonance.

PubMed

Mavrogordatos, Th K; Morris, S M; Wood, S M; Coles, H J; Wilkinson, T D

2013-06-01

In this article, we investigate the spontaneous emission properties of radiating molecules embedded in a chiral nematic liquid crystal, under the assumption that the electronic transition frequency is close to the photonic edge mode of the structure, i.e., at resonance. We take into account the transition broadening and the decay of electromagnetic field modes supported by the so-called "mirrorless"cavity. We employ the Jaynes-Cummings Hamiltonian to describe the electron interaction with the electromagnetic field, focusing on the mode with the diffracting polarization in the chiral nematic layer. As known in these structures, the density of photon states, calculated via the Wigner method, has distinct peaks on either side of the photonic band gap, which manifests itself as a considerable modification of the emission spectrum. We demonstrate that, near resonance, there are notable differences between the behavior of the density of states and the spontaneous emission profile of these structures. In addition, we examine in some detail the case of the logarithmic peak exhibited in the density of states in two-dimensional photonic structures and obtain analytic relations for the Lamb shift and the broadening of the atomic transition in the emission spectrum. The dynamical behavior of the atom-field system is described by a system of two first-order differential equations, solved using the Green's-function method and the Fourier transform. The emission spectra are then calculated and compared with experimental data.

The Cooling and Lubrication Performance of Graphene Platelets in Micro-Machining Environments

NASA Astrophysics Data System (ADS)

Chu, Bryan

The research presented in this thesis is aimed at investigating the use of graphene platelets (GPL) to address the challenges of excessive tool wear, reduced part quality, and high specific power consumption encountered in micro-machining processes. There are two viable methods of introducing GPL into micro-machining environments, viz., the embedded delivery method, where the platelets are embedded into the part being machined, and the external delivery method, where graphene is carried into the cutting zone by jetting or atomizing a carrier fluid. The study involving the embedded delivery method is focused on the micro-machining performance of hierarchical graphene composites. The results of this study show that the presence of graphene in the epoxy matrix improves the machinability of the composite. In general, the tool wear, cutting forces, surface roughness, and extent of delamination are all seen to be lower for the hierarchical composite when compared to the conventional two-phase glass fiber composite. These improvements are attributed to the fact that graphene platelets improve the thermal conductivity of the matrix, provide lubrication at the tool-chip interface and also improve the interface strength between the glass fibers and the matrix. The benefits of graphene are seen to also carry over to the external delivery method. The platelets provide improved cooling and lubrication performance to both environmentally-benign cutting fluids as well as to semi-synthetic cutting fluids used in micro-machining. The cutting performance is seen to be a function of the geometry (i.e., lateral size and thickness) and extent of oxygen-functionalization of the platelet. Ultrasonically exfoliated platelets (with 2--3 graphene layers and lowest in-solution characteristic lateral length of 120 nm) appear to be the most favorable for micro-machining applications. Even at the lowest concentration of 0.1 wt%, they are capable of providing a 51% reduction in the cutting temperature and a 25% reduction in the surface roughness value over that of the baseline semi-synthetic cutting fluid. For the thermally-reduced platelets (with 4--8 graphene layers and in-solution characteristic lateral length of 562--2780 nm), a concentration of 0.2 wt% appears to be optimal. An investigation into the impingement dynamics of the graphene-laden colloidal solutions on a heated substrate reveals that the most important criterion dictating their machining performance is their ability to form uniform, submicron thick films of the platelets upon evaporation of the carrier fluid. As such, the characterization of the residual platelet film left behind on a heated substrate may be an effective technique for evaluating different graphene colloidal solutions for cutting fluids applications in micromachining. Graphene platelets have also recently been shown to reduce the aggressive chemical wear of diamond tools during the machining of transition metal alloys. However, the specific mechanisms responsible for this improvement are currently unknown. The modeling work presented in this thesis uses molecular dynamics techniques to shed light on the wear mitigation mechanisms that are active during the diamond cutting of steel when in the presence of graphene platelets. The dual mechanisms responsible for graphene-induced chemical wear mitigation are: 1) The formation of a physical barrier between the metal and tool atoms, preventing graphitization; and 2) The preferential transfer of carbon from the graphene platelet rather than from the diamond tool. The results of the simulations also provide new insight into the behavior of the 2D graphene platelets in the cutting zone, specifically illustrating the mechanisms of cleaving and interlayer sliding in graphene platelets under the high pressures in cutting zones.

A novel sample preparation method to avoid influence of embedding medium during nano-indentation

Treesearch

Yujie Meng; Siqun Wang; Zhiyong Cai; Timothy M. Young; Guanben Du; Yanjun Li

2012-01-01

The effect of the embedding medium on the nano-indentation measurements of lignocellulosic materials was investigated experimentally using nano-indentation. Both the reduced elastic modulus and the hardness of nonembedded cell walls were found to be lower than those of the embedded samples, proving that the embedding medium used for specimen preparation on cellulosic...

Study of Composite Plate Damages Using Embedded PZT Sensors with Various Center Frequency

NASA Astrophysics Data System (ADS)

Kang, Kyoung-Tak; Chun, Heoung-Jae; Son, Ju-Hyun; Byun, Joon-Hyung; Um, Moon-Kwang; Lee, Sang-Kwan

This study presents part of an experimental and analytical survey of candidate methods for damage detection of composite structural. Embedded piezoceramic (PZT) sensors were excited with the high power ultrasonic wave generator generating a propagation of stress wave along the composite plate. The same embedded piezoceramic (PZT) sensors are used as receivers for acquiring stress signals. The effects of center frequency of embedded sensor were evaluated for the damage identification capability with known localized defects. The study was carried out to assess damage in composite plate by fusing information from multiple sensing paths of the embedded network. It was based on the Hilbert transform, signal correlation and probabilistic searching. The obtained results show that satisfactory detection of defects could be achieved by proposed method.

Peering at Brain Polysomes with Atomic Force Microscopy

PubMed Central

Lunelli, Lorenzo; Bernabò, Paola; Bolner, Alice; Vaghi, Valentina; Marchioretto, Marta; Viero, Gabriella

2016-01-01

The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, formed by ribosomes, mRNAs, several proteins and non-coding RNAs, represent integrated platforms where translational controls take place. However, while the ribosome has been widely studied, the organization of polysomes is still lacking comprehensive understanding. Thus much effort is required in order to elucidate polysome organization and any novel mechanism of translational control that may be embedded. Atomic force microscopy (AFM) is a type of scanning probe microscopy that allows the acquisition of 3D images at nanoscale resolution. Compared to electron microscopy (EM) techniques, one of the main advantages of AFM is that it can acquire thousands of images both in air and in solution, enabling the sample to be maintained under near physiological conditions without any need for staining and fixing procedures. Here, a detailed protocol for the accurate purification of polysomes from mouse brain and their deposition on mica substrates is described. This protocol enables polysome imaging in air and liquid with AFM and their reconstruction as three-dimensional objects. Complementary to cryo-electron microscopy (cryo-EM), the proposed method can be conveniently used for systematically analyzing polysomes and studying their organization. PMID:27023752

New interatomic potential for Mg–Al–Zn alloys with specific application to dilute Mg-based alloys

NASA Astrophysics Data System (ADS)

Dickel, Doyl E.; Baskes, Michael I.; Aslam, Imran; Barrett, Christopher D.

2018-06-01

Because of its very large c/a ratio, zinc has proven to be a difficult element to model using semi-empirical classical potentials. It has been shown, in particular, that for the modified embedded atom method (MEAM), a potential cannot simultaneously have an hcp ground state and c/a ratio greater than ideal. As an alloying element, however, useful zinc potentials can be generated by relaxing the condition that hcp be the lowest energy structure. In this paper, we present a MEAM zinc potential, which gives accurate material properties for the pure state, as well as a MEAM ternary potential for the Mg–Al–Zn system which will allow the atomistic modeling of a wide class of alloys containing zinc. The effects of zinc in simple Mg–Zn for this potential is demonstrated and these results verify the accuracy for the new potential in these systems.

DNA codes for nanoscience.

PubMed

Samorì, Bruno; Zuccheri, Giampaolo

2005-02-11

The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.

Effect of self-assembled InAs islands on the interfacial roughness of optical-switched resonant tunneling diode

PubMed Central

2012-01-01

Embedding a quantum dot [QD] layer between the double barriers of resonant tunneling diode [RTD] is proved to be an effective method to increase the sensitivity of QD-RTD single-photon detector. However, the interfacial flatness of this device would be worsened due to the introduction of quantum dots. In this paper, we demonstrate that the interfacial quality of this device can be optimized through increasing the growth temperature of AlAs up barrier. The glancing incidence X-ray reflectivity and the high-resolution transmission electron microscopy measurements show that the interfacial smoothness has been greatly improved, and the photo-luminescence test indicated that the InAs QDs were maintained at the same time. The smoother interface was attributed to the evaporation of segregated indium atoms at InGaAs surface layer. PACS 73.40.GK, 73.23._b, 73.21.La, 74.62.Dh PMID:22333518

Effect of self-assembled InAs islands on the interfacial roughness of optical-switched resonant tunneling diode.

PubMed

Tian, Haitao; Wang, Lu; Shi, Zhenwu; Gao, Huaiju; Zhang, Shuhui; Wang, Wenxin; Chen, Hong

2012-02-14

Embedding a quantum dot [QD] layer between the double barriers of resonant tunneling diode [RTD] is proved to be an effective method to increase the sensitivity of QD-RTD single-photon detector. However, the interfacial flatness of this device would be worsened due to the introduction of quantum dots. In this paper, we demonstrate that the interfacial quality of this device can be optimized through increasing the growth temperature of AlAs up barrier. The glancing incidence X-ray reflectivity and the high-resolution transmission electron microscopy measurements show that the interfacial smoothness has been greatly improved, and the photo-luminescence test indicated that the InAs QDs were maintained at the same time. The smoother interface was attributed to the evaporation of segregated indium atoms at InGaAs surface layer. PACS: 73.40.GK, 73.23._b, 73.21.La, 74.62.Dh.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals.

PubMed

Wilson, S R; Mendelev, M I

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

NASA Astrophysics Data System (ADS)

Wilson, S. R.; Mendelev, M. I.

2016-04-01

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

Atomistic calculations of interface elastic properties in noncoherent metallic bilayers

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

Mi Changwen; Jun, Sukky; Kouris, Demitris A.

2008-02-15

The paper describes theoretical and computational studies associated with the interface elastic properties of noncoherent metallic bicrystals. Analytical forms of interface energy, interface stresses, and interface elastic constants are derived in terms of interatomic potential functions. Embedded-atom method potentials are then incorporated into the model to compute these excess thermodynamics variables, using energy minimization in a parallel computing environment. The proposed model is validated by calculating surface thermodynamic variables and comparing them with preexisting data. Next, the interface elastic properties of several fcc-fcc bicrystals are computed. The excess energies and stresses of interfaces are smaller than those on free surfacesmore » of the same crystal orientations. In addition, no negative values of interface stresses are observed. Current results can be applied to various heterogeneous materials where interfaces assume a prominent role in the systems' mechanical behavior.« less

A Steganographic Embedding Undetectable by JPEG Compatibility Steganalysis

DTIC Science & Technology

2002-01-01

itd.nrl.navy.mil Abstract. Steganography and steganalysis of digital images is a cat- and-mouse game. In recent work, Fridrich, Goljan and Du introduced a method...proposed embedding method. 1 Introduction Steganography and steganalysis of digital images is a cat-and-mouse game. Ever since Kurak and McHugh’s seminal...paper on LSB embeddings in images [10], various researchers have published work on either increasing the payload, im- proving the resistance to

Alumina-coated and manganese monoxide embedded 3D carbon derived from avocado as high-performance anode for lithium-ion batteries

NASA Astrophysics Data System (ADS)

rehman, Wasif ur; Xu, Youlong; Du, Xianfeng; Sun, Xiaofei; Ullah, Inam; Zhang, Yuan; Jin, Yanling; Zhang, Baofeng; Li, Xifei

2018-07-01

Derived from avocado fruit, a three dimension (3D) carbon is prepared via a hydrothermal/pyrolysis process followed by embedding with MnO nanoparticles by a wet chemical method and coating with Al2O3 through an atomic layer deposition technique. The obtained material presents a hierarchical structure that MnO nanocrystals wrapped in 3D carbon and then encapsulated in a uniform Al2O3 layer with a thickness of about 5 nm. Benefiting from this hierarchical structure in which 3D carbon offers numerous electronic pathways to enhance the conductivity and Al2O3 nanolayer provide a shelter to keep away from dissolution of Mn4+ and volume changes during charge/discharge process. This material (marked as C/MnO@Al2O3) has exhibited high rate performance and excellent cyclability as an anode for lithium ion batteries. A high specific capacity of about 600 mA h g-1 is achieved at a current density of 1000 mA g-1 and the electrode can still deliver a high specific capacity of about 1165 mA h g-1 at 150 mA g-1 after 100 cycles. These results facilitate a green and high potential of anode materials towards promising devices for advance performance of lithium-ion batteries.

Average crystal structure(s) of the embedded meta stable η‧-phase in the Al-Mg-Zn system

NASA Astrophysics Data System (ADS)

Bøvik Larsen, Helge; Thorkildsen, Gunnar; Natland, Sølvi; Pattison, Philip

2014-05-01

Meta stable embedded nano-sized ?-particles within a single grain extracted from an alloy having the nominal composition ? have been examined with X-ray diffraction. By applying the orientational and metric relationships that exist between the hexagonal unit cell of the ?-particles and the cubic unit cell of the Al-matrix, it has been proven possible to directly collect diffracted intensity data from the ?-particle ensemble. This has been done using synchrotron radiation and a ?-diffractometer having a scintillator point detector setup. The approach has resulted in improved data quality compared to previous experiments. The interpretation of the data set, based on a combination of Patterson syntheses, direct methods and geometrical restraints, yielded two possible average structural representations: one Al-rich with the approximate stoichiometric composition ? and one Al-depleted with approximate stoichiometric composition ?. Both structures are realized in the same space group, ?, and are most probably superimposed in the crystalline system examined. The geometries are discussed within the atomic environment approach where icosahedral or near-icosahedral configurations are encountered. Comparison with previous published models and the equilibrium structure reveals a main difference related to the distribution of the Zn-sites in the unit cell. A possible transformation path is also suggested. Various aspects and challenges regarding data collection, data reduction and data quality are specifically addressed.

Electronic and chemical structure of an organic light emitter embedded in an inorganic wide-bandgap semiconductor: Photoelectron spectroscopy of layered and composite structures of Ir(BPA) and ZnSe

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

Dimamay, Mariel; Laboratoire de Chimie des Polymères Organiques, CNRS, Université de Bordeaux, UMR 5629-16 Avenue Pey-Berland, 33607 Pessac; Mayer, Thomas

Luminescent organic phases embedded in conductive inorganic matrices are proposed for hybrid organic-inorganic light-emitting diodes. In this configuration, the organic dye acts as the radiative recombination site for charge carriers injected into the inorganic matrix. Our investigation is aimed at finding a material combination where the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the organic dye are situated in between the valence and conduction bands of the inorganic matrix in order to promote electron and hole transfer from the matrix to the dye. Bilayer and composite thin films of zinc selenide (ZnSe) and a redmore » iridium complex (Ir(BPA)) organic light emitter were prepared in situ via UHV thermal evaporation technique. The electronic and atomic structures were studied applying X-ray and ultraviolet photoelectron spectroscopies. The measured energy band alignments for the ZnSe/Ir(BPA) bilayer and ZnSe+Ir(BPA) composite reveal that the HOMO and LUMO of the organic dye are positioned in the ZnSe bandgap. For the initial steps of ZnSe deposition on a dye film to form Ir(BPA)/ZnSe bilayers, zinc atoms intercalate into the dye film leaving behind an excess of selenium at the interface that partly reacts with dye molecules. Photoelectron spectroscopy of the composites shows the same species suggesting a similar mechanism. This mechanism leads to composite films with increased content of amorphous phases in the inorganic matrix, thereby affecting its conductivity, as well as to the presence of nonradiative recombination sites provided by the intercalated Zn atoms.« less

Single Atomic Iron Catalysts for Oxygen Reduction in Acidic Media: Particle Size Control and Thermal Activation

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

Zhang, Hanguang; Hwang, Sooyeon; Wang, Maoyu

To significantly reduce the cost of proton exchange membrane (PEM) fuel cells, current Pt must be replaced by platinum-metal-group (PGM)-free catalysts for the oxygen reduction reaction (ORR) in acid. We report here a new class of high-performance atomic iron dispersed carbon catalysts through controlled chemical doping of iron ions into zinc-zeolitic imidazolate framework (ZIF), a type of metal-organic framework (MOF). The novel synthetic chemistry enables accurate size control of Fe-doped ZIF catalyst particles with a wide range from 20 to 1000 nm without changing chemical properties, which provides a great opportunity to increase the density of active sites that ismore » determined by the particle size. We elucidated the active site formation mechanism by correlating the chemical and structural changes with thermal activation process for the conversion from Fe-N4 complex containing hydrocarbon networks in ZIF to highly active FeNx sites embedded into carbon. A temperature of 800oC was identified as the critical point to start forming pyridinic nitrogen doping at the edge of the graphitized carbon planes. Further increasing heating temperature to 1100oC leads to increase of graphitic nitrogen, generating possible synergistic effect with FeNx sites to promote ORR activity. The best performing catalyst, which has well-defined particle size around 50 nm and abundance of atomic FeNx sites embedded into carbon structures, achieve a new performance milestone for the ORR in acid including a half-wave potential of 0.85 V vs RHE and only 20 mV loss after 10,000 cycles in O2 saturated H2SO4 electrolyte. The new class PGM-free catalyst with approaching activity to Pt holds great promise for future PEM fuel cells.« less

Detection of a Fermi-level crossing in Si(557)-Au with inverse photoemission

NASA Astrophysics Data System (ADS)

Lipton-Duffin, J. A.; MacLeod, J. M.; McLean, A. B.

2006-06-01

The unoccupied energy bands of the quasi-one-dimensional (1D) Si(557)-Au system have been studied with momentum-resolved inverse photoemission. A band is found that lies (0.4±0.4)eV above the Fermi level at the center of the surface Brillouin zone (Γ¯) . It disperses to higher binding energy, along the Γ Kmacr direction, and crosses the Fermi level at k‖=0.5±0.1Å-1 . The corresponding direction in real space is parallel to both the rows of silicon adatoms and the rows of embedded gold atoms that are distinctive features of this surface reconstruction. The location of the crossing is in good agreement with previously published photoemission data [Altmann , Phys. Rev. B 64, 035406 (2001); Ahn , Phys. Rev. Lett. 91, 196403 (2003)], where two closely spaced bands were found to disperse from the Kmacr zone boundary to lower binding energy and then cross the Fermi level. In addition to the band mentioned above, a band was found that has parabolic dispersion along Γ Kmacr , the direction that is parallel to the rows of embedded gold atoms. The band minimum for the parabolic band lies (0.8±0.4)eV below the vacuum level and it has an effective mass m*=(1.0±0.1)me , where me is the free electron mass. Perpendicular to the rows of gold atoms, as expected for a state with quasi-1D symmetry, it has flat dispersion. This band may be an image state resonance, overlapping the silicon conduction band continuum, and it is spatially localized to the edge of the silicon terraces.

On the role of electronic friction for dissociative adsorption and scattering of hydrogen molecules at a Ru(0001) surface.

PubMed

Füchsel, Gernot; Schimka, Selina; Saalfrank, Peter

2013-09-12

The role of electronic friction and, more generally, of nonadiabatic effects during dynamical processes at the gas/metal surface interface is still a matter of discussion. In particular, it is not clear if electronic nonadiabaticity has an effect under "mild" conditions, when molecules in low rovibrational states interact with a metal surface. In this paper, we investigate the role of electronic friction on the dissociative sticking and (inelastic) scattering of vibrationally and rotationally cold H2 molecules at a Ru(0001) surface theoretically. For this purpose, classical molecular dynamics with electronic friction (MDEF) calculations are performed and compared to MD simulations without friction. The two H atoms move on a six-dimensional potential energy surface generated from gradient-corrected density functional theory (DFT), that is, all molecular degrees of freedom are accounted for. Electronic friction is included via atomic friction coefficients obtained from an embedded atom, free electron gas (FEG) model, with embedding densities taken from gradient-corrected DFT. We find that within this model, dissociative sticking probabilities as a function of impact kinetic energies and impact angles are hardly affected by nonadiabatic effects. If one accounts for a possibly enhanced electronic friction near the dissociation barrier, on the other hand, reduced sticking probabilities are observed, in particular, at high impact energies. Further, there is always an influence on inelastic scattering, in particular, as far as the translational and internal energy distribution of the reflected molecules is concerned. Additionally, our results shed light on the role played by the velocity distribution of the incident molecular beam for adsorption probabilities, where, in particular, at higher impact energies, large effects are found.

X-Ray Standing Waves on Surfaces

DTIC Science & Technology

1993-01-01

dependent distributional changes of iodine on Pt 6.3 X-ray standing wave study of a Langmuir - Blodgett multilayer film 7. Conclusions 8. Acknowledgments...4B. 6.3 X-ray standing wave study of a Langmuir - Blodgett multilayer film As mentioned previously the total external reflection condition occurs...for a Zn atom layer embedded in the top arachidate bilayer of a Langmuir - Blodgett (LB) multilayer film which was deposited on the surface of a gold

Research about Memory Detection Based on the Embedded Platform

NASA Astrophysics Data System (ADS)

Sun, Hao; Chu, Jian

As is known to us all, the resources of memory detection of the embedded systems are very limited. Taking the Linux-based embedded arm as platform, this article puts forward two efficient memory detection technologies according to the characteristics of the embedded software. Especially for the programs which need specific libraries, the article puts forwards portable memory detection methods to help program designers to reduce human errors,improve programming quality and therefore make better use of the valuable embedded memory resource.

Data embedding employing degenerate clusters of data having differences less than noise value

DOEpatents

Sanford, II, Maxwell T.; Handel, Theodore G.

1998-01-01

A method of embedding auxiliary information into a set of host data, such as a photograph, television signal, facsimile transmission, or identification card. All such host data contain intrinsic noise, allowing pixels in the host data which are nearly identical and which have values differing by less than the noise value to be manipulated and replaced with auxiliary data. As the embedding method does not change the elemental values of the host data, the auxiliary data do not noticeably affect the appearance or interpretation of the host data. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user.

Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding

PubMed Central

Tajima, Satohiro; Yanagawa, Toru; Fujii, Naotaka; Toyoizumi, Taro

2015-01-01

Brain-wide interactions generating complex neural dynamics are considered crucial for emergent cognitive functions. However, the irreducible nature of nonlinear and high-dimensional dynamical interactions challenges conventional reductionist approaches. We introduce a model-free method, based on embedding theorems in nonlinear state-space reconstruction, that permits a simultaneous characterization of complexity in local dynamics, directed interactions between brain areas, and how the complexity is produced by the interactions. We demonstrate this method in large-scale electrophysiological recordings from awake and anesthetized monkeys. The cross-embedding method captures structured interaction underlying cortex-wide dynamics that may be missed by conventional correlation-based analysis, demonstrating a critical role of time-series analysis in characterizing brain state. The method reveals a consciousness-related hierarchy of cortical areas, where dynamical complexity increases along with cross-area information flow. These findings demonstrate the advantages of the cross-embedding method in deciphering large-scale and heterogeneous neuronal systems, suggesting a crucial contribution by sensory-frontoparietal interactions to the emergence of complex brain dynamics during consciousness. PMID:26584045

Electrochemical CO 2 Reduction with Atomic Iron-Dispersed on Nitrogen-Doped Graphene

DOE PAGES

Zhang, Chenhao; Yang, Shize; Wu, Jingjie; ...

2018-03-25

Electrochemical reduction of CO 2 provides an opportunity to reach a carbon-neutral energy recycling regime, in which CO 2 emissions from fuel use are collected and converted back to fuels. The reduction of CO 2 to CO is the first step toward the synthesis of more complex carbon-based fuels and chemicals. Therefore, understanding this step is crucial for the development of high-performance electrocatalyst for CO 2 conversion to higher order products such as hydrocarbons. In this paper, atomic iron dispersed on nitrogen-doped graphene (Fe/NG) is synthesized as an efficient electrocatalyst for CO 2 reduction to CO. Fe/NG has a lowmore » reduction overpotential with high Faradic efficiency up to 80%. The existence of nitrogen-confined atomic Fe moieties on the nitrogen-doped graphene layer is confirmed by aberration-corrected high-angle annular dark-field scanning transmission electron microscopy and X-ray absorption fine structure analysis. The Fe/NG catalysts provide an ideal platform for comparative studies of the effect of the catalytic center on the electrocatalytic performance. Finally, the CO 2 reduction reaction mechanism on atomic Fe surrounded by four N atoms (Fe–N 4) embedded in nitrogen-doped graphene is further investigated through density functional theory calculations, revealing a possible promotional effect of nitrogen doping on graphene.« less

Electrochemical CO 2 Reduction with Atomic Iron-Dispersed on Nitrogen-Doped Graphene

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

Zhang, Chenhao; Yang, Shize; Wu, Jingjie

Electrochemical reduction of CO 2 provides an opportunity to reach a carbon-neutral energy recycling regime, in which CO 2 emissions from fuel use are collected and converted back to fuels. The reduction of CO 2 to CO is the first step toward the synthesis of more complex carbon-based fuels and chemicals. Therefore, understanding this step is crucial for the development of high-performance electrocatalyst for CO 2 conversion to higher order products such as hydrocarbons. In this paper, atomic iron dispersed on nitrogen-doped graphene (Fe/NG) is synthesized as an efficient electrocatalyst for CO 2 reduction to CO. Fe/NG has a lowmore » reduction overpotential with high Faradic efficiency up to 80%. The existence of nitrogen-confined atomic Fe moieties on the nitrogen-doped graphene layer is confirmed by aberration-corrected high-angle annular dark-field scanning transmission electron microscopy and X-ray absorption fine structure analysis. The Fe/NG catalysts provide an ideal platform for comparative studies of the effect of the catalytic center on the electrocatalytic performance. Finally, the CO 2 reduction reaction mechanism on atomic Fe surrounded by four N atoms (Fe–N 4) embedded in nitrogen-doped graphene is further investigated through density functional theory calculations, revealing a possible promotional effect of nitrogen doping on graphene.« less

PREFACE: Nanoelectronics, sensors and single molecule biophysics Nanoelectronics, sensors and single molecule biophysics

NASA Astrophysics Data System (ADS)

Tao, Nongjian

2012-04-01

This special section of Journal of Physics: Condensed Matter (JPCM) is dedicated to Professor Stuart M Lindsay on the occasion of his 60th birthday and in recognition of his outstanding contributions to multiple research areas, including light scattering spectroscopy, scanning probe microscopy, biophysics, solid-liquid interfaces and molecular and nanoelectronics. It contains a collection of 14 papers in some of these areas, including a feature article by Lindsay. Each paper was subject to the normal rigorous review process of JPCM. In Lindsay's paper, he discusses the next generations of hybrid chemical-CMOS devices for low cost and personalized medical diagnosis. The discussion leads to several papers on nanotechnology for biomedical applications. Kawaguchi et al report on the detection of single pollen allergen particles using electrode embedded microchannels. Stern et al describe a structural study of three-dimensional DNA-nanoparticle assemblies. Hihath et al measure the conductance of methylated DNA, and discuss the possibility of electrical detection DNA methylation. Portillo et al study the electrostatic effects on the aggregation of prion proteins and peptides with atomic force microscopy. In an effort to understand the interactions between nanostructures and cells, Lamprecht et al report on the mapping of the intracellular distribution of carbon nanotubes with a confocal Raman imaging technique, and Wang et al focus on the intracellular delivery of gold nanoparticles using fluorescence microscopy. Park and Kristic provide theoretical analysis of micro- and nano-traps and their biological applications. This section also features several papers on the fundamentals of electron transport in single atomic wires and molecular junctions. The papers by Xu et al and by Wandlowksi et al describe new methods to measure conductance and forces in single molecule junctions and metallic atomic wires. Scullion et al report on the conductance of molecules with similar lengths but different energy barrier profiles in order to elucidate electron transport in the molecular junctions. Kiguchi and Murakoshi study metallic atomic wires under electrochemical potential control. Asai reports on a theoretical study of rectification in substituted atomic wires. Finally, Weiss et al report on a new method to pattern and functionalize oxide-free germanium surfaces with self-assembled organic monolayers, which provides interfaces between inorganic semiconductors and organic molecules. Nanoelectronics, sensors and single molecule biophysics contents Biochemistry and semiconductor electronics—the next big hit for silicon?Stuart Lindsay Electrical detection of single pollen allergen particles using electrode-embedded microchannelsChihiro Kawaguchi, Tetsuya Noda, Makusu Tsutsui, Masateru Taniguchi, Satoyuki Kawano and Tomoji Kawai Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structuresAvigail Stern, Dvir Rotem, Inna Popov and Danny Porath Effects of cytosine methylation on DNA charge transportJoshua Hihath, Shaoyin Guo, Peiming Zhang and Nongjian Tao Effect of electrostatics on aggregation of prion protein Sup35 peptideAlexander M Portillo, Alexey V Krasnoslobodtsev and Yuri L Lyubchenko Mapping the intracellular distribution of carbon nanotubes after targeted delivery to carcinoma cells using confocal Raman imaging as a label-free techniqueC Lamprecht, N Gierlinger, E Heister, B Unterauer, B Plochberger, M Brameshuber, P Hinterdorfer, S Hild and A Ebner Caveolae-mediated endocytosis of biocompatible gold nanoparticles in living Hela cellsXian Hao, Jiazhen Wu, Yuping Shan, Mingjun Cai, Xin Shang, Junguang Jiang and Hongda Wang Stability of an aqueous quadrupole micro-trapJae Hyun Park and Predrag S Krstić Electron transport properties of single molecular junctions under mechanical modulationsJianfeng Zhou, Cunlan Guo and Bingqian Xu An approach to measure electromechanical properties of atomic and molecular junctionsIlya V Pobelov, Gábor Mészáros, Koji Yoshida, Artem Mishchenko, Murat Gulcur, Martin R Bryce and Thomas Wandlowski Single-molecule conductance determinations on HS(CH2)4O(CH2)4SH and HS(CH2)2O(CH2)2O(CH2)2SH, and comparison with alkanedithiols of the same lengthLisa E Scullion, Edmund Leary, Simon J Higgins and Richard J Nichols Metal atomic contact under electrochemical potential controlManabu Kiguchi and Kei Murakoshi Rectification in substituted atomic wires: a theoretical insightYoshihiro Asai High-fidelity chemical patterning on oxide-free germaniumJ Nathan Hohman, Moonhee Kim, Jeffrey A Lawrence, Patrick D McClanahan and Paul S Weiss

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

PubMed

Devaraj, Arun; Colby, Robert; Vurpillot, François; Thevuthasan, Suntharampillai

2014-04-17

Oxide-supported metal nanoparticles are widely used in heterogeneous catalysis. The increasingly detailed design of such catalysts necessitates three-dimensional characterization with high spatial resolution and elemental selectivity. Laser-assisted atom probe tomography (APT) is uniquely suited to the task but faces challenges with the evaporation of metal/insulator systems. Correlation of APT with aberration-corrected scanning transmission electron microscopy (STEM), for Au nanoparticles embedded in MgO, reveals preferential evaporation of the MgO and an inaccurate assessment of nanoparticle composition. Finite element field evaporation modeling is used to illustrate the evolution of the evaporation front. Nanoparticle composition is most accurately predicted when the MgO is treated as having a locally variable evaporation field, indicating the importance of considering laser-oxide interactions and the evaporation of various molecular oxide ions. These results demonstrate the viability of APT for analysis of oxide-supported metal nanoparticles, highlighting the need for developing a theoretical framework for the evaporation of heterogeneous materials.

Growth of vertically aligned nanowires in metal-oxide nanocomposites: kinetic Monte-Carlo modeling versus experiments.

PubMed

Hennes, M; Schuler, V; Weng, X; Buchwald, J; Demaille, D; Zheng, Y; Vidal, F

2018-04-26

We employ kinetic Monte-Carlo simulations to study the growth process of metal-oxide nanocomposites obtained via sequential pulsed laser deposition. Using Ni-SrTiO3 (Ni-STO) as a model system, we reduce the complexity of the computational problem by choosing a coarse-grained approach mapping Sr, Ti and O atoms onto a single effective STO pseudo-atom species. With this ansatz, we scrutinize the kinetics of the sequential synthesis process, governed by alternating deposition and relaxation steps, and analyze the self-organization propensity of Ni atoms into straight vertically aligned nanowires embedded in the surrounding STO matrix. We finally compare the predictions of our binary toy model with experiments and demonstrate that our computational approach captures fundamental aspects of self-assembled nanowire synthesis. Despite its simplicity, our modeling strategy successfully describes the impact of relevant parameters like the concentration or laser frequency on the final nanoarchitecture of metal-oxide thin films grown via pulsed laser deposition.

Embedding Quantitative Methods by Stealth in Political Science: Developing a Pedagogy for Psephology

ERIC Educational Resources Information Center

Gunn, Andrew

2017-01-01

Student evaluations of quantitative methods courses in political science often reveal they are characterised by aversion, alienation and anxiety. As a solution to this problem, this paper describes a pedagogic research project with the aim of embedding quantitative methods by stealth into the first-year undergraduate curriculum. This paper…

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

NASA Astrophysics Data System (ADS)

Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

2010-12-01

Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

Mixed methods research in mental health nursing.

PubMed

Kettles, A M; Creswell, J W; Zhang, W

2011-08-01

Mixed methods research is becoming more widely used in order to answer research questions and to investigate research problems in mental health and psychiatric nursing. However, two separate literature searches, one in Scotland and one in the USA, revealed that few mental health nursing studies identified mixed methods research in their titles. Many studies used the term 'embedded' but few studies identified in the literature were mixed methods embedded studies. The history, philosophical underpinnings, definition, types of mixed methods research and associated pragmatism are discussed, as well as the need for mixed methods research. Examples of mental health nursing mixed methods research are used to illustrate the different types of mixed methods: convergent parallel, embedded, explanatory and exploratory in their sequential and concurrent combinations. Implementing mixed methods research is also discussed briefly and the problem of identifying mixed methods research in mental and psychiatric nursing are discussed with some possible solutions to the problem proposed. © 2011 Blackwell Publishing.

Optimization of the formation of embedded multicellular spheroids of MCF-7 cells: How to reliably produce a biomimetic 3D model.

PubMed

Zhang, Wenli; Li, Caibin; Baguley, Bruce C; Zhou, Fang; Zhou, Weisai; Shaw, John P; Wang, Zhen; Wu, Zimei; Liu, Jianping

2016-12-15

To obtain a multicellular MCF-7 spheroid model to mimic the three-dimensional (3D) of tumors, the microwell liquid overlay (A) and hanging-drop/agar (B) methods were first compared for their technical parameters. Then a method for embedding spheroids within collagen was optimized. For method A, centrifugation assisted cells form irregular aggregates but not spheroids. For method B, an extended sedimentation period of over 24 h for cell suspensions and increased viscosity of the culture medium using methylcellulose were necessary to harvest a dense and regular cell spheroid. When the number was less than 5000 cells/drop, embedded spheroids showed no tight cores and higher viability than the unembedded. However, above 5000 cells/drop, cellular viability of embedded spheroids was not significantly different from unembedded spheroids and cells invading through the collagen were in a sun-burst pattern with tight cores. Propidium Iodide staining indicated that spheroids had necrotic cores. The doxorubicin cytotoxicity demonstrated that spheroids were less susceptible to DOX than their monolayer cells. A reliable and reproducible method for embedding spheroids using the hanging-drop/agarose method within collagen is described herein. The cell culture model can be used to guide experimental manipulation of 3D cell cultures and to evaluate anticancer drug efficacy. Copyright © 2016 Elsevier Inc. All rights reserved.

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.

PubMed

Dai, Hanjun; Umarov, Ramzan; Kuwahara, Hiroyuki; Li, Yu; Song, Le; Gao, Xin

2017-11-15

An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these hidden Markov models into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA datasets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods. Our program is freely available at https://github.com/ramzan1990/sequence2vec. xin.gao@kaust.edu.sa or lsong@cc.gatech.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Can't Count or Won't Count? Embedding Quantitative Methods in Substantive Sociology Curricula: A Quasi-Experiment.

PubMed

Williams, Malcolm; Sloan, Luke; Cheung, Sin Yi; Sutton, Carole; Stevens, Sebastian; Runham, Libby

2016-06-01

This paper reports on a quasi-experiment in which quantitative methods (QM) are embedded within a substantive sociology module. Through measuring student attitudes before and after the intervention alongside control group comparisons, we illustrate the impact that embedding has on the student experience. Our findings are complex and even contradictory. Whilst the experimental group were less likely to be distrustful of statistics and appreciate how QM inform social research, they were also less confident about their statistical abilities, suggesting that through 'doing' quantitative sociology the experimental group are exposed to the intricacies of method and their optimism about their own abilities is challenged. We conclude that embedding QM in a single substantive module is not a 'magic bullet' and that a wider programme of content and assessment diversification across the curriculum is preferential.

Scalable Methods for Electronic Excitations and Optical Responses of Nanostructures: Mathematics to Algorithms to Observables

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

Carter, Emily A

2013-02-02

Kohn-Sham density functional theory (DFT) is a powerful, well-established tool for the study of condensed phase electronic structure. However, there are still a number of situations where its applicability is limited. The basic theme of our research is the development of first principles electronic structure approaches for condensed matter that goes beyond what can currently be done with standard implementations ofKohn-Sham DFT. Our efforts to this end have focused on two classes or' methods. The first addresses the well-lmown inability of DFT to handle strong, many-body electron correlation effects. Our approach is a DFT -based embedding theory, to treat localizedmore » features (e.g. impurity, adsorbate, vacancy, etc.) embedded in a periodic, metallic crystal. A description for the embedded region is provided by explicitly correlated, ab initio wave function methods. DFT, as a fo1n1ally ground state theory, does not give a good description of excited states; an additional feature of our approach is the ability to obtain excitations localized in this region. We apply our method to a first-principles study of the adsorption of a single magnetic Co ada tom on non-magnetic Cu( 111 ), a known Kondo system whose behavior is governed by strong electron correlation. The second class of methods that we are developing is an orbital-free density functional theory (OFDFT), which addresses the speed limitations ofKohn-Sham DFT. OFDFT is a powerful, O(N) scaling method for electronic structure calculations. Unlike Kohn-Sham DFT, OFDFT goes back to the original Hohenberg-Kohn idea of directly optimizing an energy functional which is an explicit functional of the density, without invoking an orbital description. This eliminates the need to manipulate orbitals, which leads to O(N{sup 3}) scaling in the Kahn-Sham approach. The speed of OFDFT allows direct electronic structure calculations on large systems on the order of thousands to tens of thousands of atoms, an expensive feat within Kohn-Sham. Due to our incomplete knowledge of the exact, universal energy density functional, this speedup comes at the cost of some accuracy with respect to Kohn-Sham methods. However, OFDFT has been shown to be remarkably accurate with respect to Kohn-Sham when used in the study of nearly-free-electron-like metals, e.g., AI, for which good density functionals have been derived. Examples of past applications of OFDFT include the prediction of properties of bulk crystals, surfaces, vacancies, vacancy clusters, nanoclusters, and dislocations, as well as OFDFT -based multiscale simulations of nanoindentation in AI and Al-Mg alloys.« less

Embedding objects during 3D printing to add new functionalities.

PubMed

Yuen, Po Ki

2016-07-01

A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication. These 3D printed glass bottom casting molds would result in PDMS replicas with a flat smooth bottom surface for better bonding and adhesion.

Efficient sidelobe ASK based dual-function radar-communications

NASA Astrophysics Data System (ADS)

Hassanien, Aboulnasr; Amin, Moeness G.; Zhang, Yimin D.; Ahmad, Fauzia

2016-05-01

Recently, dual-function radar-communications (DFRC) has been proposed as means to mitigate the spectrum congestion problem. Existing amplitude-shift keying (ASK) methods for information embedding do not take full advantage of the highest permissable sidelobe level. In this paper, a new ASK-based signaling strategy for enhancing the signal-to-noise ratio (SNR) at the communication receiver is proposed. The proposed method employs one reference waveform and simultaneously transmits a number of orthogonal waveforms equals to the number of 1's in the binary sequence being embedded. 3 dB SNR gain is achieved using the proposed method as compared to existing sidelobe ASK methods. The effectiveness of the proposed information embedding strategy is verified using simulations examples.

A biomolecular detection method based on charge pumping in a nanogap embedded field-effect-transistor biosensor

NASA Astrophysics Data System (ADS)

Kim, Sungho; Ahn, Jae-Hyuk; Park, Tae Jung; Lee, Sang Yup; Choi, Yang-Kyu

2009-06-01

A unique direct electrical detection method of biomolecules, charge pumping, was demonstrated using a nanogap embedded field-effect-transistor (FET). With aid of a charge pumping method, sensitivity can fall below the 1 ng/ml concentration regime in antigen-antibody binding of an avian influenza case. Biomolecules immobilized in the nanogap are mainly responsible for the acute changes of the interface trap density due to modulation of the energy level of the trap. This finding is supported by a numerical simulation. The proposed detection method for biomolecules using a nanogap embedded FET represents a foundation for a chip-based biosensor capable of high sensitivity.

Data embedding employing degenerate clusters of data having differences less than noise value

DOEpatents

Sanford, M.T. II; Handel, T.G.

1998-10-06

A method of embedding auxiliary information into a set of host data, such as a photograph, television signal, facsimile transmission, or identification card. All such host data contain intrinsic noise, allowing pixels in the host data which are nearly identical and which have values differing by less than the noise value to be manipulated and replaced with auxiliary data. As the embedding method does not change the elemental values of the host data, the auxiliary data do not noticeably affect the appearance or interpretation of the host data. By a substantially reverse process, the embedded auxiliary data can be retrieved easily by an authorized user. 35 figs.

Ultrathin Au film on polymer surface for surface plasmon polariton waveguide application

NASA Astrophysics Data System (ADS)

Liu, Tong; Ji, Lanting; He, Guobing; Sun, Xiaoqiang; Wang, Fei; Zhang, Daming

2017-11-01

Formation of laterally continuous ultrathin gold films on polymer substrates is a technological challenge. In this work, the vacuum thermal evaporation method is adopted to form continuous Au films in the thickness range of 7-17 nm on polymers of Poly(methyl-methacrylate-glycidly-methacrylate) and SU-8 film surface without using the adhesion or metallic seeding layers. Absorption spectrum, scanning electron microscope and atomic force microscope images are used to characterize the Au film thickness, roughness and optical loss. The result shows that molecular-scale structure, surface energy and electronegativity have impacts on the Au film morphology on polymers. Wet chemical etching is used to fabricate 7-nm thick Au stripes embedded in polymer claddings. These long-range surface plasmon polariton waveguides demonstrate the favorable morphological configurations and cross-sectional states. Through the end-fire excitation method, propagation losses of 6-μm wide Au stripes are compared to theoretical values and analyzed from practical film status. The smooth, patternable gold films on polymer provide potential applications to plasmonic waveguides, biosensing, metamaterials and optical antennas.

Effect of rapid thermal annealing temperature on the dispersion of Si nanocrystals in SiO2 matrix

NASA Astrophysics Data System (ADS)

Saxena, Nupur; Kumar, Pragati; Gupta, Vinay

2015-05-01

Effect of rapid thermal annealing temperature on the dispersion of silicon nanocrystals (Si-NC's) embedded in SiO2 matrix grown by atom beam sputtering (ABS) method is reported. The dispersion of Si NCs in SiO2 is an important issue to fabricate high efficiency devices based on Si-NC's. The transmission electron microscopy studies reveal that the precipitation of excess silicon is almost uniform and the particles grow in almost uniform size upto 850 °C. The size distribution of the particles broadens and becomes bimodal as the temperature is increased to 950 °C. This suggests that by controlling the annealing temperature, the dispersion of Si-NC's can be controlled. The results are supported by selected area diffraction (SAED) studies and micro photoluminescence (PL) spectroscopy. The discussion of effect of particle size distribution on PL spectrum is presented based on tight binding approximation (TBA) method using Gaussian and log-normal distribution of particles. The study suggests that the dispersion and consequently emission energy varies as a function of particle size distribution and that can be controlled by annealing parameters.

A tungsten-rhenium interatomic potential for point defect studies

DOE PAGES

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-28

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

A tungsten-rhenium interatomic potential for point defect studies

NASA Astrophysics Data System (ADS)

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-01

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).

AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

PubMed Central

Tian, Ye; Schwieters, Charles D.; Opella, Stanley J.; Marassi, Francesca M.

2011-01-01

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes. PMID:22036904

High-Throughput Fabrication of Ultradense Annular Nanogap Arrays for Plasmon-Enhanced Spectroscopy.

PubMed

Cai, Hongbing; Meng, Qiushi; Zhao, Hui; Li, Mingling; Dai, Yanmeng; Lin, Yue; Ding, Huaiyi; Pan, Nan; Tian, Yangchao; Luo, Yi; Wang, Xiaoping

2018-06-13

The confinement of light into nanometer-sized metallic nanogaps can lead to an extremely high field enhancement, resulting in dramatically enhanced absorption, emission, and surface-enhanced Raman scattering (SERS) of molecules embedded in nanogaps. However, low-cost, high-throughput, and reliable fabrication of ultra-high-dense nanogap arrays with precise control of the gap size still remains a challenge. Here, by combining colloidal lithography and atomic layer deposition technique, a reproducible method for fabricating ultra-high-dense arrays of hexagonal close-packed annular nanogaps over large areas is demonstrated. The annular nanogap arrays with a minimum diameter smaller than 100 nm and sub-1 nm gap width have been produced, showing excellent SERS performance with a typical enhancement factor up to 3.1 × 10 6 and a detection limit of 10 -11 M. Moreover, it can also work as a high-quality field enhancement substrate for studying two-dimensional materials, such as MoSe 2 . Our method provides an attractive approach to produce controllable nanogaps for enhanced light-matter interaction at the nanoscale.

A tungsten-rhenium interatomic potential for point defect studies

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

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

Crystal structure of (1-eth­oxy­ethyl­idene)di­methyl­aza­nium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2015-01-01

In the cation of the title salt, C6H14NO+·C24H20B−, the C—N bond lengths are 1.297 (2), 1.464 (2) and 1.468 (2) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.309 (2) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. In the crystal, C—H⋯π inter­actions between the iminium H atoms and the phenyl C atoms of the anion are present. The phenyl rings form aromatic pockets, in which the iminium ions are embedded. PMID:26870564

Thermal conductivity of silicon using reverse non-equilibrium molecular dynamics

NASA Astrophysics Data System (ADS)

El-Genk, Mohamed S.; Talaat, Khaled; Cowen, Benjamin J.

2018-05-01

Simulations are performed using the reverse non-equilibrium molecular dynamics (rNEMD) method and the Stillinger-Weber (SW) potential to determine the input parameters for achieving ±1% convergence of the calculated thermal conductivity of silicon. These parameters are then used to investigate the effects of the interatomic potentials of SW, Tersoff II, Environment Dependent Interatomic Potential (EDIP), Second Nearest Neighbor, Modified Embedded-Atom Method (MEAM), and Highly Optimized Empirical Potential MEAM on determining the bulk thermal conductivity as a function of temperature (400-1000 K). At temperatures > 400 K, data collection and swap periods of 15 ns and 150 fs, system size ≥6 × 6 UC2 and system lengths ≥192 UC are adequate for ±1% convergence with all potentials, regardless of the time step size (0.1-0.5 fs). This is also true at 400 K, except for the SW potential, which requires a data collection period ≥30 ns. The calculated bulk thermal conductivities using the rNEMD method and the EDIP potential are close to, but lower than experimental values. The 10% difference at 400 K increases gradually to 20% at 1000 K.

A statistical model of a metallic inclusion in semiconducting media

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

Shikin, V. B., E-mail: shikin@issp.ac.ru

The properties of an isolated multicharged atom embedded into a semiconducting medium are discussed. The analysis generalizes the results of the known Thomas–Fermi theory for a multicharged (Z ≫ 1) atom in vacuum when it is immersed into an electron–hole gas of finite temperature. The Thomas–Fermi–Debye (TFD) atom problem is directly related to the properties of donors in low-doped semiconductors and is alternative in its conclusions to the ideal scenario of dissociation of donors. In the existing ideal statistics, an individual donor under infinitely low doping is completely ionized (a charged center does not hold its neutralizing counter-ions). A Thomas–Fermi–Debyemore » atom (briefly, a TFD donor) remains a neutral formation that holds its screening “coat” even for infinitely low doping level, i.e., in the region of n{sub d}λ{sub 0}{sup 3} ≪ 1, where n{sub d} is the concentration of the doping impurity and λ{sub 0} is the Debye length with the parameters of intrinsic semiconductor. Various observed consequences in the behavior of a TFD donor are discussed that allow one to judge the reality of the implications of the TFD donor model.« less

Pulsed-voltage atom probe tomography of low conductivity and insulator materials by application of ultrathin metallic coating on nanoscale specimen geometry.

PubMed

Adineh, Vahid R; Marceau, Ross K W; Chen, Yu; Si, Kae J; Velkov, Tony; Cheng, Wenlong; Li, Jian; Fu, Jing

2017-10-01

We present a novel approach for analysis of low-conductivity and insulating materials with conventional pulsed-voltage atom probe tomography (APT), by incorporating an ultrathin metallic coating on focused ion beam prepared needle-shaped specimens. Finite element electrostatic simulations of coated atom probe specimens were performed, which suggest remarkable improvement in uniform voltage distribution and subsequent field evaporation of the insulated samples with a metallic coating of approximately 10nm thickness. Using design of experiment technique, an experimental investigation was performed to study physical vapor deposition coating of needle specimens with end tip radii less than 100nm. The final geometries of the coated APT specimens were characterized with high-resolution scanning electron microscopy and transmission electron microscopy, and an empirical model was proposed to determine the optimal coating thickness for a given specimen size. The optimal coating strategy was applied to APT specimens of resin embedded Au nanospheres. Results demonstrate that the optimal coating strategy allows unique pulsed-voltage atom probe analysis and 3D imaging of biological and insulated samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Location and Electronic Nature of Phosphorus in the Si Nanocrystal − SiO2 System

PubMed Central

König, Dirk; Gutsch, Sebastian; Gnaser, Hubert; Wahl, Michael; Kopnarski, Michael; Göttlicher, Jörg; Steininger, Ralph; Zacharias, Margit; Hiller, Daniel

2015-01-01

Up to now, no consensus exists about the electronic nature of phosphorus (P) as donor for SiO2-embedded silicon nanocrystals (SiNCs). Here, we report on hybrid density functional theory (h-DFT) calculations of P in the SiNC/SiO2 system matching our experimental findings. Relevant P configurations within SiNCs, at SiNC surfaces, within the sub-oxide interface shell and in the SiO2 matrix were evaluated. Atom probe tomography (APT) and its statistical evaluation provide detailed spatial P distributions. For the first time, we obtain ionisation states of P atoms in the SiNC/SiO2 system at room temperature using X-ray absorption near edge structure (XANES) spectroscopy, eliminating structural artefacts due to sputtering as occurring in XPS. K energies of P in SiO2 and SiNC/SiO2 superlattices (SLs) were calibrated with non-degenerate P-doped Si wafers. results confirm measured core level energies, connecting and explaining XANES spectra with h-DFT electronic structures. While P can diffuse into SiNCs and predominantly resides on interstitial sites, its ionization probability is extremely low, rendering P unsuitable for introducing electrons into SiNCs embedded in SiO2. Increased sample conductivity and photoluminescence (PL) quenching previously assigned to ionized P donors originate from deep defect levels due to P. PMID:25997696

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

Molecular dynamics investigation of dynamical heterogeneity and local structure in the supercooled liquid and glass states of Al

NASA Astrophysics Data System (ADS)

Li, Maozhi; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Ho, Kai-Ming

2008-05-01

Molecular dynamics simulations are performed to study the structure and dynamical heterogeneity in the liquid and glass states of Al using a frequently employed embedded atom potential. While the pair correlation function of the glass and liquid states displays only minor differences, the icosahedral short-range order (ISRO) and the dynamics of the two states are very different. The ISRO is much stronger in the glass than in the liquid. It is also found that both the most mobile and the most immobile atoms in the glass state tend to form clusters, and the clusters formed by the immobile atoms are more compact. In order to investigate the local environment of each atom in the liquid and glass states, a local density is defined to characterize the local atomic packing. There is a strong correlation between the local packing density and the mobility of the atoms. These results indicate that dynamical heterogeneity in glasses is directly correlated to the local structure. We also analyze the diffusion mechanisms of atoms in the liquid and glass states. It is found that for the mobile atoms in the glass state, initially they are confined in the cages formed by their nearest neighbors and vibrating. On the time scale of β relaxation, the mobile atoms try to break up the cage confinement and hop into new cages. In the supercooled liquid states, however, atoms continuously diffuse. Furthermore, it is found that on the time scale of β relaxation, some of the mobile atoms in the glass state cooperatively hop, which is facilitated by the stringlike cluster structures. On the longer time scale, it is found that a certain fraction of atoms can simultaneously hop, although they are not nearest neighbors. Further analysis shows that these hopping atoms form big and more compact clusters than the characterized most mobile atoms. The cooperative rearrangement of these big compact clusters might facilitate the simultaneous hopping of atoms in the glass states on the long time scale.

Rapid embedding methods into epoxy and LR White resins for morphological and immunological analysis of cryofixed biological specimens.

PubMed

McDonald, Kent L

2014-02-01

A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100°C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives.

GPU surface extraction using the closest point embedding

NASA Astrophysics Data System (ADS)

Kim, Mark; Hansen, Charles

2015-01-01

Isosurface extraction is a fundamental technique used for both surface reconstruction and mesh generation. One method to extract well-formed isosurfaces is a particle system; unfortunately, particle systems can be slow. In this paper, we introduce an enhanced parallel particle system that uses the closest point embedding as the surface representation to speedup the particle system for isosurface extraction. The closest point embedding is used in the Closest Point Method (CPM), a technique that uses a standard three dimensional numerical PDE solver on two dimensional embedded surfaces. To fully take advantage of the closest point embedding, it is coupled with a Barnes-Hut tree code on the GPU. This new technique produces well-formed, conformal unstructured triangular and tetrahedral meshes from labeled multi-material volume datasets. Further, this new parallel implementation of the particle system is faster than any known methods for conformal multi-material mesh extraction. The resulting speed-ups gained in this implementation can reduce the time from labeled data to mesh from hours to minutes and benefits users, such as bioengineers, who employ triangular and tetrahedral meshes

Electronic damping of anharmonic adsorbate vibrations at metallic surfaces

NASA Astrophysics Data System (ADS)

Tremblay, Jean Christophe; Monturet, Serge; Saalfrank, Peter

2010-03-01

The nonadiabatic coupling of an adsorbate close to a metallic surface leads to electronic damping of adsorbate vibrations and line broadening in vibrational spectroscopy. Here, a perturbative treatment of the electronic contribution to the lifetime broadening serves as a building block for a new approach, in which anharmonic vibrational transition rates are calculated from a position-dependent coupling function. Different models for the coupling function will be tested, all related to embedding theory. The first two are models based on a scattering approach with (i) a jellium-type and (ii) a density functional theory based embedding density, respectively. In a third variant a further refined model is used for the embedding density, and a semiempirical approach is taken in which a scaling factor is chosen to match harmonic, single-site, first-principles transition rates, obtained from periodic density functional theory. For the example of hydrogen atoms on (adsorption) and below (subsurface absorption) a Pd(111) surface, lifetimes of and transition rates between vibrational levels are computed. The transition rates emerging from different models serve as input for the selective subsurface adsorption of hydrogen in palladium starting from an adsorption site, by using sequences of infrared laser pulses in a laser distillation scheme.

[Evaluation of 3 methods of DNA extraction from paraffin-embedded material for the amplification of genomic DNA using PCR].

PubMed

Mesquita, R A; Anzai, E K; Oliveira, R N; Nunes, F D

2001-01-01

There are several protocols reported in the literature for the extraction of genomic DNA from formalin-fixed paraffin-embedded samples. Genomic DNA is utilized in molecular analyses, including PCR. This study compares three different methods for the extraction of genomic DNA from formalin-fixed paraffin-embedded (inflammatory fibrous hyperplasia) and non-formalin-fixed (normal oral mucosa) samples: phenol with enzymatic digestion, and silica with and without enzymatic digestion. The amplification of DNA by means of the PCR technique was carried out with primers for the exon 7 of human keratin type 14. Amplicons were analyzed by means of electrophoresis in an 8% polyacrylamide gel with 5% glycerol, followed by silver-staining visualization. The phenol/enzymatic digestion and the silica/enzymatic digestion methods provided amplicons from both tissue samples. The method described is a potential aid in the establishment of the histopathologic diagnosis and in retrospective studies with archival paraffin-embedded samples.

Design method of ARM based embedded iris recognition system

NASA Astrophysics Data System (ADS)

Wang, Yuanbo; He, Yuqing; Hou, Yushi; Liu, Ting

2008-03-01

With the advantages of non-invasiveness, uniqueness, stability and low false recognition rate, iris recognition has been successfully applied in many fields. Up to now, most of the iris recognition systems are based on PC. However, a PC is not portable and it needs more power. In this paper, we proposed an embedded iris recognition system based on ARM. Considering the requirements of iris image acquisition and recognition algorithm, we analyzed the design method of the iris image acquisition module, designed the ARM processing module and its peripherals, studied the Linux platform and the recognition algorithm based on this platform, finally actualized the design method of ARM-based iris imaging and recognition system. Experimental results show that the ARM platform we used is fast enough to run the iris recognition algorithm, and the data stream can flow smoothly between the camera and the ARM chip based on the embedded Linux system. It's an effective method of using ARM to actualize portable embedded iris recognition system.

Parametric embedding for class visualization.

PubMed

Iwata, Tomoharu; Saito, Kazumi; Ueda, Naonori; Stromsten, Sean; Griffiths, Thomas L; Tenenbaum, Joshua B

2007-09-01

We propose a new method, parametric embedding (PE), that embeds objects with the class structure into a low-dimensional visualization space. PE takes as input a set of class conditional probabilities for given data points and tries to preserve the structure in an embedding space by minimizing a sum of Kullback-Leibler divergences, under the assumption that samples are generated by a gaussian mixture with equal covariances in the embedding space. PE has many potential uses depending on the source of the input data, providing insight into the classifier's behavior in supervised, semisupervised, and unsupervised settings. The PE algorithm has a computational advantage over conventional embedding methods based on pairwise object relations since its complexity scales with the product of the number of objects and the number of classes. We demonstrate PE by visualizing supervised categorization of Web pages, semisupervised categorization of digits, and the relations of words and latent topics found by an unsupervised algorithm, latent Dirichlet allocation.

Method for preparing hydrous zirconium oxide gels and spherules

DOEpatents

Collins, Jack L.

2003-08-05

Methods for preparing hydrous zirconium oxide spherules, hydrous zirconium oxide gels such as gel slabs, films, capillary and electrophoresis gels, zirconium monohydrogen phosphate spherules, hydrous zirconium oxide spherules having suspendable particles homogeneously embedded within to form a composite sorbent, zirconium monohydrogen phosphate spherules having suspendable particles of at least one different sorbent homogeneously embedded within to form a composite sorbent having a desired crystallinity, zirconium oxide spherules having suspendable particles homogeneously embedded within to form a composite, hydrous zirconium oxide fiber materials, zirconium oxide fiber materials, hydrous zirconium oxide fiber materials having suspendable particles homogeneously embedded within to form a composite, zirconium oxide fiber materials having suspendable particles homogeneously embedded within to form a composite and spherules of barium zirconate. The hydrous zirconium oxide spherules and gel forms prepared by the gel-sphere, internal gelation process are useful as inorganic ion exchangers, catalysts, getters and ceramics.

Delay differential analysis of time series.

PubMed

Lainscsek, Claudia; Sejnowski, Terrence J

2015-03-01

Nonlinear dynamical system analysis based on embedding theory has been used for modeling and prediction, but it also has applications to signal detection and classification of time series. An embedding creates a multidimensional geometrical object from a single time series. Traditionally either delay or derivative embeddings have been used. The delay embedding is composed of delayed versions of the signal, and the derivative embedding is composed of successive derivatives of the signal. The delay embedding has been extended to nonuniform embeddings to take multiple timescales into account. Both embeddings provide information on the underlying dynamical system without having direct access to all the system variables. Delay differential analysis is based on functional embeddings, a combination of the derivative embedding with nonuniform delay embeddings. Small delay differential equation (DDE) models that best represent relevant dynamic features of time series data are selected from a pool of candidate models for detection or classification. We show that the properties of DDEs support spectral analysis in the time domain where nonlinear correlation functions are used to detect frequencies, frequency and phase couplings, and bispectra. These can be efficiently computed with short time windows and are robust to noise. For frequency analysis, this framework is a multivariate extension of discrete Fourier transform (DFT), and for higher-order spectra, it is a linear and multivariate alternative to multidimensional fast Fourier transform of multidimensional correlations. This method can be applied to short or sparse time series and can be extended to cross-trial and cross-channel spectra if multiple short data segments of the same experiment are available. Together, this time-domain toolbox provides higher temporal resolution, increased frequency and phase coupling information, and it allows an easy and straightforward implementation of higher-order spectra across time compared with frequency-based methods such as the DFT and cross-spectral analysis.

Ion beam-induced shaping of Ni nanoparticles embedded in a silica matrix: from spherical to prolate shape

PubMed Central

2011-01-01

Present work reports the elongation of spherical Ni nanoparticles (NPs) parallel to each other, due to bombardment with 120 MeV Au+9 ions at a fluence of 5 × 1013 ions/cm2. The Ni NPs embedded in silica matrix have been prepared by atom beam sputtering technique and subsequent annealing. The elongation of Ni NPs due to interaction with Au+9 ions as investigated by cross-sectional transmission electron microscopy (TEM) shows a strong dependence on initial Ni particle size and is explained on the basis of thermal spike model. Irradiation induces a change from single crystalline nature of spherical particles to polycrystalline nature of elongated particles. Magnetization measurements indicate that changes in coercivity (Hc) and remanence ratio (Mr/Ms) are stronger in the ion beam direction due to the preferential easy axis of elongated particles in the beam direction. PMID:21711659

Local electric dipole moments for periodic systems via density functional theory embedding.

PubMed

Luber, Sandra

2014-12-21

We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange-correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

Generation of vortex array laser beams with Dove prism embedded unbalanced Mach-Zehnder interferometer

NASA Astrophysics Data System (ADS)

Chu, Shu-Chun

2009-02-01

This paper introduces a scheme for generation of vortex laser beams from a solid-state laser with off-axis laser-diode pumping. The proposed system consists of a Dove prism embedded in an unbalanced Mach-Zehnder interferometer configuration. This configuration allows controlled construction of p × p vortex array beams from Ince-Gaussian modes, IGep,p modes. An incident IGe p,p laser beam of variety order p can easily be generated from an end-pumped solid-state laser with an off-axis pumping mechanism. This study simulates this type of vortex array laser beam generation and discusses beam propagation effects. The formation of ordered transverse emission patterns have applications in a variety of areas such as optical data storage, distribution, and processing that exploit the robustness of soliton and vortex fields and optical manipulations of small particles and atoms in the featured intensity distribution.

Relationship between microstructure and optical properties of a novel perovskite C12PbI4 embedded in matrix of porous alumina

NASA Astrophysics Data System (ADS)

Zaghdoudi, W.; Bardaoui, A.; Khalifa, N.; Chtourou, R.

2013-01-01

In this study, organic-inorganic hybrid perovskite multiple quantum wells (PbI QWs) embedded in porous anodic alumina (PAA) thin films on glass and aluminum substrates are investigated in detail. The pore height and diameter of the nanoscale structure of porous anodic alumina (PAA) film produced by the anodization technique are controllable. The synthesized films are characterized morphologically using the atomic force microscopy (AFM). Scanning electron microscopy (SEM) study showed granular surface. The structural and optical properties were investigated by X-ray diffraction (XRD), photoluminescence (PL) and UV-Vis-NIR spectrophotometer. The effect of the two different substrates on the impregnation of the PbI QW in the PAA is presented. Both PL and AFM studies show a better penetration of the PbI QW in the case of the Al substrate providing a wider pore diameter. Remarkable enhancement of quantum confinement is demonstrated.

Mathematical modeling of elementary trapping-reduction processes in positron annihilation lifetime spectroscopy: methodology of Ps-to-positron trapping conversion

NASA Astrophysics Data System (ADS)

Shpotyuk, Ya; Cebulski, J.; Ingram, A.; Shpotyuk, O.

2017-12-01

Methodological possibilities of positron annihilation lifetime (PAL) spectroscopy in application to nanostructurized substances treated within three-term fitting procedure are reconsidered to parameterize their atomic-deficient structural arrangement. In contrast to conventional three-term fitting analysis of the detected PAL spectra based on admixed positron trapping and positronium (Ps) decaying, the nanostructurization due to guest nanoparticles embedded in host matrix is considered as producing modified trapping, which involves conversion between these channels. The developed approach referred to as x3-x2-coupling decomposition algorithm allows estimation free volumes of interfacial voids responsible for positron trapping and bulk lifetimes in nanoparticle-embedded substances. This methodology is validated using experimental data of Chakraverty et al. [Phys. Rev. B71 (2005) 024115] on PAL study of composites formed by guest NiFe2O4 nanocrystals grown in host SiO2 matrix.

Can’t Count or Won’t Count? Embedding Quantitative Methods in Substantive Sociology Curricula: A Quasi-Experiment

PubMed Central

Williams, Malcolm; Sloan, Luke; Cheung, Sin Yi; Sutton, Carole; Stevens, Sebastian; Runham, Libby

2015-01-01

This paper reports on a quasi-experiment in which quantitative methods (QM) are embedded within a substantive sociology module. Through measuring student attitudes before and after the intervention alongside control group comparisons, we illustrate the impact that embedding has on the student experience. Our findings are complex and even contradictory. Whilst the experimental group were less likely to be distrustful of statistics and appreciate how QM inform social research, they were also less confident about their statistical abilities, suggesting that through ‘doing’ quantitative sociology the experimental group are exposed to the intricacies of method and their optimism about their own abilities is challenged. We conclude that embedding QM in a single substantive module is not a ‘magic bullet’ and that a wider programme of content and assessment diversification across the curriculum is preferential. PMID:27330225

Closed-form solution of temperature and heat flux in embedded cooling channels

NASA Astrophysics Data System (ADS)

Griggs, Steven Craig

1997-11-01

An analytical method is discussed for predicting temperature in a layered composite material with embedded cooling channels. The cooling channels are embedded in the material to maintain its temperature at acceptable levels. Problems of this type are encountered in the aerospace industry and include high-temperature or high-heat-flux protection for advanced composite-material skins of high-speed air vehicles; thermal boundary-layer flow control on supersonic transports; or infrared signature suppression on military vehicles. A Green's function solution of the diffusion equation is used to simultaneously predict the global and localized effects of temperature in the material and in the embedded cooling channels. The integral method is used to solve the energy equation with fluid flow to find the solution of temperature and heat flux in the cooling fluid and material simultaneously. This method of calculation preserves the three-dimensional nature of this problem.

Structural determination of Bi-doped magnetite multifunctional nanoparticles for contrast imaging.

PubMed

Laguna-Marco, M A; Piquer, C; Roca, A G; Boada, R; Andrés-Vergés, M; Veintemillas-Verdaguer, S; Serna, C J; Iadecola, A; Chaboy, J

2014-09-14

To determine with precision how Bi atoms are distributed in Bi-doped iron oxide nanoparticles their structural characterization has been carried out by X-ray absorption spectroscopy (XAS) recorded at the K edge of Fe and at the L3 edge of Bi. The inorganic nanoparticles are nominally hybrid structures integrating an iron oxide core and a bismuth oxide shell. Fe K-edge XAS indicates the formation of a structurally ordered, non-stoichiometric magnetite (Fe3-δO4) phase for all the nanoparticles. The XAS spectra show that, in the samples synthesized by precipitation in aqueous media and laser pyrolysis, the Bi atoms neither enter into the iron oxide spinel lattice nor form any other mixed Bi-Fe oxides. No modification of the local structure around the Fe atoms induced by the Bi atoms is observed at the Fe K edge. In addition, contrary to expectations, our results indicate that the Bi atoms do not form a well-defined Bi oxide structure. The XAS study at the Bi L3 edge indicates that the environment around Bi atoms is highly disordered and only a first oxygen coordination shell is observed. Indefinite [BiO6-x(OH)x] units (isolated or aggregated forming tiny amorphous clusters) bonded through hydroxyl bridges to the nanoparticle, rather than a well defined Bi2O3 shell, surround the nanoparticle. On the other hand, the XAS study indicates that, in the samples synthesized by thermal decomposition, the Bi atoms are embedded in a longer range ordered structure showing the first and second neighbors.

Embedded high-contrast distributed grating structures

DOEpatents

Zubrzycki, Walter J.; Vawter, Gregory A.; Allerman, Andrew A.

2002-01-01

A new class of fabrication methods for embedded distributed grating structures is claimed, together with optical devices which include such structures. These new methods are the only known approach to making defect-free high-dielectric contrast grating structures, which are smaller and more efficient than are conventional grating structures.

An accurate full-dimensional potential energy surface for H-Au(111): Importance of nonadiabatic electronic excitation in energy transfer and adsorption.

PubMed

Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander

2015-09-28

We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.

Enhanced production of low energy electrons by alpha particle impact

PubMed Central

Kim, Hong-Keun; Titze, Jasmin; Schöffler, Markus; Trinter, Florian; Waitz, Markus; Voigtsberger, Jörg; Sann, Hendrik; Meckel, Moritz; Stuck, Christian; Lenz, Ute; Odenweller, Matthias; Neumann, Nadine; Schössler, Sven; Ullmann-Pfleger, Klaus; Ulrich, Birte; Fraga, Rui Costa; Petridis, Nikos; Metz, Daniel; Jung, Annika; Grisenti, Robert; Czasch, Achim; Jagutzki, Ottmar; Schmidt, Lothar; Jahnke, Till; Schmidt-Böcking, Horst; Dörner, Reinhard

2011-01-01

Radiation damage to living tissue stems not only from primary ionizing particles but to a substantial fraction from the dissociative attachment of secondary electrons with energies below the ionization threshold. We show that the emission yield of those low energy electrons increases dramatically in ion–atom collisions depending on whether or not the target atoms are isolated or embedded in an environment. Only when the atom that has been ionized and excited by the primary particle impact is in immediate proximity of another atom is a fragmentation route known as interatomic Coulombic decay (ICD) enabled. This leads to the emission of a low energy electron. Over the past decade ICD was explored in several experiments following photoionization. Most recent results show its observation even in water clusters. Here we show the quantitative role of ICD for the production of low energy electrons by ion impact, thus approaching a scenario closer to that of radiation damage by alpha particles: We choose ion energies on the maximum of the Bragg peak where energy is most efficiently deposited in tissue. We compare the electron production after colliding He+ ions on isolated Ne atoms and on Ne dimers (Ne2). In the latter case the Ne atom impacted is surrounded by a most simple environment already opening ICD as a deexcitation channel. As a consequence, we find a dramatically enhanced low energy electron yield. The results suggest that ICD may have a significant influence on cell survival after exposure to ionizing radiation. PMID:21730184

Degradation of lindane by a novel embedded bio-nano hybrid system in aqueous environment.

PubMed

Salam, Jaseetha Abdul; Das, Nilanjana

2015-03-01

The objective of this study was to evaluate the effect of an embedded bio-nano hybrid system using nanoscale zinc oxide (n-ZnO) and lindane-degrading yeast Candida VITJzN04 for lindane degradation. Nano-embedding of the yeast was done with chemically synthesized n-ZnO particles (50 mg/mL) and was visualized by atomic force microscope (AFM) and scanning electron microscope (SEM). Nanoparticles were embedded substantially on the surfaces of the yeast cells and translocated into the cell cytoplasm without causing any lethal effect to the cell until 50 mg/mL. Lindane (600 mg/L) degradation was studied both in the individual and hybrid system. Rapid reductive-dechlorination of lindane was attained with n-ZnO under illuminated conditions, with the generation of chlorobenzene and benzene as dechlorination products. The bio-nano hybrid was found to be more effective compared to the native yeasts for lindane degradation and resulted in complete removal within 3 days. The kinetic data analysis implied that the half-life of lindane was 9 h for bio-nano hybrid and 28 h for Candida VITJzN04. The enhanced lindane degradation by bio-nano hybrid might be due to increased porosity and permeability of the yeast cell membrane, facilitating the easy entry of lindane into cell cytoplasm and n-ZnO-mediated dechlorination. To the best of our knowledge, this report, for the first time, suggests the use of n-ZnO-mediated dechlorination of lindane and the novel bio-nano hybrid system that reduces the half-life to one third of the time taken by the yeast alone. The embedded bio-nano hybrid system may be exploited as an effective remediation tool for the treatment of lindane-contaminated wastewaters.

Structural and electronic properties of GaN nanowires with embedded In{sub x}Ga{sub 1−x}N nanodisks

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

Kioseoglou, J., E-mail: sifisl@auth.gr; Pavloudis, Th.; Kehagias, Th.

2015-07-21

In the present study, the effects of various types of strain and indium concentration on the total energy and optoelectronic properties of GaN nanowires (NWs) with embedded In{sub x}Ga{sub 1−x}N nanodisks (NDs) are examined. In particular, the bi-axial, hydrostatic, and uniaxial strain states of the embedded In{sub x}Ga{sub 1−x}N NDs are investigated for multiple In concentrations. Density functional theory is employed to calculate the band structure of the NWs. The theoretical analysis finds that the supercell-size-dependent characteristics calculated for our 972-atom NW models are very close to the infinite supercell-size limit. It is established that the embedded In{sub x}Ga{sub 1−x}Nmore » NDs do not induce deep states in the band gap of the NWs. A bowing parameter of 1.82 eV is derived from our analysis in the quadratic Vegard's formula for the band gaps at the various In concentrations of the investigated In{sub x}Ga{sub 1−x}N NDs in GaN NW structures. It is concluded that up to ∼10% of In, the hydrostatic strain state is competitive with the bi-axial due to the radial absorption of the strain on the surfaces. Above this value, the dominant strain state is the bi-axial one. Thus, hydrostatic and bi-axial strain components coexist in the embedded NDs, and they are of different physical origin. The bi-axial strain comes from growth on lattice mismatched substrates, while the hydrostatic strain originates from the lateral relaxation of the surfaces.« less

Method for preparing hydrous iron oxide gels and spherules

DOEpatents

Collins, Jack L.; Lauf, Robert J.; Anderson, Kimberly K.

2003-07-29

The present invention is directed to methods for preparing hydrous iron oxide spherules, hydrous iron oxide gels such as gel slabs, films, capillary and electrophoresis gels, iron monohydrogen phosphate spherules, hydrous iron oxide spherules having suspendable particles homogeneously embedded within to form composite sorbents and catalysts, iron monohydrogen phosphate spherules having suspendable particles of at least one different sorbent homogeneously embedded within to form a composite sorbent, iron oxide spherules having suspendable particles homogeneously embedded within to form a composite of hydrous iron oxide fiber materials, iron oxide fiber materials, hydrous iron oxide fiber materials having suspendable particles homogeneously embedded within to form a composite, iron oxide fiber materials having suspendable particles homogeneously embedded within to form a composite, dielectric spherules of barium, strontium, and lead ferrites and mixtures thereof, and composite catalytic spherules of barium or strontium ferrite embedded with oxides of Mg, Zn, Pb, Ce and mixtures thereof. These variations of hydrous iron oxide spherules and gel forms prepared by the gel-sphere, internal gelation process offer more useful forms of inorganic ion exchangers, catalysts, getters, dielectrics, and ceramics.

Metric Optimization for Surface Analysis in the Laplace-Beltrami Embedding Space

PubMed Central

Lai, Rongjie; Wang, Danny J.J.; Pelletier, Daniel; Mohr, David; Sicotte, Nancy; Toga, Arthur W.

2014-01-01

In this paper we present a novel approach for the intrinsic mapping of anatomical surfaces and its application in brain mapping research. Using the Laplace-Beltrami eigen-system, we represent each surface with an isometry invariant embedding in a high dimensional space. The key idea in our system is that we realize surface deformation in the embedding space via the iterative optimization of a conformal metric without explicitly perturbing the surface or its embedding. By minimizing a distance measure in the embedding space with metric optimization, our method generates a conformal map directly between surfaces with highly uniform metric distortion and the ability of aligning salient geometric features. Besides pairwise surface maps, we also extend the metric optimization approach for group-wise atlas construction and multi-atlas cortical label fusion. In experimental results, we demonstrate the robustness and generality of our method by applying it to map both cortical and hippocampal surfaces in population studies. For cortical labeling, our method achieves excellent performance in a cross-validation experiment with 40 manually labeled surfaces, and successfully models localized brain development in a pediatric study of 80 subjects. For hippocampal mapping, our method produces much more significant results than two popular tools on a multiple sclerosis study of 109 subjects. PMID:24686245

Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-03-01

In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call "Hamiltonian dielectric solvent" (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography.

PubMed

Trépout, Sylvain; Bastin, Philippe; Marco, Sergio

2017-03-12

This report describes a protocol for preparing thick biological specimens for further observation using a scanning transmission electron microscope. It also describes an imaging method for studying the 3D structure of thick biological specimens by scanning transmission electron tomography. The sample preparation protocol is based on conventional methods in which the sample is fixed using chemical agents, treated with a heavy atom salt contrasting agent, dehydrated in a series of ethanol baths, and embedded in resin. The specific imaging conditions for observing thick samples by scanning transmission electron microscopy are then described. Sections of the sample are observed using a through-focus method involving the collection of several images at various focal planes. This enables the recovery of in-focus information at various heights throughout the sample. This particular collection pattern is performed at each tilt angle during tomography data collection. A single image is then generated, merging the in-focus information from all the different focal planes. A classic tilt-series dataset is then generated. The advantage of the method is that the tilt-series alignment and reconstruction can be performed using standard tools. The collection of through-focal images allows the reconstruction of a 3D volume that contains all of the structural details of the sample in focus.

Research and Design of Embedded Wireless Meal Ordering System Based on SQLite

NASA Astrophysics Data System (ADS)

Zhang, Jihong; Chen, Xiaoquan

The paper describes features and internal architecture and developing method of SQLite. And then it gives a design and program of meal ordering system. The system realizes the information interaction among the users and embedded devices with SQLite as database system. The embedded database SQLite manages the data and achieves wireless communication by using Bluetooth. A system program based on Qt/Embedded and Linux drivers realizes the local management of environmental data.

Method and apparatus for quantum information processing using entangled neutral-atom qubits

DOEpatents

Jau, Yuan Yu; Biedermann, Grant; Deutsch, Ivan

2018-04-03

A method for preparing an entangled quantum state of an atomic ensemble is provided. The method includes loading each atom of the atomic ensemble into a respective optical trap; placing each atom of the atomic ensemble into a same first atomic quantum state by impingement of pump radiation; approaching the atoms of the atomic ensemble to within a dipole-dipole interaction length of each other; Rydberg-dressing the atomic ensemble; during the Rydberg-dressing operation, exciting the atomic ensemble with a Raman pulse tuned to stimulate a ground-state hyperfine transition from the first atomic quantum state to a second atomic quantum state; and separating the atoms of the atomic ensemble by more than a dipole-dipole interaction length.

On the solid phase crystallization of In{sub 2}O{sub 3}:H transparent conductive oxide films prepared by atomic layer deposition

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

Macco, Bart; Verheijen, Marcel A.; Black, Lachlan E.

2016-08-28

Hydrogen-doped indium oxide (In{sub 2}O{sub 3}:H) has emerged as a highly transparent and conductive oxide, finding its application in a multitude of optoelectronic devices. Recently, we have reported on an atomic layer deposition (ALD) process to prepare high quality In{sub 2}O{sub 3}:H. This process consists of ALD of In{sub 2}O{sub 3}:H films at 100 °C, followed by a solid phase crystallization step at 150–200 °C. In this work, we report on a detailed electron microscopy study of this crystallization process which reveals new insights into the crucial aspects for achieving the large grain size and associated excellent properties of the material. Themore » key finding is that the best optoelectronic properties are obtained by preparing the films at the lowest possible temperature prior to post-deposition annealing. Electron microscopy imaging shows that such films are mostly amorphous, but feature a very low density of embedded crystallites. Upon post-deposition annealing, crystallization proceeds merely from isotropic crystal grain growth of these embedded crystallites rather than by the formation of additional crystallites. The relatively high hydrogen content of 4.2 at. % in these films is thought to cause the absence of additional nucleation, thereby rendering the final grain size and optoelectronic properties solely dependent on the density of embedded crystallites. The temperature-dependent grain growth rate has been determined, from which an activation energy of (1.39 ± 0.04) eV has been extracted. Finally, on the basis of the observed crystallization mechanism, a simple model to fully describe the crystallization process has been developed. This model has been validated with a numerical implementation thereof, which accurately predicts the observed temperature-dependent crystallization behaviour.« less

LC Circuits for Diagnosing Embedded Piezoelectric Devices

NASA Technical Reports Server (NTRS)

Chattin, Richard L.; Fox, Robert Lee; Moses, Robert W.; Shams, Qamar A.

2005-01-01

A recently invented method of nonintrusively detecting faults in piezoelectric devices involves measurement of the resonance frequencies of inductor capacitor (LC) resonant circuits. The method is intended especially to enable diagnosis of piezoelectric sensors, actuators, and sensor/actuators that are embedded in structures and/or are components of multilayer composite material structures.

Dimension from covariance matrices.

PubMed

Carroll, T L; Byers, J M

2017-02-01

We describe a method to estimate embedding dimension from a time series. This method includes an estimate of the probability that the dimension estimate is valid. Such validity estimates are not common in algorithms for calculating the properties of dynamical systems. The algorithm described here compares the eigenvalues of covariance matrices created from an embedded signal to the eigenvalues for a covariance matrix of a Gaussian random process with the same dimension and number of points. A statistical test gives the probability that the eigenvalues for the embedded signal did not come from the Gaussian random process.

High-speed event detector for embedded nanopore bio-systems.

PubMed

Huang, Yiyun; Magierowski, Sebastian; Ghafar-Zadeh, Ebrahim; Wang, Chengjie

2015-08-01

Biological measurements of microscopic phenomena often deal with discrete-event signals. The ability to automatically carry out such measurements at high-speed in a miniature embedded system is desirable but compromised by high-frequency noise along with practical constraints on filter quality and sampler resolution. This paper presents a real-time event-detection method in the context of nanopore sensing that helps to mitigate these drawbacks and allows accurate signal processing in an embedded system. Simulations show at least a 10× improvement over existing on-line detection methods.

Cell Kinetic and Histomorphometric Analysis of Microgravitational Osteopenia: PARE.03B

NASA Technical Reports Server (NTRS)

Roberts, W. Eugene; Garetto, Lawrence P.

1998-01-01

Previous methods of identifying cells undergoing DNA synthesis (S-phase) utilized H-3 thymidine (3HT) autoradiography. 5-Bromo-2'-deoxyuridine (BrdU) immunohistochemistry is a nonradioactive alternative method. This experiment compared the two methods using the nuclear volume model for osteoblast histogenesis in two different embedding media. Twenty Sprague-Dawley rats were used, with half receiving 3HT (1 micro Ci/g) and the other half BrdU (50 microgram/g). Condyies were embedded (one side in paraffin, the other in plastic) and S-phase nuclei were identified using either autoradiography or immunohistochemistry. The fractional distribution of preosteoblast cell types and the percentage of labeled cells (within each cell fraction and label index) were calculated and expressed as mean q standard error. Chi-Square analysis showed only a minor difference in the fractional distribution of cell types. However, there were significant differences (p less than 0.05) by ANOVA, in the nuclear labeling of specific cell types. With the exception of the less-differentiated A+A'cells, more BrdU label was consistently detected in paraffin than in plastic-embedded sections. In general, more nuclei were labeled with 3H-thymidine than with BrdU in both types of embedding media. Labeling index data (labeled cells/total cells sampled x 100) indicated that BrdU in paraffin, but not plastic gave the same results as 3HT in either embedding method. Thus, we conclude that the two labeling methods do not yield the same results for the nuclear volume model and that embedding media is an important factor whenusing BrdU. As a result of this work, 3HT was chosen for used in the PARE.03 flight experiments.

Atomic Structure of Intrinsic and Electron-Irradiation-Induced Defects in MoTe2

PubMed Central

2018-01-01

Studying the atomic structure of intrinsic defects in two-dimensional transition-metal dichalcogenides is difficult since they damage quickly under the intense electron irradiation in transmission electron microscopy (TEM). However, this can also lead to insights into the creation of defects and their atom-scale dynamics. We first show that MoTe2 monolayers without protection indeed quickly degrade during scanning TEM (STEM) imaging, and discuss the observed atomic-level dynamics, including a transformation from the 1H phase into 1T′, 3-fold rotationally symmetric defects, and the migration of line defects between two 1H grains with a 60° misorientation. We then analyze the atomic structure of MoTe2 encapsulated between two graphene sheets to mitigate damage, finding the as-prepared material to contain an unexpectedly large concentration of defects. These include similar point defects (or quantum dots, QDs) as those created in the nonencapsulated material and two different types of line defects (or quantum wires, QWs) that can be transformed from one to the other under electron irradiation. Our density functional theory simulations indicate that the QDs and QWs embedded in MoTe2 introduce new midgap states into the semiconducting material and may thus be used to control its electronic and optical properties. Finally, the edge of the encapsulated material appears amorphous, possibly due to the pressure caused by the encapsulation. PMID:29503509

Spatial shaping for generating arbitrary optical dipole traps for ultracold degenerate gases

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

Lee, Jeffrey G., E-mail: jglee@umd.edu; Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742; Hill, W. T., E-mail: wth@umd.edu

2014-10-15

We present two spatial-shaping approaches – phase and amplitude – for creating two-dimensional optical dipole potentials for ultracold neutral atoms. When combined with an attractive or repulsive Gaussian sheet formed by an astigmatically focused beam, atoms are trapped in three dimensions resulting in planar confinement with an arbitrary network of potentials – a free-space atom chip. The first approach utilizes an adaptation of the generalized phase-contrast technique to convert a phase structure embedded in a beam after traversing a phase mask, to an identical intensity profile in the image plane. Phase masks, and a requisite phase-contrast filter, can be chemicallymore » etched into optical material (e.g., fused silica) or implemented with spatial light modulators; etching provides the highest quality while spatial light modulators enable prototyping and realtime structure modification. This approach was demonstrated on an ensemble of thermal atoms. Amplitude shaping is possible when the potential structure is made as an opaque mask in the path of a dipole trap beam, followed by imaging the shadow onto the plane of the atoms. While much more lossy, this very simple and inexpensive approach can produce dipole potentials suitable for containing degenerate gases. High-quality amplitude masks can be produced with standard photolithography techniques. Amplitude shaping was demonstrated on a Bose-Einstein condensate.« less

(Tl, Au)/Si(1 1 1){\\sqrt7 \\times \\sqrt7} 2D compound: an ordered array of identical Au clusters embedded in Tl matrix

NASA Astrophysics Data System (ADS)

Mihalyuk, A. N.; Hsing, C. R.; Wei, C. M.; Eremeev, S. V.; Bondarenko, L. V.; Tupchaya, A. Y.; Gruznev, D. V.; Zotov, A. V.; Saranin, A. A.

2018-01-01

Formation of the highly-ordered \\sqrt7 × \\sqrt7 -periodicity 2D compound has been detected in the (Tl, Au)/Si(1 1 1) system as a result of Au deposition onto the Tl/Si(1 1 1) surface, its composition, structure and electronic properties have been characterized using scanning tunneling microscopy, angle-resolved photoelectron spectroscopy and density-functional-theory calculations. On the basis of these data, the structural model of the Tl-Au compound has been proposed, which adopts 12 Tl atoms and 10 Au atoms (in total, 22 atoms) per \\sqrt7 × \\sqrt7 unit cell, i.e.  ˜1.71 ML of Tl and  ˜1.43 ML of Au (in total, ˜3.14 ML). Qualitatively, the model can be visualized as consisting of truncated-pyramid-like Au clusters with a Tl atom on top, while the other Tl atoms form a double layer around the Au clusters. The (Tl, Au)/Si(1 1 1)\\sqrt7 × \\sqrt7 compound has been found to exhibit pronounced metallic properties at least down to temperatures as low as  ˜25 K, which makes it a promising object for studying electrical transport phenomena in the 2D metallic systems.

A systematic composite service design modeling method using graph-based theory.

PubMed

Elhag, Arafat Abdulgader Mohammed; Mohamad, Radziah; Aziz, Muhammad Waqar; Zeshan, Furkh

2015-01-01

The composite service design modeling is an essential process of the service-oriented software development life cycle, where the candidate services, composite services, operations and their dependencies are required to be identified and specified before their design. However, a systematic service-oriented design modeling method for composite services is still in its infancy as most of the existing approaches provide the modeling of atomic services only. For these reasons, a new method (ComSDM) is proposed in this work for modeling the concept of service-oriented design to increase the reusability and decrease the complexity of system while keeping the service composition considerations in mind. Furthermore, the ComSDM method provides the mathematical representation of the components of service-oriented design using the graph-based theoryto facilitate the design quality measurement. To demonstrate that the ComSDM method is also suitable for composite service design modeling of distributed embedded real-time systems along with enterprise software development, it is implemented in the case study of a smart home. The results of the case study not only check the applicability of ComSDM, but can also be used to validate the complexity and reusability of ComSDM. This also guides the future research towards the design quality measurement such as using the ComSDM method to measure the quality of composite service design in service-oriented software system.

A Systematic Composite Service Design Modeling Method Using Graph-Based Theory

PubMed Central

Elhag, Arafat Abdulgader Mohammed; Mohamad, Radziah; Aziz, Muhammad Waqar; Zeshan, Furkh

2015-01-01

The composite service design modeling is an essential process of the service-oriented software development life cycle, where the candidate services, composite services, operations and their dependencies are required to be identified and specified before their design. However, a systematic service-oriented design modeling method for composite services is still in its infancy as most of the existing approaches provide the modeling of atomic services only. For these reasons, a new method (ComSDM) is proposed in this work for modeling the concept of service-oriented design to increase the reusability and decrease the complexity of system while keeping the service composition considerations in mind. Furthermore, the ComSDM method provides the mathematical representation of the components of service-oriented design using the graph-based theoryto facilitate the design quality measurement. To demonstrate that the ComSDM method is also suitable for composite service design modeling of distributed embedded real-time systems along with enterprise software development, it is implemented in the case study of a smart home. The results of the case study not only check the applicability of ComSDM, but can also be used to validate the complexity and reusability of ComSDM. This also guides the future research towards the design quality measurement such as using the ComSDM method to measure the quality of composite service design in service-oriented software system. PMID:25928358

Effects of Surface Structure and of Embedded-Atom Pair Functionals on Adatom Diffusion on FCC Metallic Surfaces

DTIC Science & Technology

1992-11-01

total-energy calculations that this complex mechanism for diffusion can be invoked for surface self-diffusion on the (100) surface ( Kellog and...Woodland Hills, CA 91364 National Science Foundation 3 SRI International ATIN: A.B. Harvey ATIN: G. Smith Washington, DC 20550 D. Crosley D. Golden...Aeronautics and Astronautics ATTN: H. Krier ATfN: J.R. Osborn 144MEB, 1206 W. Green St. Grissom Hall Urbana, IL 61801 West Lafayette, IN 47906 The Johns

Rapid Precipitation of Amorphous Silica in Experimental Systems with Nontronite (NAu-1) and Shewanella oneidensis MR-1

DTIC Science & Technology

2007-01-15

law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB...report, we focus on the rapid bio- life because much of our current understanding of early life mineralization of amorphous silica. comes from...matter. The Nanoplast-embedded sample was atomic emission spectroscopy (ICP). After pH analysis ultrathin-sectioned, and examined with JEOL3010 TEM with a

Active tuning of high-Q dielectric metasurfaces

DOE PAGES

Parry, Matthew; Komar, Andrei; Hopkins, Ben; ...

2017-08-02

Here, we demonstrate the active tuning of all-dielectric metasurfaces exhibiting high-quality factor (high-Q) resonances. The active control is provided by embedding the asymmetric silicon meta-atoms with liquid crystals, which allows the relative index of refraction to be controlled through heating. It is found that high quality factor resonances (Q = 270 ± 30) can be tuned over more than three resonance widths. Our results demonstrate the feasibility of using all-dielectric metasurfaces to construct tunable narrow-band filters.

H(D) → D(H) + Cu(111) collision system: Molecular dynamics study of surface temperature effects

PubMed Central

Vurdu, Can D.; Güvenç, Ziya B.

2011-01-01

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London–Eyring–Polanyi–Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. PMID:21528959

H(D) → D(H) + Cu(111) collision system: molecular dynamics study of surface temperature effects.

PubMed

Vurdu, Can D; Güvenç, Ziya B

2011-04-28

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London-Eyring-Polanyi-Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures.