Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

NASA Astrophysics Data System (ADS)

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah; Dicken, Quinten; Thevuthasan, S. Theva; Browning, Nigel D.; Evans, James E.

2016-02-01

Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

PubMed Central

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah; Dicken, Quinten; Thevuthasan, S. Theva; Browning, Nigel D.; Evans, James E.

2016-01-01

Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment. PMID:26924804

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.

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.

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.

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.

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.

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.

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.

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.

Phonon dispersion on Ag (100) surface: A modified analytic embedded atom method study

NASA Astrophysics Data System (ADS)

Xiao-Jun, Zhang; Chang-Le, Chen

2016-01-01

Within the harmonic approximation, the analytic expression of the dynamical matrix is derived based on the modified analytic embedded atom method (MAEAM) and the dynamics theory of surface lattice. The surface phonon dispersions along three major symmetry directions , and X¯M¯ are calculated for the clean Ag (100) surface by using our derived formulas. We then discuss the polarization and localization of surface modes at points X¯ and M¯ by plotting the squared polarization vectors as a function of the layer index. The phonon frequencies of the surface modes calculated by MAEAM are compared with the available experimental and other theoretical data. It is found that the present results are generally in agreement with the referenced experimental or theoretical results, with a maximum deviation of 10.4%. The agreement shows that the modified analytic embedded atom method is a reasonable many-body potential model to quickly describe the surface lattice vibration. It also lays a significant foundation for studying the surface lattice vibration in other metals. Project supported by the National Natural Science Foundation of China (Grant Nos. 61471301 and 61078057), the Scientific Research Program Funded by Shaanxi Provincial Education Department, China (Grant No. 14JK1301), and the Specialized Research Fund for the Doctoral Program of Higher Education, China (Grant No. 20126102110045).

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

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

Sorella, S., E-mail: sorella@sissa.it; Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr

2015-12-28

We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wavemore » function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.« less

Vibrational properties of TaW alloy using modified embedded atom method potential

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

Chand, Manesh, E-mail: maneshchand@gmail.com; Uniyal, Shweta; Joshi, Subodh

2016-05-06

Force-constants up to second neighbours of pure transition metal Ta and TaW alloy are determined using the modified embedded atom method (MEAM) potential. The obtained force-constants are used to calculate the phonon dispersion of pure Ta and TaW alloy. As a further application of MEAM potential, the force-constants are used to calculate the local vibrational density of states and mean square thermal displacements of pure Ta and W impurity atoms with Green’s function method. The calculated results are found to be in agreement with the experimental measurements.

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.

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.

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.

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.

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

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

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

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

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.

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.

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

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.

Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set

NASA Astrophysics Data System (ADS)

Bennie, Simon J.; Stella, Martina; Miller, Thomas F.; Manby, Frederick R.

2015-07-01

Methods where an accurate wavefunction is embedded in a density-functional description of the surrounding environment have recently been simplified through the use of a projection operator to ensure orthogonality of orbital subspaces. Projector embedding already offers significant performance gains over conventional post-Hartree-Fock methods by reducing the number of correlated occupied orbitals. However, in our first applications of the method, we used the atomic-orbital basis for the full system, even for the correlated wavefunction calculation in a small, active subsystem. Here, we further develop our method for truncating the atomic-orbital basis to include only functions within or close to the active subsystem. The number of atomic orbitals in a calculation on a fixed active subsystem becomes asymptotically independent of the size of the environment, producing the required O ( N 0 ) scaling of cost of the calculation in the active subsystem, and accuracy is controlled by a single parameter. The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of SN2 substitution of fluorine by chlorine in α-fluoroalkanes.

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.

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

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.

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.

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.

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.

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

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.

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.

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.

Tight-binding calculation studies of vacancy and adatom defects in graphene

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

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

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

Defect structures induced by high-energy displacement cascades in γ uranium

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

Miao, Yinbin; Beeler, Benjamin; Deo, Chaitanya

Displacement cascade simulations were conducted for the c uranium system based on molecular dynamics. A recently developed modified embedded atom method (MEAM) potential was employed to replicate the atomic interactions while an embedded atom method (EAM) potential was adopted to help characterize the defect structures induced by the displacement cascades. The atomic displacement process was studied by providing primary knock-on atoms (PKAs) with kinetic energies from 1 keV to 50 keV. The influence of the PKA incident direction was examined. The defect structures were analyzed after the systems were fully relaxed. The states of the self-interstitial atoms (SIAs) were categorizedmore » into various types of dumbbells, the crowdion, and the octahedral interstitial. The voids were determined to have a polyhedral shape with {110} facets. The size distribution of the voids was also obtained. The results of this study not only expand the knowledge of the microstructural evolution in irradiated c uranium, but also provide valuable references for the radiation-induced defects in uranium alloy fuels.« less

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.

Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A

PubMed Central

Davis, Joseph E.; Patel, Sandeep

2009-01-01

Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modelled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, headgroup orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation, since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties. PMID:19526999

Effective scheme for partitioning covalent bonds in density-functional embedding theory: From molecules to extended covalent systems.

PubMed

Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele

2016-12-28

Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.

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.

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.

A Comparison of the Predictive Capabilities of the Embedded-Atom Method and Modified Embedded-Atom Method Potentials for Lithium

DOE PAGES

Vella, Joseph R.; Stillinger, Frank H.; Panagiotopoulos, Athanassios Z.; ...

2015-07-23

Here, we compare six lithium potentials by examining their ability to predict coexistence properties and liquid structure using molecular dynamics. All potentials are of the embedded-atom-method (EAM) type. The coexistence properties we focus on are the melting curve, vapor pressure, saturated liquid density, and vapor-liquid surface tension. For each property studied, the simulation results are compared to available experimental data in order to properly assess the accuracy of each potential. We find that the Cui 2NN MEAM is the most robust potential, giving adequate agreement with most of the properties examined. For example, the zero-pressure melting point of this potentialmore » is shown to be around 443 K, while experimentally is it about 454 K. This potential also gives excellent agreement with saturated liquid densities, even though no liquid properties were used in the fitting procedure. Our study allows us to conclude that the Cui 2NN MEAM should be used for further simulations of lithiums.« less

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.

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.

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.

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

MEAM interatomic force calculation subroutine for LAMMPS

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

Stukowski, A.

2010-10-25

Interatomic force and energy calculation subroutine tobe used with the molecular dynamics simulation code LAMMPS (Ref a.). The code evaluates the total energy and atomic forces (energy gradient) according to cubic spine-based variant (Ref b.) of the Modified Embedded Atom Method (MEAM).

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

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.

In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

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)

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

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 model for the dimeric FO region of mitochondrial ATP synthase.

PubMed

Guo, Hui; Bueler, Stephanie A; Rubinstein, John L

2017-11-17

Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F O region turns the rotor that drives ATP synthesis in the soluble F 1 region. Although crystal structures of the F 1 region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F O region. Using cryo-electron microscopy, we determined the structure of the dimeric F O complex from Saccharomyces cerevisiae at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae. Copyright © 2017, American Association for the Advancement of Science.

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.

(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.

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.

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.

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.

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

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.

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.

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

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.

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

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.

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

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).

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.

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.

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

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.

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 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.

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

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.

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.

Feature-based component model for design of embedded systems

NASA Astrophysics Data System (ADS)

Zha, Xuan Fang; Sriram, Ram D.

2004-11-01

An embedded system is a hybrid of hardware and software, which combines software's flexibility and hardware real-time performance. Embedded systems can be considered as assemblies of hardware and software components. An Open Embedded System Model (OESM) is currently being developed at NIST to provide a standard representation and exchange protocol for embedded systems and system-level design, simulation, and testing information. This paper proposes an approach to representing an embedded system feature-based model in OESM, i.e., Open Embedded System Feature Model (OESFM), addressing models of embedded system artifacts, embedded system components, embedded system features, and embedded system configuration/assembly. The approach provides an object-oriented UML (Unified Modeling Language) representation for the embedded system feature model and defines an extension to the NIST Core Product Model. The model provides a feature-based component framework allowing the designer to develop a virtual embedded system prototype through assembling virtual components. The framework not only provides a formal precise model of the embedded system prototype but also offers the possibility of designing variation of prototypes whose members are derived by changing certain virtual components with different features. A case study example is discussed to illustrate the embedded system model.

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.

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.

Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, John H.; Cantrell, Sean A.

2010-01-01

The interaction of the cantilever tip of an atomic force microscope (AFM) with the sample surface is obtained by treating the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. The volume element is subjected to a restoring force from the remainder of the sample that provides dynamical equilibrium for the combined systems. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any) via a basis set of set of orthogonal functions that may be generalized to account for arbitrary cantilever shapes. The basis set is extended to include nonlinear cantilever modes. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. The effects of oscillatory excitation forces applied either to the cantilever or to the sample surface (or to both) are obtained from the solution set and applied to the to the assessment of phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) modalities. The influence of bistable cantilever modes of on AFM signal generation is discussed. The effects on the cantilever-sample surface dynamics of subsurface features embedded in the sample that are perturbed by surface-generated oscillatory excitation forces and carried to the cantilever via wave propagation are accounted by the Bolef-Miller propagating wave model. Expressions pertaining to signal generation and image contrast in A-AFM are obtained and applied to amplitude modulation (intermittent contact) atomic force microscopy and resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM). The influence of phase accumulation in A-AFM on image contrast is discussed, as is the effect of hard contact and maximum nonlinearity regimes of A-AFM operation.

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.

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.

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.

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.

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.

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.

Beyond packing of hard spheres: The effects of core softness, non-additivity, intermediate-range repulsion, and many-body interactions on the glass-forming ability of bulk metallic glasses

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

Zhang, Kai; Fan, Meng; Liu, Yanhui

When a liquid is cooled well below its melting temperature at a rate that exceeds the critical cooling rate R{sub c}, the crystalline state is bypassed and a metastable, amorphous glassy state forms instead. R{sub c} (or the corresponding critical casting thickness d{sub c}) characterizes the glass-forming ability (GFA) of each material. While silica is an excellent glass-former with small R{sub c} < 10{sup −2} K/s, pure metals and most alloys are typically poor glass-formers with large R{sub c} > 10{sup 10} K/s. Only in the past thirty years have bulk metallic glasses (BMGs) been identified with R{sub c} approachingmore » that for silica. Recent simulations have shown that simple, hard-sphere models are able to identify the atomic size ratio and number fraction regime where BMGs exist with critical cooling rates more than 13 orders of magnitude smaller than those for pure metals. However, there are a number of other features of interatomic potentials beyond hard-core interactions. How do these other features affect the glass-forming ability of BMGs? In this manuscript, we perform molecular dynamics simulations to determine how variations in the softness and non-additivity of the repulsive core and form of the interatomic pair potential at intermediate distances affect the GFA of binary alloys. These variations in the interatomic pair potential allow us to introduce geometric frustration and change the crystal phases that compete with glass formation. We also investigate the effect of tuning the strength of the many-body interactions from zero to the full embedded atom model on the GFA for pure metals. We then employ the full embedded atom model for binary BMGs and show that hard-core interactions play the dominant role in setting the GFA of alloys, while other features of the interatomic potential only change the GFA by one to two orders of magnitude. Despite their perturbative effect, understanding the detailed form of the intermetallic potential is important for designing BMGs with cm or greater casting thickness.« less

Reputation Effects in Social Networks Do Not Promote Cooperation: An Experimental Test of the Raub & Weesie Model

PubMed Central

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. PMID:27366907

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

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.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

NASA Astrophysics Data System (ADS)

Sanyal, Tanmoy; Shell, M. Scott

2016-07-01

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

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.

Radiating dipoles in photonic crystals

PubMed

Busch; Vats; John; Sanders

2000-09-01

The radiation dynamics of a dipole antenna embedded in a photonic crystal are modeled by an initially excited harmonic oscillator coupled to a non-Markovian bath of harmonic oscillators representing the colored electromagnetic vacuum within the crystal. Realistic coupling constants based on the natural modes of the photonic crystal, i.e., Bloch waves and their associated dispersion relation, are derived. For simple model systems, well-known results such as decay times and emission spectra are reproduced. This approach enables direct incorporation of realistic band structure computations into studies of radiative emission from atoms and molecules within photonic crystals. We therefore provide a predictive and interpretative tool for experiments in both the microwave and optical regimes.

Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

PubMed

Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

2014-09-16

Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.

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

The role of HH interactions in the formation of ordered structures on Ni and Pd single crystals

NASA Astrophysics Data System (ADS)

Muscat, J. P.

1981-09-01

The interaction between H adatoms on a surface is calculated within the embedded cluster model of chemisorption. The model is first applied to the case of two H atoms on a free electron surface. The interaction energy is found to be an oscillatory function of the H-H separation Rab. Application of the free electron model to the problem of chemisorption on transition metal surfaces leads to unphysical results with the prediction of formation of ordered H overlayers which are not observed in LEED experiments. We next include the l = 2 TM muffin tins. Results for H adsorption on the low index faces of Ni and Pd substrates are presented. Graphitic structures are predicted for the (111) faces of both Ni and Pd with the H atoms occupying both types of three-fold hollow sites on the surface. This agrees with the results of LEED experiments for H/Ni(111). Comparison with experiment is not possible in the case of H/Pd(111) owing to the lack of low temperature studies for that system. Zig-zag chains with the H atoms adsorbed in sites of three-fold coordination on alternate sides of the TM(110) rows are predicted for both Ni and Pd. This is in agreement with the results of He diffraction experiments for H/Ni(110). No structure determination has been done for H/Pd(110). Adsorption in the four-fold centre sites for H on the (100) faces of Ni and Pd is found to be unfavourable. The H atoms are expected to adsorb in sites of three-fold symmetry below the (100) surface for H on Pd with formation of a c(2 × 2) structure in agreement with the LEED observations. For H/Ni(100) the H atoms are believed to adsorb above the surface, away from the centre site and to bond to two surface Ni atoms. No short-range ordered structures are predicted in this case.

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

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.

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.

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.

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

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

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

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

Optimal control of the strong-field ionization of silver clusters in helium droplets

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

Truong, N. X.; Goede, S.; Przystawik, A.

Optimal control techniques combined with femtosecond laser pulse shaping are applied to steer and enhance the strong-field induced emission of highly charged atomic ions from silver clusters embedded in helium nanodroplets. With light fields shaped in amplitude and phase we observe a substantial increase of the Ag{sup q+} yield for q>10 when compared to bandwidth-limited and optimally stretched pulses. A remarkably simple double-pulse structure, containing a low-intensity prepulse and a stronger main pulse, turns out to produce the highest atomic charge states up to Ag{sup 20+}. A negative chirp during the main pulse hints at dynamic frequency locking to themore » cluster plasmon. A numerical optimal control study on pure silver clusters with a nanoplasma model converges to a similar pulse structure and corroborates that the optimal light field adapts to the resonant excitation of cluster surface plasmons for efficient ionization.« 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

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.

Theoretical evidence for a first-order liquid-liquid phase transition in gallium.

PubMed

Carvajal Jara, Diego Alejandro; Fontana Michelon, Mateus; Antonelli, Alex; de Koning, Maurice

2009-06-14

We report on theoretical results that lend support to recent experimental observations suggesting the existence of a first-order liquid-liquid phase transformation (LLPT) in gallium. Using molecular dynamics simulation based on a modified embedded-atom model, we observe a transition from a high-density to a low-density liquid in the supercooled regime. The first-order character of the transition is established through the detection of the release of latent heat and our findings suggest that the LLPT terminates in a critical point that is located in the tensile-strained domain of the metastable phase diagram.

X-ray absorption in insulators with non-Hermitian real-time time-dependent density functional theory.

PubMed

Fernando, Ranelka G; Balhoff, Mary C; Lopata, Kenneth

2015-02-10

Non-Hermitian real-time time-dependent density functional theory was used to compute the Si L-edge X-ray absorption spectrum of α-quartz using an embedded finite cluster model and atom-centered basis sets. Using tuned range-separated functionals and molecular orbital-based imaginary absorbing potentials, the excited states spanning the pre-edge to ∼20 eV above the ionization edge were obtained in good agreement with experimental data. This approach is generalizable to TDDFT studies of core-level spectroscopy and dynamics in a wide range of materials.

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

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.

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.

A simple model for molecular hydrogen chemistry coupled to radiation hydrodynamics

NASA Astrophysics Data System (ADS)

Nickerson, Sarah; Teyssier, Romain; Rosdahl, Joakim

2018-06-01

We introduce non-equilibrium molecular hydrogen chemistry into the radiation-hydrodynamics code RAMSES-RT. This is an adaptive mesh refinement grid code with radiation hydrodynamics that couples the thermal chemistry of hydrogen and helium to moment-based radiative transfer with the Eddington tensor closure model. The H2 physics that we include are formation on dust grains, gas phase formation, formation by three-body collisions, collisional destruction, photodissociation, photoionisation, cosmic ray ionisation and self-shielding. In particular, we implement the first model for H2 self-shielding that is tied locally to moment-based radiative transfer by enhancing photo-destruction. This self-shielding from Lyman-Werner line overlap is critical to H2 formation and gas cooling. We can now track the non-equilibrium evolution of molecular, atomic, and ionised hydrogen species with their corresponding dissociating and ionising photon groups. Over a series of tests we show that our model works well compared to specialised photodissociation region codes. We successfully reproduce the transition depth between molecular and atomic hydrogen, molecular cooling of the gas, and a realistic Strömgren sphere embedded in a molecular medium. In this paper we focus on test cases to demonstrate the validity of our model on small scales. Our ultimate goal is to implement this in large-scale galactic simulations.

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.

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.

Wind-embedded shocks in FASTWIND: X-ray emission and K-shell absorption

NASA Astrophysics Data System (ADS)

Carneiro, L. P.; Puls, J.; Sundqvist, J. O.; Hoffmann, T. L.

2017-11-01

EUV and X-ray radiation emitted from wind-embedded shocks can affect the ionization balance in the outer atmospheres of massive stars, and can also be the mechanism responsible for producing highly ionized atoms detected in the wind UV spectra. To investigate these processes, we implemented the emission from wind-embedded shocks and related physics into our atmosphere/spectrum synthesis code FASTWIND. We also account for the high energy absorption of the cool wind, by adding important K-shell opacities. Various tests justfying our approach have been described by Carneiro+(2016, A&A 590, A88). In particular, we studied the impact of X-ray emission on the ionization balance of important elements. In almost all the cases, the lower ionization stages (O iv, N iv, P v) are depleted and the higher stages (N v, O v, O vi) become enhanced. Moreover, also He lines (in particular He ii 1640 and He ii 4686) can be affected as well. Finally, we carried out an extensive discussion of the high-energy mass absorption coefficient, κν, regarding its spatial variation and dependence on T eff. We found that (i) the approximation of a radially constant κν can be justified for r >= 1.2R * and λ <= 18 Å, and also for many models at longer wavelengths. (ii) In order to estimate the actual value of this quantity, however, the He ii background needs to be considered from detailed modeling.

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.

Theoretical modeling of the infrared fluorescence from interstellar polycyclic aromatic hydrocarbons

NASA Technical Reports Server (NTRS)

Schutte, W. A.; Tielens, A. G. G. M.; Allamandola, L. J.

1993-01-01

We have modeled the family of interstellar IR emission bands at 3.3, 6.2, 7.7, 8.6, 11.3, and 12.7 microns by calculating the fluorescence from a size distribution of interstellar polycyclic aromatic hydrocarbons (PAHs) embedded in the radiation field of a hot star. It is found that the various emission bands are dominated by distinctly different PAHs, from molecules with much less than about 80 C atoms for the 3.3 micron feature, to molecules with 10 exp 2-10 exp 5 C atoms for the emission in the IRAS 12 and 25 micron bands. We quantitatively describe the influence on the emergent spectrum of various PAH properties such as the molecular structure, the amount of dehydrogenation, the intrinsic strength of the IR active modes, and the size distribution. Comparing our model results to the emission spectrum from the Orion Bar region, we conclude that interstellar PAHs are likely fully, or almost fully, hydrogenated. Moreover, it is found that the intrinsic strengths of the 6.2 and 7.7 micron C-C stretching modes, and the 8.6 micron C-H in-plane bending mode are 2-6 times larger than measured for neutral PAHs in the laboratory.

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).

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

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

Static electric dipole polarizability of lithium atoms in Debye plasmas

NASA Astrophysics Data System (ADS)

Ning, Li-Na; Qi, Yue-Ying

2012-12-01

The static electric dipole polarizabilities of the ground state and n <= 3 excited states of a lithium atom embedded in a weekly coupled plasma environment are investigated as a function of the plasma screening radium. The plasma screening of the Coulomb interaction is described by the Debye—Hückel potential and the interaction between the valence electron and the atomic core is described by a model potential. The electron energies and wave functions for both the bound and continuum states are calculated by solving the Schrödinger equation numerically using the symplectic integrator. The oscillator strengths, partial-wave, and total static dipole polarizabilities of the ground state and n <= 3 excited states of the lithium atom are calculated. Comparison of present results with those of other authors, when available, is made. The results for the 2s ground state demonstrated that the oscillator strengths and the static dipole polarizabilities from np orbitals do not always increase or decrease with the plasma screening effect increasing, unlike that for hydrogen-like ions, especially for 2s→3p transition there is a zero value for both the oscillator strength and the static dipole polarizability for screening length D = 10.3106a0, which is associated with the Cooper minima.

Crown ethers in graphene

DOE PAGES

Guo, Junjie; Lee, Jaekwang; Contescu, Cristian I.; ...

2014-11-13

Crown ethers, introduced by Pedersen1, are at their most basic level neutral rings constructed of oxygen atoms linked by two- or three-carbon chains. They have attracted special attention for their ability to selectively incorporate various atoms2 or molecules within the cavity formed by the ring3-6. This property has led to the use of crown ethers and their compounds in a wide range of chemical and biological applications7,8. However, crown ethers are typically highly flexible, frustrating efforts to rigidify them for many uses that demand higher binding affinity and selectivity9,10. In this Letter, we report atomic-resolution images of the same basicmore » structures of the original crown ethers embedded in graphene. This arrangement constrains the crown ethers to be rigid and planar and thus uniquely suited for the many applications that crown ethers are known for. First-principles calculations show that the close similarity of the structures seen in graphene with those of crown ether molecules also extends to their selectivity towards specific metal cations depending on the ring size. Atoms (or molecules) incorporated within the crown ethers in graphene offer a simple environment that can be easily and systematically probed and modeled. Thus, we expect that this discovery will introduce a new wave of investigations and applications of chemically functionalized graphene.« less

Simulation of Ge Dopant Emission in Indirect-Drive ICF Implosion Experiments

NASA Astrophysics Data System (ADS)

Macfarlane, J. J.; Golovkin, I.; Kulkarni, S.; Regan, S.; Epstein, R.; Mancini, R.; Peterson, K.; Suter, L. J.

2013-10-01

We present results from simulations performed to study the radiative properties of dopants used in inertial confinement fusion indirect-drive capsule implosion experiments on NIF. In Rev5 NIF ignition capsules, a Ge dopant is added to an inner region of the CH ablator to absorb hohlraum x-ray preheat. Spectrally resolved emission from ablator dopants can be used to study the degree of mixing of ablator material into the ignition hot spot. Here, we study the atomic processes that affect the radiative characteristics of these elements using a set of simulation tools to first estimate the evolution of plasma conditions in the compressed target, and then to compute the atomic kinetics of the dopant and the resultant radiative emission. Using estimates of temperature and density profiles predicted by radiation-hydrodynamics simulations, we set up simple 2-D plasma grids where we allow dopant material to be embedded in the fuel, and perform multi-dimensional collisional-radiative simulations using SPECT3D to compute non-LTE atomic level populations and spectral signatures from the dopant. Recently improved Stark-broadened line shape modeling for Ge K-shell lines has been included. The goal is to study the radiative and atomic processes that affect the emergent spectra, including the effects of inner-shell photoabsorption and K α reemission from the dopant.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

Closed-system 'economic' models for psychiatric disorders: Western atomism and its culture-bound syndromes.

PubMed

Wallace, Rodrick

2015-08-01

The stabilization of human cognition via feedback from embedding social and cultural contexts is a dynamic process deeply intertwined with it, constituting, in a sense, the riverbanks directing the flow of a stream of generalized consciousness at different scales: Cultural norms and social interaction are synergistic with individual and group cognition and their disorders. A canonical failure mode in atomistic cultures is found to be a 'ground state' collapse well represented by atomistic models of economic interaction that are increasingly characterized as divorced from reality by heterodox economists. That is, high rates of psychopathic and antisocial personality disorder and obsessive compulsive disorder emerge as culture-bound syndromes particular to Western or Westernizing societies, or to those undergoing social disintegration.

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

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.

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.

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.

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.

Hot-atom versus Eley-Rideal dynamics in hydrogen recombination on Ni(100). I. The single-adsorbate case.

PubMed

Martinazzo, R; Assoni, S; Marinoni, G; Tantardini, G F

2004-05-08

We compare the efficiency of the Eley-Rideal (ER) reaction with the formation of hot-atom (HA) species in the simplest case, i.e., the scattering of a projectile off a single adsorbate, considering the Hydrogen and Hydrogen-on-Ni(100) system. We use classical mechanics and the accurate embedded diatomics-in-molecules potential to study the collision system over a wide range of collision energies (0.10-1.50 eV), both with a rigid and a nonrigid Ni substrate and for impact on the occupied and neighboring empty cells. In the rigid model metastable and truly bound hot-atoms occur and we find that the cross section for the formation of bound hot-atoms is considerably higher than that for the ER reaction over the whole range of collision energies examined. Metastable hot-atoms form because of the inefficient energy transfer to the adsorbate and have lifetimes of the order 0.1-0.7 ps, depending on the collision energy. When considering the effects of lattice vibrations we find, on average, a consistent energy transfer to the substrate, say 0.1-0.2 eV, which forced us to devise a two-step dynamical model to get rid of the problems associated with the use of periodic boundary conditions. Results for long-lived HA formation due to scattering on the occupied cell at a surface temperature of 120 K agree well with those of the rigid model, suggesting that in the above process the substrate plays only a secondary role and further calculations at surface temperatures of 50 and 300 K are in line with these findings. However, considerably high cross sections for formation of long-lived hot-atoms result also from scattering off the neighboring cells where the energy transfer to the lattice cannot be neglected. Metastable hot-atoms are reduced in number and have usually lifetimes shorter than those of the rigid-model, say less than 0.3 ps. In addition, ER cross sections are only slightly affected by the lattice motion and show a little temperature dependence. Finally, we find also that absorption and reflection strongly depend on the correct consideration of lattice vibrations and the occurrence of trapping. (c) 2004 American Institute of Physics.

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.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

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

Sanyal, Tanmoy; Shell, M. Scott, E-mail: shell@engineering.ucsb.edu

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one atmore » which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.« less

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.

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.

Dissociation rate of bromine diatomics in an argon heat bath

NASA Technical Reports Server (NTRS)

Razner, R.; Hopkins, D.

1973-01-01

The evolution of a collection of 300 K bromine diatomics embedded in a heat bath of argon atoms at 1800 K was studied by computer, and a dissociation-rate constant for the reaction Br2 + BR + Ar yields Br + Ar was determined. Previously published probability distributions for energy and angular momentum transfers in classical three-dimensional Br2-Ar collisions were used in conjunction with a newly developed Monte Carlo scheme for this purpose. Results are compared with experimental shock-tube data and the predictions of several other theoretical models. A departure from equilibrium is obtained which is significantly greater than that predicted by any of these other theories.

Adsorption in zeolites using mechanically embedded ONIOM clusters

DOE PAGES

Patet, Ryan E.; Caratzoulas, Stavros; Vlachos, Dionisios G.

2016-09-01

Here, we have explored mechanically embedded three-layer QM/QM/MM ONIOM models for computational studies of binding in Al-substituted zeolites. In all the models considered, the high-level-theory layer consists of the adsorbate molecule and of the framework atoms within the first two coordination spheres of the Al atom and is treated at the M06-2X/6-311G(2df,p) level. For simplicity, flexibility and routine applicability, the outer, low-level-theory layer is treated with the UFF. We have modelled the intermediate-level layer quantum mechanically and investigated the performance of HF theory and of three DFT functionals, B3LYP, M06-2X and ωB97x-D, for different layer sizes and various basis sets,more » with and without BSSE corrections. We have studied the binding of sixteen probe molecules in H-MFI and compared the computed adsorption enthalpies with published experimental data. We have demonstrated that HF and B3LYP are inadequate for the description of the interactions between the probe molecules and the framework surrounding the metal site of the zeolite on account of their inability to capture dispersion forces. Both M06-2X and ωB97x-D on average converge within ca. 10% of the experimental values. We have further demonstrated transferability of the approach by computing the binding enthalpies of n-alkanes (C1–C8) in H-MFI, H-BEA and H-FAU, with very satisfactory agreement with experiment. The computed entropies of adsorption of n-alkanes in H-MFI are also found to be in good agreement with experimental data. Finally, we compare with published adsorption energies calculated by periodic-DFT for n-C3 to n-C6 alkanes, water and methanol in H-ZSM-5 and find very good agreement.« less

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.

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.

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.

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.

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.

Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements.

PubMed

Wierez-Kien, M; Craciun, A D; Pinon, A V; Roux, S Le; Gallani, J L; Rastei, M V

2018-04-01

The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically <10 3 nm 2 ) measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

Interface bonding in silicon oxide nanocontacts: interaction potentials and force measurements

NASA Astrophysics Data System (ADS)

Wierez-Kien, M.; Craciun, A. D.; Pinon, A. V.; Le Roux, S.; Gallani, J. L.; Rastei, M. V.

2018-04-01

The interface bonding between two silicon-oxide nanoscale surfaces has been studied as a function of atomic nature and size of contacting asperities. The binding forces obtained using various interaction potentials are compared with experimental force curves measured in vacuum with an atomic force microscope. In the limit of small nanocontacts (typically <103 nm2) measured with sensitive probes the bonding is found to be influenced by thermal-induced fluctuations. Using interface interactions described by Morse, embedded atom model, or Lennard-Jones potential within reaction rate theory, we investigate three bonding types of covalent and van der Waals nature. The comparison of numerical and experimental results reveals that a Lennard-Jones-like potential originating from van der Waals interactions captures the binding characteristics of dry silicon oxide nanocontacts, and likely of other nanoscale materials adsorbed on silicon oxide surfaces. The analyses reveal the importance of the dispersive surface energy and of the effective contact area which is altered by stretching speeds. The mean unbinding force is found to decrease as the contact spends time in the attractive regime. This contact weakening is featured by a negative aging coefficient which broadens and shifts the thermal-induced force distribution at low stretching speeds.

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.

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.

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.

Interaction between adatoms on surfaces: Application to the system H/Ni(111)

NASA Astrophysics Data System (ADS)

Muscat, J. P.; Newns, D. M.

1981-04-01

The interaction of adatoms on a metal surface is looked at from a novel viewpoint, using the techniques of the embedded cluster model of chemisorption. Application is made to the problem of two hydrogen atoms on a free electron surface with simple derivation of the well known R-5 asymptotic behaviour for the interaction, at large inter-adatom distances R, compared to the corresponding R-3 behaviour for two impurities in a bulk free electron gas. Application of the free electron model to the case of H/Ni(111) does not reproduce the experimental observation of formation of a graphitic structure on the surface. Inclusion of the l = 2 nickel muffin tins corrects for this anomaly, and is seen to favour the formation of the above mentioned structure.

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

Rayleigh scattering in an emitter-nanofiber-coupling system

NASA Astrophysics Data System (ADS)

Tang, Shui-Jing; Gao, Fei; Xu, Da; Li, Yan; Gong, Qihuang; Xiao, Yun-Feng

2017-04-01

Scattering is a general process in both fundamental and applied physics. In this paper, we investigate Rayleigh scattering of a solid-state-emitter coupled to a nanofiber, by S -matrix-like theory in k -space description. Under this model, both Rayleigh scattering and dipole interaction are studied between a two-level artificial atom embedded in a nanocrystal and fiber modes (guided and radiation modes). It is found that Rayleigh scattering plays a critical role in the transport properties and quantum statistics of photons. On the one hand, Rayleigh scattering produces the transparency in the optical transmitted field of the nanofiber, accompanied by the change of atomic phase, population, and frequency shift. On the other hand, the interference between two kinds of scattering fields by Rayleigh scattering and dipole transition modifies the photon statistics (second-order autocorrelation function) of output fields, showing a strong wavelength dependence. This study provides guidance for the solid-state emitter acting as a single-photon source and can be extended to explore the scattering effect in many-body physics.

Formation of H̅ in p̅-Ps collisions embedded in plasmas

NASA Astrophysics Data System (ADS)

Ratnavelu, Kuru; Ghoshal, Arijit; Nayek, Sujay; Bhattacharya, Arka; Mohamed Kamali, Mohd Zahurin

2016-04-01

Screening effects of plasmas on the formation of antihydrogen (H̅) in an arbitrary s-state from the ground state of the positronium atom (Ps) by antiproton (p̅) impact have been studied within the framework of charge-conjugation and time-reversal invariance. Two types of plasma environments have been considered, namely weakly coupled plasma and dense quantum plasma. For weakly coupled plasma, the interactions among the charged particles in plasma have been represented by Debye-Huckel screening model, whereas for dense quantum plasma, interactions among the charged particles in plasma have been represented by exponential cosine-screened Coulomb potentials. Effects of plasma screening on the antihydrogen formation cross section have been studied in the energy range 15-400 keV of incident antiproton. For the free atomic case, our results agree well with some of the most accurate results available in the literature. Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.

A national facility for biological cryo-electron microscopy

PubMed Central

Saibil, Helen R.; Grünewald, Kay; Stuart, David I.

2015-01-01

Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback. PMID:25615867

Simulation of Ge Dopant Emission in Indirect-Drive ICF Implosion Experiments

NASA Astrophysics Data System (ADS)

Macfarlane, Joseph; Golovkin, I.; Regan, S.; Epstein, R.; Mancini, R.; Peterson, K.; Suter, L.

2012-10-01

We present results from simulations performed to study the radiative properties of dopants used in inertial confinement fusion indirect-drive capsule implosion experiments on NIF. In Rev5 NIF ignition capsules, a Ge dopant is added to an inner region of the CH ablator to absorb hohlraum x-ray preheat. Spectrally resolved emission from ablator dopants can be used to study the degree of mixing of ablator material into the ignition hot spot. Here, we study the atomic processes that affect the radiative characteristics of these elements using a set of simulation tools to first estimate the evolution of plasma conditions in the compressed target, and then to compute the atomic kinetics of the dopant and the resultant radiative emission. Using estimates of temperature and density profiles predicted by radiation-hydrodynamics simulations, we set up simple plasma grids where we allow dopant material to be embedded in the fuel, and perform multi-dimensional collisional-radiative simulations using SPECT3D to compute non-LTE atomic level populations and spectral signatures from the dopant. Recently improved Stark-broadened line shape modeling for Ge K-shell lines has been included. The goal is to study the radiative and atomic processes that affect the emergent spectra, including the effects of inner-shell photoabsorption and Kα reemission from the dopant, and to study the sensitivity of the emergent spectra to the dopant and the hot spot and ablator conditions.

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

Fe embedded in ice: The impacts of sublimation and energetic particle bombardment

NASA Astrophysics Data System (ADS)

Frankland, Victoria L.; Plane, John M. C.

2015-05-01

Icy particles containing a variety of Fe compounds are present in the upper atmospheres of planets such as the Earth and Saturn. In order to explore the role of ice sublimation and energetic ion bombardment in releasing Fe species into the gas phase, Fe-dosed ice films were prepared under UHV conditions in the laboratory. Temperature-programmed desorption studies of Fe/H2O films revealed that no Fe atoms or Fe-containing species co-desorbed along with the H2O molecules. This implies that when noctilucent ice cloud particles sublimate in the terrestrial mesosphere, the metallic species embedded in them will coalesce to form residual particles. Sputtering of the Fe-ice films by energetic Ar+ ions was shown to be an efficient mechanism for releasing Fe into the gas phase, with a yield of 0.08 (Ar+ energy=600 eV). Extrapolating with a semi-empirical sputtering model to the conditions of a proton aurora indicates that sputtering by energetic protons (>100 keV) should also be efficient. However, the proton flux in even an intense aurora will be too low for the resulting injection of Fe species into the gas phase to compete with that from meteoric ablation. In contrast, sputtering of the icy particles in the main rings of Saturn by energetic O+ ions may be the source of recently observed Fe+ in the Saturnian magnetosphere. Electron sputtering (9.5 keV) produced no detectable Fe atoms or Fe-containing species. Finally, it was observed that Fe(OH)2 was produced when Fe was dosed onto an ice film at 140 K (but not at 95 K). Electronic structure theory shows that the reaction which forms this hydroxide from adsorbed Fe has a large barrier of about 0.7 eV, from which we conclude that the reaction requires both translationally hot Fe atoms and mobile H2O molecules on the ice surface.

Crystal structures and atomic model of NADPH oxidase.

PubMed

Magnani, Francesca; Nenci, Simone; Millana Fananas, Elisa; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W; Mattevi, Andrea

2017-06-27

NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.

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.

NUMERICAL SIMULATION OF NANOINDENTATION AND PATCH CLAMP EXPERIMENTS ON MECHANOSENSITIVE CHANNELS OF LARGE CONDUCTANCE IN ESCHERICHIA COLI

PubMed Central

Tang, Yuye; Chen, Xi; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang

2010-01-01

A hierarchical simulation framework that integrates information from all-atom simulations into a finite element model at the continuum level is established to study the mechanical response of a mechanosensitive channel of large conductance (MscL) in bacteria Escherichia Coli (E.coli) embedded in a vesicle formed by the dipalmitoylphosphatidycholine (DPPC) lipid bilayer. Sufficient structural details of the protein are built into the continuum model, with key parameters and material properties derived from molecular mechanics simulations. The multi-scale framework is used to analyze the gating of MscL when the lipid vesicle is subjective to nanoindentation and patch clamp experiments, and the detailed structural transitions of the protein are obtained explicitly as a function of external load; it is currently impossible to derive such information based solely on all-atom simulations. The gating pathways of E.coli-MscL qualitatively agree with results from previous patch clamp experiments. The gating mechanisms under complex indentation-induced deformation are also predicted. This versatile hierarchical multi-scale framework may be further extended to study the mechanical behaviors of cells and biomolecules, as well as to guide and stimulate biomechanics experiments. PMID:21874098

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.

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.

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.

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.

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.

Intermolecular Interactions and Electrostatic Properties of the [beta]-Hydroquinone Apohost: Implications for Supramolecular Chemistry

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

Clausen, Henrik F.; Chen, Yu-Sheng; Jayatilaka, Dylan

2012-02-07

The crystal structure of the {beta}-polymorph of hydroquinone ({beta}-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated withmore » the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/{angstrom}{sup 2} (0.27 V/{angstrom}) 1 {angstrom} along the 3-fold axis and 0.0105 e/{angstrom}{sup 2} (0.15 V/{angstrom}) 1 {angstrom} along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.« less

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.

Alternative Z ' bosons in E 6

NASA Astrophysics Data System (ADS)

Rojas, Eduardo; Erler, Jens

2015-10-01

We classify the quantum numbers of the extra U(1)' symmetries contained in E 6. In particular, we categorize the cases with rational charges and present the full list of models which arise from the chains of the maximal subgroups of E 6. As an application, the classification allows us to determine all embeddings of the Standard Model fermions in all possible decompositions of the fundamental representation of E 6 under its maximal subgroups. From this we find alternative chains of subgroups for Grand Unified Theories. We show how many of the known models including some new ones appear in alternative breaking patterns. We also use low energy constraints coming from parity-violating asymmetry measurements and atomic parity non-conservation to set limits on the E 6 motivated parameter space for a Z ' boson mass of 1.2 TeV. We include projected limits for the present and upcoming QWEAK, MOLLER and SOLID experiments.

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...

Resonance fluorescence spectrum in a two-band photonic bandgap crystal

NASA Astrophysics Data System (ADS)

Lee, Ray-Kuang; Lai, Yinchieh

2003-05-01

Steady state resonance fluorescence spectra from a two-level atom embedded in a photonic bandgap crystal and resonantly driven by a classical pump light are calculated. The photonic crystal is considered to be with a small bandgap which is in the order of magnitude of the Rabi frequency and is modeled by the anisotropic two-band dispersion relation. Non-Markovian noises caused by the non-uniform distribution of photon density states near the photonic bandgap are taken into account by a new approach which linearizes the optical Bloch equations by using the Liouville operator expansion. Fluorescence spectra that only exhibit sidebands of the Mollow triplet are found, indicating that there is no coherent Rayleigh scattering process.

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.

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.

Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework

PubMed Central

Chen, Xi; Cui, Qiang; Tang, Yuye; Yoo, Jejoong; Yethiraj, Arun

2008-01-01

A hierarchical simulation framework that integrates information from molecular dynamics (MD) simulations into a continuum model is established to study the mechanical response of mechanosensitive channel of large-conductance (MscL) using the finite element method (FEM). The proposed MD-decorated FEM (MDeFEM) approach is used to explore the detailed gating mechanisms of the MscL in Escherichia coli embedded in a palmitoyloleoylphosphatidylethanolamine lipid bilayer. In Part I of this study, the framework of MDeFEM is established. The transmembrane and cytoplasmic helices are taken to be elastic rods, the loops are modeled as springs, and the lipid bilayer is approximated by a three-layer sheet. The mechanical properties of the continuum components, as well as their interactions, are derived from molecular simulations based on atomic force fields. In addition, analytical closed-form continuum model and elastic network model are established to complement the MDeFEM approach and to capture the most essential features of gating. In Part II of this study, the detailed gating mechanisms of E. coli-MscL under various types of loading are presented and compared with experiments, structural model, and all-atom simulations, as well as the analytical models established in Part I. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction. PMID:18390626

Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers

DOE PAGES

Moskovitz, Yevgeny; Yang, Hui

2015-01-08

Our objective was to study molecular processes that might be responsible for inert gas narcosis and high-pressure nervous syndrome. The classical molecular dynamics trajectories (200 ns-long) of dioleoylphosphatidylcholine (DOPC) bilayers simulated by the Berger force field were evaluated for water and the atomic distribution of noble gases around DOPC molecules at a pressure range of 1 - 1000 bar and temperature of 310 Kelvin. Xenon and argon have been tested as model gases for general anesthetics, and neon has been investigated for distortions that are potentially responsible for neurological tremor at hyperbaric conditions. The analysis of stacked radial pair distributionmore » functions of DOPC headgroup atoms revealed the explicit solvation potential of gas molecules, which correlates with their dimensions. The orientational dynamics of water molecules at the biomolecular interface should be considered as an influential factor; while excessive solvation effects appearing in the lumen of membrane-embedded ion channels could be a possible cause of inert gas narcosis. All the noble gases tested exhibit similar patterns of the order parameter for both DOPC acyl chains, which is opposite to the patterns found for the order parameter curve at high hydrostatic pressures in intact bilayers. This finding supports the ‘critical volume’ hypothesis of anesthesia pressure reversal. The irregular lipid headgroup-water boundary observed in DOPC bilayers saturated with neon in the pressure range of 1 - 100 bar could be associated with the possible manifestation of neurological tremor at the atomic scale. The non-immobilizer neon also demonstrated the highest momentum impact on the normal component of the DOPC diffusion coefficient representing monolayers undulations rate, which indicates enhanced diffusivity, rather than atom size, as the key factor.« less

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.

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.

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.

Strain gradient drives shear banding in metallic glasses

NASA Astrophysics Data System (ADS)

Tian, Zhi-Li; Wang, Yun-Jiang; Chen, Yan; Dai, Lan-Hong

2017-09-01

Shear banding is a nucleation-controlled process in metallic glasses (MGs) involving multiple temporal-spatial scales, which hinders a concrete understanding of its structural origin down to the atomic scale. Here, inspired by the morphology of composite materials, we propose a different perspective of MGs as a hard particle-reinforced material based on atomic-scale structural heterogeneity. The local stable structures indicated by a high level of local fivefold symmetry (L5FS) act as hard "particles" which are embedded in the relatively soft matrix. We demonstrate this concept by performing atomistic simulations of shear banding in CuZr MG. A shear band is prone to form in a sample with a high degree of L5FS which is slowly quenched from the liquid. An atomic-scale analysis on strain and the structural evolution reveals that it is the strain gradient effect that has originated from structural heterogeneity that facilitates shear transformation zones (STZs) to mature shear bands. An artificial composite model with a high degree of strain gradient, generated by inserting hard MG strips into a soft MG matrix, demonstrates a great propensity for shear banding. It therefore confirms the critical role strain gradient plays in shear banding. The strain gradient effect on shear banding is further quantified with a continuum model and a mechanical instability analysis. These physical insights might highlight the strain gradient as the hidden driving force in transforming STZs into shear bands in MGs.

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.

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…

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

Mechanism of morphology transformation during annealing of nanostructured gold films on glass.

PubMed

Karakouz, Tanya; Tesler, Alexander B; Sannomiya, Takumi; Feldman, Yishay; Vaskevich, Alexander; Rubinstein, Israel

2013-04-07

Nanostructured, just-percolated gold films were prepared by evaporation on bare glass. Annealing of the films at temperatures close to or higher than the softening temperature of the glass substrate induces morphological transformation to discrete Au islands and gradual embedding of the formed islands in the glass. The mechanism and kinetics of these processes are studied here using a combination of in situ high-temperature optical spectroscopy; ex situ characterization of the island shape by high-resolution scanning electron microscopy (HRSEM), atomic force microcopy (AFM) and cross-sectional transmission electron microscopy (TEM); and numerical simulations of transmission spectra using the Multiple Multipole Program (MMP) approach. It is shown that the morphological transformation of just-percolated, 10 nm (nominal thickness) Au films evaporated on glass and annealed at 600 °C, i.e., in the vicinity of the substrate glass transition temperature (Tg = 557 °C), proceeds via three processes exhibiting different time scales: (i) fast recrystallization and dewetting, leading to formation of single-crystalline islands (minutes); the initial spectrum characteristic of a continuous Au film is transformed to that of an island film, displaying a surface plasmon (SP) absorption band. (ii) Reshaping and faceting of the single-crystalline islands accompanied by formation of circumferential glass rims around them (first few hours); the overall optical response shows a blue shift of the SP band. (iii) Gradual island embedding in the glass substrate (tens of hours), seen as a characteristic red shift of the SP band. The influence of the annealing atmosphere (air, vacuum) on the embedding process is found to be minor. Numerical modeling of the extinction cross-section corresponding to the morphological transformations during island recrystallization and embedding is in qualitative agreement with the experimental data.

Nonlinear soil parameter effects on dynamic embedment of offshore pipeline on soft clay

NASA Astrophysics Data System (ADS)

Yu, Su Young; Choi, Han Suk; Lee, Seung Keon; Park, Kyu-Sik; Kim, Do Kyun

2015-06-01

In this paper, the effects of nonlinear soft clay on dynamic embedment of offshore pipeline were investigated. Seabed embedment by pipe-soil interactions has impacts on the structural boundary conditions for various subsea structures such as pipeline, riser, pile, and many other systems. A number of studies have been performed to estimate real soil behavior, but their estimation of seabed embedment has not been fully identified and there are still many uncertainties. In this regards, comparison of embedment between field survey and existing empirical models has been performed to identify uncertainties and investigate the effect of nonlinear soil parameter on dynamic embedment. From the comparison, it is found that the dynamic embedment with installation effects based on nonlinear soil model have an influence on seabed embedment. Therefore, the pipe embedment under dynamic condition by nonlinear parameters of soil models was investigated by Dynamic Embedment Factor (DEF) concept, which is defined as the ratio of the dynamic and static embedment of pipeline, in order to overcome the gap between field embedment and currently used empirical and numerical formula. Although DEF through various researches is suggested, its range is too wide and it does not consider dynamic laying effect. It is difficult to find critical parameters that are affecting to the embedment result. Therefore, the study on dynamic embedment factor by soft clay parameters of nonlinear soil model was conducted and the sensitivity analyses about parameters of nonlinear soil model were performed as well. The tendency on dynamic embedment factor was found by conducting numerical analyses using OrcaFlex software. It is found that DEF was influenced by shear strength gradient than other factors. The obtained results will be useful to understand the pipe embedment on soft clay seabed for applying offshore pipeline designs such as on-bottom stability and free span analyses.

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

Computer simulation of backscattering spectra from paint

NASA Astrophysics Data System (ADS)

Mayer, M.; Silva, T. F.

2017-09-01

To study the role of lateral non-homogeneity on backscattering analysis of paintings, a simplified model of paint consisting of randomly distributed spherical pigment particles embedded in oil/binder has been developed. Backscattering spectra for lead white pigment particles in linseed oil have been calculated for 3 MeV H+ at a scattering angle of 165° for pigment volume concentrations ranging from 30 vol.% to 70 vol.% using the program STRUCTNRA. For identical pigment volume concentrations the heights and shapes of the backscattering spectra depend on the diameter of the pigment particles: This is a structural ambiguity for identical mean atomic concentrations but different lateral arrangement of materials. Only for very small pigment particles the resulting spectra are close to spectra calculated supposing atomic mixing and assuming identical concentrations of all elements. Generally, a good fit can be achieved when evaluating spectra from structured materials assuming atomic mixing of all elements and laterally homogeneous depth distributions. However, the derived depth profiles are inaccurate by a factor of up to 3. The depth range affected by this structural ambiguity ranges from the surface to a depth of roughly 0.5-1 pigment particle diameters. Accurate quantitative evaluation of backscattering spectra from paintings therefore requires taking the correct microstructure of the paint layer into account.

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.

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.

The Herschel-PACS Legacy of Low-mass Protostars: The Properties of Warm and Hot Gas Components and Their Origin in Far-UV Illuminated Shocks

NASA Astrophysics Data System (ADS)

Karska, Agata; Kaufman, Michael J.; Kristensen, Lars E.; van Dishoeck, Ewine F.; Herczeg, Gregory J.; Mottram, Joseph C.; Tychoniec, Łukasz; Lindberg, Johan E.; Evans, Neal J., II; Green, Joel D.; Yang, Yao-Lun; Gusdorf, Antoine; Itrich, Dominika; Siódmiak, Natasza

2018-04-01

Recent observations from Herschel allow the identification of important mechanisms responsible both for the heating of the gas that surrounds low-mass protostars and for its subsequent cooling in the far-infrared. Shocks are routinely invoked to reproduce some properties of the far-IR spectra, but standard models fail to reproduce the emission from key molecules, e.g., H2O. Here, we present the Herschel Photodetector Array Camera and Spectrometer (PACS) far-IR spectroscopy of 90 embedded low-mass protostars (Class 0/I). The Herschel-PACS spectral maps, covering ∼55–210 μm with a field of view of ∼50″, are used to quantify the gas excitation conditions and spatial extent using rotational transitions of H2O, high-J CO, and OH, as well as [O I] and [C II]. We confirm that a warm (∼300 K) CO reservoir is ubiquitous and that a hotter component (760 ± 170 K) is frequently detected around protostars. The line emission is extended beyond ∼1000 au spatial scales in 40/90 objects, typically in molecular tracers in Class 0 and atomic tracers in Class I objects. High-velocity emission (≳90 km s‑1) is detected in only 10 sources in the [O I] line, suggesting that the bulk of [O I] arises from gas that is moving slower than typical jets. Line flux ratios show an excellent agreement with models of C-shocks illuminated by ultraviolet (UV) photons for pre-shock densities of ∼105 cm‑3 and UV fields 0.1–10 times the interstellar value. The far-IR molecular and atomic lines are a unique diagnostic of feedback from UV emission and shocks in envelopes of deeply embedded protostars.

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.

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

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).

Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape

PubMed Central

Sodt, Alexander J.; Pastor, Richard W.

2014-01-01

Molecular dynamics simulations of an amphipathic helix embedded in a lipid bilayer indicate that it will induce substantial positive curvature (e.g., a tube of diameter 20 nm at 16% surface coverage). The induction is twice that of a continuum model prediction that only considers the shape of the inclusion. The discrepancy is explained in terms of the additional presence of specific interactions described only by the molecular model. The conclusion that molecular shape alone is insufficient to quantitatively model curvature is supported by contrasting molecular and continuum models of lipids with large and small headgroups (choline and ethanolamine, respectively), and of the removal of a lipid tail (modeling a lyso-lipid). For the molecular model, curvature propensity is analyzed by computing the derivative of the free energy with respect to bending. The continuum model predicts that the inclusion will soften the bilayer near the headgroup region, an effect that may weaken curvature induction. The all-atom predictions are consistent with experimental observations of the degree of tubulation by amphipathic helices and variation of the free energy of binding to liposomes. PMID:24806928

RAPID COMMUNICATION: Improving prediction accuracy of GPS satellite clocks with periodic variation behaviour

NASA Astrophysics Data System (ADS)

Heo, Youn Jeong; Cho, Jeongho; Heo, Moon Beom

2010-07-01

The broadcast ephemeris and IGS ultra-rapid predicted (IGU-P) products are primarily available for use in real-time GPS applications. The IGU orbit precision has been remarkably improved since late 2007, but its clock products have not shown acceptably high-quality prediction performance. One reason for this fact is that satellite atomic clocks in space can be easily influenced by various factors such as temperature and environment and this leads to complicated aspects like periodic variations, which are not sufficiently described by conventional models. A more reliable prediction model is thus proposed in this paper in order to be utilized particularly in describing the periodic variation behaviour satisfactorily. The proposed prediction model for satellite clocks adds cyclic terms to overcome the periodic effects and adopts delay coordinate embedding, which offers the possibility of accessing linear or nonlinear coupling characteristics like satellite behaviour. The simulation results have shown that the proposed prediction model outperforms the IGU-P solutions at least on a daily basis.

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

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.

Study of Outflow and Molecular Lines from the Observations of BHR71 by The Herschel Key Program,``Dust, Ice, and Gas In Time" (DIGIT)

NASA Astrophysics Data System (ADS)

Yang, Yao-Lun; Green, Joel D.

2014-07-01

The infall and outflow processes initiated by the collapse a dense core are widely observed in Class 0 protostars, and significantly change the density and temperature structure of the prestellar core as well as the following disk and envelope evolution. Since the Class 0 protostars are usually embedded in the cold molecular envelope preventing them from being observed at visible or near-IR wavelengths, the spectral analyses of the far-IR spectra provide us a window to look through the envelope and constrain the physical properties of the envelope and the core. BHR71, a Class 0 embedded protostar, is located in an isolated neighborhood with a collimated bipolar outflow and shows a rich far-IR spectrum as observed in the DIGIT program (PI: Neal Evans) with Herschel. It has numerous molecular and atomic features that can constrain its physical properties and the density structure well. In this research, we developed a robust data reduction (Green et al. 2013a, b) and automatic line fitting package that ensures all of the molecular and atomic lines are extracted to the same standard and it can be easily used for any other protostars observed by Herschel as well. We found 44 and 28 emission lines in the central spaxel in the PACS and the SPIRE bands respectively, including CO, 13CO, OH, and H2O. The extended feature observed at low-J CO and several H2O lines are consistent to the outflow direction but less collimated and a heterogeneous environment is concluded from the rotational diagram analysis. A dust Monte Carlo radiative transfer simulation using RADMC-3D will reveal the embedded structure with a dust density profile of a flared disk and a spherical envelope with bipolar outflow cavity. We will use a line radiative transfer simulation for multiple species to constrain the chemical abundance distributions and their temperature profiles.With high sensitivity spatial resolved spectra and simulated internal structure analysis of BHR71 will provide a good test of theoretical models of the infall and outflow.

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

Calculations of the electrostatic potential adjacent to model phospholipid bilayers.

PubMed

Peitzsch, R M; Eisenberg, M; Sharp, K A; McLaughlin, S

1995-03-01

We used the nonlinear Poisson-Boltzmann equation to calculate electrostatic potentials in the aqueous phase adjacent to model phospholipid bilayers containing mixtures of zwitterionic lipids (phosphatidylcholine) and acidic lipids (phosphatidylserine or phosphatidylglycerol). The aqueous phase (relative permittivity, epsilon r = 80) contains 0.1 M monovalent salt. When the bilayers contain < 11% acidic lipid, the -25 mV equipotential surfaces are discrete domes centered over the negatively charged lipids and are approximately twice the value calculated using Debye-Hückel theory. When the bilayers contain > 25% acidic lipid, the -25 mV equipotential profiles are essentially flat and agree well with the values calculated using Gouy-Chapman theory. When the bilayers contain 100% acidic lipid, all of the equipotential surfaces are flat and agree with Gouy-Chapman predictions (including the -100 mV surface, which is located only 1 A from the outermost atoms). Even our model bilayers are not simple systems: the charge on each lipid is distributed over several atoms, these partial charges are non-coplanar, there is a 2 A ion-exclusion region (epsilon r = 80) adjacent to the polar headgroups, and the molecular surface is rough. We investigated the effect of these four factors using smooth (or bumpy) epsilon r = 2 slabs with embedded point charges: these factors had only minor effects on the potential in the aqueous phase.

Calculations of the electrostatic potential adjacent to model phospholipid bilayers.

PubMed Central

Peitzsch, R M; Eisenberg, M; Sharp, K A; McLaughlin, S

1995-01-01

We used the nonlinear Poisson-Boltzmann equation to calculate electrostatic potentials in the aqueous phase adjacent to model phospholipid bilayers containing mixtures of zwitterionic lipids (phosphatidylcholine) and acidic lipids (phosphatidylserine or phosphatidylglycerol). The aqueous phase (relative permittivity, epsilon r = 80) contains 0.1 M monovalent salt. When the bilayers contain < 11% acidic lipid, the -25 mV equipotential surfaces are discrete domes centered over the negatively charged lipids and are approximately twice the value calculated using Debye-Hückel theory. When the bilayers contain > 25% acidic lipid, the -25 mV equipotential profiles are essentially flat and agree well with the values calculated using Gouy-Chapman theory. When the bilayers contain 100% acidic lipid, all of the equipotential surfaces are flat and agree with Gouy-Chapman predictions (including the -100 mV surface, which is located only 1 A from the outermost atoms). Even our model bilayers are not simple systems: the charge on each lipid is distributed over several atoms, these partial charges are non-coplanar, there is a 2 A ion-exclusion region (epsilon r = 80) adjacent to the polar headgroups, and the molecular surface is rough. We investigated the effect of these four factors using smooth (or bumpy) epsilon r = 2 slabs with embedded point charges: these factors had only minor effects on the potential in the aqueous phase. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:7756540

Fractionation and current time trends of PCB congeners: evolvement of distributions 1950-2010 studied using a global atmosphere-ocean general circulation model

NASA Astrophysics Data System (ADS)

Lammel, G.; Stemmler, I.

2012-05-01

PCBs are ubiquitous environmental pollutants expected to decline in abiotic environmental media in response to decreasing primary emissions since the 1970s. A coupled atmosphere-ocean general circulation model with embedded dynamic sub-models for atmospheric aerosols and the marine biogeochemistry and air-surface exchange processes with soils, vegetation and the cryosphere is used to study the transport and fate of four PCB congeners covering a range of 3-7 chlorine atoms. The change of the geographic distribution of the PCB mixture reflects the sources and sinks' evolvement over time. Globally, secondary emissions (re-volatilisation from surfaces) are on the long term increasingly gaining importance over primary emissions. They are most important for congeners of medium hydrophobicity (5-6 chlorine atoms). Their levels are predicted to decrease slowest. Congeners' fractionation is characterized both geographically and temporally. It causes enrichment of the lighter, less persistent congeners and more delayed decreasing levels in high latitudes in response to decreasing emissions. Delivery of contaminants to high latitudes is predicted to be more efficient than previously suggested. The results suggest furthermore that the effectiveness of emission control measures may significantly vary among substances: trends of decline in abiotic environmental media do not only vary with latitude (slow in high latitudes), but do also show longitudinal gradients

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.

Superfluid-ferromagnet-superfluid junction and the {pi} phase in a superfluid Fermi gas

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

Kashimura, Takashi; Tsuchiya, Shunji; CREST

2010-09-15

We investigate the possibility of a superfluid-ferromagnet-superfluid (SFS) junction in a superfluid Fermi gas. To examine this possibility in a simple manner, we consider an attractive Hubbard model at T=0 within the mean-field theory. When a potential barrier is embedded in a superfluid Fermi gas with population imbalance (N{sub {up_arrow}}>N{sub {down_arrow}}, where N{sub {sigma}} is the number of atoms with pseudospin {sigma}= {up_arrow}, {down_arrow}), this barrier is shown to be magnetized in the sense that excess {up_arrow}-spin atoms are localized around it. The resulting superfluid Fermi gas is spatially divided into two by this ferromagnet, so that one obtains amore » junction similar to the superconductor-ferromagnet-superconductor junction discussed in superconductivity. Indeed, we show that the so-called {pi} phase, which is a typical phenomenon in the SFS junction, is realized, where the superfluid order parameter changes its sign across the junction. Our results would be useful for the study of magnetic effects on fermion superfluidity using an ultracold Fermi gas.« less

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].

All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

PubMed Central

Mohammadiarani, Hossein; Vashisth, Harish

2016-01-01

The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID:27379020

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.

Nanodroplet impact onto solid platinum surface: Spreading and bouncing

NASA Astrophysics Data System (ADS)

Lussier, Daniel; Ventikos, Yiannis

2009-11-01

The impact of droplets onto solid surfaces is found in a huge variety of natural and technological applications, from rain drops splashing on the pavement, to material manufacturing by molten droplet deposition. Taking inspiration from existing microfluidic technologies (i.e. lab-on-chip), there is increasing interest in the use of nanodroplets (D < 100 nm) for a number of applications such as drug delivery and semiconductor device manufacturing. However, as the size of the droplet is reduced into the nanoscale, the direct use of previously obtained macroscopic results is not guaranteed. At the nanoscale, important effects due to the molecular nature of the fluid, thermal fluctuations and reduced dimensionality can play a critical role in determining system dynamics. In this paper we present the results of large-scale, fully atomistic, three-dimensional molecular dynamics (MD) simulation of an argon nanodroplet (D = 18 nm, 54 000 atoms) impact onto a solid platinum surface, using the LAMMPS software package. The fluid argon is modeled using the well-known Lennard-Jones (LJ) potential, while the embedded-atom model (EAM) potential is used for the solid platinum. By varying both the impact velocities (10-1000 m/s) and the wettability of the solid surface a wide range of impact behaviors is observed, from smooth spreading, to bouncing recoil, pointing towards a wide array of potential applications.

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

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

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

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.

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

Multi-scale modeling of diffusion-controlled reactions in polymers: renormalisation of reactivity parameters.

PubMed

Everaers, Ralf; Rosa, Angelo

2012-01-07

The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we show that the adjustments are independent of chain length. As a consequence, it is possible to match reactions times between descriptions with different resolution for relatively short reference chains and to use the coarse-grained model to make quantitative predictions for longer chains. We illustrate our results by a detailed discussion of the classical problem of chain cyclization in the Rouse model, which offers the simplest example of a multi-scale descriptions, if we consider differently discretized Rouse models for the same physical system. Moreover, we are able to explore different combinations of compact and non-compact diffusion in the local and large-scale dynamics by varying the embedding dimension.

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.

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

PubMed

Surles, M C; Richardson, J S; Richardson, D C; Brooks, F P

1994-02-01

We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions. Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrange-multiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded beta-ribbon into an approximate beta-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and (2) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed.

Nano-Indentation of Aluminium Reinforced Metallic Glass Composites: A Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

Yadav, D.; Gupta, P.; Yedla, N.

2018-03-01

Molecular dynamics (MD) simulations are performed for nanoindentation on metal (Al)-metallic glass (Cu50Zr50) reinforced composites to investigate the mechanical properties and the effects of volume percentage on behavior of the load-displacement curves. The interaction among Al-Cu-Zr is modelled using a EAM (Embedded Atom Method) potential. Simulation box size of 100 Å (x) × 100 Å (y) × 100 Å (z) is modelled for investigating the properties of the sintered models by altering the volume percentage on the scale of 5%-20%. Nanoindentation is done along y-direction with a spherical diamond indenter at temperature of 300 K with constant indentation speed of 100 m/s. NVT ensemble is used with a timestep of 0.002 ps. Investigations on the effect of volume percentage show that as volume percentage of Metallic Glass (MG) increases, the corresponding Load required to penetrate inside the sample also increases. As a result of this Hardness also increase as volume percentage varies from 5% to 20%.

SchNet - A deep learning architecture for molecules and materials

NASA Astrophysics Data System (ADS)

Schütt, K. T.; Sauceda, H. E.; Kindermans, P.-J.; Tkatchenko, A.; Müller, K.-R.

2018-06-01

Deep learning has led to a paradigm shift in artificial intelligence, including web, text, and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning, in general, and deep learning, in particular, are ideally suitable for representing quantum-mechanical interactions, enabling us to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for molecules and materials, where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study on the quantum-mechanical properties of C20-fullerene that would have been infeasible with regular ab initio molecular dynamics.

Grain boundary phase transformations in PtAu and relevance to thermal stabilization of bulk nanocrystalline metals

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

O’Brien, C. J.; Barr, C. M.; Price, P. M.

There has recently been a great deal of interest in employing immiscible solutes to stabilize nanocrystalline microstructures. Existing modeling efforts largely rely on mesoscale Monte Carlo approaches that employ a simplified model of the microstructure and result in highly homogeneous segregation to grain boundaries. However, there is ample evidence from experimental and modeling studies that demonstrates segregation to grain boundaries is highly non-uniform and sensitive to boundary character. This work employs a realistic nanocrystalline microstructure with experimentally relevant global solute concentrations to illustrate inhomogeneous boundary segregation. Furthermore, experiments quantifying segregation in thin films are reported that corroborate the prediction thatmore » grain boundary segregation is highly inhomogeneous. In addition to grain boundary structure modifying the degree of segregation, the existence of a phase transformation between low and high solute content grain boundaries is predicted. In order to conduct this study, new embedded atom method interatomic potentials are developed for Pt, Au, and the PtAu binary alloy.« less

Grain boundary phase transformations in PtAu and relevance to thermal stabilization of bulk nanocrystalline metals

DOE PAGES

O’Brien, C. J.; Barr, C. M.; Price, P. M.; ...

2017-10-31

There has recently been a great deal of interest in employing immiscible solutes to stabilize nanocrystalline microstructures. Existing modeling efforts largely rely on mesoscale Monte Carlo approaches that employ a simplified model of the microstructure and result in highly homogeneous segregation to grain boundaries. However, there is ample evidence from experimental and modeling studies that demonstrates segregation to grain boundaries is highly non-uniform and sensitive to boundary character. This work employs a realistic nanocrystalline microstructure with experimentally relevant global solute concentrations to illustrate inhomogeneous boundary segregation. Furthermore, experiments quantifying segregation in thin films are reported that corroborate the prediction thatmore » grain boundary segregation is highly inhomogeneous. In addition to grain boundary structure modifying the degree of segregation, the existence of a phase transformation between low and high solute content grain boundaries is predicted. In order to conduct this study, new embedded atom method interatomic potentials are developed for Pt, Au, and the PtAu binary alloy.« less

Spatial network surrogates for disentangling complex system structure from spatial embedding of nodes

NASA Astrophysics Data System (ADS)

Wiedermann, Marc; Donges, Jonathan F.; Kurths, Jürgen; Donner, Reik V.

2016-04-01

Networks with nodes embedded in a metric space have gained increasing interest in recent years. The effects of spatial embedding on the networks' structural characteristics, however, are rarely taken into account when studying their macroscopic properties. Here, we propose a hierarchy of null models to generate random surrogates from a given spatially embedded network that can preserve certain global and local statistics associated with the nodes' embedding in a metric space. Comparing the original network's and the resulting surrogates' global characteristics allows one to quantify to what extent these characteristics are already predetermined by the spatial embedding of the nodes and links. We apply our framework to various real-world spatial networks and show that the proposed models capture macroscopic properties of the networks under study much better than standard random network models that do not account for the nodes' spatial embedding. Depending on the actual performance of the proposed null models, the networks are categorized into different classes. Since many real-world complex networks are in fact spatial networks, the proposed approach is relevant for disentangling the underlying complex system structure from spatial embedding of nodes in many fields, ranging from social systems over infrastructure and neurophysiology to climatology.

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.

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

Majorana spin in magnetic atomic chain systems

NASA Astrophysics Data System (ADS)

Li, Jian; Jeon, Sangjun; Xie, Yonglong; Yazdani, Ali; Bernevig, B. Andrei

2018-03-01

In this paper, we establish that Majorana zero modes emerging from a topological band structure of a chain of magnetic atoms embedded in a superconductor can be distinguished from trivial localized zero energy states that may accidentally form in this system using spin-resolved measurements. To demonstrate this key Majorana diagnostics, we study the spin composition of magnetic impurity induced in-gap Shiba states in a superconductor using a hybrid model. By examining the spin and spectral densities in the context of the Bogoliubov-de Gennes (BdG) particle-hole symmetry, we derive a sum rule that relates the spin densities of localized Shiba states with those in the normal state without superconductivity. Extending our investigations to a ferromagnetic chain of magnetic impurities, we identify key features of the spin properties of the extended Shiba state bands, as well as those associated with a localized Majorana end mode when the effect of spin-orbit interaction is included. We then formulate a phenomenological theory for the measurement of the local spin densities with spin-polarized scanning tunneling microscopy (STM) techniques. By combining the calculated spin densities and the measurement theory, we show that spin-polarized STM measurements can reveal a sharp contrast in spin polarization between an accidental-zero-energy trivial Shiba state and a Majorana zero mode in a topological superconducting phase in atomic chains. We further confirm our results with numerical simulations that address generic parameter settings.

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.

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.

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.

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.

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

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

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.

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.

Hamiltonian vs Lagrangian Embedding of a Massive Spin-One Theory Involving Two-Form Field

NASA Astrophysics Data System (ADS)

Harikumar, E.; Sivakumar, M.

We consider the Hamiltonian and Lagrangian embedding of a first-order, massive spin-one, gauge noninvariant theory involving antisymmetric tensor field. We apply the BFV-BRST generalized canonical approach to convert the model to a first class system and construct nilpotent BFV-BRST charge and a unitarizing Hamiltonian. The canonical analysis of the Stückelberg formulation of this model is presented. We bring out the contrasting feature in the constraint structure, specifically with respect to the reducibility aspect, of the Hamiltonian and the Lagrangian embedded model. We show that to obtain manifestly covariant Stückelberg Lagrangian from the BFV embedded Hamiltonian, phase space has to be further enlarged and show how the reducible gauge structure emerges in the embedded model.

Privacy-Preserving Predictive Modeling: Harmonization of Contextual Embeddings From Different Sources.

PubMed

Huang, Yingxiang; Lee, Junghye; Wang, Shuang; Sun, Jimeng; Liu, Hongfang; Jiang, Xiaoqian

2018-05-16

Data sharing has been a big challenge in biomedical informatics because of privacy concerns. Contextual embedding models have demonstrated a very strong representative capability to describe medical concepts (and their context), and they have shown promise as an alternative way to support deep-learning applications without the need to disclose original data. However, contextual embedding models acquired from individual hospitals cannot be directly combined because their embedding spaces are different, and naive pooling renders combined embeddings useless. The aim of this study was to present a novel approach to address these issues and to promote sharing representation without sharing data. Without sacrificing privacy, we also aimed to build a global model from representations learned from local private data and synchronize information from multiple sources. We propose a methodology that harmonizes different local contextual embeddings into a global model. We used Word2Vec to generate contextual embeddings from each source and Procrustes to fuse different vector models into one common space by using a list of corresponding pairs as anchor points. We performed prediction analysis with harmonized embeddings. We used sequential medical events extracted from the Medical Information Mart for Intensive Care III database to evaluate the proposed methodology in predicting the next likely diagnosis of a new patient using either structured data or unstructured data. Under different experimental scenarios, we confirmed that the global model built from harmonized local models achieves a more accurate prediction than local models and global models built from naive pooling. Such aggregation of local models using our unique harmonization can serve as the proxy for a global model, combining information from a wide range of institutions and information sources. It allows information unique to a certain hospital to become available to other sites, increasing the fluidity of information flow in health care. ©Yingxiang Huang, Junghye Lee, Shuang Wang, Jimeng Sun, Hongfang Liu, Xiaoqian Jiang. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 16.05.2018.

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

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.

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.

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

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

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

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.

Atmospheric NLTE models for the spectroscopic analysis of blue stars with winds. III. X-ray emission from wind-embedded shocks

NASA Astrophysics Data System (ADS)

Carneiro, L. P.; Puls, J.; Sundqvist, J. O.; Hoffmann, T. L.

2016-05-01

Context. Extreme ultraviolet (EUV) and X-ray radiation emitted from wind-embedded shocks in hot, massive stars can affect the ionization balance in their outer atmospheres and can be the mechanism responsible for producing highly ionized atomic species detected in stellar wind UV spectra. Aims: To allow for these processes in the context of spectral analysis, we have implemented the emission from wind-embedded shocks and related physics into our unified, NLTE model atmosphere/spectrum synthesis code FASTWIND. Methods: The shock structure and corresponding emission is calculated as a function of user-supplied parameters (volume filling factor, radial stratification of shock strength, and radial onset of emission). We account for a temperature and density stratification inside the postshock cooling zones, calculated for radiative and adiabatic cooling in the inner and outer wind, respectively. The high-energy absorption of the cool wind is considered by adding important K-shell opacities, and corresponding Auger ionization rates have been included in the NLTE network. To test our implementation and to check the resulting effects, we calculated a comprehensive model grid with a variety of X-ray emission parameters. Results: We tested and verified our implementation carefully against corresponding results from various alternative model atmosphere codes, and studied the effects from shock emission for important ions from He, C, N, O, Si, and P. Surprisingly, dielectronic recombination turned out to play an essential role for the ionization balance of O iv/O v (particularly in dwarfs with Teff~ 45 000 K). Finally, we investigated the frequency dependence and radial behavior of the mass absorption coefficient, κν(r), which is important in the context of X-ray line formation in massive star winds. Conclusions: In almost all of the cases considered, direct ionization is of major influence because of the enhanced EUV radiation field, and Auger ionization only affects N vi and O vi significantly. The approximation of a radially constant κν is justified for r ≳ 1.2 R∗ and λ ≲ 18 Å and also for many models at longer wavelengths. To estimate the actual value of this quantity, however, the He II opacities need to be calculated from detailed NLTE modeling, at least for wavelengths longer than 18 to 20 Å, and information on the individual CNO abundances has to be present.

'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

Hammerstein system represention of financial volatility processes

NASA Astrophysics Data System (ADS)

Capobianco, E.

2002-05-01

We show new modeling aspects of stock return volatility processes, by first representing them through Hammerstein Systems, and by then approximating the observed and transformed dynamics with wavelet-based atomic dictionaries. We thus propose an hybrid statistical methodology for volatility approximation and non-parametric estimation, and aim to use the information embedded in a bank of volatility sources obtained by decomposing the observed signal with multiresolution techniques. Scale dependent information refers both to market activity inherent to different temporally aggregated trading horizons, and to a variable degree of sparsity in representing the signal. A decomposition of the expansion coefficients in least dependent coordinates is then implemented through Independent Component Analysis. Based on the described steps, the features of volatility can be more effectively detected through global and greedy algorithms.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Equivalent crystal theory of alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John

1991-01-01

Equivalent Crystal Theory (ECT) is a new, semi-empirical approach to calculating the energetics of a solid with defects. The theory has successfully reproduced surface energies in metals and semiconductors. The theory of binary alloys to date, both with first-principles and semi-empirical models, has not been very successful in predicting the energetics of alloys. This procedure is used to predict the heats of formation, cohesive energy, and lattice parameter of binary alloys of Cu, Ni, Al, Ag, Au, Pd, and Pt as functions of composition. The procedure accurately reproduces the heats of formation versus composition curves for a variety of binary alloys. The results are then compared with other approaches such as the embedded atom and lattice parameters of alloys from pure metal properties more accurately than Vegard's law is presented.

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.

Two diverse models of embedding class one

NASA Astrophysics Data System (ADS)

Kuhfittig, Peter K. F.

2018-05-01

Embedding theorems have continued to be a topic of interest in the general theory of relativity since these help connect the classical theory to higher-dimensional manifolds. This paper deals with spacetimes of embedding class one, i.e., spacetimes that can be embedded in a five-dimensional flat spacetime. These ideas are applied to two diverse models, a complete solution for a charged wormhole admitting a one-parameter group of conformal motions and a new model to explain the flat rotation curves in spiral galaxies without the need for dark matter.

Fractionation and current time trends of PCB congeners: evolvement of distributions 1950-2010 studied using a global atmosphere-ocean general circulation model

NASA Astrophysics Data System (ADS)

Lammel, G.; Stemmler, I.

2012-08-01

PCBs are ubiquitous environmental pollutants expected to decline in abiotic environmental media in response to decreasing primary emissions since the 1970s. A coupled atmosphere-ocean general circulation model with embedded dynamic sub-models for atmospheric aerosols and the marine biogeochemistry and air-surface exchange processes with soils, vegetation and the cryosphere is used to study the transport and fate of four PCB congeners covering a range of 3-7 chlorine atoms. The change of the geographic distribution of the PCB mixture reflects the sources and sinks' evolvement over time. Globally, secondary emissions (re-volatilisation from surfaces) are on the long term increasingly gaining importance over primary emissions. Secondary emissions are most important for the congeners with 5-6 chlorine atoms. Correspondingly, the levels of these congeners are predicted to decrease slowest. Changes in congener mixture composition (fractionation) are characterized both geographically and temporally. In high latitudes enrichment of the lighter, less persistent congeners and more delayed decreasing levels in response to decreasing emissions are found. The delivery of the contaminants to high latitudes is predicted to be more efficient than previously suggested. The results suggest furthermore that the effectiveness of emission control measures may significantly vary among substances. The trends of decline of organic contaminant levels in the abiotic environmental media do not only vary with latitude (slow in high latitudes), but do also show longitudinal gradients.

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.

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.

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.

Mechanosensitive Ion Channels in Bacteria: Functional Domains and Mechanisms of Gating

NASA Technical Reports Server (NTRS)

Sukharev, Sergei

2003-01-01

The past funding period was productive for the group. The progress in the mechanosensitive channel field was critically affected in the end of 1998 by the solution of the crystal structure of the mycobacterial homolog of MscL by our colleagues from Caltech. Having the structure of TbMscL in the closed state, we developed a detailed homology model of EcoMscL, and related the structural model with the wealth of functional phenomenology available for the E. coli version of the channel (EcoMscL). The biophysical properties of the open MscL helped to model the open conformation and infer the pathway for the entire gating transition. The following experiments provided strong support to the atomic model of the gating process, and allowed to make further predictions. The work has advanced our understanding of tension-driven conformational transitions in membrane-embedded mechanosensory proteins, determine major energetic contributions and set the stage for further exploration of the whole family of mechanosensitive channels. The results have been published in seven experimental and theoretical papers, with three other papers currently in press or in preparation.

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

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

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

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Fernández-Perea, Ricardo; Madzharova, Fani

2016-06-28

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet thismore » challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He–Mg pair potentials is also presented, as an improvement of the approximation using isolated He–Mg pairs.« less

Structural relaxation in a binary metallic melt: Molecular dynamics computer simulation of undercooled Al80Ni20

NASA Astrophysics Data System (ADS)

Das, Subir K.; Horbach, Jürgen; Voigtmann, Thomas

2008-08-01

Molecular dynamics computer simulations are performed to study structure and structural relaxation in the glassforming metallic alloy Al80Ni20 . The interactions between the particles are modeled by an effective potential of the embedded atom type. Our model of Al80Ni20 exhibits chemical short-range order (CSRO) that is reflected in a broad prepeak around a wave number of 1.8Å-1 in the partial static structure factor for the Ni-Ni correlations. The CSRO is due to the preference of Ni atoms to have Al rather than Ni atoms as nearest neighbors. By analyzing incoherent and coherent intermediate scattering functions as well as self-diffusion constants and shear viscosity, we discuss how the chemical ordering is reflected in the dynamics of the deeply undercooled melt. The q dependence of the α relaxation time as well as the Debye-Waller factor for the Al-Al correlations show oscillations at the location of the prepeak in the partial static structure factor for the Ni-Ni correlations. The latter feature of the Debye-Waller factor is well reproduced by a calculation in the framework of the mode coupling theory (MCT) of the glass transition, using the partial static structure factors from the simulation as input. We also check the validity of the Stokes-Einstein-Sutherland formula that relates the self-diffusion coefficients with the shear viscosity. We show that it breaks down already far above the mode coupling critical temperature Tc . The failure of the Stokes-Einstein-Sutherland relation is not related to the specific chemical ordering in Al80Ni20 .

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

NASA Astrophysics Data System (ADS)

de Lara-Castells, María Pilar; Fernández-Perea, Ricardo; Madzharova, Fani; Voloshina, Elena

2016-06-01

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He-Mg pair potentials is also presented, as an improvement of the approximation using isolated He-Mg pairs.

Prediction of folding preference of 10 kDa silk-like proteins using a Lego approach and ab initio calculations.

PubMed

Pohl, Gábor; Beke, Tamás; Borbély, János; Perczel, András

2006-11-15

Because of their great flexibility and strength resistance, both spider silks and silkworm silks are of increasing scientific and commercial interest. Despite numerous spectroscopic and theoretical studies, several structural properties at the atomic level have yet to be identified. The present theoretical investigation focuses on these issues by studying three silk-like model peptides: (AG)(64), [(AG)(4)EG](16), and [(AG)(4)PEG](16), using a Lego-type approach to construct these polypeptides. On the basis of these examples it is shown that thermoneutral isodesmic reactions and ab initio calculations provide a capable method to investigate structural properties of repetitive polypeptides. The most probable overall fold schema of these molecules with respect to the type of embedded hairpin structures were determined at the ab initio level of theory (RHF/6-311++G(d,p)//RHF/3-21G). Further on, analysis is carried out on the possible hairpin and turn regions and on their effect on the global fold. In the case of the (AG)(64) model peptide, the optimal beta-sheet/turn ratio was also determined, which provided good support for experimental observations. In addition, lateral shearing of a hairpin "folding unit" was investigated at the quantum chemical level to explain the mechanical properties of spider silk. The unique mechanical characteristics of silk bio-compounds are now investigated at the atomic level.

Comparison of the corrosion of fasteners embedded in wood measured in outdoor exposure with the predictions from a combined hygrothermal-corrosion model

Treesearch

Samuel L. Zelinka; Samuel V. Glass; Charles R. Boardman; Dominique Derome

2016-01-01

This paper examines the accuracy of a recently developed hygrothermal-corrosion model which predictsthe corrosion of fasteners embedded in wood by comparing the results of the model to a one year fieldtest. Steel and galvanized steel fasteners were embedded into untreated and preservative treated woodand exposed outdoors while weather data were collected. Qualitatively...

A national facility for biological cryo-electron microscopy

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

Saibil, Helen R., E-mail: h.saibil@mail.cryst.bbk.ac.uk; Grünewald, Kay; Stuart, David I.

2015-01-01

This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron. Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided ofmore » the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.« less

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.

Experience, Challenges, and Opportunities of Being Fully Embedded in a User Group.

PubMed

Wu, Lin; Thornton, Joel

2017-01-01

Embedded librarian models can assume different forms and levels, depending on patron needs and a library's choice of delivery services. An academic health sciences library decided to enhance its service delivery model by integrating a librarian into the College of Pharmacy, approximately 250 miles away from the main library. This article describes the embedded librarian's first-year experience, challenges, and opportunities working as a library faculty in the college. The comparison of one-year recorded statistics on preembedded and postembedded activities demonstrated the effectiveness and impact of such an embedded librarian model.

Bringing nanomagnetism to the mesoscale with artificial amorphous structures

NASA Astrophysics Data System (ADS)

Muscas, G.; Brucas, R.; Jönsson, P. E.

2018-05-01

In the quest for materials with emergent or improved properties, an effective route is to create artificial superstructures. Novel properties emerge from the coupling between the phases, but the strength of this coupling depends on the quality of the interfaces. Atomic control of crystalline interfaces is notoriously complicated and to elude that obstacle, we suggest here an all-amorphous design. Starting from a model amorphous iron alloy, we locally tune the magnetic behavior by creating boron-doped regions by means of ion implantation through a lithographic mask. This process preserves the amorphous environment, creating a non-topographic magnetic superstructure with smooth interfaces and no structural discontinuities. The absence of inhomogeneities acting as pinning centers for the magnetization reversal is demonstrated by the formation of magnetic vortexes for ferromagnetic disks as large as 20 µm in diameter embedded within a paramagnetic matrix. Rigid exchange coupling between two amorphous ferromagnetic phases in a microstructured sample is evidenced by an investigation involving first-order reversal curves. The sample consists of a soft matrix with embedded elements constituting a hard phase where the anisotropy originates from an elongated shape of the elements. We provide an intuitive explanation for the micrometer-range exchange coupling mechanism and discuss how to tailor the properties of all-amorphous superstructures.

Simultaneous electrical and optical study of spoke rotation, merging and splitting in HiPIMS plasma

NASA Astrophysics Data System (ADS)

Klein, P.; Lockwood Estrin, F.; Hnilica, J.; Vašina, P.; Bradley, J. W.

2017-01-01

To gain more information on the temporal and spatial behaviour of self-organized spoke structures in HiPIMS plasmas, a correlation between the broadband optical image of an individual spoke (taken over 200 ns) and the current it delivers to the target has been made for a range of magnetron operating conditions. As a spoke passes over a set of embedded probes in the niobium cathode target, a distinct modulation in the local current density is observed, (typically up to twice the average value), matching very well the radially integrated optical emission intensities (obtained remotely with an ICCD camera). The dual diagnostic system allows the merging and splitting of a set of spokes to be studied as they rotate. It is observed that in the merger of two spokes, the trailing spoke maintains its velocity while the leading spoke either decreases its velocity or increases its azimuthal length. In the spoke splitting process, the total charge collected by an embedded probe is conserved. A simple phenomenological model is developed that relates the spoke mode number m to the spoke dimensions, spoke velocity and gas atom velocity. The results are discussed in the context of the observations of spoke dynamics made by Hecimovic et al (2015 Plasma Sources Sci. Technol. 24 045005)

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

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

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.

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.

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.

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.

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.

Time-Centric Models For Designing Embedded Cyber-physical Systems

DTIC Science & Technology

2009-10-09

Time -centric Models For Designing Embedded Cyber- physical Systems John C. Eidson Edward A. Lee Slobodan Matic Sanjit A. Seshia Jia Zou Electrical... Time -centric Models For Designing Embedded Cyber-physical Systems ∗ John C. Eidson , Edward A. Lee, Slobodan Matic, Sanjit A. Seshia, Jia Zou...implementations, such a uniform notion of time cannot be precisely realized. Time triggered networks [10] and time synchronization [9] can be used to

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.

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

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.

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.

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.

Cooling rate dependence of simulated Cu{sub 64.5}Zr{sub 35.5} metallic glass structure

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

Ryltsev, R. E.; Ural Federal University, 19 Mira Str., 620002 Ekaterinburg; L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 2 Kosygina Str., 119334 Moscow

Using molecular dynamics simulations with embedded atom model potential, we study structural evolution of Cu{sub 64.5}Zr{sub 35.5} alloy during the cooling in a wide range of cooling rates γ ∈ (1.5 ⋅ 10{sup 9}, 10{sup 13}) K/s. Investigating short- and medium-range orders, we show that the structure of Cu{sub 64.5}Zr{sub 35.5} metallic glass essentially depends on cooling rate. In particular, a decrease of the cooling rate leads to an increase of abundances of both the icosahedral-like clusters and Frank-Kasper Z16 polyhedra. The amounts of these clusters in the glassy state drastically increase at the γ{sub min} = 1.5 ⋅ 10{supmore » 9} K/s. Analysing the structure of the glass at γ{sub min}, we observe the formation of nano-sized crystalline grain of Cu{sub 2}Zr intermetallic compound with the structure of Cu{sub 2}Mg Laves phase. The structure of this compound is isomorphous with that for Cu{sub 5}Zr intermetallic compound. Both crystal lattices consist of two types of clusters: Cu-centered 13-atom icosahedral-like cluster and Zr-centered 17-atom Frank-Kasper polyhedron Z16. That suggests the same structural motifs for the metallic glass and intermetallic compounds of Cu–Zr system and explains the drastic increase of the abundances of these clusters observed at γ{sub min}.« less

Co Modeling and Co Synthesis of Safety Critical Multi threaded Embedded Software for Multi Core Embedded Platforms

DTIC Science & Technology

2017-03-20

computation, Prime Implicates, Boolean Abstraction, real- time embedded software, software synthesis, correct by construction software design , model...types for time -dependent data-flow networks". J.-P. Talpin, P. Jouvelot, S. Shukla. ACM-IEEE Conference on Methods and Models for System Design ...information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing   data sources, gathering and

Assessing frequency-dependent site polarisabilities in linear response polarisable embedding

NASA Astrophysics Data System (ADS)

Nørby, Morten S.; Vahtras, Olav; Norman, Patrick; Kongsted, Jacob

2017-01-01

In this paper, we discuss the impact of using a frequency-dependent embedding potential in quantum chemical embedding calculations of response properties. We show that the introduction of a frequency-dependent embedding potential leads to further model complications upon solving the central equations defining specific molecular properties. On the other hand, we also show from a numerical point of view that the consequences of using such a frequency-dependent embedding potential is almost negligible. Thus, for the kind of systems and processes studied in this paper the general recommendation is to use frequency-independent embedding potentials since this leads to less complicated model issues. However, larger effects are expected if the absorption bands of the environment are closer to that of the region treated using quantum mechanics.

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.

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.

A Technology-Enhanced Unit of Modeling Static Electricity: Integrating scientific explanations and everyday observations

NASA Astrophysics Data System (ADS)

Shen, Ji; Linn, Marcia C.

2011-08-01

What trajectories do students follow as they connect their observations of electrostatic phenomena to atomic-level visualizations? We designed an electrostatics unit, using the knowledge integration framework to help students link observations and scientific ideas. We analyze how learners integrate ideas about charges, charged particles, energy, and observable events. We compare learning enactments in a typical school and a magnet school in the USA. We use pre-tests, post-tests, embedded notes, and delayed post-tests to capture the trajectories of students' knowledge integration. We analyze how visualizations help students grapple with abstract electrostatics concepts such as induction. We find that overall students gain more sophisticated ideas. They can interpret dynamic, interactive visualizations, and connect charge- and particle-based explanations to interpret observable events. Students continue to have difficulty in applying the energy-based explanation.

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

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.

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.

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

Logic flowgraph methodology - A tool for modeling embedded systems

NASA Technical Reports Server (NTRS)

Muthukumar, C. T.; Guarro, S. B.; Apostolakis, G. E.

1991-01-01

The logic flowgraph methodology (LFM), a method for modeling hardware in terms of its process parameters, has been extended to form an analytical tool for the analysis of integrated (hardware/software) embedded systems. In the software part of a given embedded system model, timing and the control flow among different software components are modeled by augmenting LFM with modified Petrinet structures. The objective of the use of such an augmented LFM model is to uncover possible errors and the potential for unanticipated software/hardware interactions. This is done by backtracking through the augmented LFM mode according to established procedures which allow the semiautomated construction of fault trees for any chosen state of the embedded system (top event). These fault trees, in turn, produce the possible combinations of lower-level states (events) that may lead to the top event.

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

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.

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.

Fracture Mechanics Method for Word Embedding Generation of Neural Probabilistic Linguistic Model.

PubMed

Bi, Size; Liang, Xiao; Huang, Ting-Lei

2016-01-01

Word embedding, a lexical vector representation generated via the neural linguistic model (NLM), is empirically demonstrated to be appropriate for improvement of the performance of traditional language model. However, the supreme dimensionality that is inherent in NLM contributes to the problems of hyperparameters and long-time training in modeling. Here, we propose a force-directed method to improve such problems for simplifying the generation of word embedding. In this framework, each word is assumed as a point in the real world; thus it can approximately simulate the physical movement following certain mechanics. To simulate the variation of meaning in phrases, we use the fracture mechanics to do the formation and breakdown of meaning combined by a 2-gram word group. With the experiments on the natural linguistic tasks of part-of-speech tagging, named entity recognition and semantic role labeling, the result demonstrated that the 2-dimensional word embedding can rival the word embeddings generated by classic NLMs, in terms of accuracy, recall, and text visualization.

Embedded-explicit emergent literacy intervention I: Background and description of approach.

PubMed

Justice, Laura M; Kaderavek, Joan N

2004-07-01

This article, the first of a two-part series, provides background information and a general description of an emergent literacy intervention model for at-risk preschoolers and kindergartners. The embedded-explicit intervention model emphasizes the dual importance of providing young children with socially embedded opportunities for meaningful, naturalistic literacy experiences throughout the day, in addition to regular structured therapeutic interactions that explicitly target critical emergent literacy goals. The role of the speech-language pathologist (SLP) in the embedded-explicit model encompasses both indirect and direct service delivery: The SLP consults and collaborates with teachers and parents to ensure the highest quality and quantity of socially embedded literacy-focused experiences and serves as a direct provider of explicit interventions using structured curricula and/or lesson plans. The goal of this integrated model is to provide comprehensive emergent literacy interventions across a spectrum of early literacy skills to ensure the successful transition of at-risk children from prereaders to readers.

Embedded Librarians: Just-in-Time or Just-in-Case? A Research Study

ERIC Educational Resources Information Center

Heathcock, Kristin

2015-01-01

Embedded librarians in online courses provide a wealth of service and information to students. Though students indicate that these services are valuable, the librarians providing embedded services frequently note that these projects are very time consuming. This study examines the provision of a less time-intensive model of embedded librarianship…

Nested Interrupt Analysis of Low Cost and High Performance Embedded Systems Using GSPN Framework

NASA Astrophysics Data System (ADS)

Lin, Cheng-Min

Interrupt service routines are a key technology for embedded systems. In this paper, we introduce the standard approach for using Generalized Stochastic Petri Nets (GSPNs) as a high-level model for generating CTMC Continuous-Time Markov Chains (CTMCs) and then use Markov Reward Models (MRMs) to compute the performance for embedded systems. This framework is employed to analyze two embedded controllers with low cost and high performance, ARM7 and Cortex-M3. Cortex-M3 is designed with a tail-chaining mechanism to improve the performance of ARM7 when a nested interrupt occurs on an embedded controller. The Platform Independent Petri net Editor 2 (PIPE2) tool is used to model and evaluate the controllers in terms of power consumption and interrupt overhead performance. Using numerical results, in spite of the power consumption or interrupt overhead, Cortex-M3 performs better than ARM7.

Reliability Analysis and Optimal Release Problem Considering Maintenance Time of Software Components for an Embedded OSS Porting Phase

NASA Astrophysics Data System (ADS)

Tamura, Yoshinobu; Yamada, Shigeru

OSS (open source software) systems which serve as key components of critical infrastructures in our social life are still ever-expanding now. Especially, embedded OSS systems have been gaining a lot of attention in the embedded system area, i.e., Android, BusyBox, TRON, etc. However, the poor handling of quality problem and customer support prohibit the progress of embedded OSS. Also, it is difficult for developers to assess the reliability and portability of embedded OSS on a single-board computer. In this paper, we propose a method of software reliability assessment based on flexible hazard rates for the embedded OSS. Also, we analyze actual data of software failure-occurrence time-intervals to show numerical examples of software reliability assessment for the embedded OSS. Moreover, we compare the proposed hazard rate model for the embedded OSS with the typical conventional hazard rate models by using the comparison criteria of goodness-of-fit. Furthermore, we discuss the optimal software release problem for the porting-phase based on the total expected software maintenance cost.

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

An embedded multi-core parallel model for real-time stereo imaging

NASA Astrophysics Data System (ADS)

He, Wenjing; Hu, Jian; Niu, Jingyu; Li, Chuanrong; Liu, Guangyu

2018-04-01

The real-time processing based on embedded system will enhance the application capability of stereo imaging for LiDAR and hyperspectral sensor. The task partitioning and scheduling strategies for embedded multiprocessor system starts relatively late, compared with that for PC computer. In this paper, aimed at embedded multi-core processing platform, a parallel model for stereo imaging is studied and verified. After analyzing the computing amount, throughout capacity and buffering requirements, a two-stage pipeline parallel model based on message transmission is established. This model can be applied to fast stereo imaging for airborne sensors with various characteristics. To demonstrate the feasibility and effectiveness of the parallel model, a parallel software was designed using test flight data, based on the 8-core DSP processor TMS320C6678. The results indicate that the design performed well in workload distribution and had a speed-up ratio up to 6.4.

The interpretation of polycrystalline coherent inelastic neutron scattering from aluminium

PubMed Central

Roach, Daniel L.; Ross, D. Keith; Gale, Julian D.; Taylor, Jon W.

2013-01-01

A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the (Q, ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available. PMID:24282332

Structural and functional properties of spatially embedded scale-free networks.

PubMed

Emmerich, Thorsten; Bunde, Armin; Havlin, Shlomo

2014-06-01

Scale-free networks have been studied mostly as non-spatially embedded systems. However, in many realistic cases, they are spatially embedded and these constraints should be considered. Here, we study the structural and functional properties of a model of scale-free (SF) spatially embedded networks. In our model, both the degree and the length of links follow power law distributions as found in many real networks. We show that not all SF networks can be embedded in space and that the largest degree of a node in the network is usually smaller than in nonembedded SF networks. Moreover, the spatial constraints (each node has only few neighboring nodes) introduce degree-degree anticorrelations (disassortativity) since two high degree nodes cannot stay close in space. We also find significant effects of space embedding on the hopping distances (chemical distance) and the vulnerability of the networks.

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.

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.

eXtended CASA Line Analysis Software Suite (XCLASS)

NASA Astrophysics Data System (ADS)

Möller, T.; Endres, C.; Schilke, P.

2017-02-01

The eXtended CASA Line Analysis Software Suite (XCLASS) is a toolbox for the Common Astronomy Software Applications package (CASA) containing new functions for modeling interferometric and single dish data. Among the tools is the myXCLASS program which calculates synthetic spectra by solving the radiative transfer equation for an isothermal object in one dimension, whereas the finite source size and dust attenuation are considered as well. Molecular data required by the myXCLASS program are taken from an embedded SQLite3 database containing entries from the Cologne Database for Molecular Spectroscopy (CDMS) and JPL using the Virtual Atomic and Molecular Data Center (VAMDC) portal. Additionally, the toolbox provides an interface for the model optimizer package Modeling and Analysis Generic Interface for eXternal numerical codes (MAGIX), which helps to find the best description of observational data using myXCLASS (or another external model program), that is, finding the parameter set that most closely reproduces the data. http://www.astro.uni-koeln.de/projects/schilke/myXCLASSInterface A copy of the code is available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/598/A7

Symbiotic stars

NASA Technical Reports Server (NTRS)

Kafatos, M.; Michalitsianos, A. G.

1984-01-01

The physical characteristics of symbiotic star systems are discussed, based on a review of recent observational data. A model of a symbiotic star system is presented which illustrates how a cool red-giant star is embedded in a nebula whose atoms are ionized by the energetic radiation from its hot compact companion. UV outbursts from symbiotic systems are explained by two principal models: an accretion-disk-outburst model which describes how material expelled from the tenuous envelope of the red giant forms an inwardly-spiralling disk around the hot companion, and a thermonuclear-outburst model in which the companion is specifically a white dwarf which superheats the material expelled from the red giant to the point where thermonuclear reactions occur and radiation is emitted. It is suspected that the evolutionary course of binary systems is predetermined by the initial mass and angular momentum of the gas cloud within which binary stars are born. Since red giants and Mira variables are thought to be stars with a mass of one or two solar mass, it is believed that the original cloud from which a symbiotic system is formed can consist of no more than a few solar masses of gas.

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

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

Characterization and application of shape-changing panels with embedded rubber muscle actuators

NASA Astrophysics Data System (ADS)

Peel, Larry D.; Molina, Enrique, Jr.; Baur, Jeffery W.; Justice, Ryan S.

2013-09-01

Cylindrical soft actuators efficiently convert fluid pressure into mechanical energy and thus offer excellent force-to-weight ratios while behaving similar to biological muscle. McKibben-like rubber muscle actuators (RMAs) were embedded into neat elastomer and act as shape-changing panels. The effect of actuator spacing and modeling methods on the performance of these panels was investigated. Simulations from nonlinear finite element models were compared with results from test panels containing four RMAs that were spaced 0, 1/2, 1, and 1.3 RMA diameters apart. Nonlinear ‘laminated plate’ and ‘rod & plate’ finite element (FE) models of individual (non-embedded) RMAs and panels with embedded RMAs were developed. Due to model complexity and resource limitations, several simplified 2D and 3D FE model types, including a 3D ‘Unit Cell’ were created. After subtracting the ‘activation pressure’ needed to initiate contraction, all the models for the individual actuators produced forces consistent with experimental values, but only the more resource-intensive rod & plate models replicated fiber/braid re-orientation and produced more realistic values for actuator contraction. For panel models, the Full 3D rod & plate model appeared to be the most accurate for panel contraction and force, but was not completed for all configurations due to resource limitations. Most embedded panel FE models produced maximum panel actuator force and maximum contraction when the embedded actuators are spaced between 1/2 and 1 diameter apart. Seven panels with embedded RMAs were experimentally fabricated and tested. Panel tests confirmed that maximum or optimal performance occurs when the RMAs are spaced between 1/2 and 1 diameter apart. The tested actuator force was fairly constant in this range, suggesting that minor design or manufacturing differences may not significantly affect panel performance. However, the amount of axial force and contraction decreases significantly at greater than optimal spacing. This multi-faceted work provides useful design, simulation fabrication, and test characteristics for shape-adaptive panels. Bending panels were demonstrated but not modeled. Developers of future shape-adaptive air vehicles have been provided with additional simulation and design tools.

"Bohr's Atomic Model."

ERIC Educational Resources Information Center

Willden, Jeff

2001-01-01

"Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…

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

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

All-atom molecular dynamics simulation of a photosystem i/detergent complex.

PubMed

Harris, Bradley J; Cheng, Xiaolin; Frymier, Paul

2014-10-09

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

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

All-atom molecular dynamics simulation of a photosystem I/detergent complex

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

Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

2014-09-18

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein detergent complexmore » to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Moreover, we find that the docking of soluble electron mediators such as cytochrome c 6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.« less

Nano-extrusion: a promising tool for continuous manufacturing of solid nano-formulations.

PubMed

Baumgartner, Ramona; Eitzlmayr, Andreas; Matsko, Nadejda; Tetyczka, Carolin; Khinast, Johannes; Roblegg, Eva

2014-12-30

Since more than 40% of today's drugs have low stability, poor solubility and/or limited ability to cross certain biological barriers, new platform technologies are required to address these challenges. This paper describes a novel continuous process that converts a stabilized aqueous nano-suspension into a solid oral formulation in a single step (i.e., the NANEX process) in order to improve the solubility of a model drug (phenytoin). Phenytoin nano-suspensions were prepared via media milling using different stabilizers. A stable nano-suspension was obtained using Tween(®) 80 as a stabilizer. The matrix material (Soluplus(®)) was gravimetrically fed into the hot melt extruder. The suspension was introduced through a side feeding device and mixed with the molten polymer to immediately devolatilize the water in the nano-suspension. Phenytoin nano-crystals were dispersed and embedded in the molten polymer. Investigation of the nano-extrudates via transmission electron microscopy and atomic force microscopy showed that the nano-crystals were embedded de-aggregated in the extrudates. Furthermore, no changes in the crystallinity (due to the mechanical and thermal stress) occurred. The dissolution studies confirmed that the prepared nano-extrudates increased the solubility of nano-crystalline phenytoin, regardless of the polymer. Our work demonstrates that NANEX represents a promising new platform technology in the design of novel drug delivery systems to improve drug performance. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

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.

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).

The X-ray emitting galaxy Centaurus A

NASA Technical Reports Server (NTRS)

Mushotzky, R. F.; Serlemitsos, P. J.; Boldt, E. A.; Holt, S. S.; Becker, R. H.

1978-01-01

OSO-8 X-ray observations of Cen A in 1975 and 1976 are reported. The source spectrum can be well fitted in both years by a power law of number index 1.66 and absorption due to 1.3 by 10 to the 23rd power atoms/sq cm. The total flux varied by a factor of 2 between 1975 and 1976. In 1976 there were flux variations of approximately 40% on a time scale of days. Measurements of the 6.4-keV Fe fluorescent line and the 7.1-keV absorption edge imply Fe/H of approximately 0.000016. Simultaneous radio measurements show variation in phase with X-ray variability. Consideration of radio, millimeter, infrared, and X-ray data shows that all the data can be accounted for by a model in which the X-rays are due to a synchrotron self-Compton source embedded in a cold H2 cloud.

Predicting the solid state phase diagram for glass-forming alloys of copper and zirconium

NASA Astrophysics Data System (ADS)

Tang, C.; Harrowell, Peter

2012-06-01

The free energies of six crystal structures associated with Cu-Zr alloys—Cu (face centred cubic), Cu2Zr, Cu10Zr7, CuZr, CuZr2 and Zr (hexagonal close packed)—are calculated using the embedded atom potential of Mendelev et al (2009 Phil. Mag. 89 967). We find that the observed low temperature stability of the Cu10Zr7 and CuZr2 phases is not reproduced. Instead, the model predicts that the CuZr phase remains stable down to T = 0 K. This discrepancy is largely removed when the interaction potentials are cut off at a short distance, such as that used by Duan et al (2005 Phys. Rev. B 71 224208). We present evidence, however, that the cut-off distance necessary to achieve the change in phase stability results in pathological artefacts in the energetics of some crystal phases.

De Novo Computational Design of Retro-Aldol Enzymes

PubMed Central

Jiang, Lin; Althoff, Eric A.; Clemente, Fernando R.; Doyle, Lindsey; Röthlisberger, Daniela; Zanghellini, Alexandre; Gallaher, Jasmine L.; Betker, Jamie L.; Tanaka, Fujie; Barbas, Carlos F.; Hilvert, Donald; Houk, Kendall N.; Stoddard, Barry L.; Baker, David

2012-01-01

The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model. PMID:18323453

Analog quantum simulation of the Rabi model in the ultra-strong coupling regime.

PubMed

Braumüller, Jochen; Marthaler, Michael; Schneider, Andre; Stehli, Alexander; Rotzinger, Hannes; Weides, Martin; Ustinov, Alexey V

2017-10-03

The quantum Rabi model describes the fundamental mechanism of light-matter interaction. It consists of a two-level atom or qubit coupled to a quantized harmonic mode via a transversal interaction. In the weak coupling regime, it reduces to the well-known Jaynes-Cummings model by applying a rotating wave approximation. The rotating wave approximation breaks down in the ultra-strong coupling regime, where the effective coupling strength g is comparable to the energy ω of the bosonic mode, and remarkable features in the system dynamics are revealed. Here we demonstrate an analog quantum simulation of an effective quantum Rabi model in the ultra-strong coupling regime, achieving a relative coupling ratio of g/ω ~ 0.6. The quantum hardware of the simulator is a superconducting circuit embedded in a cQED setup. We observe fast and periodic quantum state collapses and revivals of the initial qubit state, being the most distinct signature of the synthesized model.An analog quantum simulation scheme has been explored with a quantum hardware based on a superconducting circuit. Here the authors investigate the time evolution of the quantum Rabi model at ultra-strong coupling conditions, which is synthesized by slowing down the system dynamics in an effective frame.

Fish Passage in Large Culverts with Low Flows

DOT National Transportation Integrated Search

2014-08-01

A series of physical and numerical modeling runs were completed to support the development of a design procedure for characterizing the variation in velocity within non-embedded and embedded culverts. Physical modeling of symmetrical half-section cir...

Non-uniform Continuum Model for Solvated Species Based on Frozen-Density Embedding Theory: The Study Case of Solvatochromism of Coumarin 153.

PubMed

Shedge, Sapana V; Zhou, Xiuwen; Wesolowski, Tomasz A

2014-09-01

Recent application of the Frozen-Density Embedding Theory based continuum model of the solvent, which is used for calculating solvatochromic shifts in the UV/Vis range, are reviewed. In this model, the solvent is represented as a non-uniform continuum taking into account both the statistical nature of the solvent and specific solute-solvent interactions. It offers, therefore, a computationally attractive alternative to methods in which the solvent is described at atomistic level. The evaluation of the solvatochromic shift involves only two calculations of excitation energy instead of at least hundreds needed to account for inhomogeneous broadening. The present review provides a detailed graphical analysis of the key quantities of this model: the average charge density of the solvent (<ρB>) and the corresponding Frozen-Density Embedding Theory derived embedding potential for coumarin 153.

Heartbeat-based error diagnosis framework for distributed embedded systems

NASA Astrophysics Data System (ADS)

Mishra, Swagat; Khilar, Pabitra Mohan

2012-01-01

Distributed Embedded Systems have significant applications in automobile industry as steer-by-wire, fly-by-wire and brake-by-wire systems. In this paper, we provide a general framework for fault detection in a distributed embedded real time system. We use heartbeat monitoring, check pointing and model based redundancy to design a scalable framework that takes care of task scheduling, temperature control and diagnosis of faulty nodes in a distributed embedded system. This helps in diagnosis and shutting down of faulty actuators before the system becomes unsafe. The framework is designed and tested using a new simulation model consisting of virtual nodes working on a message passing system.

Heartbeat-based error diagnosis framework for distributed embedded systems

NASA Astrophysics Data System (ADS)

Mishra, Swagat; Khilar, Pabitra Mohan

2011-12-01

Distributed Embedded Systems have significant applications in automobile industry as steer-by-wire, fly-by-wire and brake-by-wire systems. In this paper, we provide a general framework for fault detection in a distributed embedded real time system. We use heartbeat monitoring, check pointing and model based redundancy to design a scalable framework that takes care of task scheduling, temperature control and diagnosis of faulty nodes in a distributed embedded system. This helps in diagnosis and shutting down of faulty actuators before the system becomes unsafe. The framework is designed and tested using a new simulation model consisting of virtual nodes working on a message passing system.

Information-theoretic model selection for optimal prediction of stochastic dynamical systems from data

NASA Astrophysics Data System (ADS)

Darmon, David

2018-03-01

In the absence of mechanistic or phenomenological models of real-world systems, data-driven models become necessary. The discovery of various embedding theorems in the 1980s and 1990s motivated a powerful set of tools for analyzing deterministic dynamical systems via delay-coordinate embeddings of observations of their component states. However, in many branches of science, the condition of operational determinism is not satisfied, and stochastic models must be brought to bear. For such stochastic models, the tool set developed for delay-coordinate embedding is no longer appropriate, and a new toolkit must be developed. We present an information-theoretic criterion, the negative log-predictive likelihood, for selecting the embedding dimension for a predictively optimal data-driven model of a stochastic dynamical system. We develop a nonparametric estimator for the negative log-predictive likelihood and compare its performance to a recently proposed criterion based on active information storage. Finally, we show how the output of the model selection procedure can be used to compare candidate predictors for a stochastic system to an information-theoretic lower bound.

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

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.

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

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.

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

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.

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.

Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: difference between atomistic and coarse-grained simulations.

PubMed

Nishizawa, Manami; Nishizawa, Kazuhisa

2014-08-21

Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT(OPLS)). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT(OPLS) PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT(CHARMM)) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16-22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT(OPLS) PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA)3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret CG and AT simulation results on membrane proteins.

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.

Streamflow Prediction based on Chaos Theory

NASA Astrophysics Data System (ADS)

Li, X.; Wang, X.; Babovic, V. M.

2015-12-01

Chaos theory is a popular method in hydrologic time series prediction. Local model (LM) based on this theory utilizes time-delay embedding to reconstruct the phase-space diagram. For this method, its efficacy is dependent on the embedding parameters, i.e. embedding dimension, time lag, and nearest neighbor number. The optimal estimation of these parameters is thus critical to the application of Local model. However, these embedding parameters are conventionally estimated using Average Mutual Information (AMI) and False Nearest Neighbors (FNN) separately. This may leads to local optimization and thus has limitation to its prediction accuracy. Considering about these limitation, this paper applies a local model combined with simulated annealing (SA) to find the global optimization of embedding parameters. It is also compared with another global optimization approach of Genetic Algorithm (GA). These proposed hybrid methods are applied in daily and monthly streamflow time series for examination. The results show that global optimization can contribute to the local model to provide more accurate prediction results compared with local optimization. The LM combined with SA shows more advantages in terms of its computational efficiency. The proposed scheme here can also be applied to other fields such as prediction of hydro-climatic time series, error correction, etc.

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.

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.

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.

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.

The I3E Model for Embedding Education for Sustainability within Higher Education Institutions

ERIC Educational Resources Information Center

Cebrián, Gisela

2018-01-01

This paper presents an evidence-based model (the I3E model) for embedding education for sustainability (EfS) within a higher education institution. This model emerged from a doctoral research that examined organisational learning and change processes at the University of Southampton to build EfS into the university curriculum. The researcher aimed…

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.

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.

Patron perception and utilization of an embedded librarian program.

PubMed

Blake, Lindsay; Ballance, Darra; Davies, Kathy; Gaines, Julie K; Mears, Kim; Shipman, Peter; Connolly-Brown, Maryska; Burchfield, Vicki

2016-07-01

The study measured the perceived value of an academic library's embedded librarian service model. The study took place at the health sciences campuses of a research institution. A web-based survey was distributed that asked respondents a series of questions about their utilization of and satisfaction with embedded librarians and services. Over 58% of respondents reported being aware of their embedded librarians, and 95% of these were satisfied with provided services. The overall satisfaction with services was encouraging, but awareness of the embedded program was low, suggesting an overall need for marketing of services.

Dynamics of essential collective motions in proteins: Theory

NASA Astrophysics Data System (ADS)

Stepanova, Maria

2007-11-01

A general theoretical background is introduced for characterization of conformational motions in protein molecules, and for building reduced coarse-grained models of proteins, based on the statistical analysis of their phase trajectories. Using the projection operator technique, a system of coupled generalized Langevin equations is derived for essential collective coordinates, which are generated by principal component analysis of molecular dynamic trajectories. The number of essential degrees of freedom is not limited in the theory. An explicit analytic relation is established between the generalized Langevin equation for essential collective coordinates and that for the all-atom phase trajectory projected onto the subspace of essential collective degrees of freedom. The theory introduced is applied to identify correlated dynamic domains in a macromolecule and to construct coarse-grained models representing the conformational motions in a protein through a few interacting domains embedded in a dissipative medium. A rigorous theoretical background is provided for identification of dynamic correlated domains in a macromolecule. Examples of domain identification in protein G are given and employed to interpret NMR experiments. Challenges and potential outcomes of the theory are discussed.

Anatomy of a Photodissociation Region: High angular resolution images of molecular emission in the Orion Bar

NASA Technical Reports Server (NTRS)

Tauber, Jan A.; Tielens, A. G. G. M.; Meixner, Margaret; Foldsmith, Paul F.

1994-01-01

We present observations of the molecular component of the Orion Bar, a prototypical Photodissociation Region (PDR) illuminated by the Trapezium cluster. The high angular resolution (6 sec-10 sec) that we have achieved by combining single-dish and interferometric observations has allowed us to examine in detail the spatial and kinematic morphology of this region and to estimate the physical characteristics of the molecular gas it contains. Our observations indicate that this PDR can be essentially described as a homogeneously distributed slab of moderately dense material (approximately 5 x 10(exp 4)/cu cm), in which are embedded a small number of dense (greater than 10(exp 6)/cu cm) clumps. The latter play little or no role in determining the thickness and kinetic temperature structure of this PDR. This observational picture is largely supported by PDR model calculations for this region, which we describe in detail in this work. We also find our model predictions of the intensities of a variety of atomic and molecular lines to be in good general agreement with a number of previous observations.

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

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

Homology Model of the GABAA Receptor Examined Using Brownian Dynamics

PubMed Central

O'Mara, Megan; Cromer, Brett; Parker, Michael; Chung, Shin-Ho

2005-01-01

We have developed a homology model of the GABAA receptor, using the subunit combination of α1β2γ2, the most prevalent type in the mammalian brain. The model is produced in two parts: the membrane-embedded channel domain and the extracellular N-terminal domain. The pentameric transmembrane domain model is built by modeling each subunit by homology with the equivalent subunit of the heteropentameric acetylcholine receptor transmembrane domain. This segment is then joined with the extracellular domain built by homology with the acetylcholine binding protein. The all-atom model forms a wide extracellular vestibule that is connected to an oval chamber near the external surface of the membrane. A narrow, cylindrical transmembrane channel links the outer segment of the pore to a shallow intracellular vestibule. The physiological properties of the model so constructed are examined using electrostatic calculations and Brownian dynamics simulations. A deep energy well of ∼80 kT accommodates three Cl− ions in the narrow transmembrane channel and seven Cl− ions in the external vestibule. Inward permeation takes place when one of the ions queued in the external vestibule enters the narrow segment and ejects the innermost ion. The model, when incorporated into Brownian dynamics, reproduces key experimental features, such as the single-channel current-voltage-concentration profiles. Finally, we simulate the γ2 K289M epilepsy inducing mutation and examine Cl− ion permeation through the mutant receptor. PMID:15749776

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.

Conceptual Models and Theory-Embedded Principles on Effective Schooling.

ERIC Educational Resources Information Center

Scheerens, Jaap

1997-01-01

Reviews models and theories on effective schooling. Discusses four rationality-based organization theories and a fifth perspective, chaos theory, as applied to organizational functioning. Discusses theory-embedded principles flowing from these theories: proactive structuring, fit, market mechanisms, cybernetics, and self-organization. The…

Improving End-of-Life Care: Palliative Care Embedded in an Oncology Clinic Specializing in Targeted and Immune-Based Therapies.

PubMed

Einstein, David J; DeSanto-Madeya, Susan; Gregas, Matthew; Lynch, Jessica; McDermott, David F; Buss, Mary K

2017-09-01

Patients with advanced cancer benefit from early involvement of palliative care. The ideal method of palliative care integration remains to be determined, as does its effectiveness for patients treated with targeted and immune-based therapies. We studied the impact of an embedded palliative care team that saw patients in an academic oncology clinic specializing in targeted and immune-based therapies. Patients seen on a specific day accessed the embedded model, on the basis of automatic criteria; patients seen other days could be referred to a separate palliative care clinic (usual care). We abstracted data from the medical records of 114 patients who died during the 3 years after this model's implementation. Compared with usual care (n = 88), patients with access to the embedded model (n = 26) encountered palliative care as outpatients more often ( P = .003) and earlier (mean, 231 v 109 days before death; P < .001). Hospice enrollment rates were similar ( P = .303), but duration was doubled (mean, 57 v 25 days; P = .006), and enrollment > 7 days before death-a core Quality Oncology Practice Initiative metric-was higher in the embedded model (odds ratio, 5.60; P = .034). Place of death ( P = .505) and end-of-life chemotherapy (odds ratio, 0.361; P = .204) did not differ between the two arms. A model of embedded and automatically triggered palliative care among patients treated exclusively with targeted and immune-based therapies was associated with significant improvements in use and timing of palliative care and hospice, compared with usual practice.

Failure and recovery in dynamical networks.

PubMed

Böttcher, L; Luković, M; Nagler, J; Havlin, S; Herrmann, H J

2017-02-03

Failure, damage spread and recovery crucially underlie many spatially embedded networked systems ranging from transportation structures to the human body. Here we study the interplay between spontaneous damage, induced failure and recovery in both embedded and non-embedded networks. In our model the network's components follow three realistic processes that capture these features: (i) spontaneous failure of a component independent of the neighborhood (internal failure), (ii) failure induced by failed neighboring nodes (external failure) and (iii) spontaneous recovery of a component. We identify a metastable domain in the global network phase diagram spanned by the model's control parameters where dramatic hysteresis effects and random switching between two coexisting states are observed. This dynamics depends on the characteristic link length of the embedded system. For the Euclidean lattice in particular, hysteresis and switching only occur in an extremely narrow region of the parameter space compared to random networks. We develop a unifying theory which links the dynamics of our model to contact processes. Our unifying framework may help to better understand controllability in spatially embedded and random networks where spontaneous recovery of components can mitigate spontaneous failure and damage spread in dynamical networks.

Modeling the mechanics of axonal fiber tracts using the embedded finite element method.

PubMed

Garimella, Harsha T; Kraft, Reuben H

2017-05-01

A subject-specific human head finite element model with embedded axonal fiber tractography obtained from diffusion tensor imaging was developed. The axonal fiber tractography finite element model was coupled with the volumetric elements in the head model using the embedded element method. This technique enables the calculation of axonal strains and real-time tracking of the mechanical response of the axonal fiber tracts. The coupled model was then verified using pressure and relative displacement-based (between skull and brain) experimental studies and was employed to analyze a head impact, demonstrating the applicability of this method in studying axonal injury. Following this, a comparison study of different injury criteria was performed. This model was used to determine the influence of impact direction on the extent of the axonal injury. The results suggested that the lateral impact loading is more dangerous compared to loading in the sagittal plane, a finding in agreement with previous studies. Through this analysis, we demonstrated the viability of the embedded element method as an alternative numerical approach for studying axonal injury in patient-specific human head models. Copyright © 2016 John Wiley & Sons, Ltd.

Coaches Coaching Coaches

ERIC Educational Resources Information Center

Burkins, Jan Miller; Ritchie, Scott

2007-01-01

Researchers have argued that "job-embedded" professional learning is the most valuable model for teachers (Joyce & Showers, 2002). But there is little or no corresponding literature regarding job-embedded professional learning for literacy coaches. In this paper, the authors offer an example of one such model, the Coach-to-Coach…

Raman Monte Carlo simulation for light propagation for tissue with embedded objects

NASA Astrophysics Data System (ADS)

Periyasamy, Vijitha; Jaafar, Humaira Bte; Pramanik, Manojit

2018-02-01

Monte Carlo (MC) stimulation is one of the prominent simulation technique and is rapidly becoming the model of choice to study light-tissue interaction. Monte Carlo simulation for light transport in multi-layered tissue (MCML) is adapted and modelled with different geometry by integrating embedded objects of various shapes (i.e., sphere, cylinder, cuboid and ellipsoid) into the multi-layered structure. These geometries would be useful in providing a realistic tissue structure such as modelling for lymph nodes, tumors, blood vessels, head and other simulation medium. MC simulations were performed on various geometric medium. Simulation of MCML with embedded object (MCML-EO) was improvised for propagation of the photon in the defined medium with Raman scattering. The location of Raman photon generation is recorded. Simulations were experimented on a modelled breast tissue with tumor (spherical and ellipsoidal) and blood vessels (cylindrical). Results were presented in both A-line and B-line scans for embedded objects to determine spatial location where Raman photons were generated. Studies were done for different Raman probabilities.

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

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.

GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations

PubMed Central

Staritzbichler, René; Anselmi, Claudio; Forrest, Lucy R.; Faraldo-Gómez, José D.

2014-01-01

As new atomic structures of membrane proteins are resolved, they reveal increasingly complex transmembrane topologies, and highly irregular surfaces with crevices and pores. In many cases, specific interactions formed with the lipid membrane are functionally crucial, as is the overall lipid composition. Compounded with increasing protein size, these characteristics pose a challenge for the construction of simulation models of membrane proteins in lipid environments; clearly, that these models are sufficiently realistic bears upon the reliability of simulation-based studies of these systems. Here, we introduce GRIFFIN, which uses a versatile framework to automate and improve a widely-used membrane-embedding protocol. Initially, GRIFFIN carves out lipid and water molecules from a volume equivalent to that of the protein, so as to conserve the system density. In the subsequent optimization phase GRIFFIN adds an implicit grid-based protein force-field to a molecular dynamics simulation of the pre-carved membrane. In this force-field, atoms inside the implicit protein volume experience an outward force that will expel them from that volume, whereas those outside are subject to electrostatic and van-der-Waals interactions with the implicit protein. At each step of the simulation, these forces are updated by GRIFFIN and combined with the intermolecular forces of the explicit lipid-water system. This procedure enables the construction of realistic and reproducible starting configurations of the protein-membrane interface within a reasonable timeframe and with minimal intervention. GRIFFIN is a standalone tool designed to work alongside any existing molecular dynamics package, such as NAMD or GROMACS. PMID:24707227

Embedded CLIPS for SDI BM/C3 simulation and analysis

NASA Technical Reports Server (NTRS)

Gossage, Brett; Nanney, Van

1990-01-01

Nichols Research Corporation is developing the BM/C3 Requirements Analysis Tool (BRAT) for the U.S. Army Strategic Defense Command. BRAT uses embedded CLIPS/Ada to model the decision making processes used by the human commander of a defense system. Embedding CLlPS/Ada in BRAT allows the user to explore the role of the human in Command and Control (C2) and the use of expert systems for automated C2. BRAT models assert facts about the current state of the system, the simulated scenario, and threat information into CLIPS/Ada. A user-defined rule set describes the decision criteria for the commander. We have extended CLIPS/Ada with user-defined functions that allow the firing of a rule to invoke a system action such as weapons release or a change in strategy. The use of embedded CLIPS/Ada will provide a powerful modeling tool for our customer at minimal cost.

Effect of Longitudinal Magnetic Field on Vibration Characteristics of Single-Walled Carbon Nanotubes in a Viscoelastic Medium

NASA Astrophysics Data System (ADS)

Zhang, D. P.; Lei, Y.; Shen, Z. B.

2017-12-01

The effect of longitudinal magnetic field on vibration response of a sing-walled carbon nanotube (SWCNT) embedded in viscoelastic medium is investigated. Based on nonlocal Euler-Bernoulli beam theory, Maxwell's relations, and Kelvin viscoelastic foundation model, the governing equations of motion for vibration analysis are established. The complex natural frequencies and corresponding mode shapes in closed form for the embedded SWCNT with arbitrary boundary conditions are obtained using transfer function method (TFM). The new analytical expressions for the complex natural frequencies are also derived for certain typical boundary conditions and Kelvin-Voigt model. Numerical results from the model are presented to show the effects of nonlocal parameter, viscoelastic parameter, boundary conditions, aspect ratio, and strength of the magnetic field on vibration characteristics for the embedded SWCNT in longitudinal magnetic field. The results demonstrate the efficiency of the proposed methods for vibration analysis of embedded SWCNTs under magnetic field.

Modeling of Embedded Human Systems

DTIC Science & Technology

2013-07-01

ISAT study [7] for DARPA in 20051 concretized the notion of an embedded human, who is a necessary component of the system. The proposed work integrates...Technology, IEEE Transactions on, vol. 16, no. 2, pp. 229–244, March 2008. [7] C. J. Tomlin and S. S. Sastry, “Embedded humans,” tech. rep., DARPA ISAT

The Embedded Librarian Online or Face-to-Face: American University's Experiences

ERIC Educational Resources Information Center

Matos, Michael A.; Matsuoka-Motley, Nobue; Mayer, William

2010-01-01

This article examines the role online communication and tools play in embedded librarianship at American University. Two embedded models of user engagement, traditional and hybrid, are discussed. The librarians operating in each mode share their experiences providing tailored support to the departments of music/performing arts and business. The…

AADL and Model-based Engineering

DTIC Science & Technology

2014-10-20

and MBE Feiler, Oct 20, 2014 © 2014 Carnegie Mellon University We Rely on Software for Safe Aircraft Operation Embedded software systems ...D eveloper Compute Platform Runtime Architecture Application Software Embedded SW System Engineer Data Stream Characteristics Latency...confusion Hardware Engineer Why do system level failures still occur despite fault tolerance techniques being deployed in systems ? Embedded software

H.264/AVC digital fingerprinting based on spatio-temporal just noticeable distortion

NASA Astrophysics Data System (ADS)

Ait Saadi, Karima; Bouridane, Ahmed; Guessoum, Abderrezak

2014-01-01

This paper presents a robust adaptive embedding scheme using a modified Spatio-Temporal noticeable distortion (JND) model that is designed for tracing the distribution of the H.264/AVC video content and protecting them from unauthorized redistribution. The Embedding process is performed during coding process in selected macroblocks type Intra 4x4 within I-Frame. The method uses spread-spectrum technique in order to obtain robustness against collusion attacks and the JND model to dynamically adjust the embedding strength and control the energy of the embedded fingerprints so as to ensure their imperceptibility. Linear and non linear collusion attacks are performed to show the robustness of the proposed technique against collusion attacks while maintaining visual quality unchanged.

Dynamics of embedded curves by doubly-nonlocal reaction-diffusion systems

NASA Astrophysics Data System (ADS)

von Brecht, James H.; Blair, Ryan

2017-11-01

We study a class of nonlocal, energy-driven dynamical models that govern the motion of closed, embedded curves from both an energetic and dynamical perspective. Our energetic results provide a variety of ways to understand physically motivated energetic models in terms of more classical, combinatorial measures of complexity for embedded curves. This line of investigation culminates in a family of complexity bounds that relate a rather broad class of models to a generalized, or weighted, variant of the crossing number. Our dynamic results include global well-posedness of the associated partial differential equations, regularity of equilibria for these flows as well as a more detailed investigation of dynamics near such equilibria. Finally, we explore a few global dynamical properties of these models numerically.

A probabilistic method for determining the volume fraction of pre-embedded capsules in self-healing materials

NASA Astrophysics Data System (ADS)

Lv, Zhong; Chen, Huisu

2014-10-01

Autonomous healing of cracks using pre-embedded capsules containing healing agent is becoming a promising approach to restore the strength of damaged structures. In addition to the material properties, the size and volume fraction of capsules influence crack healing in the matrix. Understanding the crack and capsule interaction is critical in the development and design of structures made of self-healing materials. Assuming that the pre-embedded capsules are randomly dispersed we theoretically model flat ellipsoidal crack interaction with capsules and determine the probability of a crack intersecting the pre-embedded capsules i.e. the self-healing probability. We also develop a probabilistic model of a crack simultaneously meeting with capsules and catalyst carriers in two-component self-healing system matrix. Using a risk-based healing approach, we determine the volume fraction and size of the pre-embedded capsules that are required to achieve a certain self-healing probability. To understand the effect of the shape of the capsules on self-healing we theoretically modeled crack interaction with spherical and cylindrical capsules. We compared the results of our theoretical model with Monte-Carlo simulations of crack interaction with capsules. The formulae presented in this paper will provide guidelines for engineers working with self-healing structures in material selection and sustenance.

Sustaining librarian vitality: embedded librarianship model for health sciences libraries.

PubMed

Wu, Lin; Mi, Misa

2013-01-01

With biomedical information widely accessible from anywhere at any time, health sciences libraries have become less centralized, and they are challenged to stay relevant and vital to the mission and strategic goals of their home institution. One solution is to embed librarians at strategic points in health professions' education, research, and patient care. This article discusses a proposed five-level model of embedded librarianship within the context of health sciences libraries and describes different roles, knowledge, and skills desirable for health sciences librarians working as embedded librarians.

An IPA-Embedded Model for Evaluating Creativity Curricula

ERIC Educational Resources Information Center

Chang, Chi-Cheng

2014-01-01

How to diagnose the effectiveness of creativity-related curricula is a crucial concern in the pursuit of educational excellence. This paper introduces an importance-performance analysis (IPA)-embedded model for curriculum evaluation, using the example of an IT project implementation course to assess the creativity performance deduced from student…

Effects of '"Environmental Chemistry" Elective Course via Technology-Embedded Scientific Inquiry Model on Some Variables

ERIC Educational Resources Information Center

Çalik, Muammer; Özsevgeç, Tuncay; Ebenezer, Jazlin; Artun, Hüseyin; Küçük, Zeynel

2014-01-01

The purpose of this study is to examine the effects of "environmental chemistry" elective course via Technology-Embedded Scientific Inquiry (TESI) model on senior science student teachers' (SSSTs) conceptions of environmental chemistry concepts/issues, attitudes toward chemistry, and technological pedagogical content knowledge…

Gear Fatigue Crack Diagnosis by Vibration Analysis Using Embedded Modeling

DTIC Science & Technology

2001-04-05

gave references on Wigner - Ville Distribution ( WVD ) and some statistical based methods including FM4, NA4 and NB4. There are limitations for vibration...Embedded Modeling DISTRIBUTION : Approved for public release, distribution unlimited This paper is part of the following report: TITLE: New Frontiers in

Embedding Academic Literacy Skills: Towards a Best Practice Model

ERIC Educational Resources Information Center

McWilliams, Robyn; Allan, Quentin

2014-01-01

Learning advisors provide academic literacy development support in a variety of configurations, ranging from one-on-one consultations through to large-scale lectures. Such lectures can be generic, stand-alone modules or embedded within a discipline-specific course. Pragmatic and institutional considerations suggest that a generic model of delivery…

Data management in the mission data system

NASA Technical Reports Server (NTRS)

Wagner, David A.

2005-01-01

As spacecraft evolve from simple embedded devices to become more sophisticated computing platforms with complex behaviors it is increasingly necessary to model and manage the flow of data, and to provide uniform models for managing data that promote adaptability, yet pay heed to the physical limitations of the embedded and space environments.

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

PubMed

Riniker, Sereina; van Gunsteren, Wilfred F

2011-02-28

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models.

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

Atomic study of effects of crystal structure and temperature on structural evolution of Au nanowires under torsion

NASA Astrophysics Data System (ADS)

Wu, Cheng-Da; Tsai, Hsing-Wei

2018-06-01

The effect of temperature on the structural evolution of nanocrystalline (NC) and single-crystalline (SC) Au nanowires (NWs) under torsional deformation is studied using molecular dynamics simulations based on the many-body embedded-atom potential. The effect is investigated using common neighbor analysis and discussed in terms of shear strain distribution and atomic flow field. The simulation results show that deformation for NC NWs is mainly driven by the nucleation and propagation of dislocations and the gliding of grain boundaries (GBs) and that for SC NWs is mainly driven by dislocations and the formation of disordered structures. Dislocations for NC and SC NWs easily nucleate at GBs and free surfaces, respectively. For NC NWs, torsional buckling occurs easily at GBs with large gliding. SC NWs have a more uniform and larger elastic deformation under torsion compared to that for NC NWs due to the former's lack of grains. SC NWs have a long period of elastic deformation transforming into plastic deformation. Increasing temperature facilitates stress transmission throughout NWs.

Monte Carlo investigations on surface elastic energy of spin-crossover solids: Direct access to image pressure and the Eshelby constant

NASA Astrophysics Data System (ADS)

Boukheddaden, Kamel

2013-10-01

We present theoretical investigations on surface elastic energy in spin-crossover (SC) solids studied in the frame of a microscopic elastic model, coupling spin, and lattice deformations. Although surface energy plays a crucial role in driving the SC transition, specific quantitative investigations on its effect have been neglected in most of the recent theoretical works based on atomistic descriptions of the SC transitions, resolved by Monte Carlo or by molecular dynamics simulations. Here, we perform a quantitative study of the surface energy resulting from an inserted high-spin (HS) domain in a low-spin (LS) lattice. This situation may be produced experimentally in SC solids, at low temperature, through a photoexcitation by a single pulse laser shot. We demonstrate that the surface energy depends on the ratio between the local molecular volume misfit (between the LS and HS sites) δυ and the lattice volume V, such as Esurf˜δυ2/V for the HS atom at the center of lattice, while it is Esurf˜δυ2/L (L is the length of the lattice) in the case of the HS atom located on the edge of the lattice. We then derived the image pressure (negative in the case of embedded dilatation centers) through the work of the free surface atoms and evaluated the Eshelby constant, which was found equal to γ˜1.90, in very good agreement with the available data of literature. Energetic configuration diagrams in the homogeneous (HS and LS) and heterogeneous (coexistence of HS and LS) are calculated, from which estimations of the macroscopic bulk modulus were deduced.

A computer model for liquid jet atomization in rocket thrust chambers

NASA Astrophysics Data System (ADS)

Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Yang, H. Q.; Ibrahim, E.; Chuech, S.; Przekwas, A. J.

1991-12-01

The process of atomization has been used as an efficient means of burning liquid fuels in rocket engines, gas turbine engines, internal combustion engines, and industrial furnaces. Despite its widespread application, this complex hydrodynamic phenomenon has not been well understood, and predictive models for this process are still in their infancy. The difficulty in simulating the atomization process arises from the relatively large number of parameters that influence it, including the details of the injector geometry, liquid and gas turbulence, and the operating conditions. In this study, numerical models are developed from first principles, to quantify factors influencing atomization. For example, the surface wave dynamics theory is used for modeling the primary atomization and the droplet energy conservation principle is applied for modeling the secondary atomization. The use of empirical correlations has been minimized by shifting the analyses to fundamental levels. During applications of these models, parametric studies are performed to understand and correlate the influence of relevant parameters on the atomization process. The predictions of these models are compared with existing experimental data. The main tasks of this study were the following: development of a primary atomization model; development of a secondary atomization model; development of a model for impinging jets; development of a model for swirling jets; and coupling of the primary atomization model with a CFD code.

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

Promotional effect of surface hydroxyls on electrochemical reduction of CO 2 over SnO x/Sn electrode

DOE PAGES

Cui, Chaonan; Han, Jinyu; Zhu, Xinli; ...

2016-01-16

In this study, tin oxide (SnO x) formation on tin-based electrode surfaces during CO 2 electrochemical reduction can have a significant impact on the activity and selectivity of the reaction. In the present study, density functional theory (DFT) calculations have been performed to understand the role of SnO x in CO 2 reduction using a SnO monolayer on the Sn(112) surface as a model for SnO x. Water molecules have been treated explicitly and considered actively participating in the reaction. The results showed that H 2O dissociates on the perfect SnO monolayer into two hydroxyl groups symmetrically on the surface.more » CO 2 energetically prefers to react with the hydroxyl, forming a bicarbonate (HCO 3(t)*) intermediate, which can then be reduced to either formate (HCOO*) by hydrogenating the carbon atom or carboxyl (COOH*) by protonating the oxygen atom. Both steps involve a simultaneous Csingle bondO bond breaking. Further reduction of HCOO* species leads to the formation of formic acid in the acidic solution at pH < 4, while the COOH* will decompose to CO and H 2O via protonation. Whereas the oxygen vacancy (VO) in the oxide monolayer maybe formed by the reduction, it can be recovered by H 2O dissociation, resulting in two embedded hydroxyl groups. The results show that the hydroxylated surface with two symmetric hydroxyls is energetically more favorable for CO 2 reduction than the hydroxylated VO surface with two embedded hydroxyls. The reduction potential for the former has a limiting-potential of –0.20 V (RHE), lower than that for the latter (–0.74 V (RHE)). Compared to the pure Sn electrode, the formation of SnO x monolayer on the electrode under the operating conditions promotes CO 2 reduction more effectively by forming surface hydroxyls, thereby providing a new channel via COOH* to the CO formation, although formic acid is still the major reduction product.« less

Technology Demonstration Missions

NASA Technical Reports Server (NTRS)

McDougal, John; French, Raymond; Adams-Fogle, Beth; Stephens, Karen

2015-01-01

Technology Demonstration Missions (TDM) is in its third year of execution, being initiated in 2010 and baselined in January of 2012. There are 11 projects that NASA Marshall Space Flight Center (MSFC) has contributed to or led: (1) Evolvable Cryogenics (eCryo): Cyrogenic Propellant Storage and Transfer Engineering Development Unit (EDU), a proof of manufacturability effort, used to enhance knowledge and technology related to handling cryogenic propellants, specifically liquid hydrogen. (2) Composites for Exploration Upper Stage (CEUS): Design, build, test, and address flight certification of a large composite shell suitable for the second stage of the Space Launch System (SLS). (3) Deep Space Atomic Clock (DSAC): Spaceflight to demo small, low-mass atomic clock that can provide unprecedented stability for deep space navigation. (4) Green Propellant Infusion Mission (GPIM): Demo of high-performance, green propellant propulsion system suitable for Evolved Expendable Launch Vehicle (EELV) Secondary Payload Adapter (ESPA)-class spacecraft. (5) Human Exploration Telerobotics (HET): Demonstrating how telerobotics, remote control of a variety of robotic systems, can take routine, highly repetitive, dangerous or long-duration tasks out of human hands. (6) Laser Communication Relay Demo (LCRD): Demo to advance optical communications technology toward infusion into deep space and near Earth operational systems, while growing the capabilities of industry sources. (7) Low Density Supersonic Decelerator (LDSD): Demo new supersonic inflatable decelerator and parachute technologies to enable Mars landings of larger payloads with greater precision at a wider range of altitudes. (8) Mars Science Laboratory (MSL) Entry Descent & Landing Instrumentation (MEDLI): Demo of embedded sensors embedded in the MSL heat shield, designed to record the heat and atmospheric pressure experienced during the spacecraft's high-speed, hot entry in the Martian atmosphere. (9) Solar Electric Propulsion (SEP): 50-kW class spacecraft that uses flexible blanket solar arrays for power generation and an electric propulsion system that delivers payload from low-Earth orbit to higher orbits. (10) Solar Sail Demonstration (SSD): Demo to validate sail deployment techniques for solar sails that are propelled by the pressure of sunlight. (11) Terrestrial HIAD Orbit Reentry (THOR): Demo of a 3.7-m Hypersonic Inflatable Aerodynamic Decelerator (HIAD) entry vehicle to test second generation aerothermal performance and modeling.

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

NASA Astrophysics Data System (ADS)

Yang, Liqiu

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

The Effect of an Embedded Pedagogical Agent on the Students' Science Achievement

ERIC Educational Resources Information Center

Kizilkaya, Gonca; Askar, Petek

2008-01-01

Purpose: The purpose of this paper is to investigate the effect of an embedded pedagogical agent into a tutorial on achievement. Design/methodology/approach: Research methodology is designed according to the post test control group model in which the experimental group (69 students) was exposed to a tutorial with an embedded pedagogical agent;…

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

Structural investigations in helium implanted cubic zirconia using grazing incidence XRD and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Kuri, G.; Degueldre, C.; Bertsch, J.; Döbeli, M.

2010-06-01

The crystal structure and local atom arrangements surrounding Zr atoms were determined for a helium implanted cubic stabilized zirconia (CSZ) using X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, respectively, measured at glancing angles. The implanted specimen was prepared at a helium fluence of 2 × 10 16 cm -2 using He + beams at two energies (2.54 and 2.74 MeV) passing through a 8.0 μm Al absorber foil. XRD results identified the formation of a new rhombohedral phase in the helium embedded layer, attributed to internal stress as a result of expansion of the CSZ-lattice. Zr K-edge EXAFS data suggested loss of crystallinity in the implanted lattice and disorder of the Zr atoms environment. EXAFS Fourier transforms analysis showed that the average first-shell radius of the Zr sbnd O pair in the implanted sample was slightly larger than that of the CSZ standard. Common general disorder features were explained by rhombohedral type short-range ordered clusters. The average structural parameters estimated from the EXAFS data of unimplanted and implanted CSZ are compared and discussed. Potential of EXAFS as a local probe of atomic-scale structural modifications induced by helium implantation in CSZ is demonstrated.

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.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

H-atom addition and abstraction reactions in mixed CO, H2CO and CH3OH ices - an extended view on complex organic molecule formation

NASA Astrophysics Data System (ADS)

Chuang, K.-J.; Fedoseev, G.; Ioppolo, S.; van Dishoeck, E. F.; Linnartz, H.

2016-01-01

Complex organic molecules (COMs) have been observed not only in the hot cores surrounding low- and high-mass protostars, but also in cold dark clouds. Therefore, it is interesting to understand how such species can be formed without the presence of embedded energy sources. We present new laboratory experiments on the low-temperature solid state formation of three complex molecules - methyl formate (HC(O)OCH3), glycolaldehyde (HC(O)CH2OH) and ethylene glycol (H2C(OH)CH2OH) - through recombination of free radicals formed via H-atom addition and abstraction reactions at different stages in the CO→H2CO→CH3OH hydrogenation network at 15 K. The experiments extend previous CO hydrogenation studies and aim at resembling the physical-chemical conditions typical of the CO freeze-out stage in dark molecular clouds, when H2CO and CH3OH form by recombination of accreting CO molecules and H-atoms on ice grains. We confirm that H2CO, once formed through CO hydrogenation, not only yields CH3OH through ongoing H-atom addition reactions, but is also subject to H-atom-induced abstraction reactions, yielding CO again. In a similar way, H2CO is also formed in abstraction reactions involving CH3OH. The dominant methanol H-atom abstraction product is expected to be CH2OH, while H-atom additions to H2CO should at least partially proceed through CH3O intermediate radicals. The occurrence of H-atom abstraction reactions in ice mantles leads to more reactive intermediates (HCO, CH3O and CH2OH) than previously thought, when assuming sequential H-atom addition reactions only. This enhances the probability to form COMs through radical-radical recombination without the need of UV photolysis or cosmic rays as external triggers.

A Prototype Embedding of Bluespec System Verilog in the PVS Theorem Prover

NASA Technical Reports Server (NTRS)

Richards, Dominic; Lester, David

2010-01-01

Bluespec SystemVerilog (BSV) is a Hardware Description Language based on the guarded action model of concurrency. It has an elegant semantics, which makes it well suited for formal reasoning. To date, a number of BSV designs have been verified with hand proofs, but little work has been conducted on the application of automated reasoning. We present a prototype shallow embedding of BSV in the PVS theorem prover. Our embedding is compatible with the PVS model checker, which can automatically prove an important class of theorems, and can also be used in conjunction with the powerful proof strategies of PVS to verify a broader class of properties than can be achieved with model checking alone.

AtomDB Progress Report: Atomic data and new models for X-ray spectroscopy.

NASA Astrophysics Data System (ADS)

Smith, Randall K.; Foster, Adam; Brickhouse, Nancy S.; Stancil, Phillip C.; Cumbee, Renata; Mullen, Patrick Dean; AtomDB Team

2018-06-01

The AtomDB project collects atomic data from both theoretical and observational/experimental sources, providing both a convenient interface (http://www.atomdb.org/Webguide/webguide.php) as well as providing input to spectral models for many types of astrophysical X-ray plasmas. We have released several updates to AtomDB in response to the Hitomi data, including new data for the Fe K complex, and have expanded the range of models available in AtomDB to include the Kronos charge exchange models from Mullen at al. (2016, ApJS, 224, 2). Combined with the previous AtomDB charge exchange model (http://www.atomdb.org/CX/), these data enable a velocity-dependent model for X-ray and EUV charge exchange spectra. We also present a new Kappa-distribution spectral model, enabling plasmas with non-Maxwellian electron distributions to be modeled with AtomDB. Tools are provided within pyAtomDB to explore and exploit these new plasma models. This presentation will review these enhancements and describe plans for the new few years of database and code development in preparation for XARM, Athena, and (hopefully) Arcus.

Connes' embedding problem and winning strategies for quantum XOR games

NASA Astrophysics Data System (ADS)

Harris, Samuel J.

2017-12-01

We consider quantum XOR games, defined in the work of Regev and Vidick [ACM Trans. Comput. Theory 7, 43 (2015)], from the perspective of unitary correlations defined in the work of Harris and Paulsen [Integr. Equations Oper. Theory 89, 125 (2017)]. We show that the winning bias of a quantum XOR game in the tensor product model (respectively, the commuting model) is equal to the norm of its associated linear functional on the unitary correlation set from the appropriate model. We show that Connes' embedding problem has a positive answer if and only if every quantum XOR game has entanglement bias equal to the commuting bias. In particular, the embedding problem is equivalent to determining whether every quantum XOR game G with a winning strategy in the commuting model also has a winning strategy in the approximate finite-dimensional model.

'A device for being able to book P&L': the organizational embedding of the Gaussian copula.

PubMed

MacKenzie, Donald; Spears, Taylor

2014-06-01

This article, the second of two articles on the Gaussian copula family of models, discusses the attitude of 'quants' (modellers) to these models, showing that contrary to some accounts, those quants were not 'model dopes' who uncritically accepted the outputs of the models. Although sometimes highly critical of Gaussian copulas - even 'othering' them as not really being models --they nevertheless nearly all kept using them, an outcome we explain with reference to the embedding of these models in inter- and intra-organizational processes: communication, risk control and especially the setting of bonuses. The article also examines the role of Gaussian copula models in the 2007-2008 global crisis and in a 2005 episode known as 'the correlation crisis'. We end with the speculation that all widely used derivatives models (and indeed the evaluation culture in which they are embedded) help generate inter-organizational co-ordination, and all that is special in this respect about the Gaussian copula is that its status as 'other' makes this role evident.

Regularized Embedded Multiple Kernel Dimensionality Reduction for Mine Signal Processing.

PubMed

Li, Shuang; Liu, Bing; Zhang, Chen

2016-01-01

Traditional multiple kernel dimensionality reduction models are generally based on graph embedding and manifold assumption. But such assumption might be invalid for some high-dimensional or sparse data due to the curse of dimensionality, which has a negative influence on the performance of multiple kernel learning. In addition, some models might be ill-posed if the rank of matrices in their objective functions was not high enough. To address these issues, we extend the traditional graph embedding framework and propose a novel regularized embedded multiple kernel dimensionality reduction method. Different from the conventional convex relaxation technique, the proposed algorithm directly takes advantage of a binary search and an alternative optimization scheme to obtain optimal solutions efficiently. The experimental results demonstrate the effectiveness of the proposed method for supervised, unsupervised, and semisupervised scenarios.

Single-step synthesis of crystalline h-BN quantum- and nanodots embedded in boron carbon nitride films

NASA Astrophysics Data System (ADS)

Matsoso, Boitumelo J.; Ranganathan, Kamalakannan; Mutuma, Bridget K.; Lerotholi, Tsenolo; Jones, Glenn; Coville, Neil J.

2017-03-01

Herein we report on the synthesis and characterization of novel crystalline hexagonal boron nitride (h-BN) quantum- and nanodots embedded in large-area boron carbon nitride (BCN) films. The films were grown on a Cu substrate by an atmospheric pressure chemical vapour deposition technique. Methane, ammonia, and boric acid were used as precursors for C, N and B to grow these few atomic layer thick uniform films. We observed that both the size of the h-BN quantum/nanodots and thickness of the BCN films were influenced by the vaporization temperature of boric acid as well as the H3BO3 (g) flux over the Cu substrate. These growth conditions were easily achieved by changing the position of the solid boric acid in the reactor with respect to the Cu substrate. Atomic force microscope (AFM) and TEM analyses show a variation in the h-BN dot size distribution, ranging from nanodots (˜224 nm) to quantum dots (˜11 nm) as the B-source is placed further away from the Cu foil. The distance between the B-source and the Cu foil gave an increase in the C atomic composition (42 at% C-65 at% C) and a decrease in both B and N contents (18 at% B and 14 at% N to 8 at% B and 7 at% N). UV-vis absorption spectra showed a higher band gap energy for the quantum dots (5.90 eV) in comparison with the nanodots (5.68 eV) due to a quantum confinement effect. The results indicated that the position of the B-source and its reaction with ammonia plays a significant role in controlling the nucleation of the h-BN quantum- and nanodots. The films are proposed to be used in solar cells. A mechanism to explain the growth of h-BN quantum/nanodots in BCN films is reported.

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

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.

Ultrafine Ceramic Grains Embedded in Metallic Glass Matrix: Achieving Superior Wear Resistance via Increase in Both Hardness and Toughness.

PubMed

Yang, Lina; Wen, Mao; Dai, Xuan; Cheng, Gang; Zhang, Kan

2018-05-09

As structural materials, crystalline or metallic glass materials have attracted scientific and practical interests. However, some mechanisms involving critical size and shear bands have adverse effects on their mechanical properties. Here, we counter these two effects by introducing a special structure with ultrafine ceramic grains (with a diameter of ∼2.0 nm) embedded into a metallic glass matrix, wherein the grains are mainly composed of a Ta-W-N solid solution structure in nature, surrounded by a W-based amorphous matrix that contains Ta and N atoms. Such a structure is in situ formed during preparation, which combines the merits of both phases to achieve simultaneous increase in hardness and toughness relative to references (pure TaN and W) and thus superior wear resistance. Even more remarkable, a favorable variation of increased hardness but reduced elasticity modulus can be induced by this structure. Intrinsically, ultrafine ceramic grains (free of dislocations), embedded in the metallic glass matrix, could prevent shear band propagation within the glass matrix and further improve the hardness of the matrix material. In return, such glass matrix allows for stiffness neutralization and structural relaxation to reduce the elasticity modulus of ceramic grains. This study will offer a new guidance to fabricate ultrahigh-performance metal-based composites.

Moving from Introverted to Extraverted Embedded Librarian Services: An Example of a Proactive Model

ERIC Educational Resources Information Center

Knight, Valerie R.; Loftis, Charissa

2012-01-01

Librarians at Wayne State College have developed an extraverted online embedded librarian model whereby librarians proactively push out content to students at time-appropriate moments. This article outlines why extraverted approaches are more effective than introverted approaches. It also details how to develop an extraverted program. First,…

Site-occupation embedding theory using Bethe ansatz local density approximations

NASA Astrophysics Data System (ADS)

Senjean, Bruno; Nakatani, Naoki; Tsuchiizu, Masahisa; Fromager, Emmanuel

2018-06-01

Site-occupation embedding theory (SOET) is an alternative formulation of density functional theory (DFT) for model Hamiltonians where the fully interacting Hubbard problem is mapped, in principle exactly, onto an impurity-interacting (rather than a noninteracting) one. It provides a rigorous framework for combining wave-function (or Green function)-based methods with DFT. In this work, exact expressions for the per-site energy and double occupation of the uniform Hubbard model are derived in the context of SOET. As readily seen from these derivations, the so-called bath contribution to the per-site correlation energy is, in addition to the latter, the key density functional quantity to model in SOET. Various approximations based on Bethe ansatz and perturbative solutions to the Hubbard and single-impurity Anderson models are constructed and tested on a one-dimensional ring. The self-consistent calculation of the embedded impurity wave function has been performed with the density-matrix renormalization group method. It has been shown that promising results are obtained in specific regimes of correlation and density. Possible further developments have been proposed in order to provide reliable embedding functionals and potentials.

A generalized self-consistent polycrystal model for the yield strength of nanocrystalline materials

NASA Astrophysics Data System (ADS)

Jiang, B.; Weng, G. J.

2004-05-01

Inspired by recent molecular dynamic simulations of nanocrystalline solids, a generalized self-consistent polycrystal model is proposed to study the transition of yield strength of polycrystalline metals as the grain size decreases from the traditional coarse grain to the nanometer scale. These atomic simulations revealed that a significant portion of atoms resides in the grain boundaries and the plastic flow of the grain-boundary region is responsible for the unique characteristics displayed by such materials. The proposed model takes each oriented grain and its immediate grain boundary to form a pair, which in turn is embedded in the infinite effective medium with a property representing the orientational average of all these pairs. We make use of the linear comparison composite to determine the nonlinear behavior of the nanocrystalline polycrystal through the concept of secant moduli. To this end an auxiliary problem of Christensen and Lo (J. Mech. Phys. Solids 27 (1979) 315) superimposed on the eigenstrain field of Luo and Weng (Mech. Mater. 6 (1987) 347) is first considered, and then the nonlinear elastoplastic polycrystal problem is addressed. The plastic flow of each grain is calculated from its crystallographic slips, but the plastic behavior of the grain-boundary phase is modeled as that of an amorphous material. The calculated yield stress for Cu is found to follow the classic Hall-Petch relation initially, but as the gain size decreases it begins to depart from it. The yield strength eventually attains a maximum at a critical grain size and then the Hall-Petch slope turns negative in the nano-range. It is also found that, when the Hall-Petch relation is observed, the plastic behavior of the polycrystal is governed by crystallographic slips in the grains, but when the slope is negative it is governed by the grain boundaries. During the transition both grains and grain boundaries contribute competitively.