Learning molecular energies using localized graph kernels

NASA Astrophysics Data System (ADS)

Ferré, Grégoire; Haut, Terry; Barros, Kipton

2017-03-01

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

A cluster expansion model for predicting activation barrier of atomic processes

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

Rehman, Tafizur; Jaipal, M.; Chatterjee, Abhijit, E-mail: achatter@iitk.ac.in

2013-06-15

We introduce a procedure based on cluster expansion models for predicting the activation barrier of atomic processes encountered while studying the dynamics of a material system using the kinetic Monte Carlo (KMC) method. Starting with an interatomic potential description, a mathematical derivation is presented to show that the local environment dependence of the activation barrier can be captured using cluster interaction models. Next, we develop a systematic procedure for training the cluster interaction model on-the-fly, which involves: (i) obtaining activation barriers for handful local environments using nudged elastic band (NEB) calculations, (ii) identifying the local environment by analyzing the NEBmore » results, and (iii) estimating the cluster interaction model parameters from the activation barrier data. Once a cluster expansion model has been trained, it is used to predict activation barriers without requiring any additional NEB calculations. Numerical studies are performed to validate the cluster expansion model by studying hop processes in Ag/Ag(100). We show that the use of cluster expansion model with KMC enables efficient generation of an accurate process rate catalog.« less

Pressure/temperature fluid cell apparatus for the neutron powder diffractometer instrument: probing atomic structure in situ.

PubMed

Wang, Hsiu-Wen; Fanelli, Victor R; Reiche, Helmut M; Larson, Eric; Taylor, Mark A; Xu, Hongwu; Zhu, Jinlong; Siewenie, Joan; Page, Katharine

2014-12-01

This contribution describes a new local structure compatible gas/liquid cell apparatus for probing disordered materials at high pressures and variable temperatures in the Neutron Powder Diffraction instrument at the Lujan Neutron Scattering Center, Los Alamos National Laboratory. The new sample environment offers choices for sample canister thickness and canister material type. Finite element modeling is utilized to establish maximum allowable working pressures of 414 MPa at 15 K and 121 MPa at 600 K. High quality atomic pair distribution function data extraction and modeling have been demonstrated for a calibration standard (Si powder) and for supercritical and subcritical CO2 measurements. The new sample environment was designed to specifically target experimental studies of the local atomic structures involved in geologic CO2 sequestration, but will be equally applicable to a wide variety of energy applications, including sorption of fluids on nano/meso-porous solids, clathrate hydrate formation, catalysis, carbon capture, and H2 and natural gas uptake/storage.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE PAGES

Belianinov, Alex; Panchapakesan, G.; Lin, Wenzhi; ...

2014-12-02

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signaturemore » and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

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

Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified bymore » their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Local atomic and magnetic structure of dilute magnetic semiconductor (Ba ,K ) (Zn,Mn ) 2As2

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; Banerjee, Soham; Chen, Bijuan; Jin, Changqing; Feygenson, Mikhail; Uemura, Yasutomo J.; Billinge, Simon J. L.

2016-09-01

We have studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba ,K )(Zn ,Mn )2As2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. We detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5 Å , resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment of Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. We discuss these results in the context of other experiments and theoretical studies on this system.

Ab initio local-energy and local-stress analysis of tensile behaviours of tilt grain boundaries in Al and Cu

NASA Astrophysics Data System (ADS)

Wang, Hao; Kohyama, Masanori; Tanaka, Shingo; Shiihara, Yoshinori

2017-01-01

Tensile deformation and failure of Σ9 tilt grain boundaries (GBs) in Al and Cu have been examined by first-principles tensile tests (FPTTs). Local-energy and local-stress schemes were applied to clarify the variations of local energies and local hydrostatic stresses for all atoms during the deformation process. The GBs in Al and Cu exhibited quite different tensile behaviours in the FPTTs, despite their similar initial configurations. For the Al GB, there are two stages of deformation before failure. In the first stage, the back bonds of the interfacial bonds are mainly stretched, due to special high strength of the interfacial reconstructed bonds. In the second stage, the interfacial bonds begin to be significantly stretched due to high concentrated stresses, while stretching of the back bonds is suppressed. The atoms at the interfacial, back and bulk bonds have very different variations of local energies and local stresses during each stage, because the behaviour of each atom is significantly dependent on each local structural change due to the high sensitivity of sp electrons to the local environment in Al. The Cu GB has much higher tensile strength, and a natural introduction of stacking faults (SFs) occurs via the {111}< 112> shear slip in the bulk regions between the interfaces before the maximum stress is reached. This is caused by the smaller SF energy and lower ideal shear strength of Cu than Al, and is triggered by highly accumulated local energies and stress at the interface atoms. The local-energy distribution around the SF is consistent with the previous theoretical estimation. After the introduction of the SF, the local energies and stresses of all the atoms in the Cu GB supercell tend to become similar to each other during the tensile process, in contrast to the inhomogeneity in the Al GB. The origins of the different tensile behaviours observed for Al and Cu GBs are discussed with respect to the different bonding natures of Al and Cu, which are dominated by three sp valence electrons per atom for Al and by fully occupied d bands and s electrons for Cu.

Learning molecular energies using localized graph kernels

DOE PAGES

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

2017-03-21

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

Learning molecular energies using localized graph kernels

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

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

Challenges and constraints of dynamically emerged source and sink in atomtronic circuits: From closed-system to open-system approaches

PubMed Central

Lai, Chen-Yen; Chien, Chih-Chun

2016-01-01

While batteries offer electronic source and sink for electronic devices, atomic analogues of source and sink and their theoretical descriptions have been a challenge in cold-atom systems. Here we consider dynamically emerged local potentials as controllable source and sink for bosonic atoms. Although a sink potential can collect bosons in equilibrium and indicate its usefulness in the adiabatic limit, sudden switching of the potential exhibits low effectiveness in pushing bosons into it. This is due to conservation of energy and particle in isolated systems such as cold atoms. By varying the potential depth and interaction strength, the systems can further exhibit averse response, where a deeper emerged potential attracts less bosonic atoms into it. To explore possibilities for improving the effectiveness, we investigate what types of system-environment coupling can help bring bosons into a dynamically emerged sink, and a Lindblad operator corresponding to local cooling is found to serve the purpose. PMID:27849034

Atomistic material behavior at extreme pressures

DOE PAGES

Beland, Laurent K.; Osetskiy, Yury N.; Stoller, Roger E.

2016-08-05

Computer simulations are routinely performed to model the response of materials to extreme environments, such as neutron (or ion) irradiation. The latter involves high-energy collisions from which a recoiling atom creates a so-called atomic displacement cascade. These cascades involve coordinated motion of atoms in the form of supersonic shockwaves. These shockwaves are characterized by local atomic pressures >15 GPa and interatomic distances <2 Å. Similar pressures and interatomic distances are observed in other extreme environment, including short-pulse laser ablation, high-impact ballistic collisions and diamond anvil cells. Displacement cascade simulations using four different force fields, with initial kinetic energies ranging frommore » 1 to 40 keV, show that there is a direct relationship between these high-pressure states and stable defect production. An important shortcoming in the modeling of interatomic interactions at these short distances, which in turn determines final defect production, is brought to light.« less

Pressure/temperature fluid cell apparatus for the neutron powder diffractometer instrument: Probing atomic structure in situ

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

Wang, Hsiu-Wen; Fanelli, Victor R.; Reiche, Helmut M.

This contribution describes a new local structure compatible gas/liquid cell apparatus for probing disordered materials at high pressures and variable temperatures in the Neutron Powder Diffraction instrument at the Lujan Neutron Scattering Center, Los Alamos National Laboratory. The new sample environment offers choices for sample canister thickness and canister material type. Finite element modeling is utilized to establish maximum allowable working pressures of 414 MPa at 15 K and 121 MPa at 600 K. High quality atomic pair distribution function data extraction and modeling have been demonstrated for a calibration standard (Si powder) and for supercritical and subcritical CO{sub 2}more » measurements. The new sample environment was designed to specifically target experimental studies of the local atomic structures involved in geologic CO{sub 2} sequestration, but will be equally applicable to a wide variety of energy applications, including sorption of fluids on nano/meso-porous solids, clathrate hydrate formation, catalysis, carbon capture, and H{sub 2} and natural gas uptake/storage.« less

Pressure/temperature fluid cell apparatus for the neutron powder diffractometer instrument: Probing atomic structure in situ

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

Wang, Hsiu -Wen; Fanelli, Victor R.; Reiche, Helmut M.

This contribution describes a new local structure compatible gas/liquid cell apparatus for probing disordered materials at high pressures and variable temperatures in the Neutron Powder Diffraction instrument at the Lujan Neutron Scattering Center, Los Alamos National Laboratory. The new sample environment offers choices for sample canister thickness and canister material type. Finite element modeling is utilized to establish maximum allowable working pressures of 414 MPa at 15 K and 121 MPa at 600 K. High quality atomic pair distribution function data extraction and modeling have been demonstrated for a calibration standard (Si powder) and for supercritical and subcritical CO 2measurements.more » As a result, the new sample environment was designed to specifically target experimental studies of the local atomic structures involved in geologic CO 2 sequestration, but will be equally applicable to a wide variety of energy applications, including sorption of fluids on nano/meso-porous solids, clathrate hydrate formation, catalysis, carbon capture, and H 2 and natural gas uptake/storage.« less

Pressure/temperature fluid cell apparatus for the neutron powder diffractometer instrument: Probing atomic structure in situ

DOE PAGES

Wang, Hsiu -Wen; Fanelli, Victor R.; Reiche, Helmut M.; ...

2014-12-24

This contribution describes a new local structure compatible gas/liquid cell apparatus for probing disordered materials at high pressures and variable temperatures in the Neutron Powder Diffraction instrument at the Lujan Neutron Scattering Center, Los Alamos National Laboratory. The new sample environment offers choices for sample canister thickness and canister material type. Finite element modeling is utilized to establish maximum allowable working pressures of 414 MPa at 15 K and 121 MPa at 600 K. High quality atomic pair distribution function data extraction and modeling have been demonstrated for a calibration standard (Si powder) and for supercritical and subcritical CO 2measurements.more » As a result, the new sample environment was designed to specifically target experimental studies of the local atomic structures involved in geologic CO 2 sequestration, but will be equally applicable to a wide variety of energy applications, including sorption of fluids on nano/meso-porous solids, clathrate hydrate formation, catalysis, carbon capture, and H 2 and natural gas uptake/storage.« less

Optimal atomic structure of amorphous silicon obtained from density functional theory calculations

NASA Astrophysics Data System (ADS)

Pedersen, Andreas; Pizzagalli, Laurent; Jónsson, Hannes

2017-06-01

Atomic structure of amorphous silicon consistent with several reported experimental measurements has been obtained from annealing simulations using electron density functional theory calculations and a systematic removal of weakly bound atoms. The excess energy and density with respect to the crystal are well reproduced in addition to radial distribution function, angular distribution functions, and vibrational density of states. No atom in the optimal configuration is locally in a crystalline environment as deduced by ring analysis and common neighbor analysis, but coordination defects are present at a level of 1%-2%. The simulated samples provide structural models of this archetypal disordered covalent material without preconceived notion of the atomic ordering or fitting to experimental data.

VEDA: a web-based virtual environment for dynamic atomic force microscopy.

PubMed

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

NASA Astrophysics Data System (ADS)

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

DOE PAGES

Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

2016-06-30

We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

Influence of the local environment on Mn acceptors in GaAs

NASA Astrophysics Data System (ADS)

Lee, Donghun; Gohlke, David; Benjamin, Anne; Gupta, Jay A.

2015-04-01

As transistors continue to shrink toward nanoscale dimensions, their characteristics are increasingly dependent on the statistical variations of impurities in the semiconductor material. The scanning tunneling microscope (STM) can be used to not only study prototype devices with atomically precise placement of impurity atoms, but can also probe how the properties of these impurities depend on the local environment. Tunneling spectroscopy of Mn acceptors in GaAs indicates that surface-layer Mn act as a deep acceptor, with a hole binding energy that can be tuned by positioning charged defects nearby. Band bending induced by the tip or by these defects can also tune the ionization state of the acceptor complex, evident as a ring-like contrast in STM images. The interplay of these effects is explored over a wide range of defect distances, and understood using iterative simulations of tip-induced band bending.

Soviet Developments in Material Science No. 1, January - June 1975

DTIC Science & Technology

1975-11-30

Zotova, T. Makhanbetaliyev, B. Ya. Mel’tser, and D. N. Nasledov. Effect of fluctuations in local composition of solid solutions on...289-297. Gurin, N. T., D. G. Semak, and V. V. Fedak. Threshold switching and local states in chalcogenide glasses. FTP, no. 4, 1975...L. N. Seregina. Crystal-glass transition in Ge0 .-Te- p. and its effect on local environment of germanium atoms. FTT, no. 2, 1975, 633

Atomic structure and glass forming ability of Cu46Zr46Al8 bulk metallic glass

NASA Astrophysics Data System (ADS)

Wang, X. D.; Jiang, Q. K.; Cao, Q. P.; Bednarcik, J.; Franz, H.; Jiang, J. Z.

2008-11-01

By using a combination of state-of-the-art experimental and computational methods, the high glass forming ability (GFA) of Cu46Zr46Al8 alloy is studied from the view of its atomic packing. Three-dimensional atomic configuration is well established. It is found that Al atoms almost homogeneously distribute around Cu and Zr atoms without segregation, causing the local environment around Cu and Zr atoms in Cu46Zr46Al8 bulk metallic glass different from that of the major competing phase of Cu10Zr7. Furthermore, the addition of Al not only increases the amount of icosahedronlike clusters but also makes them more homogeneous distribution, which can enhance the GFA by increasing the structural incompatibility with the competing crystalline phases.

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.

Local atomic and magnetic structure of dilute magnetic semiconductor ( Ba , K ) ( Zn , Mn ) 2 As 2

DOE PAGES

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; ...

2016-09-06

We studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba,K)(Zn,Mn) 2As 2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. Furthermore, we detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5Å, resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment ofmore » Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. Finally, we discuss these results in the context of other experiments and theoretical studies on this system.« less

AtomPy: an open atomic-data curation environment

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

Electronic structure of oxygen-vacancy defects in amorphous In-Ga-Zn-O semiconductors

NASA Astrophysics Data System (ADS)

Noh, Hyeon-Kyun; Chang, K. J.; Ryu, Byungki; Lee, Woo-Jin

2011-09-01

We perform first-principles density functional calculations to investigate the atomic and electronic properties of various O-vacancy (VO) defects in amorphous indium gallium zinc oxides (a-IGZO). The formation energies of VO have a tendency to increase with increasing number of neighboring Ga atoms, whereas they are generally low in the environment surrounded with In atoms. Thus, adding Ga atoms suppresses the formation of O-deficiency defects, which are considered as the origin of device instability in a-IGZO-based thin film transistors. The conduction band edge state is characterized by the In s orbital and insensitive to disorder, in good agreement with the experimental finding that increasing the In content enhances the carrier density and mobility. In a-IGZO, while most VO defects are deep donors, some of the defects act as shallow donors due to local environments different from those in crystalline oxides. As ionized O vacancies can capture electrons, it is suggested that these defects are responsible for positive shifts of the threshold voltage observed under positive gate bias stress. Under light illumination stress, VO defects can be ionized, becoming VO2+ defects due to the negative-U behavior. When electrons are captured by applying a negative bias voltage, ionized VO2+ defects return to the original neutral charge state. Through molecular dynamics simulations, we find that the initial neutral state is restored by annealing, in good agreement with experiments, although the annealing temperature depends on the local environment. Our calculations show that VO defects play an important role in the instability of a-IGZO-based devices.

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.

Quantum phase transitions of light in a dissipative Dicke-Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Wu, Ren-Cun; Tan, Lei; Zhang, Wen-Xuan; Liu, Wu-Ming

2017-09-01

The impact that the environment has on the quantum phase transition of light in the Dicke-Bose-Hubbard model is investigated. Based on the quasibosonic approach, mean-field theory, and perturbation theory, the formulation of the Hamiltonian, the eigenenergies, and the superfluid order parameter are obtained analytically. Compared with the ideal cases, the order parameter of the system evolves with time as the photons naturally decay in their environment. When the system starts with the superfluid state, the dissipation makes the photons more likely to localize, and a greater hopping energy of photons is required to restore the long-range phase coherence of the localized state of the system. Furthermore, the Mott lobes depend crucially on the numbers of atoms and photons (which disappear) of each site, and the system tends to be classical with the number of atoms increasing; however, the atomic number is far lower than that expected under ideal circumstances. As there is an inevitable interaction between the coupled-cavity array and its surrounding environment in the actual experiments, the system is intrinsically dissipative. The results obtained here provide a more realistic image for characterizing the dissipative nature of quantum phase transitions in lossy platforms, which will offer valuable insight into quantum simulation of a dissipative system and which are helpful in guiding experimentalists in open quantum systems.

Global Anisotropies in TeV Cosmic Rays Related to the Sun's Local Galactic Environment from IBEX

NASA Technical Reports Server (NTRS)

Schwadron, N. A.; Adams, F. C.; Christian, E. R.; Desiati, P.; Frisch, P.; Funsten, H. O.; Jokipii, J. R.; McComas, D. J.; Moebius, E.; Zank, G. P.

2014-01-01

Observations with the Interstellar Boundary Explorer (IBEX) have shown enhanced energetic neutral atom (ENA) emission from a narrow, circular ribbon likely centered on the direction of the local interstellar medium (LISM) magnetic field. Here, we show that recent determinations of the local interstellar velocity, based on interstellar atom measurements with IBEX, are consistent with the interstellar modulation of high-energy (tera-electron volts, TeV) cosmic rays and diffusive propagation from supernova sources revealed in global anisotropy maps of ground-based high-energy cosmic-ray observatories (Milagro, Asg, and IceCube). Establishing a consistent local interstellar magnetic field direction using IBEX ENAs at hundreds to thousands of eV and galactic cosmic rays at tens of TeV has wide-ranging implications for the structure of our heliosphere and its interactions with the LISM, which is particularly important at the time when the Voyager spacecraft are leaving our heliosphere.

The hybrid lattice of K(x)Fe(2-y)Se2: where superconductivity and magnetism coexist.

PubMed

Louca, Despina; Park, Keeseong; Li, Bing; Neuefeind, Joerg; Yan, Jiaqiang

2013-01-01

Much remains unknown of the microscopic origin of superconductivity in atomically disordered systems of amorphous alloys or in crystals riddled with defects. A manifestation of this conundrum is envisaged in the highly defective superconductor of K(x)Fe(2-y)Se2. How can superconductivity survive under such crude conditions that call for strong electron localization? Here, we show that the Fe sublattice is locally distorted and accommodates two kinds of Fe valence environments giving rise to a bimodal bond-distribution, with short and long Fe bonds. The bimodal bonds are present even as the system becomes superconducting in the presence of antiferromagnetism, with the weight continuously shifting from the short to the long with increasing K content. Such a hybrid state is most likely found in cuprates as well while our results point to the importance of the local atomic symmetry by which exchange interactions between local moments materialize.

Global anisotropies in TeV cosmic rays related to the Sun's local galactic environment from IBEX.

PubMed

Schwadron, N A; Adams, F C; Christian, E R; Desiati, P; Frisch, P; Funsten, H O; Jokipii, J R; McComas, D J; Moebius, E; Zank, G P

2014-02-28

Observations with the Interstellar Boundary Explorer (IBEX) have shown enhanced energetic neutral atom (ENA) emission from a narrow, circular ribbon likely centered on the direction of the local interstellar medium (LISM) magnetic field. Here, we show that recent determinations of the local interstellar velocity, based on interstellar atom measurements with IBEX, are consistent with the interstellar modulation of high-energy (tera-electron volts, TeV) cosmic rays and diffusive propagation from supernova sources revealed in global anisotropy maps of ground-based high-energy cosmic-ray observatories (Milagro, Asγ, and IceCube). Establishing a consistent local interstellar magnetic field direction using IBEX ENAs at hundreds to thousands of eV and galactic cosmic rays at tens of TeV has wide-ranging implications for the structure of our heliosphere and its interactions with the LISM, which is particularly important at the time when the Voyager spacecraft are leaving our heliosphere.

Effect of magnetism and atomic order on static atomic displacements in the Invar alloy Fe-27 at.% Pt

NASA Astrophysics Data System (ADS)

Sax, C. R.; Schönfeld, B.; Ruban, A. V.

2015-08-01

Fe-27 at.% Pt was aged at 1123 K and quenched to room temperature (RT) to set up a state of thermal equilibrium. The local atomic arrangement was studied by diffuse x-ray scattering above (at 427 K) and below (at RT) the Curie temperature as well as at RT under a saturating magnetic field. The separated short-range order scattering remained unchanged for all three states, with maxima at 100 positions. Effective pair interaction parameters determined by the inverse Monte Carlo method gave an order-disorder transition temperature of about 1088 K, close to direct experimental findings. The species-dependent static atomic displacements for the first two shells show large differences, with a strong increase in magnitude from the state at 427 K over RT to the state under saturating magnetic field. This outcome is in agreement with an increase in atomic volume of Fe with increasing local magnetic moment. Electronic-structure calculations closely reproduce the values for the static atomic displacements in the ferromagnetic state, and predict their dependence on the atomic configuration. They also reveal a strong dependence of the magnetic exchange interactions in Fe-Pt on the atomic configuration state and lattice parameter. In particular, the increase of the Curie temperature in a random state relative to that in the ordered one is demonstrated to be related to the corresponding change of the magnetic exchange interactions due to the different local atomic chemical environment. There exists a similar strong concentration dependence of the chemical interactions as in the case of magnetic exchange interactions. Theoretical effective interactions for Fe-27 at.% Pt alloy are in good agreement with experimental results, and they also reproduce well the L1 2-A1 transition temperature.

Observing heliospheric neutral atoms at 1 AU

NASA Astrophysics Data System (ADS)

Heerikhuisen, Jacob; Pogorelov, Nikolai; Florinski, Vladimir; Zank, Gary

2006-09-01

Although in situ observations of distant heliospheric plasma by the Voyagers has proven to be extremely enlightening, such point observations need to be complemented with global measurements taken remotely to obtain a complete picture of the heliosphere and local interstellar environment. Neutral atoms, with their contempt for magnetic fields, provide useful probes of the plasma that generated them. However, there will be a number of ambiguities in neutral atom readings that require a deeper understanding of the plasma processes generating neutral atoms, as well as the loss mechanisms on their flight to the observation point. We introduce a procedure for generating all-sky maps of energetic H-atoms, calculated directly in our Monte-Carlo neutral atom code. Results obtained for a self-consistent axisymmetric MHD-Boltzmann calculation, as well as several non-selfconsistent 3D sky maps, will be presented.

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

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

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

Oxygen atom reaction with shuttle materials at orbital altitudes

NASA Technical Reports Server (NTRS)

Leger, L. J.

1983-01-01

Significant effects of the environment on payload bay materials observed on all flights are discussed. The STS 5 experiment is described. Increased outgassing rates resulting in possible localized effects on experiments, changes in optical control surfaces, and photoemission from reaction products are considered.

EXAFS and electrical studies of new narrow-gap semiconductors: InTe1-xSex and In1-xGaxTe

NASA Astrophysics Data System (ADS)

Lebedev, A. I.; Michurin, A. V.; Sluchinskaya, I. A.; Demin, V. N.; Munro, I. H.

2000-12-01

The local environment of Ga, Se and Tl atoms in InTe-based solid solutions was studied by EXAFS technique. It was shown that all investigated atoms are substitutional impurities, which enter the In(1), Te and In(2) positions in the InTe structure, respectively. The electrical measurements revealed that In1-xGaxTe and InTe1-xSex solid solutions become semiconductors at x>0.24 and >0.15, respectively.

Rapid insights from remote sensing in the geosciences

NASA Astrophysics Data System (ADS)

Plaza, Antonio

2015-03-01

The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. Dept. of Energy's National Nuclear Security Admin. under Contract DE-AC04-94AL85000.

Chemical Environment Effects on K[beta]/K[alpha] Intensity Ratio: An X-Ray Fluorescence Experiment on Periodic Trends

ERIC Educational Resources Information Center

Durham, Chaney R.; Chase, Jeffery M.; Nivens, Delana A.; Baird, William H.; Padgett, Clifford W.

2011-01-01

X-ray fluorescence (XRF) data from an energy-dispersive XRF instrument were used to investigate the chlorine K[alpha] and K[beta] peaks in several group 1 salts. The ratio of the peak intensity is sensitive to the local chemical environment of the chlorine atoms studied in this experiment and it shows a periodic trend for these salts. (Contains 1…

Atomic-Scale Fingerprint of Mn Dopant at the Surface of Sr3(Ru1−xMnx)2O7

PubMed Central

Li, Guorong; Li, Qing; Pan, Minghu; Hu, Biao; Chen, Chen; Teng, Jing; Diao, Zhenyu; Zhang, Jiandi; Jin, Rongying; Plummer, E. W.

2013-01-01

Chemical doping in materials is known to give rise to emergent phenomena. These phenomena are extremely difficult to predict a priori, because electron-electron interactions are entangled with local environment of assembled atoms. Scanning tunneling microscopy and low energy electron diffraction are combined to investigate how the local electronic structure is correlated with lattice distortion on the surface of Sr3(Ru1−xMnx)2O7, which has double-layer building blocks formed by (Ru/Mn)O6 octahedra with rotational distortion. The presence of doping-dependent tilt distortion of (Ru/Mn)O6 octahedra at the surface results in a C2v broken symmetry in contrast with the bulk C4v counterpart. It also enables us to observe two Mn sites associated with the octahedral rotation in the bulk through the “chirality” of local electronic density of states surrounding Mn, which is randomly distributed. These results serve as fingerprint of chemical doping on the atomic scale. PMID:24108411

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal.

PubMed

Shibuta, Yasushi; Sakane, Shinji; Miyoshi, Eisuke; Okita, Shin; Takaki, Tomohiro; Ohno, Munekazu

2017-04-05

Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.

IBEX Observations and Simulations of the Ribbon: Implications for the Very Local Interstellar Medium

NASA Astrophysics Data System (ADS)

Zirnstein, E.

2017-12-01

The crossing of the Voyager 1 spacecraft into the very local interstellar medium (VLISM) in 2012 August opened a new chapter in humankind's exploration of space. Voyager 1 has been measuring interstellar plasma properties outside the heliosphere, including the galactic cosmic ray flux, (indirectly) the compressed interstellar plasma, as well as the compressed interstellar magnetic field draped around the heliosphere. Interstellar Boundary Explorer (IBEX) neutral atom observations complement the only in situ observations of the VLISM made by Voyager 1. IBEX is an Earth-orbiting spacecraft equipped with two single-pixel cameras that detect neutral atoms produced by the interaction of the solar wind (SW) with the VLISM, as well as neutral atoms flowing into the heliosphere from the VLISM itself. After its launch in 2009, IBEX discovered the unexpected existence of the "ribbon," a nearly circular arc across the sky of enhanced hydrogen ENA fluxes observed at keV energies. The ribbon fluxes originate from look directions perpendicular to the local interstellar magnetic field draped around the heliosphere, and can be used to derive the VLISM magnetic field magnitude and direction far from the heliopause. Thus, IBEX observations of the ribbon complement Voyager 1 in situ observations of the VLISM magnetic field, and provide insight into what Voyager 2 will observe after it crosses the heliopause. This talk will review key IBEX observations of the VLISM environment related to the ribbon and the VLISM magnetic field observed by Voyager 1, and their implications for the VLISM environment.

Extended electron energy loss fine structure simulation of the local boron environment in sodium aluminoborosilicate glasses containing gadolinium

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

Qian, Morris; Li, Hong; Li, Liyu

Gadolinium can be dissolved in sodium-alumino-borosilicate glasses up to 47 wt% in a baseline borosilicate glass (mol%) 20 B2O3, 5 Al2O3, 60 SiO2,and 20 Na2O. Understanding of Gd dissolution in borosilicate melts is important in glass formulation optimization. Electron energy loss fine structure (ELFS) spectroscopy is chosen, which provides well resolved local atomic structure information for both amorphous and crystalline materials with high sensitivity to low Z elements such as Al, B, Na, O, and Si where the x-ray absorption fine structure (XAFS) technique faces experimental difficulty. In this study, we report our results of boron K-edge ELFS study. Twomore » borosilicate glass samples with 30 and 47 mass% Gd2O3, B20Gd30 and B20Gd47were chosen for B K-edge ELFS study. EEL spectra were acquired on a Philips 430 TEM equipped with Gatan PEELS system 666 and EL/P 2.1 software with Custom function AcqLong. The ELFS data analysis was performed using UWELFS, UWXAFS and FEFF software. From our Gd solubility study, the local structure of Gd in the borate environment possibly resembles double chain structure found in crystalline Gd(BO2)3 as proposed by Chakraborty et al. The B/Gd ratio's in both glasses are smaller then 3, which means the excess Gd atoms in the Si-sites would be 17 and 60 mol% of the total Gd atoms, respectively according to the model, yet the local environment of borate sites saturated with Gd should be remained. To verity above hypothesis, the double chain structure model was applied to fit boron K-edge. The model was shown to well fit experimental boron K-edge EELS spectra for both glasses with some degree of distance distortion which is understandable in amorphous structure. Therefore, it is very likely that Gd stabilized in borate sites has a local structure resembling the double chain Gd(BO2)3 structure as proposed by our solubility study and literature.« less

Atomic Evolution and Entanglement of Two Qubits in Photon Superfluid

NASA Astrophysics Data System (ADS)

Yin, Miao; Zhang, Xiongfeng; Deng, Yunlong; Deng, Huaqiu

2018-07-01

By using reservoir theory, we investigate the evolution of an atom placed in photon superfluid and study the entanglement properties of two qubits interacting with photon superfluid. It is found that the atomic decay rate in photon superfluid changes periodically with position of the atom and the decay rate can be inhibited compared to that in usual electromagnetic environment without photon superfluid. It is also found that when two atoms are separately immersed in their own local photon-superfluid reservoir, the entanglement sudden death or birth occurs or not only depends on the initial state of the qubits. What is more, we find a possible case that the concurrence between two qubits can remain a constant value by choosing proper values of parameters of the system, which may provide a new way to preserve quantum entanglement.

Combining density functional theory (DFT) and pair distribution function (PDF) analysis to solve the structure of metastable materials: the case of metakaolin.

PubMed

White, Claire E; Provis, John L; Proffen, Thomas; Riley, Daniel P; van Deventer, Jannie S J

2010-04-07

Understanding the atomic structure of complex metastable (including glassy) materials is of great importance in research and industry, however, such materials resist solution by most standard techniques. Here, a novel technique combining thermodynamics and local structure is presented to solve the structure of the metastable aluminosilicate material metakaolin (calcined kaolinite) without the use of chemical constraints. The structure is elucidated by iterating between least-squares real-space refinement using neutron pair distribution function data, and geometry optimisation using density functional modelling. The resulting structural representation is both energetically feasible and in excellent agreement with experimental data. This accurate structural representation of metakaolin provides new insight into the local environment of the aluminium atoms, with evidence of the existence of tri-coordinated aluminium. By the availability of this detailed chemically feasible atomic description, without the need to artificially impose constraints during the refinement process, there exists the opportunity to tailor chemical and mechanical processes involving metakaolin and other complex metastable materials at the atomic level to obtain optimal performance at the macro-scale.

The hybrid lattice of KxFe2−ySe2: where superconductivity and magnetism coexist

PubMed Central

Louca, Despina; Park, Keeseong; Li, Bing; Neuefeind, Joerg; Yan, Jiaqiang

2013-01-01

Much remains unknown of the microscopic origin of superconductivity in atomically disordered systems of amorphous alloys or in crystals riddled with defects. A manifestation of this conundrum is envisaged in the highly defective superconductor of KxFe2−ySe2. How can superconductivity survive under such crude conditions that call for strong electron localization? Here, we show that the Fe sublattice is locally distorted and accommodates two kinds of Fe valence environments giving rise to a bimodal bond-distribution, with short and long Fe bonds. The bimodal bonds are present even as the system becomes superconducting in the presence of antiferromagnetism, with the weight continuously shifting from the short to the long with increasing K content. Such a hybrid state is most likely found in cuprates as well while our results point to the importance of the local atomic symmetry by which exchange interactions between local moments materialize. PMID:23782976

The hybrid lattice of K xFe 2-ySe 2: where superconductivity and magnetism coexist

DOE PAGES

Yang, Junjie; Duan, Chunruo; Huang, Qing; ...

2013-01-01

Much remains unknown of the microscopic origin of superconductivity in atomically disordered systems of amorphous alloys or in crystals riddled with defects. A manifestation of this conundrum is envisaged in the highly defective superconductor of K xFe 2-ySe 2. How can superconductivity survive under such crude conditions that call for strong electron localization? Here, we show that the Fe sublattice is locally distorted and accommodates two kinds of Fe valence environments giving rise to a bimodal bond-distribution, with short and long Fe bonds. The bimodal bonds are present even as the system becomes superconducting in the presence of antiferromagnetism, withmore » the weight continuously shifting from the short to the long with increasing K content. Such a hybrid state is most likely found in cuprates as well while our results point to the importance of the local atomic symmetry by which exchange interactions between local moments materialize.« less

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of Mn K -edge XANES data

NASA Astrophysics Data System (ADS)

Monesi, C.; Meneghini, C.; Bardelli, F.; Benfatto, M.; Mobilio, S.; Manju, U.; Sarma, D. D.

2005-11-01

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K -edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3 . The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K -edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

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

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

DOE PAGES

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs; ...

2018-05-25

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural Network Approach for Characterizing Structural Transformations by X-Ray Absorption Fine Structure Spectroscopy

NASA Astrophysics Data System (ADS)

Timoshenko, Janis; Anspoks, Andris; Cintins, Arturs; Kuzmin, Alexei; Purans, Juris; Frenkel, Anatoly I.

2018-06-01

The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its in situ changes directly from the x-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from a body-centered to a face-centered cubic arrangement of iron atoms. This method is attractive for a broad range of materials and experimental conditions.

Homogeneity of Pb(Zr ,Ti)O3 thin films by chemical solution deposition: Extended x-ray absorption fine structure spectroscopy study of zirconium local environment

NASA Astrophysics Data System (ADS)

Malic, Barbara; Arcon, Iztok; Kodre, Alojz; Kosec, Marija

2006-09-01

Sols for Pb(Zr0.53Ti0.47)O3 (PZT) thin films were prepared by 2-methoxyethanol route from lead acetate, titanium n-propoxide, and zirconium n-propoxide, the latter either unmodified or modified with acetylacetone or acetic acid in a 2/1 molar ratio and deposited on sapphire (0001). By Zr K-edge extended x-ray absorption fine structure (EXAFS) spectroscopy, the structural changes in the Zr local environment, induced by the addition of the two modifiers, were followed from the synthesis of the PZT sol to the transition to the amorphous film. In the unmodified PZT sol segregation of Zr species occurs from the original dimers present in the Zr propoxide solution in 2-methoxyethanol. The immediate neighborhood of Zr atoms changes markedly at the transition from the sol to the amorphous film: the local structure around Zr atoms is similar to the one found in tetragonal zirconia particles. The modification of Zr propoxide with acetylacetone in 2-methoxyethanol results in Zr monomers. In PZT sol, clustering of Zr species is observed continuing into the amorphous film. By modification with acetic acid the original dimeric structure of the Zr precursor is retained in the PZT sol and further in the amorphous film. Selective modification of Zr propoxide with acetic acid therefore results in a more homogeneous distribution of Zr atoms in the PZT sol and amorphous film than in both as-received and acetylacetone-modified Zr propoxide.

Tunneling spectroscopy of a phosphorus impurity atom on the Ge(111)-(2 × 1) surface

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

Savinov, S. V.; Oreshkin, A. I., E-mail: oreshkin@spmlab.phys.msu.su, E-mail: oreshkin@spmlab.ru; Oreshkin, S. I.

2015-06-15

We numerically model the Ge(111)-(2 × 1) surface electronic properties in the vicinity of a P donor impurity atom located near the surface. We find a notable increase in the surface local density of states (LDOS) around the surface dopant near the bottom of the empty surface state band π*, which we call a split state due to its limited spatial extent and energetic position inside the band gap. We show that despite the well-established bulk donor impurity energy level position at the very bottom of the conduction band, a surface donor impurity on the Ge(111)-(2 × 1) surface mightmore » produce an energy level below the Fermi energy, depending on the impurity atom local environment. It is demonstrated that the impurity located in subsurface atomic layers is visible in a scanning tunneling microscope (STM) experiment on the Ge(111)-(2 × 1) surface. The quasi-1D character of the impurity image, observed in STM experiments, is confirmed by our computer simulations with a note that a few π-bonded dimer rows may be affected by the presence of the impurity atom. We elaborate a model that allows classifying atoms on the experimental low-temperature STM image. We show the presence of spatial oscillations of the LDOS by the density-functional theory method.« less

High-dimensional atom localization via spontaneously generated coherence in a microwave-driven atomic system.

PubMed

Wang, Zhiping; Chen, Jinyu; Yu, Benli

2017-02-20

We investigate the two-dimensional (2D) and three-dimensional (3D) atom localization behaviors via spontaneously generated coherence in a microwave-driven four-level atomic system. Owing to the space-dependent atom-field interaction, it is found that the detecting probability and precision of 2D and 3D atom localization behaviors can be significantly improved via adjusting the system parameters, the phase, amplitude, and initial population distribution. Interestingly, the atom can be localized in volumes that are substantially smaller than a cubic optical wavelength. Our scheme opens a promising way to achieve high-precision and high-efficiency atom localization, which provides some potential applications in high-dimensional atom nanolithography.

Investigation of the Structural Stability of Ion-Implanted Gd 2Ti 2-xSn xO 7 Pyrochlore-Type Oxides by Glancing Angle X-ray Absorption Spectroscopy

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

Aluri, Esther Rani; Hayes, John R.; Walker, James D.S.

2016-03-24

Rare-earth titanate and stannate pyrochlore-type oxides have been investigated in the past for the sequestration of nuclear waste elements because of their resistance to radiation-induced structural damage. In order to enhance this property, it is necessary to understand the effect of radioactive decay of the incorporated actinide elements on the local chemical environment. In this study, Gd 2Ti 2–xSn xO 7 materials have been implanted with Au– ions to simulate radiation-induced structural damage. Glancing angle X-ray absorption near-edge spectroscopy (GA-XANES), glancing angle X-ray absorption fine structure (GA-EXAFS) analysis, and powder X-ray diffraction have been used to investigate changes in themore » local coordination environment of the metal atoms in the damaged surface layer. Examination of GA-XANES/EXAFS spectra from the implanted Gd 2Ti 2–xSn xO 7 materials collected at various glancing angles allowed for an investigation of how the local coordination environment around the absorbing atoms changed at different depths in the damaged surface layer. This study has shown the usefulness of GA-XANES to the examination of ion-implanted materials and has suggested that Gd 2Ti 2–xSn xO 7 becomes more susceptible to ion-beam-induced structural damage with increasing Sn concentration.« less

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.

The Thermochemical and Kinetic Properties of Ascorbate are Tuned by its Local Environment: Solution Chemistry and Biochemical Implications

PubMed Central

Warren, Jeffrey J.; Mayer, James M.

2010-01-01

Ascorbate (Vitamin C) is a ubiquitous biological cofactor. While its aqueous solution chemistry has long been studied, many in vivo reactions of ascorbate occur in enzyme active sites or at membrane interfaces, which have varying local environments. This report shows that the rate and driving force of oxidations of two ascorbate derivatives by the TEMPO radical (2,2′-6,6′-tetramethylpiperidine-1-oxyl) in acetonitrile are very sensitive to the presence of various additives. These reactions proceed by the transfer of a proton and an electron (a hydrogen atom), as is typical of biological ascorbate reactions. The measured rate and equilibrium constants vary substantially with added water or other polar solutes in acetonitrile solutions, indicating large shifts in the reducing power of ascorbate. The correlation of rate and equilibrium constants indicates that this effect has a thermochemical origin rather than being a purely kinetic effect. This contrasts with previous examples of solvent effects on hydrogen atom transfer reactions. Potential biological implications of this apparently unique effect are discussed. PMID:20476757

Sound Source Localization through 8 MEMS Microphones Array Using a Sand-Scorpion-Inspired Spiking Neural Network.

PubMed

Beck, Christoph; Garreau, Guillaume; Georgiou, Julius

2016-01-01

Sand-scorpions and many other arachnids perceive their environment by using their feet to sense ground waves. They are able to determine amplitudes the size of an atom and locate the acoustic stimuli with an accuracy of within 13° based on their neuronal anatomy. We present here a prototype sound source localization system, inspired from this impressive performance. The system presented utilizes custom-built hardware with eight MEMS microphones, one for each foot, to acquire the acoustic scene, and a spiking neural model to localize the sound source. The current implementation shows smaller localization error than those observed in nature.

Chemical contrast in STM imaging of transition metal aluminides

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

Duguet, T.; Thiel, Patricia A.

2012-08-01

The present manuscript reviews recent scanning tunnelling microscopy (STM) studies of transition metal (TM) aluminide surfaces. It provides a general perspective on the contrast between Al atoms and TM atoms in STM imaging. A general trend is the much stronger bias dependence of TM atoms, or TM-rich regions of the surface. This dependence can be attenuated by the local chemical arrangements and environments. Al atoms can show a stronger bias dependence when their chemical environment, such as their immediate subsurface, is populated with TM. All this is well explained in light of combined results of STM and both theoretical andmore » experimental electronic and crystallographic structure determinations. Since STM probes the Fermi surface, the electronic structure in the vicinity of the Fermi level (EF) is essential for understanding contrast and bias dependence. Hence, partial density of states provides information about the TM d band position and width, s–p–d hybridization or interactions, or charge transfer between constituent elements. In addition, recent developments in STM image simulations are very interesting for elucidating chemical contrast at Al–TM alloy surfaces, and allow direct atomic identification, when the surface does not show too much disorder. Overall, we show that chemically-specific imaging is often possible at these surfaces.« less

Self-consistent mapping of the ab initio calculations to the multi-orbital p- d model: Magnetism in α-FeSi2 films as the effect of the local environment

NASA Astrophysics Data System (ADS)

Zhandun, V.; Zamkova, N.; Ovchinnikov, S.; Sandalov, I.

2017-11-01

To accurately translate the results obtained within density functional theory (DFT) to the language of many-body theory we suggest and test the following approach: the parameters of the formulated model are to be found from the requirement that the model self-consistent electron density and density of electron states are as close as possible to the ones found from the DFT-based calculations. The investigation of the phase diagram of the model allows us to find the critical regions in magnetic properties. Then the behavior of the real system in these regions is checked by the ab initio calculations. As an example, we studied the physics of magnetic moment (MM) formation due to substitutions of Si by Fe-atoms or vice versa in the otherwise non-magnetic alloy α-FeSi2. We find that the MM formation is essentially controlled by the interaction of Fe atoms with its next nearest atoms (NNN) and by their particular arrangement. The latter may result in different magnetic states at the same concentrations of constituents. Moreover, one of arrangements produces the counterintuitive result: a ferromagnetism arises due to an increase in Si concentration in Fe1-xSi2+ x ordered alloy. The existing phenomenological models associate the destruction of magnetic moment only with the number of Fe-Si nearest neighbors. The presented results show that the crucial role in MM formation is played by the particular local NNN environment of the metal atom in the transition metal-metalloid alloy.

Specific features of the atomic structure of metallic layers of multilayered (CoFeZr/SiO2)32 and (CoFeZr/ a-Si)40 nanostructures with different interlayers

NASA Astrophysics Data System (ADS)

Domashevskaya, E. P.; Guda, A. A.; Chernyshev, A. V.; Sitnikov, V. G.

2017-02-01

Multilayered nanostructures (MN) were prepared by ion-beam successive sputtering from two targets, one of which was a metallic Co45Fe45Zr10 alloy plate and another target was a quartz (SiO2) or silicon plate on the surface of a rotating glass-ceramic substrate in an argon atmosphere. The Co and Fe K edges X-ray absorption fine structure of XANES in the (CoFeZr/SiO2)32 sample with oxide interlayers was similar to XANES of metallic Fe foil. This indicated the existence in metallic layers of multilayered CoFeZr nanocrystals with a local environment similar to the atomic environment in solid solutions on the base of bcc Fe structure, which is also confirmed by XRD data. XANES near the Co and Fe K edges absorption in another multilayered nanostructure with silicon interlayers (CoFeZr/ a-Si)40 differs from XANES of MN with dielectric SiO2 interlayer, which demonstrates a dominant influence of the Fe-Si and Co-Si bonds in the local environment of 3 d Co and Fe metals when they form CoFeSi-type silicide phases in thinner bilayers of this MN.

Localized magnetism in liquid Al80Mn20 alloys: A first-principles investigation

NASA Astrophysics Data System (ADS)

Jakse, N.; LeBacq, O.; Pasturel, A.

2006-04-01

We present first-principles investigations of the formation of magnetic moments in liquid Al80Mn20 alloys as a function of temperature. We predict the existence of large magnetic moments on Mn atoms which are close to that of the single-impurity limit. The wide distribution of moments can be understood in terms of fluctuations in the local environment. Our calculations also predict that thermal expansion effects within the single-impurity model mainly explain the striking increase of magnetism with temperature.

Lattice instability and elastic response of metastable Mo1-xSix thin films

NASA Astrophysics Data System (ADS)

Fillon, A.; Jaouen, C.; Michel, A.; Abadias, G.; Tromas, C.; Belliard, L.; Perrin, B.; Djemia, Ph.

2013-11-01

We present a detailed experimental study on Mo1-xSix thin films, an archetypal alloy system combining metallic and semiconductor materials. The correlations between structure and elastic response are comprehensively investigated. We focus on assessing trends for understanding the evolution of elastic properties upon Si alloying in relation to the structural state (crystalline vs amorphous), bonding character (metallic vs covalent), and local atomic environment. By combining picosecond ultrasonics and Brillouin light scattering techniques, a complete set of effective elastic constants and mechanical moduli (B, G, E) is provided in the whole compositional range, covering bcc solid solutions (x < 0.20) and the amorphous phase (0.20 < x < 1.0). A softening of the shear and Young moduli and a concomitant decrease of the Debye temperature is revealed for crystalline alloys, with a significant drop being observed at x ˜ 0.2 corresponding to the limit of crystal lattice stability. Amorphous alloys exhibit a more complex elastic response, related to variations in coordination number, atomic volume, and bonding state, depending on Si content. Finally, distinct evolutions of the G/B ratio as a function of Cauchy pressure are reported for crystalline and amorphous alloys, enabling us to identify signatures of ductility vs brittleness in the features of the local atomic environment. This work paves the way to design materials with improved mechanical properties by appropriate chemical substitution or impurity incorporation during thin-film growth.

Three-dimensional atom localization via electromagnetically induced transparency in a three-level atomic system.

PubMed

Wang, Zhiping; Cao, Dewei; Yu, Benli

2016-05-01

We present a new scheme for three-dimensional (3D) atom localization in a three-level atomic system via measuring the absorption of a weak probe field. Owing to the space-dependent atom-field interaction, the position probability distribution of the atom can be directly determined by measuring the probe absorption. It is found that, by properly varying the parameters of the system, the probability of finding the atom in 3D space can be almost 100%. Our scheme opens a promising way to achieve high-precision and high-efficiency 3D atom localization, which provides some potential applications in laser cooling or atom nano-lithography via atom localization.

The evolution of structural and chemical heterogeneity during rapid solidification at gas atomization

NASA Astrophysics Data System (ADS)

Golod, V. M.; Sufiiarov, V. Sh

2017-04-01

Gas atomization is a high-performance process for manufacturing superfine metal powders. Formation of the powder particles takes place primarily through the fragmentation of alloy melt flow with high-pressure inert gas, which leads to the formation of non-uniform sized micron-scale particles and subsequent their rapid solidification due to heat exchange with gas environment. The article presents results of computer modeling of crystallization process, simulation and experimental studies of the cellular-dendrite structure formation and microsegregation in different size particles. It presents results of adaptation of the approach for local nonequilibrium solidification to conditions of crystallization at gas atomization, detected border values of the particle size at which it is possible a manifestation of diffusionless crystallization.

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

Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures.more » The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.« less

Resonance fluorescence based two- and three-dimensional atom localization

NASA Astrophysics Data System (ADS)

Wahab, Abdul; Rahmatullah; Qamar, Sajid

2016-06-01

Two- and three-dimensional atom localization in a two-level atom-field system via resonance fluorescence is suggested. For the two-dimensional localization, the atom interacts with two orthogonal standing-wave fields, whereas for the three-dimensional atom localization, the atom interacts with three orthogonal standing-wave fields. The effect of the detuning and phase shifts associated with the corresponding standing-wave fields is investigated. A precision enhancement in position measurement of the single atom can be noticed via the control of the detuning and phase shifts.

X-ray absorption investigation of local structural disorder in Ni 1-xFe x (x=0.10, 0.20, 0.35, and 0.50) alloys

DOE PAGES

Zhang, Fuxiang X.; Jin, Ke; Zhao, Shijun; ...

2017-04-27

Defect energetics in structural materials has long been recognized to be affected by specific alloy compositions. Significantly enhanced radiation resistance has recently been observed in concentrated solid-solution alloys. However, the link between local structural disorder and modified defect dynamics in solid solutions remains unclear. To reveal the atomic-level lattice distortion, the local structures of Ni and Fe in Ni 1-xFe x (x=0.1, 0.2, 0.35 and 0.5) solid solution alloys were measured with extended X-ray absorption fine structure (EXAFS) technique. The lattice constant and the first-neighbor distances increase with the increase of Fe content in the solid solutions. EXAFS measurements havemore » revealed that the bond length of Fe with surrounding atoms is 0.01-0.03 larger than that of Ni in the alloy systems. Debye-Waller factor of the Fe-Fe bonds in all the systems is also slightly larger than that of the Ni-Ni bond. EXAFS fitting suggests that the local structural disorder is enhanced with the addition of Fe elements in the solid solution. The local bonding environments from ab initio calculation are in good agreement with the experimental results, which suggest that the Fe has a larger first-neighbor bonding distance than that of Ni, and thus Ni atom inside the Ni-Fe solid solution alloys undergoes compressive strain.« less

X-ray absorption investigation of local structural disorder in Ni 1-xFe x (x=0.10, 0.20, 0.35, and 0.50) alloys

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

Zhang, Fuxiang X.; Jin, Ke; Zhao, Shijun

Defect energetics in structural materials has long been recognized to be affected by specific alloy compositions. Significantly enhanced radiation resistance has recently been observed in concentrated solid-solution alloys. However, the link between local structural disorder and modified defect dynamics in solid solutions remains unclear. To reveal the atomic-level lattice distortion, the local structures of Ni and Fe in Ni 1-xFe x (x=0.1, 0.2, 0.35 and 0.5) solid solution alloys were measured with extended X-ray absorption fine structure (EXAFS) technique. The lattice constant and the first-neighbor distances increase with the increase of Fe content in the solid solutions. EXAFS measurements havemore » revealed that the bond length of Fe with surrounding atoms is 0.01-0.03 larger than that of Ni in the alloy systems. Debye-Waller factor of the Fe-Fe bonds in all the systems is also slightly larger than that of the Ni-Ni bond. EXAFS fitting suggests that the local structural disorder is enhanced with the addition of Fe elements in the solid solution. The local bonding environments from ab initio calculation are in good agreement with the experimental results, which suggest that the Fe has a larger first-neighbor bonding distance than that of Ni, and thus Ni atom inside the Ni-Fe solid solution alloys undergoes compressive strain.« less

Effects of surface structural disorder and surface coverage on isotopic fractionation during Zn(II) adsorption onto quartz and amorphous silica surfaces

DOE PAGES

Nelson, Joey; Wasylenki, Laura; Bargar, John R.; ...

2017-08-05

Metal ion-mineral surface interactions and the attendant isotopic fractionation depend on the properties of the mineral surface and the local atomic-level chemical environment. Furthermore, these factors have not been systematically examined for phases of the same composition with different levels of surface disorder.

Effects of surface structural disorder and surface coverage on isotopic fractionation during Zn(II) adsorption onto quartz and amorphous silica surfaces

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

Nelson, Joey; Wasylenki, Laura; Bargar, John R.

Metal ion-mineral surface interactions and the attendant isotopic fractionation depend on the properties of the mineral surface and the local atomic-level chemical environment. Furthermore, these factors have not been systematically examined for phases of the same composition with different levels of surface disorder.

A New Role for Local Police in Radiological Security

DTIC Science & Technology

2007-09-01

levels of polonium 210 to warrant a health 63 International Atomic Energy Commission, 21. 64...Probability of occur. (P) Area affected Effects on Man’s health Environment/ Economics Psychological Effects Risk...isotope such as Polonium 210 , the material that was used to kill former KGB officer Alexander Litvinenko, has been proposed by Zimmeran as a

Nanotribological effects of hair care products and environment on human hair using atomic force microscopy

NASA Astrophysics Data System (ADS)

Latorre, Carmen; Bhushan, Bharat

2005-07-01

Tribological properties are useful in the study of human hair and other biological materials. Major sources of investigation for conditioner treated hair includes localization of conditioner, mechanisms related to changes in surface roughness, friction, and adhesion on the nanoscale due to conditioner agents, and how the products change the microstructure of the cuticle. The paper presents nanotribological studies investigating surface roughness, friction, and adhesion using atomic force/friction force microscopy (AFM/FFM). Test samples include virgin and chemically damaged hair, both with and without commercial conditioner treatment, as well as chemically damaged hair with experimental conditioner treatments. Friction force mapping provides insight into the localized change in friction caused by the application of hair care materials. Adhesive force maps to study adhesion on the cuticle surface provide information about localization and distribution of conditioner as well. A discussion is presented on these properties of hair as a function of relative humidity, temperature, durability, and conditioning treatments.

Enhancing AFLOW Visualization using Jmol

NASA Astrophysics Data System (ADS)

Lanasa, Jacob; New, Elizabeth; Stefek, Patrik; Honaker, Brigette; Hanson, Robert; Aflow Collaboration

The AFLOW library is a database of theoretical solid-state structures and calculated properties created using high-throughput ab initio calculations. Jmol is a Java-based program capable of visualizing and analyzing complex molecular structures and energy landscapes. In collaboration with the AFLOW consortium, our goal is the enhancement of the AFLOWLIB database through the extension of Jmol's capabilities in the area of materials science. Modifications made to Jmol include the ability to read and visualize AFLOW binary alloy data files, the ability to extract from these files information using Jmol scripting macros that can be utilized in the creation of interactive web-based convex hull graphs, the capability to identify and classify local atomic environments by symmetry, and the ability to search one or more related crystal structures for atomic environments using a novel extension of inorganic polyhedron-based SMILES strings

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

Ferré, Grégoire; Maillet, Jean-Bernard; Stoltz, Gabriel

We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables us to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e., fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the root mean square distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal frameworkmore » is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e., their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity.« less

Local-order metric for condensed-phase environments

NASA Astrophysics Data System (ADS)

Martelli, Fausto; Ko, Hsin-Yu; Oǧuz, Erdal C.; Car, Roberto

2018-02-01

We introduce a local order metric (LOM) that measures the degree of order in the neighborhood of an atomic or molecular site in a condensed medium. The LOM maximizes the overlap between the spatial distribution of sites belonging to that neighborhood and the corresponding distribution in a suitable reference system. The LOM takes a value tending to zero for completely disordered environments and tending to one for environments that perfectly match the reference. The site-averaged LOM and its standard deviation define two scalar order parameters, S and δ S , that characterize with excellent resolution crystals, liquids, and amorphous materials. We show with molecular dynamics simulations that S , δ S , and the LOM provide very insightful information in the study of structural transformations, such as those occurring when ice spontaneously nucleates from supercooled water or when a supercooled water sample becomes amorphous upon progressive cooling.

Permutation-invariant distance between atomic configurations

NASA Astrophysics Data System (ADS)

Ferré, Grégoire; Maillet, Jean-Bernard; Stoltz, Gabriel

2015-09-01

We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables us to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e., fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the root mean square distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e., their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity.

Near-neighbor mixing and bond dilation in mechanically alloyed Cu-Fe

NASA Astrophysics Data System (ADS)

Harris, V. G.; Kemner, K. M.; Das, B. N.; Koon, N. C.; Ehrlich, A. E.; Kirkland, J. P.; Woicik, J. C.; Crespo, P.; Hernando, A.; Garcia Escorial, A.

1996-09-01

Extended x-ray-absorption fine-structure (EXAFS) measurements were used to obtain element-specific, structural, and chemical information of the local environments around Cu and Fe atoms in high-energy ball-milled CuxFe1-x samples (x=0.50 and 0.70). Analysis of the EXAFS data shows both Fe and Cu atoms reside in face-centered-cubic sites where the first coordination sphere consists of a mixture of Fe and Cu atoms in a ratio which reflects the as-prepared stoichiometry. The measured bond distances indicate a dilation in the bonds between unlike neighbors which accounts for the lattice expansion measured by x-ray diffraction. These results indicate that metastable alloys having a positive heat of mixing can be prepared via the high-energy ball-milling process.

Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.

Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of 'atom typing' QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the 'size' of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and transferable models for the interactions between the quantum mechanical system and their solvated surroundings.

Local environment effects in the magnetic properties and electronic structure of disordered FePt

NASA Astrophysics Data System (ADS)

Khan, Saleem Ayaz; Minár, Ján; Ebert, Hubert; Blaha, Peter; Šipr, Ondřej

2017-01-01

Local aspects of magnetism of disordered FePt are investigated by ab initio fully relativistic full-potential calculations, employing the supercell approach and the coherent potential approximation (CPA). The focus is on trends of the spin and orbital magnetic moments with chemical composition and with bond lengths around the Fe and Pt atoms. A small but distinct difference between average magnetic moments obtained when using the supercells and when relying on the CPA is identified and linked to the neglect of the Madelung potential in the CPA.

Temperature-dependent local structural properties of redox Pt nanoparticles on TiO 2 and ZrO 2 supports

DOE PAGES

Jeong, Eun -Suk; Park, Chang -In; Jin, Zhenlan; ...

2015-01-21

This paper examined the local structural properties of Pt nanoparticles on SiO 2, TiO 2–SiO 2, and ZrO 2–SiO 2 supports to better understand the impact of oxide-support type on the performance of Pt-based catalysts. In situ X-ray absorption fine structure (XAFS) measurements were taken for the Pt L3-edge in a temperature range from 300 to 700 K in He, H 2, and O 2 gas environments. The XAFS measurements demonstrated that Pt atoms were highly dispersed on TiO 2–SiO 2 and ZrO 2–SiO 2 forming pancake-shaped nanoparticles, whereas Pt atoms formed larger particles of hemispherical shapes on SiO 2more » supports. Contrary to the SiO 2 case, the coordination numbers for Pt, Ti, and Zr around Pt atoms on the TiO 2–SiO 2 and ZrO 2–SiO 2 supports were nearly constant from 300 to 700 K under the different gas environments. These results are consistent with the improvements in thermal stability of Pt nanoparticles achieved by incorporating TiO 2 or ZrO 2 on the surface of SiO 2 supports. XAFS analysis further indicated that the enhanced dispersion and stability of Pt were a consequence of the strong metal support interaction via Pt–Ti and Pt–Zr bonds.« less

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.

Overview of Three-Dimensional Atomic-Resolution Holography and Imaging Techniques: Recent Advances in Local-Structure Science

NASA Astrophysics Data System (ADS)

Daimon, Hiroshi

2018-06-01

Local three-dimensional (3D) atomic arrangements without periodicity have not been able to be studied until recently. Recently, several holographies and related techniques have been developed to reveal the 3D atomic arrangement around specific atoms with no translational symmetry. This review gives an overview of these new local 3D atomic imaging techniques.

Temperature and composition dependence of short-range order and entropy, and statistics of bond length: the semiconductor alloy (GaN)(1-x)(ZnO)(x).

PubMed

Liu, Jian; Pedroza, Luana S; Misch, Carissa; Fernández-Serra, Maria V; Allen, Philip B

2014-07-09

We present total energy and force calculations for the (GaN)1-x(ZnO)x alloy. Site-occupancy configurations are generated from Monte Carlo (MC) simulations, on the basis of a cluster expansion model proposed in a previous study. Local atomic coordinate relaxations of surprisingly large magnitude are found via density-functional calculations using a 432-atom periodic supercell, for three representative configurations at x = 0.5. These are used to generate bond-length distributions. The configurationally averaged composition- and temperature-dependent short-range order (SRO) parameters of the alloys are discussed. The entropy is approximated in terms of pair distribution statistics and thus related to SRO parameters. This approximate entropy is compared with accurate numerical values from MC simulations. An empirical model for the dependence of the bond length on the local chemical environments is proposed.

Potential Engineering of Fermi-Hubbard Systems using a Quantum Gas Microscope

NASA Astrophysics Data System (ADS)

Ji, Geoffrey; Mazurenko, Anton; Chiu, Christie; Parsons, Maxwell; Kanász-Nagy, Márton; Schmidt, Richard; Grusdt, Fabian; Demler, Eugene; Greif, Daniel; Greiner, Markus

2017-04-01

Arbitrary control of optical potentials has emerged as an important tool in manipulating ultracold atomic systems, especially when combined with the single-site addressing afforded by quantum gas microscopy. Already, experiments have used digital micromirror devices (DMDs) to initialize and control ultracold atomic systems in the context of studying quantum walks, quantum thermalization, and many-body localization. Here, we report on progress in using a DMD located in the image plane of a quantum gas microscope to explore static and dynamic properties of a 2D Fermi-Hubbard system. By projecting a large, ring-shaped anti-confining potential, we demonstrate entropy redistribution and controlled doping of the system. Moreover, we use the DMD to prepare localized holes, which upon release interact with and disrupt the surrounding spin environment. These techniques pave the way for controlled investigations of dynamics in the low-temperature phases of the Hubbard model.

Quantum optical tests of complementarity: Quantum eraser and the decoherence time of a local measurement process

NASA Astrophysics Data System (ADS)

Abranyos, Yonatan

1999-10-01

Quantum optical tests of the fundamental principles of quantum mechanics, in particular, complementarity, entanglement and non-locality, are the central themes of this dissertation. A which-path experiment is implemented based on a recent experiment by Eichmann et al. [1] involving two four-level atoms. In the version considered here a continuous Broad Band Excitation field drives the two trapped atoms and, depending on the type of scattering, information about which atom scattered the light is stored in the internal degrees of the atoms. Entanglement of the atoms-photon system is intimately connected to the availability of ``which way'' information. The quantum eraser disentangles the atoms-photon system and consequently ``which way'' information is lost leading to interference. Two different experimental schemes based on the Eichmann et al. experiment are proposed for the implementation of the quantum eraser. The quantum eraser schemes erase the ``which way'' information and interference is observed in the second order correlation function. With a slight modification of the experiment, a scheme that allows to verify recently derived inequalities by Englert [2] in connection with distinguishability and visibility in a two-way interferometer is proposed. These inequalities, in some sense, can be regarded as quantifying the notion of wave-particle duality. The visibility of interference depends on the detected polarization direction of the scattered light, and a reading out of the internal atomic states of one of the two atoms provides for partial ``which way'' information or distinguishability of the two different paths. Finally, the quantum eraser is used to measure the decoherence time of a local measurement process. The experiment proposed is similar to the quantum eraser setup and contains the complete measurement process of system-meter-environment interaction. The decoherence time is quantitatively expressed in the amount of reduction of the visibility in the second order correlation function. In addition, it explores how we can cast the question of quantum coherence of mesoscopic or macroscopic systems with a quantum eraser or in general interference experiments.

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

NASA Astrophysics Data System (ADS)

Matsui, Fumihiko; Matsushita, Tomohiro; Daimon, Hiroshi

2018-06-01

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

Atoms in Action: Observing Atomic Motion with Dynamic in situ X-ray Diffraction

NASA Astrophysics Data System (ADS)

Cox, Jordan Michael

Metal-organic framework (MOF) materials are rich in both structural diversity and application. These materials are comprised of metal atoms or clusters which are connected in a three-dimensional polymer-like network by bridging organic linker molecules. One of the major attractive features in MOFs is their permanent pore space which can potentially be used to adsorb or exchange foreign molecules from/with the surrounding environment. While MOFs are an active area of scientific interest, MOF materials are still relatively new, only 20 years old. As such, there is still much that needs to be understood about these materials before they can be effectively applied to widespread chemical problems like CO2 sequestration or low-pressure hydrogen fuel storage. One of the most important facets of MOF chemistry to understand in order to rationally design MOF materials with tailor-made properties is the relationship between the structural features in a MOF and the chemical and physical properties of that material. By examining in detail the atomic structure of a MOF with known properties under a variety of conditions, scientists can begin to unravel the guiding principles which govern these relationships. X-ray diffraction remains one of the most effective tools for determining the structure of a crystalline material with atomic resolution, and has been applied to the determination of MOF structures for years. Typically these experiments have been carried out using powder X-ray diffraction, but this technique lacks the high-resolution structural information found in single-crystal methods. Some studies have been reported which use specialized devices, sometimes called Environmental Control Cells, to study single crystalline MOFs under non-ambient chemical conditions in situ . However, these in situ studies are performed under static conditions. Even in cases where the ECC provides continued access to the local chemical environment during diffraction data collections, the environment is left static or data is not collected until after the material has equilibrated to its new environment. First, a unique ECC has been designed and constructed which allows continuous access to the local chemical environment of a single-crystal sample while maintaining ease of use, minimizing size, and which is easily adaptable to a wide variety of gaseous and liquid chemical stimuli. Novel methods have been developed and are herein described for utilizing this ECC and in situ X-ray diffraction methods in a dynamic manner for monitoring the structural responses of single crystals to changes in their local chemical environment. These methods provide the opportunity for the determination of changes in unit cell parameters and even complete crystal structures during adsorption, desorption, and exchange processes in MOF materials. The application of these methods to the determination of the dehydration process of a previously reported cobalt-based MOF have revealed surprising structural and dynamics data. Several new intermediate structures have been determined in this process, including one metastable species and several actively transitioning species during the dehydration process. Applying these methods to the ethanol solvation process in the same material again yielded results which were richer in structural information than the previously reported ex situ structures. A computational study of rotational potential energy surfaces in a family of photochromic MOF linkers revealed the important role rotational stereoisomers can play in maintaining light-activated functionality when these linkers are incorporated into next-generation functional MOF materials. Finally, the application of novel photocrystallography techniques were used in conjunction with spectroscopic methods to determine the nature of the anomalous behavior of a photochromic diarylethene single-crystal.

Simulation-based Extraction of Key Material Parameters from Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Alsafi, Huseen; Peninngton, Gray

Models for the atomic force microscopy (AFM) tip and sample interaction contain numerous material parameters that are often poorly known. This is especially true when dealing with novel material systems or when imaging samples that are exposed to complicated interactions with the local environment. In this work we use Monte Carlo methods to extract sample material parameters from the experimental AFM analysis of a test sample. The parameterized theoretical model that we use is based on the Virtual Environment for Dynamic AFM (VEDA) [1]. The extracted material parameters are then compared with the accepted values for our test sample. Using this procedure, we suggest a method that can be used to successfully determine unknown material properties in novel and complicated material systems. We acknowledge Fisher Endowment Grant support from the Jess and Mildred Fisher College of Science and Mathematics,Towson University.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Local Viscoelastic Properties of Live Cells Investigated Using Dynamic and Quasi-Static Atomic Force Microscopy Methods

PubMed Central

Cartagena, Alexander; Raman, Arvind

2014-01-01

The measurement of viscoelasticity of cells in physiological environments with high spatio-temporal resolution is a key goal in cell mechanobiology. Traditionally only the elastic properties have been measured from quasi-static force-distance curves using the atomic force microscope (AFM). Recently, dynamic AFM-based methods have been proposed to map the local in vitro viscoelastic properties of living cells with nanoscale resolution. However, the differences in viscoelastic properties estimated from such dynamic and traditional quasi-static techniques are poorly understood. In this work we quantitatively reconstruct the local force and dissipation gradients (viscoelasticity) on live fibroblast cells in buffer solutions using Lorentz force excited cantilevers and present a careful comparison between mechanical properties (local stiffness and damping) extracted using dynamic and quasi-static force spectroscopy methods. The results highlight the dependence of measured viscoelastic properties on both the frequency at which the chosen technique operates as well as the interactions with subcellular components beyond certain indentation depth, both of which are responsible for differences between the viscoelasticity property maps acquired using the dynamic AFM method against the quasi-static measurements. PMID:24606928

Materials selection for long life in low earth orbit - A critical evaluation of atomic oxygen testing with thermal atom systems

NASA Technical Reports Server (NTRS)

Koontz, S. L.; Albyn, K.; Leger, L.

1990-01-01

The use of thermal atom test methods as a materials selection and screening technique for low-earth orbit (LEO) spacecraft is critically evaluated. The chemistry and physics of thermal atom environments are compared with the LEO environment. The relative reactivities of a number of materials determined in thermal atom environments are compared with those observed in LEO and in high-quality LEO simulations. Reaction efficiencies (cu cm/atom) measured in a new type of thermal atom apparatus are one-thousandth to one ten-thousandth those observed in LEO, and many materials showing nearly identical reactivities in LEO show relative reactivities differing by as much as a factor of eight in thermal atom systems. A simple phenomenological kinetic model for the reaction of oxygen atoms with organic materials can be used to explain the differences in reactivity in different environments. Certain speciic thermal atom test environments can be used as reliable materials screening tools.

Resonance fluorescence microscopy via three-dimensional atom localization

NASA Astrophysics Data System (ADS)

Panchadhyayee, Pradipta; Dutta, Bibhas Kumar; Das, Nityananda; Mahapatra, Prasanta Kumar

2018-02-01

A scheme is proposed to realize three-dimensional (3D) atom localization in a driven two-level atomic system via resonance fluorescence. The field arrangement for the atom localization involves the application of three mutually orthogonal standing-wave fields and an additional traveling-wave coupling field. We have shown the efficacy of such field arrangement in tuning the spatially modulated resonance in all directions. Under different parametric conditions, the 3D localization patterns originate with various shapes such as sphere, sheets, disk, bowling pin, snake flute, flower vase. High-precision localization is achieved when the radiation field detuning equals twice the combined Rabi frequencies of the standing-wave fields. Application of a traveling-wave field of suitable amplitude at optimum radiation field detuning under symmetric standing-wave configuration leads to 100% detection probability even in sub-wavelength domain. Asymmetric field configuration is also taken into consideration to exhibit atom localization with appreciable precision compared to that of the symmetric case. The momentum distribution of the localized atoms is found to follow the Heisenberg uncertainty principle under the validity of Raman-Nath approximation. The proposed field configuration is suitable for application in the study of atom localization in an optical lattice arrangement.

CMAPS_ASPS_DATA-LCM_GTC

EPA Pesticide Factsheets

Total mercury in precipitation collected using ASPS automated wet-only instrument and analyzed by cold vapor atomic fluorescence spectroscopy.This dataset is associated with the following publication:Lynam, M., J.T. Dvonch, J. Barres, M. Landis , and A. Kamal. Investigating the impact of local urban sources on total atmospheric mercury wet deposition in Cleveland, Ohio, USA. ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 127: 262-271, (2016).

Atomic Force Microscopy Mechanical Mapping of Micropatterned Cells Shows Adhesion Geometry-Dependent Mechanical Response on Local and Global Scales

PubMed Central

Rigato, Annafrancesca; Rico, Felix; Eghiaian, Frédéric; Piel, Mathieu; Scheuring, Simon

2015-01-01

In multicellular organisms cell shape and organization are dictated by cell-cell or cell-extracellular matrix adhesion interactions. Adhesion complexes crosstalk with the cytoskeleton enabling cells to sense their mechanical environment. Unfortunately, most of cell biology studies, and cell mechanics studies in particular, are conducted on cultured cells adhering to a hard, homogeneous and unconstrained substrate with non-specific adhesion sites – thus far from physiological and reproducible conditions. Here, we grew cells on three different fibronectin patterns with identical overall dimensions but different geometries (▽, T and Y), and investigated their topography and mechanics by atomic force microscopy (AFM). The obtained mechanical maps were reproducible for cells grown on patterns of the same geometry, revealing pattern-specific subcellular differences. We found that local Young’s moduli variations are related to the cell adhesion geometry. Additionally, we detected local changes of cell mechanical properties induced by cytoskeletal drugs. We thus provide a method to quantitatively and systematically investigate cell mechanics and their variations, and present further evidence for a tight relation between cell adhesion and mechanics. PMID:26013956

Atomic Force Microscopy Mechanical Mapping of Micropatterned Cells Shows Adhesion Geometry-Dependent Mechanical Response on Local and Global Scales.

PubMed

Rigato, Annafrancesca; Rico, Felix; Eghiaian, Frédéric; Piel, Mathieu; Scheuring, Simon

2015-06-23

In multicellular organisms, cell shape and organization are dictated by cell-cell or cell-extracellular matrix adhesion interactions. Adhesion complexes crosstalk with the cytoskeleton enabling cells to sense their mechanical environment. Unfortunately, most of cell biology studies, and cell mechanics studies in particular, are conducted on cultured cells adhering to a hard, homogeneous, and unconstrained substrate with nonspecific adhesion sites, thus far from physiological and reproducible conditions. Here, we grew cells on three different fibronectin patterns with identical overall dimensions but different geometries (▽, T, and Y), and investigated their topography and mechanics by atomic force microscopy (AFM). The obtained mechanical maps were reproducible for cells grown on patterns of the same geometry, revealing pattern-specific subcellular differences. We found that local Young's moduli variations are related to the cell adhesion geometry. Additionally, we detected local changes of cell mechanical properties induced by cytoskeletal drugs. We thus provide a method to quantitatively and systematically investigate cell mechanics and their variations, and present further evidence for a tight relation between cell adhesion and mechanics.

High-precision two-dimensional atom localization from four-wave mixing in a double-Λ four-level atomic system

NASA Astrophysics Data System (ADS)

Shui, Tao; Yang, Wen-Xing; Chen, Ai-Xi; Liu, Shaopeng; Li, Ling; Zhu, Zhonghu

2018-03-01

We propose a scheme for high-precision two-dimensional (2D) atom localization via the four-wave mixing (FWM) in a four-level double-Λ atomic system. Due to the position-dependent atom-field interaction, the 2D position information of the atoms can be directly determined by the measurement of the normalized light intensity of output FWM-generated field. We further show that, when the position-dependent generated FWM field has become sufficiently intense, efficient back-coupling to the FWM generating state becomes important. This back-coupling pathway leads to competitive multiphoton destructive interference of the FWM generating state by three supplied and one internally generated fields. We find that the precision of 2D atom localization can be improved significantly by the multiphoton destructive interference and depends sensitively on the frequency detunings and the pump field intensity. Interestingly enough, we show that adjusting the frequency detunings and the pump field intensity can modify significantly the FWM efficiency, and consequently lead to a redistribution of the atoms. As a result, the atom can be localized in one of four quadrants with holding the precision of atom localization.

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

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2003-01-01

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

Surface structure and chemistry of Pt/Cu/Pt(1 1 1) near surface alloy model catalyst in CO

NASA Astrophysics Data System (ADS)

Zeng, Shibi; Nguyen, Luan; Cheng, Fang; Liu, Lacheng; Yu, Ying; Tao, Franklin (Feng)

2014-11-01

Near surface alloy (NSA) model catalyst Pt/Cu/Pt(1 1 1) was prepared on Pt(1 1 1) through a controlled vapor deposition of Cu atoms. Different coordination environments of Pt atoms of the topmost Pt layer with the underneath Cu atoms in the subsurface result in different local electronic structures of surface Pt atoms. Surface structure and chemistry of the NAS model catalyst in Torr pressure of CO were studied with high pressure scanning tunneling microscopy (HP-STM) and ambient pressure X-ray photoelectron spectroscopy (AP-XPS). In Torr pressure of CO, the topmost Pt layer of Pt/Cu/Pt(1 1 1) is restructured to thin nanoclusters with size of about 1 nm. Photoemission feature of O 1s of CO on Pt/Cu/Pt(1 1 1) suggests CO adsorbed on both edge and surface of these formed nanoclusters. This surface is active for CO oxidation. Atomic layers of carbon are formed on Pt/Cu/Pt(1 1 1) at 573 K in 2 Torr of CO.

Unraveling orbital hybridization of triplet emitters at the metal-organic interface.

PubMed

Ewen, Pascal R; Sanning, Jan; Doltsinis, Nikos L; Mauro, Matteo; Strassert, Cristian A; Wegner, Daniel

2013-12-27

We have investigated the structural and electronic properties of phosphorescent planar platinum(II) complexes at the interface of Au(111) with submolecular resolution using combined scanning tunneling microscopy and spectroscopy as well as density functional theory. Our analysis shows that molecule-substrate coupling and lateral intermolecular interactions are weak. While the ligand orbitals remain essentially unchanged upon contact with the substrate, we found modified electronic behavior at the Pt atom due to local hybridization and charge transfer to the substrate. Thus, this novel class of phosphorescent molecules exhibits well-defined and tunable interaction with its local environment.

Drifts and Environmental Disturbances in Atomic Clock Subsystems: Quantifying Local Oscillator, Control Loop, and Ion Resonance Interactions.

PubMed

Enzer, Daphna G; Diener, William A; Murphy, David W; Rao, Shanti R; Tjoelker, Robert L

2017-03-01

Linear ion trap frequency standards are among the most stable continuously operating frequency references and clocks. Depending on the application, they have been operated with a variety of local oscillators (LOs), including quartz ultrastable oscillators, hydrogen-masers, and cryogenic sapphire oscillators. The short-, intermediate-, and long-term stability of the frequency output is a complicated function of the fundamental performances, the time dependence of environmental disturbances, the atomic interrogation algorithm, the implemented control loop, and the environmental sensitivity of the LO and the atomic system components. For applications that require moving these references out of controlled lab spaces and into less stable environments, such as fieldwork or spaceflight, a deeper understanding is needed of how disturbances at different timescales impact the various subsystems of the clock and ultimately the output stability. In this paper, we analyze which perturbations have an impact and to what degree. We also report on a computational model of a control loop, which keeps the microwave source locked to the ion resonance. This model is shown to agree with laboratory measurements of how well the feedback removes various disturbances and also with a useful analytic approach we developed for predicting these impacts.

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

Local bonding structure of tellurium and antimony in the phase change chalcogenides germanium-antimony-tellurium: A nuclear magnetic resonance study

NASA Astrophysics Data System (ADS)

Bobela, David C.

Recent technological applications of some chalcogenide materials, compounds containing a group VI atom, have prompted studies of the local atomic structure of the amorphous phase. In the case of Ge2Sb2Te 5, metastability in the local bonding structure is responsible for its usefulness as a phase-change memory material. There is no consensus on the exact phase-change mechanism, which is partly due to the inadequacy of standard scattering techniques to probe the structure of the amorphous phase. Nuclear magnetic resonance methods, on the other hand, are well suited to study local structural order even in the absence of a periodic lattice. In this technique, structural information is encoded as an oscillating voltage caused by the nuclear spin. For the tellurium isotope, 125Te (spin = 1/2 in the ground state), the dominant interaction comes from the core and valence electrons that carry angular momentum. This interaction is helpful in identifying Te sites of different local coordination since the number of neighboring atoms should markedly change the local electronic structure. The antimony isotope 125Sb has a spin = 5/2 in the ground state and possesses an asymmetric nuclear charge. This quadrupole moment will interact with an electric field gradient at the nuclear site, which is provided by an asymmetric electron cloud surrounding the nucleus. The frequency-space spectra will reflect the strength of the interaction as well as the symmetry of the local electronic environment. This work investigates the nuclear magnetic resonance spectrum of 125Te and 125Sb in the crystalline and amorphous forms of several GexSbyTe 1-x-y compounds where 0 < (x, y) < 1. Results from the crystalline phase 125Te data show a trend in the spectral position that can be related to the tellurium bonded to three and six neighbors. In the amorphous phase, the same trend is observed, and the nuclear magnetic resonance fingerprint of two-fold and three-fold coordinated tellurium is obtained. It is concluded, based upon this comparison that the Te atoms see a dramatically different bonding environment depending on which phase the lattice has. The 125Sb data for the crystalline phase indicate electric field gradients that are consistent with similarly bonded quadrupolar nuclei, such as Sb atoms in crystalline Sb or five-fold coordinated Sb in crystalline MnSb. The NMR data exemplify the consequences of combinatorial disorder on the spectra via the absence of certain line-shape features. In the amorphous phase, the electric field gradients are approximately seven times larger, and the fingerprints of both highly-symmetric and asymmetric antimony sites emerge. Details of field gradient, i.e. the magnitude and symmetry, are remarkably similar to those found in Sb containing compounds where the Sb sites are three-fold pyramidal, such as in crystalline Sb2X3 where X = O, S, or Se. The observations from the NMR data provide a critical litmus test for recent structural models of the amorphous phase. In particular, the amorphous phase data provides clear evidence that the Te atoms are two-fold and three-fold coordinated while the Sb atoms are most likely bonded in three-fold pyramidal configurations. These observations imply a structural model of the amorphous phase that agrees best with a models based upon the "8 minus n", or "8-n" rule for chemical bonding in amorphous semiconductors. Thus, the lattice of these compounds is arranged such that the constituent elements have enough bonds, on average, to satisfy their valence requirement. The implications of the NMR data on theoretical modeling data are immediate. Theoretical models of these systems must possess some aspect of the "8-n" mentality. With this idea as a foundation for physically realistic representations of the amorphous phase, the origin of the phase-change mechanism may be unraveled, which will ultimately speed the process of compositional optimization of phase-change materials.

The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

DOE PAGES

Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; ...

2014-09-25

To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na 7Sn 3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Namore » 9Sn 4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na 14.78Sn 4 (Pnma), better described as Na 16-xSn 4, is Na-richer than cubic Na 15Sn 4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na 7Sn 3 and Na 15Sn 4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.« less

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

Momentum distributions for the quantum delta-kicked rotor with decoherence

PubMed

Vant; Ball; Christensen

2000-05-01

We report on the momentum distribution line shapes for the quantum delta-kicked rotor in the presence of environment induced decoherence. Experimental and numerical results are presented. In the experiment ultracold cesium atoms are subjected to a pulsed standing wave of near resonant light. Spontaneous scattering of photons destroys dynamical localization. For the scattering rates used in our experiment the momentum distribution shapes remain essentially exponential.

Science Goals for the PARCS mission on the International Space Station

NASA Astrophysics Data System (ADS)

Ashby, Neil; Hollberg, Leo; Jefferts, Steven; Klipstein, William; Seidel, David; Sullivan, Donald

2003-05-01

The PARCS (Primary Atomic Reference Clock in Space) experiment will use a laser-cooled cesium atomic clock operating in the microgravity environment aboard the International Space Station (ISS) to provide both advanced tests of gravitational theory and to demonstrate a new cold-atom clock technology for space. This presentation concentrates on the scientific goals of the PARCS mission. The microgravity space environment allows laser-cooled Cs atoms to have Ramsey times in excess of those feasible on Earth, resulting in improved clock performance. Clock stabilities of 5×10-14 at one second, and uncertainties below 10-16 are projected. The relativistic frequency shift should be measurable at least 40 times better than the previous best measurement made by Gravity Probe A. Significant improvements in testing fundamental assumptions of relativity theory, such as local position invariance (LPI), are expected. PARCS is scheduled for launch in 2007 and may very well fly with the Stanford superconducting microwave oscillator (SUMO) which will allow a Kennedy-Thorndike-type experiment with an improvement of better than three orders of magnitude compared to previous best results. PARCS will also provide a much-improved realization of the second, and a stable time reference in space. PARCS is a joint project by the National Institue of Standards and Technology (NIST), the University of Colorado (CU) and NASA's Jet Propulsion Laboratory (JPL).

Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results.

PubMed

Hahn, Seungsoo

2016-10-28

The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; Giese, Timothy J.; York, Darrin M.

2015-12-01

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom's local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion and dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the SN2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.

Correspondence: Reply to ‘Phantom phonon localization in relaxors’

DOE PAGES

Manley, Michael E.; Abernathy, Douglas L.; Budai, John D.

2017-12-05

The Correspondence by Gehring et al. mistakes Anderson phonon localization for the concept of an atomic-scale local mode. An atomic-scale local mode refers to a single atom vibrating on its own within a crystal. Such a local mode will have an almost flat intensity profile, but this is not the same as phonon localization. Anderson localization is a wave interference effect in a disordered system that results in waves becoming spatially localized. The length scale of the localized waves is set by the wavelength, which is approximately 2 nm in this case. This larger length scale in real space meansmore » narrower intensity profiles in reciprocal space. Here, we conclude that the claims in the Correspondence by Gehring et al. are incorrect because they mistakenly assume that the length scale for Anderson localization is atomic, and because the experimental observations rule out multiple scattering as the origin.« less

Correspondence: Reply to ‘Phantom phonon localization in relaxors’

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

Manley, Michael E.; Abernathy, Douglas L.; Budai, John D.

The Correspondence by Gehring et al. mistakes Anderson phonon localization for the concept of an atomic-scale local mode. An atomic-scale local mode refers to a single atom vibrating on its own within a crystal. Such a local mode will have an almost flat intensity profile, but this is not the same as phonon localization. Anderson localization is a wave interference effect in a disordered system that results in waves becoming spatially localized. The length scale of the localized waves is set by the wavelength, which is approximately 2 nm in this case. This larger length scale in real space meansmore » narrower intensity profiles in reciprocal space. Here, we conclude that the claims in the Correspondence by Gehring et al. are incorrect because they mistakenly assume that the length scale for Anderson localization is atomic, and because the experimental observations rule out multiple scattering as the origin.« less

Materials selection for long life in LEO: A critical evaluation of atomic oxygen testing with thermal atom systems

NASA Technical Reports Server (NTRS)

Koontz, S. L.; Kuminecz, J.; Leger, L.; Nordine, P.

1988-01-01

The use of thermal atom test methods as a materials selection and screening technique for low-Earth orbit (LEO) spacecraft is critically evaluated. The chemistry and physics of thermal atom environments are compared with the LEO environment. The relative reactivities of a number of materials determined to be in thermal atom environments are compared to those observed in LEO and in high quality LEO simulations. Reaction efficiencies measured in a new type of thermal atom apparatus are one-hundredth to one-thousandth those observed in LEO, and many materials showing nearly identical reactivities in LEO show relative reactivities differing by as much as a factor of 8 in thermal atom systems. A simple phenomenological kinetic model for the reaction of oxygen atoms with organic materials can be used to explain the differences in reactivity in different environments. Certain specific thermal test environments can be used as reliable materials screening tools. Using thermal atom methods to predict material lifetime in LEO requires direct calibration of the method against LEO data or high quality simulation data for each material.

Hydrogen atom in a quantum plasma environment under the influence of Aharonov-Bohm flux and electric and magnetic fields.

PubMed

Falaye, Babatunde James; Sun, Guo-Hua; Silva-Ortigoza, Ramón; Dong, Shi-Hai

2016-05-01

This study presents the confinement influences of Aharonov-Bohm (AB) flux and electric and magnetic fields directed along the z axis and encircled by quantum plasmas on the hydrogen atom. The all-inclusive effects result in a strongly attractive system while the localizations of quantum levels change and the eigenvalues decrease. We find that the combined effect of the fields is stronger than a solitary effect and consequently there is a substantial shift in the bound state energy of the system. We also find that to perpetuate a low-energy medium for the hydrogen atom in quantum plasmas, a strong electric field and weak magnetic field are required, whereas the AB flux field can be used as a regulator. The application of the perturbation technique utilized in this paper is not restricted to plasma physics; it can also be applied in molecular physics.

Reduced-temperature crystallization of thin amorphous Fe80B20 films studied via empirical modeling of extended x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Oliver, S. A.; Ayers, J. D.; Das, B. N.; Koon, N. C.

1996-04-01

The evolution of the local atomic environment around Fe atoms in very thin (15 nm), amorphous, partially crystallized and fully crystallized films of Fe80B20 was studied using extended x-ray absorption fine structure (EXAFS) measurements. The relative atomic fraction of each crystalline phase present in the annealed samples was extracted from the Fe EXAFS data by a least-squares fitting procedure, using data collected from t-Fe3B, t-Fe2B, and α-Fe standards. The type and relative fraction of the crystallization products follows the trends previously measured in Fe80B20 melt-spun ribbons, except for the fact that crystallization temperatures are ≊200 K lower than those measured in bulk equivalents. This greatly reduced crystallization temperature may arise from the dominant role of surface nucleation sites in the crystallization of very thin amorphous films.

An orbital localization criterion based on the theory of "fuzzy" atoms.

PubMed

Alcoba, Diego R; Lain, Luis; Torre, Alicia; Bochicchio, Roberto C

2006-04-15

This work proposes a new procedure for localizing molecular and natural orbitals. The localization criterion presented here is based on the partitioning of the overlap matrix into atomic contributions within the theory of "fuzzy" atoms. Our approach has several advantages over other schemes: it is computationally inexpensive, preserves the sigma/pi-separability in planar systems and provides a straightforward interpretation of the resulting orbitals in terms of their localization indices and atomic occupancies. The corresponding algorithm has been implemented and its efficiency tested on selected molecular systems. (c) 2006 Wiley Periodicals, Inc.

Collisional Cooling of Light Ions by Cotrapped Heavy Atoms.

PubMed

Dutta, Sourav; Sawant, Rahul; Rangwala, S A

2017-03-17

We experimentally demonstrate cooling of trapped ions by collisions with cotrapped, higher-mass neutral atoms. It is shown that the lighter ^{39}K^{+} ions, created by ionizing ^{39}K atoms in a magneto-optical trap (MOT), when trapped in an ion trap and subsequently allowed to cool by collisions with ultracold, heavier ^{85}Rb atoms in a MOT, exhibit a longer trap lifetime than without the localized ^{85}Rb MOT atoms. A similar cooling of trapped ^{85}Rb^{+} ions by ultracold ^{133}Cs atoms in a MOT is also demonstrated in a different experimental configuration to validate this mechanism of ion cooling by localized and centered ultracold neutral atoms. Our results suggest that the cooling of ions by localized cold atoms holds for any mass ratio, thereby enabling studies on a wider class of atom-ion systems irrespective of their masses.

Glassy nature and glass-to-crystal transition in the binary metallic glass CuZr

NASA Astrophysics Data System (ADS)

Wei, Zi-Yang; Shang, Cheng; Zhang, Xiao-Jie; Liu, Zhi-Pan

2017-06-01

The prediction for the stability of glassy material is a key challenge in physical science. Here, we report a theoretical framework to predict the glass stability based on stochastic surface walking global optimization and reaction pathway sampling. This is demonstrated by revealing for the first time the global potential energy surface (PES) of two systems, CuZr binary metallic glass and nonglassy pure Cu systems, and establishing the lowest energy pathways linking glassy/amorphous structures with crystalline structures. The CuZr system has a significant number of glassy structures on PES that are ˜0.045 eV /atom above the crystal structure. Two clear trends are identified from global PES in the glass-to-crystal transition of the CuZr system: (i) the local Zr-Cu coordination (nearest neighbor) increases, and (ii) the local Zr bonding environment becomes homogeneous. This allows us to introduce quantitative structural and energetics conditions to distinguish the glassy structures from the crystalline structures. Because of the local Zr-Cu exchange in the glass-to-crystal transition, a high reaction barrier (>0.048 eV /atom ) is present to separate the glassy structures and the crystals in CuZr. By contrast, the Cu system, although it does possess amorphous structures that appear at much higher energy (˜0.075 eV /atom ) with respect to the crystal structure, has very low reaction barriers for the crystallization of amorphous structures, i.e. <0.011 eV /atom . The quantitative data on PES now available from global optimization techniques deepens our understanding on the microscopic nature of glassy material and might eventually facilitate the design of stable glassy materials.

The Ba 4d-4f giant dipole resonance in complex Ba/Si compounds

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

Sahle, Ch. J.; Sternemann, C.; Sternemann, H.

2014-08-06

The shape of the Ba 4d–4f giant dipole resonance is studied for Ba atoms embedded inside complex Si networks covering structures consisting of Si nanocages and nanotubes, i.e. the clathrate Ba 8Si 46, the complex compound BaSi 6, and the semiconducting BaSi 2. Here, non-resonant x-ray Raman scattering is used to investigate confinement effects on the shape of the giant resonance in the vicinity of the Ba NIV, V-edge. The distinct momentum transfer dependence of the spectra is analyzed and discussed. The measurements are compared to calculations of the giant resonance within time-dependent local density approximation in the dipole limit.more » No modulation of the giant resonance's shape for Ba atoms confined in different local environments was observed, in contrast to the calculations. The absence of such shape modulation for complex Ba/Si compounds is discussed providing important implications for further studies of giant resonance phenomena utilizing both theory and experiment.« less

The Ba 4d-4f giant dipole resonance in complex Ba/Si compounds

NASA Astrophysics Data System (ADS)

Sahle, Ch J.; Sternemann, C.; Sternemann, H.; Tse, J. S.; Gordon, R. A.; Desgreniers, S.; Maekawa, S.; Yamanaka, S.; Lehmkühler, F.; Wieland, D. C. F.; Mende, K.; Huotari, S.; Tolan, M.

2014-02-01

The shape of the Ba 4d-4f giant dipole resonance is studied for Ba atoms embedded inside complex Si networks covering structures consisting of Si nanocages and nanotubes, i.e. the clathrate Ba8Si46, the complex compound BaSi6, and the semiconducting BaSi2. Here, non-resonant x-ray Raman scattering is used to investigate confinement effects on the shape of the giant resonance in the vicinity of the Ba NIV, V-edge. The distinct momentum transfer dependence of the spectra is analyzed and discussed. The measurements are compared to calculations of the giant resonance within time-dependent local density approximation in the dipole limit. No modulation of the giant resonance’s shape for Ba atoms confined in different local environments was observed, in contrast to the calculations. The absence of such shape modulation for complex Ba/Si compounds is discussed providing important implications for further studies of giant resonance phenomena utilizing both theory and experiment.

Efficient atom localization via probe absorption in an inverted-Y atomic system

NASA Astrophysics Data System (ADS)

Wu, Jianchun; Wu, Bo; Mao, Jiejian

2018-06-01

The behaviour of atom localization in an inverted-Y atomic system is theoretically investigated. For the atoms interacting with a weak probe field and several orthogonal standing-wave fields, their position information can be obtained by measuring the probe absorption. Compared with the traditional scheme, we couple the probe field to the transition between the middle and top levels. It is found that the probe absorption sensitively depends on the detuning and strength of the relevant light fields. Remarkably, the atom can be localized at a particular position in the standing-wave fields by coupling a microwave field to the transition between the two ground levels.

Local Structures of High-Entropy Alloys (HEAs) on Atomic Scales: An Overview

DOE PAGES

Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; ...

2015-08-29

The high-entropy alloys (HEAs), containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on atomic level are essential to understand the mechanical behaviors and related mechanisms. In this paper, the local structure and stress on the atomic level are reviewed by the pair-distribution function (PDF) of neutron-diffraction data, ab-initio-molecular-dynamics (AIMD) simulations, and atomic-probe microscopy (APT).

Atomistic simulation of mineral-melt trace-element partitioning

NASA Astrophysics Data System (ADS)

Allan, Neil L.; Du, Zhimei; Lavrentiev, Mikhail Yu.; Blundy, Jon D.; Purton, John A.; van Westrenen, Wim

2003-09-01

We discuss recent advances in computational approaches to trace-element incorporation in minerals and melts. It is crucial to take explicit account of the local structural environment of each ion in the solid and the change in this environment following the introduction of a foreign atom or atoms. Particular attention is paid to models using relaxation (strain) energies and solution energies, and the use of these different models for isovalent and heterovalent substitution in diopside and forsterite. Solution energies are also evaluated for pyrope and grossular garnets, and pyrope-grossular solid solutions. Unfavourable interactions between dodecahedral sites containing ions of the same size and connected by an intervening tetrahedron lead to larger solubilities of trace elements in the garnet solid solution than in either end member compound and to the failure of Goldschmidt's first rule. Our final two examples are the partitioning behaviour of noble gases, which behave as 'ions of zero charge' and the direct calculation of high-temperature partition coefficients between CaO solid and melt via Monte Carlo simulations.

Local structural environments of Ge doped in eutectic Sb-Te film before and after crystallization

NASA Astrophysics Data System (ADS)

Shin, Sang Yeol; Cheong, Byung-ki; Choi, Yong Gyu

2018-06-01

Electrical phase change device using the Ge-doped eutectic Sb-Te (e.g., Ge1Sb8Te2) film is known to exhibit improved energy efficiency thanks to lowered threshold voltage as well as decreased power consumption for the reset operation, as compared with Ge2Sb2Te5 film. Ge K-edge EXAFS analysis is employed in this study in an effort to elucidate such merits of Ge1Sb8Te2 film in connection with its local atomic arrangements. It is then verified that a Ge atom is four-fold coordinated in its nearest-neighboring shell both in the as-deposited and in the annealed films. It needs to be highlighted that approximately two Sb atoms constitute the Ge tetrahedral units in its amorphous state; however, after being crystallized, heteropolar Ge-Sb bonds hardly exist in this Ge1Sb8Te2 film. It has been known that crystallization temperature and activation energy for crystallization of this Ge1Sb8Te2 composition are greater than those of Ge2Sb2Te5 composition. In addition, these two phase change materials exhibit distinctly different crystallization mechanisms, i.e., nucleation-dominant for Ge2Sb2Te5 film but growth-dominant for Ge1Sb8Te2 film. These discrepancies in the crystallization-related properties are delineated in terms of the local structural changes verified from the present EXAFS analysis.

The characterisation of atomic structure and glass-forming ability of the Zr-Cu-Co metallic glasses studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Celtek, M.; Sengul, S.

2018-03-01

In the present work, the glass formation process and structural properties of Zr50Cu50-xCox (0 ≤ x ≤ 50) bulk metallic glasses were investigated by a molecular dynamics simulation with the many body tight-binding potentials. The evolution of structure and glass formation process with temperature were discussed using the coordination number, the radial distribution functions, the volume-temperature curve, icosahedral short-range order, glass transition temperature, Voronoi analysis, Honeycutt-Andersen pair analysis technique and the distribution of bond-angles. Results indicate that adding Co causes similar responses on the nature of the Zr50Cu50-xCox (0 ≤ x ≤ 50) alloys except for higher glass transition temperature and ideal icosahedral type ordered local atomic environment. Also, the differences of the atomic radii play the key role in influencing the atomic structure of these alloys. Both Cu and Co atoms play a significant role in deciding the chemical and topological short-range orders of the Zr50Cu50-xCox ternary liquids and amorphous alloys. The glass-forming ability of these alloys is supported by the experimental observations reported in the literature up to now.

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

Cable, J.W.

The diffuse scattering of neutrons from magnetic materials provides unique and important information regarding the spatial correlations of the atoms and the spins. Such measurements have been extensively applied to magnetically ordered systems, such as the ferromagnetic binary alloys, for which the observed correlations describe the magnetic moment fluctuations associated with local environment effects. With the advent of polarization analysis, these techniques are increasingly being applied to study disordered paramagnetic systems such as the spin-glasses and the diluted magnetic semiconductors. The spin-pair correlations obtained are essential in understanding the exchange interactions of such systems. In this paper, we describe recentmore » neutron diffuse scattering results on the atom-pair and spin-pair correlations in some of these disordered magnetic systems. 56 refs.« less

Atomic-Scale Variations of the Mechanical Response of 2D Materials Detected by Noncontact Atomic Force Microscopy.

PubMed

de la Torre, B; Ellner, M; Pou, P; Nicoara, N; Pérez, Rubén; Gómez-Rodríguez, J M

2016-06-17

We show that noncontact atomic force microscopy (AFM) is sensitive to the local stiffness in the atomic-scale limit on weakly coupled 2D materials, as graphene on metals. Our large amplitude AFM topography and dissipation images under ultrahigh vacuum and low temperature resolve the atomic and moiré patterns in graphene on Pt(111), despite its extremely low geometric corrugation. The imaging mechanisms are identified with a multiscale model based on density-functional theory calculations, where the energy cost of global and local deformations of graphene competes with short-range chemical and long-range van der Waals interactions. Atomic contrast is related with short-range tip-sample interactions, while the dissipation can be understood in terms of global deformations in the weakly coupled graphene layer. Remarkably, the observed moiré modulation is linked with the subtle variations of the local interplanar graphene-substrate interaction, opening a new route to explore the local mechanical properties of 2D materials at the atomic scale.

Probing the localization of magnetic dichroism by atomic-size astigmatic and vortex electron beams.

PubMed

Negi, Devendra Singh; Idrobo, Juan Carlos; Rusz, Ján

2018-03-05

We report localization of a magnetic dichroic signal on atomic columns in electron magnetic circular dichroism (EMCD), probed by beam distorted by four-fold astigmatism and electron vortex beam. With astigmatic probe, magnetic signal to noise ratio can be enhanced by blocking the intensity from the central part of probe. However, the simulations show that for atomic resolution magnetic measurements, vortex beam is a more effective probe, with much higher magnetic signal to noise ratio. For all considered beam shapes, the optimal SNR constrains the signal detection at low collection angles of approximately 6-8 mrad. Irrespective of the material thickness, the magnetic signal remains strongly localized within the probed atomic column with vortex beam, whereas for astigmatic probes, the magnetic signal originates mostly from the nearest neighbor atomic columns. Due to excellent signal localization at probing individual atomic columns, vortex beams are predicted to be a strong candidate for studying the crystal site specific magnetic properties, magnetic properties at interfaces, or magnetism arising from individual atomic impurities.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

2014-03-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

Ethene adsorption and dehydrogenation on clean and oxygen precovered Ni(111) studied by high resolution x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Lorenz, M. P. A.; Fuhrmann, T.; Streber, R.; Bayer, A.; Bebensee, F.; Gotterbarm, K.; Kinne, M.; Tränkenschuh, B.; Zhu, J. F.; Papp, C.; Denecke, R.; Steinrück, H.-P.

2010-07-01

The adsorption and thermal evolution of ethene (ethylene) on clean and oxygen precovered Ni(111) was investigated with high resolution x-ray photoelectron spectroscopy using synchrotron radiation at BESSY II. The high resolution spectra allow to unequivocally identify the local environment of individual carbon atoms. Upon adsorption at 110 K, ethene adsorbs in a geometry, where the two carbon atoms within the intact ethene molecule occupy nonequivalent sites, most likely hollow and on top; this new result unambiguously solves an old puzzle concerning the adsorption geometry of ethene on Ni(111). On the oxygen precovered surface a different adsorption geometry is found with both carbon atoms occupying equivalent hollow sites. Upon heating ethene on the clean surface, we can confirm the dehydrogenation to ethine (acetylene), which adsorbs in a geometry, where both carbon atoms occupy equivalent sites. On the oxygen precovered surface dehydrogenation of ethene is completely suppressed. For the identification of the adsorbed species and the quantitative analysis the vibrational fine structure of the x-ray photoelectron spectra was analyzed in detail.

Investigation of Cr substitution in Co ferrite (CoCrxFe2-xO4) using Mossbauer spectroscopy

NASA Astrophysics Data System (ADS)

Krieble, K.; Lo, C. C. H.; Melikhov, Y.; Snyder, J. E.

2006-04-01

Substitution of other metals for Fe in cobalt ferrite has been proposed as a method to tailor the magnetic and magnetoelastic properties for sensor and actuator applications [H. Zheng et al., Science 303, 661 (2004)]. However, to understand the effect of Cr substitution, one needs atomic-level information on the local environments and interactions of the transition-metal ions. In this study, Mossbauer spectroscopy was used to investigate the local environments of the Fe atoms in these materials. A series of five powder samples with compositions CoCrxFe2-xO4 (x=0.0 to 0.8) was investigated using transmission geometry. Results show two distinct six-line hyperfine patterns, indicating Fe in A and B spinel sites. Increasing Cr concentration is seen to decrease the hyperfine field strength for both A and B sites, as well as increasing the width of those distributions. Results for Cr substitution show generally similar behavior to a prior study using Mn; however, Cr substitution has more pronounced effects: the hyperfine fields decrease and distribution widths increase at greater rates for Cr substitution, and the differences between A and B site behavior are more pronounced. Results are consistent with a model in which Cr has an even stronger B-site preference than Mn, and displaces more of the Co from the B to the A sites.

Tensile properties of ADI material in water and gaseous environments

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

Rajnovic, Dragan, E-mail: draganr@uns.ac.rs; Balos, Sebastian; Sidjanin, Leposava

2015-03-15

Austempered ductile iron (ADI) is an advanced type of heat treated ductile iron, having comparable mechanical properties as forged steels. However, it was found that in contact with water the mechanical properties of austempered ductile irons decrease, especially their ductility. Despite considerable scientific attention, the cause of this phenomenon remains unclear. Some authors suggested that hydrogen or small atom chemisorption causes the weakening of the surface atomic bonds. To get additional reliable data of that phenomenon, in this paper, two different types of austempered ductile irons were tensile tested in various environments, such as: argon, helium, hydrogen gas and water.more » It was found that only the hydrogen gas and water gave a statistically significant decrease in mechanical properties, i.e. cause embrittlement. Furthermore, the fracture surface analysis revealed that the morphology of the embrittled zone near the specimen surface shares similarities to the fatigue micro-containing striation-like lines, which indicates that the morphology of the brittle zone may be caused by cyclic local-chemisorption, micro-embrittlement and local-fracture. - Highlights: • In contact with water and other liquids the ADI suddenly exhibits embrittlement. • The embrittlement is more pronounced in water than in the gaseous hydrogen. • The hydrogen chemisorption into ADI surface causes the formation of a brittle zone. • The ADI austempered at lower temperatures (300 °C) is more resistant to embrittlement.« less

Probing Local Ionic Dynamics in Functional Oxides: From Nanometer to Atomic Scale

NASA Astrophysics Data System (ADS)

Kalinin, Sergei

2014-03-01

Vacancy-mediated electrochemical reactions in oxides underpin multiple applications ranging from electroresistive memories, to chemical sensors to energy conversion systems such as fuel cells. Understanding the functionality in these systems requires probing reversible (oxygen reduction/evolution reaction) and irreversible (cathode degradation and activation, formation of conductive filaments) electrochemical processes. In this talk, I summarize recent advances in probing and controlling these transformations locally on nanometer level using scanning probe microscopy. The localized tip concentrates the electric field in the nanometer scale volume of material, inducing local transition. Measured simultaneously electromechanical response (piezoresponse) or current (conductive AFM) provides the information on the bias-induced changes in material. Here, I illustrate how these methods can be extended to study local electrochemical transformations, including vacancy dynamics in oxides such as titanates, LaxSr1-xCoO3, BiFeO3, and YxZr1-xO2. The formation of electromechanical hysteresis loops and their bias-, temperature- and environment dependences provide insight into local electrochemical mechanisms. In materials such as lanthanum-strontium cobaltite, mapping both reversible vacancy motion and vacancy ordering and static deformation is possible, and can be corroborated by post mortem STEM/EELS studies. In ceria, a broad gamut of electrochemical behaviors is observed as a function of temperature and humidity. The possible strategies for elucidation ionic motion at the electroactive interfaces in oxides using high-resolution electron microscopy and combined ex-situ and in-situ STEM-SPM studies are discussed. In the second part of the talk, probing electrochemical phenomena on in-situ grown surfaces with atomic resolution is illustrated. I present an approach based on the multivariate statistical analysis of the coordination spheres of individual atoms to reveal preferential structures and symmetries. The relevant statistical techniques including k-means clustering, principal component analysis, and Baesian unmixing are briefly intriduced. This approach is illustrated for several systems, including chemical phase identification, mapping ferroic variants, and probing topological and structural defects, and provides real space view on surface atomic processes. Research supported (SVK) by the U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division and partially performed at the Center for Nanophase Materials Sciences (AK, SJ), a DOE-BES user facility.

Hunting liquid micro-pockets in snow and ice: Phase transition in salt solutions at the bulk and interface with X-ray photoelectron spectroscopy.

NASA Astrophysics Data System (ADS)

Bartels-Rausch, Thorsten; Orlando, Fabrizio; Kong, Xiangrui; Waldner, Astrid; Artiglia, Luca; Ammann, Markus; Huthwelker, Thomas

2016-04-01

Sea salt, and in particular chloride, is an important reactant in the atmosphere. Chloride in air-borne sea salt aerosol is - once chemically converted to a molecular halogen (Cl2, BrCl) and released to the atmosphere - well known as important atmospheric reactant, driving large-scale changes to the atmospheric composition and in particular to ozone levels in remote areas, but also in coastal mega cities. Similar chemistry has been proposed for sea salt deposits in polar snow covers. A crucial factor determining the overall reactivity is the local physical environment of the chloride ion. For example, the reactivity of liquid aerosols decreases significantly upon crystallization. Surprisingly, the phases of NaCl-containing systems are still under debate, partially due to the limited availability of in situ measurements directly probing the local environment at the surface of frozen NaCl-water binary systems. Using core electron spectroscopy of the oxygen atoms in water, we previously showed that these systems follow the phase rules at the air-ice interface. This finding contrasts some earlier observations, where the presence of liquid below the eutectic point of bulk solutions was postulated. In the present study, we present new electron yield near-edge X-ray absorption fine structure spectroscopy (NEXAFS) data obtained at near-ambient pressures up to 20 mbar of NaCl frozen solutions. The method is sensitive to small changes in the local environment of the chlorine atom. The measurements were performed at the PHOENIX beamline at SLS. The study indicates frapant differences in the phases of NaCl - water mixtures at temperatures blow the freezing point for the surface of the ice vs. the bulk. This has significant impact on modelling chemical reactions in snow or ice and it's environmental consequences.

Second-Nearest-Neighbor Effects upon N NMR Shieldings in Models for Solid Si 3N 4and C 3N 4

NASA Astrophysics Data System (ADS)

Tossell, J. A.

1997-07-01

NMR shifts are generally determined mainly by the nearest-neighbor environment of an atom, with fairly small changes in the shift arising from differences in the second-nearest-neighbor environment. Previous calculations on the (SiH3)3N molecule used as a model for the local environment of N in crystalline α- and β-Si3N4gave N NMR shieldings much larger than those measured in the solids and gave the wrong order for the shifts of the inequivalent N sites (e.g., N1 and N2 in β-Si3N4). We have now calculated the N NMR shieldings in larger molecular models for the N2 site of β-Si3N4and have found that the N2 shielding is greatly reduced when additional N1 atoms (second-nearest-neighbors to the central N2) are included. The calculated N2 shieldings (using the GIAO method with the 6-31G* basis set and 6-31G* SCF optimized geometries) are 288.1, 244.7, and 206.0 ppm for the molecules (SiH3)3N, Si6N5H15, and Si9N9H21(central N2), respectively, while the experimental shielding of N2 in β-Si3N4is about 155 ppm. Second-nearest-neighbor effects of only slightly smaller magnitude are calculated for the analog C molecules. At the same time, the effects of molecule size upon Si NMR shieldings and N electric field gradients are small. The local geometries at the N2-like Ns in C6N5H15and C9N9H21are calculated to be planar, consistent with the planar local geometry recently calculated for N in crystalline C3N4using density functional theory.

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM

NASA Astrophysics Data System (ADS)

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-01

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt1/Fe2O3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water–gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe2O3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H2O molecules to the CO or H2 significantly accelerates the sintering of the Fe2O3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal–support interaction.

Stability investigation of a high number density Pt1/Fe2O3 single-atom catalyst under different gas environments by HAADF-STEM.

PubMed

Duan, Sibin; Wang, Rongming; Liu, Jingyue

2018-05-18

Catalysis by supported single metal atoms has demonstrated tremendous potential for practical applications due to their unique catalytic properties. Unless they are strongly anchored to the support surfaces, supported single atoms, however, are thermodynamically unstable, which poses a major obstacle for broad applications of single-atom catalysts (SACs). In order to develop strategies to improve the stability of SACs, we need to understand the intrinsic nature of the sintering processes of supported single metal atoms, especially under various gas environments that are relevant to important catalytic reactions. We report on the synthesis of high number density Pt 1 /Fe 2 O 3 SACs using a facial strong adsorption method and the study of the mobility of these supported Pt single atoms at 250 °C under various gas environments that are relevant to CO oxidation, water-gas shift, and hydrogenation reactions. Under the oxidative gas environment, Fe 2 O 3 supported Pt single atoms are stable even at high temperatures. The presence of either CO or H 2 molecules in the gas environment, however, facilitates the movement of the Pt atoms. The strong interaction between CO and Pt weakens the binding between the Pt atoms and the support, facilitating the movement of the Pt single atoms. The dissociation of H 2 molecules on the Pt atoms and their subsequent interaction with the oxygen species of the support surfaces dislodge the surface oxygen anchored Pt atoms, resulting in the formation of Pt clusters. The addition of H 2 O molecules to the CO or H 2 significantly accelerates the sintering of the Fe 2 O 3 supported Pt single atoms. An anchoring-site determined sintering mechanism is further proposed, which is related to the metal-support interaction.

Probing the localization of magnetic dichroism by atomic-size astigmatic and vortex electron beams

DOE PAGES

Negi, Devendra Singh; Idrobo, Juan Carlos; Rusz, Ján

2018-03-05

We report localization of a magnetic dichroic signal on atomic columns in electron magnetic circular dichroism (EMCD), probed by beam distorted by four-fold astigmatism and electron vortex beam. With astigmatic probe, magnetic signal to noise ratio can be enhanced by blocking the intensity from the central part of probe. However, the simulations show that for atomic resolution magnetic measurements, vortex beam is a more effective probe, with much higher magnetic signal to noise ratio. For all considered beam shapes, the optimal SNR constrains the signal detection at low collection angles of approximately 6–8 mrad. Irrespective of the material thickness, themore » magnetic signal remains strongly localized within the probed atomic column with vortex beam, whereas for astigmatic probes, the magnetic signal originates mostly from the nearest neighbor atomic columns. Due to excellent signal localization at probing individual atomic columns, vortex beams are predicted to be a strong candidate for studying the crystal site specific magnetic properties, magnetic properties at interfaces, or magnetism arising from individual atomic impurities.« less

Probing the localization of magnetic dichroism by atomic-size astigmatic and vortex electron beams

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

Negi, Devendra Singh; Idrobo, Juan Carlos; Rusz, Ján

We report localization of a magnetic dichroic signal on atomic columns in electron magnetic circular dichroism (EMCD), probed by beam distorted by four-fold astigmatism and electron vortex beam. With astigmatic probe, magnetic signal to noise ratio can be enhanced by blocking the intensity from the central part of probe. However, the simulations show that for atomic resolution magnetic measurements, vortex beam is a more effective probe, with much higher magnetic signal to noise ratio. For all considered beam shapes, the optimal SNR constrains the signal detection at low collection angles of approximately 6–8 mrad. Irrespective of the material thickness, themore » magnetic signal remains strongly localized within the probed atomic column with vortex beam, whereas for astigmatic probes, the magnetic signal originates mostly from the nearest neighbor atomic columns. Due to excellent signal localization at probing individual atomic columns, vortex beams are predicted to be a strong candidate for studying the crystal site specific magnetic properties, magnetic properties at interfaces, or magnetism arising from individual atomic impurities.« less

Atomic-Scale Lightning Rod Effect in Plasmonic Picocavities: A Classical View to a Quantum Effect.

PubMed

Urbieta, Mattin; Barbry, Marc; Zhang, Yao; Koval, Peter; Sánchez-Portal, Daniel; Zabala, Nerea; Aizpurua, Javier

2018-01-23

Plasmonic gaps are known to produce nanoscale localization and enhancement of optical fields, providing small effective mode volumes of about a few hundred nm 3 . Atomistic quantum calculations based on time-dependent density functional theory reveal the effect of subnanometric localization of electromagnetic fields due to the presence of atomic-scale features at the interfaces of plasmonic gaps. Using a classical model, we explain this as a nonresonant lightning rod effect at the atomic scale that produces an extra enhancement over that of the plasmonic background. The near-field distribution of atomic-scale hot spots around atomic features is robust against dynamical screening and spill-out effects and follows the potential landscape determined by the electron density around the atomic sites. A detailed comparison of the field distribution around atomic hot spots from full quantum atomistic calculations and from the local classical approach considering the geometrical profile of the atoms' electronic density validates the use of a classical framework to determine the effective mode volume in these extreme subnanometric optical cavities. This finding is of practical importance for the community of surface-enhanced molecular spectroscopy and quantum nanophotonics, as it provides an adequate description of the local electromagnetic fields around atomic-scale features with use of simplified classical methods.

Catalyst Architecture for Stable Single Atom Dispersion Enables Site-Specific Spectroscopic and Reactivity Measurements of CO Adsorbed to Pt Atoms, Oxidized Pt Clusters, and Metallic Pt Clusters on TiO2.

PubMed

DeRita, Leo; Dai, Sheng; Lopez-Zepeda, Kimberly; Pham, Nicholas; Graham, George W; Pan, Xiaoqing; Christopher, Phillip

2017-10-11

Oxide-supported precious metal nanoparticles are widely used industrial catalysts. Due to expense and rarity, developing synthetic protocols that reduce precious metal nanoparticle size and stabilize dispersed species is essential. Supported atomically dispersed, single precious metal atoms represent the most efficient metal utilization geometry, although debate regarding the catalytic activity of supported single precious atom species has arisen from difficulty in synthesizing homogeneous and stable single atom dispersions, and a lack of site-specific characterization approaches. We propose a catalyst architecture and characterization approach to overcome these limitations, by depositing ∼1 precious metal atom per support particle and characterizing structures by correlating scanning transmission electron microscopy imaging and CO probe molecule infrared spectroscopy. This is demonstrated for Pt supported on anatase TiO 2 . In these structures, isolated Pt atoms, Pt iso , remain stable through various conditions, and spectroscopic evidence suggests Pt iso species exist in homogeneous local environments. Comparing Pt iso to ∼1 nm preoxidized (Pt ox ) and prereduced (Pt metal ) Pt clusters on TiO 2 , we identify unique spectroscopic signatures of CO bound to each site and find CO adsorption energy is ordered: Pt iso ≪ Pt metal < Pt ox . Pt iso species exhibited a 2-fold greater turnover frequency for CO oxidation than 1 nm Pt metal clusters but share an identical reaction mechanism. We propose the active catalytic sites are cationic interfacial Pt atoms bonded to TiO 2 and that Pt iso exhibits optimal reactivity because every atom is exposed for catalysis and forms an interfacial site with TiO 2 . This approach should be generally useful for studying the behavior of supported precious metal atoms.

Imaging the Atomic Position of Light Cations in a Porous Network and the Europium(III) Ion Exchange Capability by Aberration-Corrected Electron Microscopy.

PubMed

Mayoral, Alvaro; Hall, Reece M; Jackowska, Roksana; Readman, Jennifer E

2016-12-23

In the present work, ETS-10 microporous titanosilicate has been synthesized and its structure characterized by means of powder XRD and aberration corrected scanning transmission electron microscopy (C s -corrected STEM). For the first time, sodium ions have been imaged sitting inside the 7-membered rings. The ion-exchange capability has been tested by the inclusion of rare earth metals (Eu, Tb and Gd) to produce a luminescent material which has been studied by atomic-resolution C s -corrected STEM. The data produced has allowed unambiguous imaging of light atoms in a microporous framework as well as determining the cationic metal positions for the first time, providing evidence of the importance of advanced electron microscopy methods for the study of the local environment of metals within zeolitic supports providing unique information of both systems (guest and support) at the same time. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhancement of low-energy electron emission in 2D radioactive films

NASA Astrophysics Data System (ADS)

Pronschinske, Alex; Pedevilla, Philipp; Murphy, Colin J.; Lewis, Emily A.; Lucci, Felicia R.; Brown, Garth; Pappas, George; Michaelides, Angelos; Sykes, E. Charles H.

2015-09-01

High-energy radiation has been used for decades; however, the role of low-energy electrons created during irradiation has only recently begun to be appreciated. Low-energy electrons are the most important component of radiation damage in biological environments because they have subcellular ranges, interact destructively with chemical bonds, and are the most abundant product of ionizing particles in tissue. However, methods for generating them locally without external stimulation do not exist. Here, we synthesize one-atom-thick films of the radioactive isotope 125I on gold that are stable under ambient conditions. Scanning tunnelling microscopy, supported by electronic structure simulations, allows us to directly observe nuclear transmutation of individual 125I atoms into 125Te, and explain the surprising stability of the 2D film as it underwent radioactive decay. The metal interface geometry induces a 600% amplification of low-energy electron emission (<10 eV; ref. ) compared with atomic 125I. This enhancement of biologically active low-energy electrons might offer a new direction for highly targeted nanoparticle therapies.

Ab initio thermodynamics and kinetics for coalescence on nanoislands and nanopits on metal(100) surfaces

NASA Astrophysics Data System (ADS)

Evans, Jim; Han, Yong; Stoldt, Conrad; Thiel, Patricia

Coalescence or sintering of nanoscale features on metal(100) surfaces is mediated by periphery or edge diffusion. These processes are highly sensitive to the multiple diffusion barriers for various local edge environments. We provide an optimal strategy to determine both thermodynamics and kinetics for these systems at the ab initio level. The former requires assessing conventional interactions between adatoms at adsorption sites. The latter requires assessing unconventional interactions between the hopping atom at a bridge site transition state and other nearby atoms. KMC simulation reveals that this formulation recovers observed sintering times for Ag nanoislands on Ag(100), including a novel size dependence. The formulation also applies for nanopits where there are additional challenges to capture kinetics. Work supported by NSF Grant CHE-1507223.

Mercury Pollution Exploration in Latvia with High-Sensitivity Zeeman Atomic Absorption Spectrometry

NASA Astrophysics Data System (ADS)

Bogans, Egils; Gavare, Zanda; Svagere, Anda; Poikane, Rita; Skudra, Jānis

2011-01-01

This research presents Hg pollution measurements performed in Latvia with sensitive method using Zeeman AAS analyzer RA-915+ and necessary attachments. Air in Riga city and water samples from a number of rivers and lakes of Latvia were analyzed for presence of low-level Hg concentrations. Ombrotrophic bog peat was analyzed to get insight into long-term trends. Environment in the sites sampled is relatively clean according to the results obtained, but there are local spots of pollution.

Bose-Hubbard lattice as a controllable environment for open quantum systems

NASA Astrophysics Data System (ADS)

Cosco, Francesco; Borrelli, Massimo; Mendoza-Arenas, Juan José; Plastina, Francesco; Jaksch, Dieter; Maniscalco, Sabrina

2018-04-01

We investigate the open dynamics of an atomic impurity embedded in a one-dimensional Bose-Hubbard lattice. We derive the reduced evolution equation for the impurity and show that the Bose-Hubbard lattice behaves as a tunable engineered environment allowing one to simulate both Markovian and non-Markovian dynamics in a controlled and experimentally realizable way. We demonstrate that the presence or absence of memory effects is a signature of the nature of the excitations induced by the impurity, being delocalized or localized in the two limiting cases of a superfluid and Mott insulator, respectively. Furthermore, our findings show how the excitations supported in the two phases can be characterized as information carriers.

Energy shift and Casimir-Polder force for an atom out of thermal equilibrium near a dielectric substrate

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Yu, Hongwei

2014-09-01

We study the energy shift and the Casimir-Polder force of an atom out of thermal equilibrium near the surface of a dielectric substrate. We first generalize, adopting the local source hypothesis, the formalism proposed by Dalibard, Dupont-Roc, and Cohen-Tannoudji [J. Phys. (Paris) 43, 1617 (1982), 10.1051/jphys:0198200430110161700; J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], which separates the contributions of thermal fluctuations and radiation reaction to the energy shift and allows a distinct treatment of atoms in the ground and excited states, to the case out of thermal equilibrium, and then we use the generalized formalism to calculate the energy shift and the Casimir-Polder force of an isotropically polarizable neutral atom. We identify the effects of the thermal fluctuations that originate from the substrate and the environment and discuss in detail how the Casimir-Polder force out of thermal equilibrium behaves in three different distance regions in both the low-temperature limit and the high-temperature limit for both the ground-state and excited-state atoms, with special attention devoted to the distinctive features as opposed to thermal equilibrium. In particular, we recover the distinctive behavior of the atom-wall force out of thermal equilibrium at large distances in the low-temperature limit recently found in a different theoretical framework, and furthermore we give a concrete region where this behavior holds.

Fragmentation inside atomic cooling haloes exposed to Lyman-Werner radiation

NASA Astrophysics Data System (ADS)

Regan, John A.; Downes, Turlough P.

2018-04-01

Supermassive stars born in pristine environments in the early Universe hold the promise of being the seeds for the supermassive black holes observed as high redshift quasars shortly after the epoch of reionisation. H2 suppression is thought to be crucial in order to negate normal Population III star formation and allow high accretion rates to drive the formation of supermassive stars. Only in the cases where vigorous fragmentation is avoided will a monolithic collapse be successful, giving rise to a single massive central object. We investigate the number of fragmentation sites formed in collapsing atomic cooling haloes subject to various levels of background Lyman-Werner flux. The background Lyman-Werner flux manipulates the chemical properties of the gas in the collapsing halo by destroying H2. We find that only when the collapsing gas cloud shifts from the molecular to the atomic cooling regime is the degree of fragmentation suppressed. In our particular case, we find that this occurs above a critical Lyman-Werner background of J ˜ 10 J21. The important criterion being the transition to the atomic cooling regime rather than the actual value of J, which will vary locally. Once the temperature of the gas exceeds T ≳ 104 K and the gas transitions to atomic line cooling, then vigorous fragmentation is strongly suppressed.

Effect of intermixing at CdS/CdTe interface on defect properties

NASA Astrophysics Data System (ADS)

Park, Ji-Sang; Yang, Ji-Hui; Barnes, Teresa; Wei, Su-Huai

2016-07-01

We investigated the stability and electronic properties of defects in CdTe1-xSx that can be formed at the CdS/CdTe interface. As the anions mix at the interface, the defect properties are significantly affected, especially those defects centered at cation sites like Cd vacancy, VCd, and Te on Cd antisite, TeCd, because the environment surrounding the defect sites can have different configurations. We show that at a given composition, the transition energy levels of VCd and TeCd become close to the valence band maximum when the defect has more S atoms in their local environment, thus improving the device performance. Such beneficial role is also found at the grain boundaries when the Te atom is replaced by S in the Te-Te wrong bonds, reducing the energy of the grain boundary level. On the other hand, the transition levels with respect to the valence band edge of CdTe1-xSx increases with the S concentration as the valence band edge decreases with the S concentration, resulting in the reduced p-type doping efficiency.

Comparison of the Atomic Oxygen Erosion Depth and Cone Height of Various Materials at Hyperthermal Energy

NASA Technical Reports Server (NTRS)

Waters, Deborah L.; Banks, Bruce A.; Thorson, Stephen D.; deGroh, Kim, K.; Miller, Sharon K.

2007-01-01

Atomic oxygen readily reacts with most spacecraft polymer materials exposed to the low Earth orbital (LEO) environment. If the atomic oxygen arrival comes from a fixed angle of impact, the resulting erosion will foster the development of a change in surface morphology as material thickness decreases. Hydrocarbon and halopolymer materials, as well as graphite, are easily oxidized and textured by directed atomic oxygen in LEO at energies of approx.4.5 eV. What has been curious is that the ratio of cone height to erosion depth is quite different for different materials. The formation of cones under fixed direction atomic oxygen attack may contribute to a reduction in material tensile strength in excess of that which would occur if the cone height to erosion depth ratio was very low because of greater opportunities for crack initiation. In an effort to understand how material composition affects the ratio of cone height to erosion depth, an experimental investigation was conducted on 18 different materials exposed to a hyperthermal energy directed atomic oxygen source (approx.70 eV). The materials were first salt-sprayed to provide microscopic local areas that would be protected from atomic oxygen. This allowed erosion depth measurements to be made by scanning microscopy inspection. The polymers were then exposed to atomic oxygen produced by an end Hall ion source that was operated on pure oxygen. Samples were exposed to an atomic oxygen effective fluence of 1.0x10(exp 20) atoms/sq cm based on Kapton H polyimide erosion. The average erosion depth and average cone height were determined using field emission scanning electron microscopy (FESEM). The experimental ratio of average cone height to erosion depth is compared to polymer composition and other properties.

The photoexcitation of crystalline ice and amorphous solid water: A molecular dynamics study of outcomes at 11 K and 125 K.

PubMed

Crouse, J; Loock, H-P; Cann, N M

2015-07-21

Photoexcitation of crystalline ice Ih and amorphous solid water at 7-9 eV is examined using molecular dynamics simulations and a fully flexible water model. The probabilities of photofragment desorption, trapping, and recombination are examined for crystalline ice at 11 K and at 125 K and for amorphous solid water at 11 K. For 11 K crystalline ice, a fully rigid water model is also employed for comparison. The kinetic energy of desorbed H atoms and the distance travelled by trapped fragments are correlated to the location and the local environment of the photoexcited water molecule. In all cases, H atom desorption is found to be the most likely outcome in the top bilayer while trapping of all photofragments is most probable deeper in the solid where the likelihood for recombination of the fragments into H2O molecules also rises. Trajectory analysis indicates that the local hydrogen bonding network in amorphous solid water is more easily distorted by a photodissociation event compared to crystalline ice. Also, simulations indicate that desorption of OH radicals and H2O molecules are more probable in amorphous solid water. The kinetic energy distributions for desorbed H atoms show a peak at high energy in crystalline ice, arising from photoexcited water molecules in the top monolayer. This peak is less pronounced in amorphous solid water. H atoms that are trapped may be displaced by up to ∼10 water cages, but migrate on average 3 water cages. Trapped OH fragments tend to stay near the original solvent cage.

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

NASA Astrophysics Data System (ADS)

Bereau, Tristan; DiStasio, Robert A.; Tkatchenko, Alexandre; von Lilienfeld, O. Anatole

2018-06-01

Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions—electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters—optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically relevant molecules. We further focus on hydrogen-bonded complexes—essential but challenging due to their directional nature—where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML for denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.

Locality of correlation in density functional theory.

PubMed

Burke, Kieron; Cancio, Antonio; Gould, Tim; Pittalis, Stefano

2016-08-07

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that EC → -AC ZlnZ + BCZ as Z → ∞, where Z is the atomic number, AC is known, and we estimate BC to be about 37 mhartree. The local density approximation yields AC exactly, but a very incorrect value for BC, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with BC a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.

Low Earth orbit atomic oxygen simulation for durability evaluation of solar reflector surfaces

NASA Technical Reports Server (NTRS)

Degroh, Kim K.; Banks, Bruce A.

1992-01-01

To evaluate the performance and durability of solar reflector surfaces in the atomic oxygen environment typical of low Earth orbit (LEO), one must expose the reflector surface either directly to LEO or to ground-laboratory atomic oxygen environments. Although actual LEO exposures are most desired, such opportunities are typically scarce, expensive, and of limited duration. As a result, ground-laboratory exposures must be relied upon as the most practical long-term durability evaluation technique. Plasma ashers are widely used as LEO simulation facilities by producing atomic oxygen environments for durability evaluation of potential spacecraft materials. Atomic oxygen arrival differs between ground and space exposure in that plasma asher exposure produces isotropic arrival and space solar tracking produces sweeping arrival. Differences in initial impact reaction probability occur, dependent upon the energy and species existing in these environments. Due to the variations in ground-laboratory and space atomic oxygen, quantification of in-space performance based on plasma asher testing is not straightforward. The various atomic oxygen interactions that can occur with reflector surfaces, such as undercutting in organic substrates at protective coating defect sites, ground-laboratory techniques recommended for evaluating the atomic oxygen durability of reflectors based on asher exposures, and computational techniques which make use of ground-laboratory atomic oxygen exposure to predict in-space LEO durability are addressed.

Localization of atomic excitation beyond the diffraction limit using electromagnetically induced transparency

NASA Astrophysics Data System (ADS)

Miles, J. A.; Das, Diptaranjan; Simmons, Z. J.; Yavuz, D. D.

2015-09-01

We experimentally demonstrate the localization of excitation between hyperfine ground states of 87Rb atoms to as small as λ /13 -wide spatial regions. We use ultracold atoms trapped in a dipole trap and utilize electromagnetically induced transparency (EIT) for the atomic excitation. The localization is achieved by combining a spatially varying coupling laser (standing wave) with the intensity dependence of EIT. The excitation is fast (150 ns laser pulses) and the dark-state fidelity can be made higher than 94% throughout the standing wave. Because the width of the localized regions is much smaller than the wavelength of the driving light, traditional optical imaging techniques cannot resolve the localized features. Therefore, to measure the excitation profile, we use an autocorrelation-like method where we perform two EIT sequences separated by a time delay, during which we move the standing wave.

Local structure and polarization resistance of Ce doped SrMnO{sub 3} using extended x-ray fine structure analysis

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

Ryu, Jiseung; Lee, Heesoo, E-mail: heesoo@pusan.ac.kr

2014-09-15

Changes to the local structure of Sr and Mn atoms in Sr{sub 1−x}Ce{sub x}MnO{sub 3} (SCM) according to increasing Ce content and the effect of the structural change on the polarization resistance of SCM were investigated. The reduction of manganese was confirmed by the absorption edge shift of the Mn K-edge toward lower energies. The noise of oscillation in extended X-ray absorption fine structure k{sup 3}χ data at Mn K-edge reveals the distortion of the local structure of Mn atoms, and the peak that indicates the bonding length of Mn-O, Sr/Ce, and -Mn decreased with the addition of Ce contentmore » in Fourier transformations of the Mn K-edge. The distortion of the local structure at Mn atoms was affected by the reduced manganese ions having larger ionic radii than Mn{sup 4+}. Meanwhile, few distortions of local atomic structures of Sr atoms occurred, and the average nearest neighboring distances of Sr-O and Sr-Mn are ∼2.13 Å and ∼2.95 Å, respectively. The average bonding lengths of the Ce-O and Ce-Mn increased because the ionic radius of substituted Ce ion with 12 coordination number is smaller than that of Sr ion, which leads the reduction of Mn ions and the distortion of local structure at the substituted A-site. Therefore, we reasoned that the distortion of the local atomic structure at Mn atoms in MnO{sub 6} and Ce atoms in A-site is one of the causes for interrupting oxygen ion transfers as a geometric factor, which results in an increase in the polarization resistance of SCM within the Ce composition range from 10 mol. % to 30 mol. %.« less

Study of diffusion and local structure of sodium-silicate liquid: the molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Hung, Pham Khac; Noritake, Fumiya; San, Luyen Thi; Van, To Ba; Vinh, Le The

2017-10-01

A systematic analysis on sodium-silicate melt with various silica contents was carried out. The simulation revealed two diffusion mechanisms occurred in the melt: the bond-breaking and hopping between sites. The local structure was analyzed through T-simplexes. It was revealed that T-clusters have a non-spherical shape and represent the diffusion channel, in which Na atoms are dominant, but no any O atoms are located. The SiO2-poor melt acquires a long channel. In contrast, the SiO2-rich melt consists of unconnected short channels. The simulation also revealed the immobile and mobile regions which differ in local structure and constituent composition. We propose a new CL-function to characterizing the spatial distribution of different atom component. The spatial distribution of mobile and immobile atoms is found quite different. In particular, the immobile atoms are concentrated in high-density regions possessing very large density of immobile atoms. The spatial distribution of mobile atoms in contrast is more homogeneous.

High viscosity environments: an unexpected route to obtain true atomic resolution with atomic force microscopy.

PubMed

Weber, Stefan A L; Kilpatrick, Jason I; Brosnan, Timothy M; Jarvis, Suzanne P; Rodriguez, Brian J

2014-05-02

Atomic force microscopy (AFM) is widely used in liquid environments, where true atomic resolution at the solid-liquid interface can now be routinely achieved. It is generally expected that AFM operation in more viscous environments results in an increased noise contribution from the thermal motion of the cantilever, thereby reducing the signal-to-noise ratio (SNR). Thus, viscous fluids such as ionic and organic liquids have been generally avoided for high-resolution AFM studies despite their relevance to, e.g. energy applications. Here, we investigate the thermal noise limitations of dynamic AFM operation in both low and high viscosity environments theoretically, deriving expressions for the amplitude, phase and frequency noise resulting from the thermal motion of the cantilever, thereby defining the performance limits of amplitude modulation, phase modulation and frequency modulation AFM. We show that the assumption of a reduced SNR in viscous environments is not inherent to the technique and demonstrate that SNR values comparable to ultra-high vacuum systems can be obtained in high viscosity environments under certain conditions. Finally, we have obtained true atomic resolution images of highly ordered pyrolytic graphite and mica surfaces, thus revealing the potential of high-resolution imaging in high viscosity environments.

High viscosity environments: an unexpected route to obtain true atomic resolution with atomic force microscopy

NASA Astrophysics Data System (ADS)

Weber, Stefan A. L.; Kilpatrick, Jason I.; Brosnan, Timothy M.; Jarvis, Suzanne P.; Rodriguez, Brian J.

2014-05-01

Atomic force microscopy (AFM) is widely used in liquid environments, where true atomic resolution at the solid-liquid interface can now be routinely achieved. It is generally expected that AFM operation in more viscous environments results in an increased noise contribution from the thermal motion of the cantilever, thereby reducing the signal-to-noise ratio (SNR). Thus, viscous fluids such as ionic and organic liquids have been generally avoided for high-resolution AFM studies despite their relevance to, e.g. energy applications. Here, we investigate the thermal noise limitations of dynamic AFM operation in both low and high viscosity environments theoretically, deriving expressions for the amplitude, phase and frequency noise resulting from the thermal motion of the cantilever, thereby defining the performance limits of amplitude modulation, phase modulation and frequency modulation AFM. We show that the assumption of a reduced SNR in viscous environments is not inherent to the technique and demonstrate that SNR values comparable to ultra-high vacuum systems can be obtained in high viscosity environments under certain conditions. Finally, we have obtained true atomic resolution images of highly ordered pyrolytic graphite and mica surfaces, thus revealing the potential of high-resolution imaging in high viscosity environments.

Synchrotron EXAFS and XANES spectroscopy studies of transition aluminas doped with La and Cr for catalytic applications

DOE PAGES

Glazoff, Michael V.

2016-03-14

Abstract Transition aluminas doped with Cr find widespread application in the dehydrogenation industry, while La-stabilized transition aluminas are used extensively for high temperature application as catalytic supports. In this work, a detailed synchrotron XAFS-spectroscopy studies were conducted to shed light upon the atomic mechanisms of catalysis and/or catalytic support stabilization. It has been demonstrated that in the samples of different transition aluminas doped with Cr, the atoms of chromium are mostly in the state of oxidation Cr3+ and enter nanoparticles of Cr-bearing phases (Cr2O3 in the case of gamma- and –chi-alumina. In the row “gamma – chi – theta –more » eta-alumina” the change of properties (in particular, of the coloration of different samples) takes place because of dramatic reduction in the average size of Cr clusters and, possibly, their appearance on the Al2O3 surface. It has been also demonstrated that the substantial change in the local coordination of the La atoms in the samples of gamma-alumina doped with La, takes place only upon heating up to 1400°C, thereby making the La-stabilized gamma-alumina a perfect catalytic support for the numerous applications, e.g. catalytic three-way conversion of automobile exhaust gases. This change manifested itself in the form of increased La-O bond lengths and the La coordination number (from 8 to 12). It has been proved that the local environment of La in this new La-bearing phase cannot be explained in terms of the LaAlO3 formation. The absence of the La atoms in the second coordination sphere favors monoatomic distribution of La atoms on grain boundaries, proving that only very small amounts of this expensive rare earth material is required to achieve full stabilization. It is inferred that the tendency of La atoms to get surrounded by oxygen atoms, and also the impossibility of going into the bulk of alumina crystal, could be a major reason of the increased thermal stability of gamma alumina doped with lanthanum.« less

Synchrotron EXAFS and XANES spectroscopy studies of transition aluminas doped with La and Cr for catalytic applications

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

Glazoff, Michael V.

Abstract Transition aluminas doped with Cr find widespread application in the dehydrogenation industry, while La-stabilized transition aluminas are used extensively for high temperature application as catalytic supports. In this work, a detailed synchrotron XAFS-spectroscopy studies were conducted to shed light upon the atomic mechanisms of catalysis and/or catalytic support stabilization. It has been demonstrated that in the samples of different transition aluminas doped with Cr, the atoms of chromium are mostly in the state of oxidation Cr3+ and enter nanoparticles of Cr-bearing phases (Cr2O3 in the case of gamma- and –chi-alumina. In the row “gamma – chi – theta –more » eta-alumina” the change of properties (in particular, of the coloration of different samples) takes place because of dramatic reduction in the average size of Cr clusters and, possibly, their appearance on the Al2O3 surface. It has been also demonstrated that the substantial change in the local coordination of the La atoms in the samples of gamma-alumina doped with La, takes place only upon heating up to 1400°C, thereby making the La-stabilized gamma-alumina a perfect catalytic support for the numerous applications, e.g. catalytic three-way conversion of automobile exhaust gases. This change manifested itself in the form of increased La-O bond lengths and the La coordination number (from 8 to 12). It has been proved that the local environment of La in this new La-bearing phase cannot be explained in terms of the LaAlO3 formation. The absence of the La atoms in the second coordination sphere favors monoatomic distribution of La atoms on grain boundaries, proving that only very small amounts of this expensive rare earth material is required to achieve full stabilization. It is inferred that the tendency of La atoms to get surrounded by oxygen atoms, and also the impossibility of going into the bulk of alumina crystal, could be a major reason of the increased thermal stability of gamma alumina doped with lanthanum.« less

PubChem atom environments.

PubMed

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many seemingly due to erroneous interpretation of structures from patent data. Compared to fragmentation statistics published 40 years ago, the exponential growth in chemistry is mirrored in a nearly eightfold increase in the number of unique chemical fragments; however, this result is clearly an upper bound estimate as earlier studies employed structure sampling approaches and this study shows that a relatively high rate of atom fragments are found in only a single chemical structure (singletons). In addition, the percentage of singletons grows as the size of the chemical fragment is increased. The observed growth of the numbers of unique fragments over time suggests that many chemically possible connections of atom types to larger fragments have yet to be explored by chemists. A dramatic drop in the relative rate of increase of atom environments from smaller to larger fragments shows that larger fragments mainly consist of diverse combinations of a limited subset of smaller fragments. This is further supported by the observed concomitant increase of singleton atom environments. Combined, these findings suggest that there is considerable opportunity for chemists to combine known fragments to novel chemical compounds. The comparison of PubChem to an older study of known chemical structures shows noticeable differences. The changes suggest advances in synthetic capabilities of chemists to combine atoms in new patterns. Log-log plots of fragment incidence show small numbers of fragments are found in many structures and that large numbers of fragments are found in very few structures, with nearly half being novel using the methods in this work. The relative decrease in the count of new fragments as a function of size further suggests considerable opportunity for more novel chemicals exists. Lastly, the differences in atom environment diversity between PubChem Substance and Compound showcase the effect of PubChem standardization protocols, but also indicate that a normalization procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PubMed Central

Dasgupta, Bhaskar; Kasahara, Kota; Kamiya, Narutoshi; Nakamura, Haruki; Kinjo, Akira R.

2014-01-01

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics. PMID:24625758

Coherent manipulation of a solid-state artificial atom with few photons.

PubMed

Giesz, V; Somaschi, N; Hornecker, G; Grange, T; Reznychenko, B; De Santis, L; Demory, J; Gomez, C; Sagnes, I; Lemaître, A; Krebs, O; Lanzillotti-Kimura, N D; Lanco, L; Auffeves, A; Senellart, P

2016-06-17

In a quantum network based on atoms and photons, a single atom should control the photon state and, reciprocally, a single photon should allow the coherent manipulation of the atom. Both operations require controlling the atom environment and developing efficient atom-photon interfaces, for instance by coupling the natural or artificial atom to cavities. So far, much attention has been drown on manipulating the light field with atomic transitions, recently at the few-photon limit. Here we report on the reciprocal operation and demonstrate the coherent manipulation of an artificial atom by few photons. We study a quantum dot-cavity system with a record cooperativity of 13. Incident photons interact with the atom with probability 0.95, which radiates back in the cavity mode with probability 0.96. Inversion of the atomic transition is achieved for 3.8 photons on average, showing that our artificial atom performs as if fully isolated from the solid-state environment.

On the relationship between residue structural environment and sequence conservation in proteins.

PubMed

Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

2017-09-01

Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

Locality of correlation in density functional theory

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

Burke, Kieron; Cancio, Antonio; Gould, Tim

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that E{sub C} → −A{sub C} ZlnZ +more » B{sub C}Z as Z → ∞, where Z is the atomic number, A{sub C} is known, and we estimate B{sub C} to be about 37 mhartree. The local density approximation yields A{sub C} exactly, but a very incorrect value for B{sub C}, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with B{sub C} a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.« less

Water adsorption in SAPO-34: elucidating the role of local heterogeneities and defects using dispersion-corrected DFT calculations.

PubMed

Fischer, Michael

2015-10-14

The chabazite-type silicoaluminophosphate SAPO-34 is a promising adsorbent for applications in thermal energy storage using water adsorption-desorption cycles. In order to develop a microscopic understanding of the impact of local heterogeneities and defects on the water adsorption properties, the interaction of different models of SAPO-34 with water was studied using dispersion-corrected density-functional theory (DFT-D) calculations. In addition to SAPO-34 with isolated silicon atoms, the calculations considered models incorporating two types of heterogeneities (silicon islands, aluminosilicate domains), and two defect-containing (partially and fully desilicated) systems. DFT-D optimisations were performed for systems with small amounts of adsorbed water, in which all H2O molecules can interact with framework protons, and systems with large amounts of adsorbed water (30 H2O molecules per unit cell). At low loadings, the host-guest interaction energy calculated for SAPO-34 with isolated Si atoms amounts to approximately -90 kJ mol(-1). While the presence of local heterogeneities leads to the creation of some adsorption sites that are energetically slightly more favourable, the interaction strength is drastically reduced in systems with defects. At high water loadings, energies in the range of -70 kJ mol(-1) are obtained for all models. The DFT-D interaction energies are in good agreement with experimentally measured heats of water adsorption. A detailed analysis of the equilibrium structures was used to gain insights into the binding modes at low coverages, and to assess the extent of framework deprotonation and changes in the coordination environment of aluminium atoms at high water loadings.

Low Earth Orbital Atomic Oxygen Interactions With Materials

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Miller, Sharon K.; deGroh, Kim K.

2004-01-01

Atomic oxygen is formed in the low Earth orbital environment (LEO) by photo dissociation of diatomic oxygen by short wavelength (< 243 nm) solar radiation which has sufficient energy to break the 5.12 eV O2 diatomic bond in an environment where the mean free path is sufficiently long ( 108 meters) that the probability of reassociation or the formation of ozone (O3) is small. As a consequence, between the altitudes of 180 and 650 km, atomic oxygen is the most abundant species. Spacecraft impact the atomic oxygen resident in LEO with sufficient energy to break hydrocarbon polymer bonds, causing oxidation and thinning of the polymers due to loss of volatile oxidation products. Mitigation techniques, such as the development of materials with improved durability to atomic oxygen attack, as well as atomic oxygen protective coatings, have been employed with varying degrees of success to improve durability of polymers in the LEO environment. Atomic oxygen can also oxidize silicones and silicone contamination to produce non-volatile silica deposits. Such contaminants are present on most LEO missions and can be a threat to performance of optical surfaces. The LEO atomic oxygen environment, its interactions with materials, results of space testing, computational modeling, mitigation techniques, and ground laboratory simulation procedures and issues are presented.

Core–Shell to Doped Quantum Dots: Evolution of the Local Environment Using XAFS

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

Saha, Avijit; Chattopadhyay, Soma; Shibata, Tomohiro

2016-09-30

Internal structure study at an atomic level is a challenging task with far reaching consequences to its material properties, specifically in the field of transition metal doping in quantum dots. Diffusion of transition metal ions in and out of quantum dots forming magnetic clusters has been a major bottleneck in this class of materials. Diffusion of the magnetic ions from the core into the nonmagnetic shell in a core/shell heterostructure architecture to attain uniform doping has been recently introduced and yet to be understood. In this work, we have studied the local structure variation of Fe as a function ofmore » CdS matrix thickness and annealing time during the overcoating of Fe 3O 4 core with CdS using X-ray absorption spectroscopy. The data reveals that Fe 3O 4 core initially forms a core/shell structure with CdS followed by alloying at the interface eventually completely diffusing all the way through the CdS matrix to form homogeneously Fe-doped CdS QDs with excellent control over size and size distribution. Study of Fe K-edge shows a complete change of Fe local environment from Fe–O to FeS.« less

Dynamics of many-body localization in the presence of particle loss

NASA Astrophysics Data System (ADS)

van Nieuwenburg, EPL; Yago Malo, J.; Daley, AJ; Fischer, MH

2018-01-01

At long times, residual couplings to the environment become relevant even in the most isolated experiments, a crucial difficulty for the study of fundamental aspects of many-body dynamics. A particular example is many-body localization in a cold-atom setting, where incoherent photon scattering introduces both dephasing and particle loss. Whereas dephasing has been studied in detail and is known to destroy localization already on the level of non-interacting particles, the effect of particle loss is less well understood. A difficulty arises due to the ‘non-local’ nature of the loss process, complicating standard numerical tools using matrix product decomposition. Utilizing symmetries of the Lindbladian dynamics, we investigate the particle loss on both the dynamics of observables, as well as the structure of the density matrix and the individual states. We find that particle loss in the presence of interactions leads to dissipation and a strong suppression of the (operator space) entanglement entropy. Our approach allows for the study of the interplay of dephasing and loss for pure and mixed initial states to long times, which is important for future experiments using controlled coupling of the environment.

Environment-Assisted Speed-up of the Field Evolution in Cavity Quantum Electrodynamics

DOE PAGES

Cimmarusti, A. D.; Yan, Z.; Patterson, B. D.; ...

2015-06-11

We measure the quantum speed of the state evolution of the field in a weakly-driven optical cavity QED system. To this end, the mode of the electromagnetic field is considered as a quantum system of interest with a preferential coupling to a tunable environment: the atoms. By controlling the environment, i.e., changing the number of atoms coupled to the optical cavity mode, an environment assisted speed-up is realized: the quantum speed of the state re-population in the optical cavity increases with the coupling strength between the optical cavity mode and this non-Markovian environment (the number of atoms).

Update on IBEX and the outer boundary of the space radiation environment

NASA Astrophysics Data System (ADS)

McComas, D. J.; IBEX Science Team

2012-11-01

The Interstellar Boundary Explorer (IBEX) mission has been remotely observing the global interaction of our heliosphere with the local interstellar medium for over three years. Initially, IBEX generated the first all-sky maps of Energetic Neutral Atoms (ENAs) emanating in from the boundaries of our heliosphere over the energy range from ˜0.1-6 keV. Using these observations, the IBEX team discovered a smoothly varying, globally distributed ENA flux overlaid by a narrow "ribbon" of significantly enhanced ENA emissions. Since the initial publication of these results in a special issue of Science magazine (November 2009), IBEX has completed five more energy-resolved sets of sky maps and discovered small but important time variations in the interaction, separated the ribbon from globally distributed ENA fluxes, measured the energy spectral shape and inferred ion source temperatures, and carried out many other observational and theoretical studies of the outer heliosphere. In a second major area of observations - direct measurements of Interstellar Neutral (ISN) atoms - just published, IBEX observations of ISN He atoms show that the speed and direction (the motion of the heliosphere with respect to the interstellar medium) is slower and from a somewhat different direction than that thought from prior Ulysses observations. These observations also show evidence for a previously unknown and unanticipated secondary population of Helium. In addition, IBEX is providing the first direct quantitative measurements of the ISN H parameters and the first direct measurements of interstellar Ne and the interstellar Neon/Oxygen abundance ratio; this ratio is significantly different than the solar abundance ratio. Finally, IBEX was recently maneuvered into a unique, long-term stable orbit, which has a very low radiation environment and requires no orbit maintenance. Thus, IBEX will likely continue to provide revolutionary observations of the outer heliosphere and local interstellar medium for many years to come.

Chemical Bonding: The Orthogonal Valence-Bond View

PubMed Central

Sax, Alexander F.

2015-01-01

Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can be calculated, but the local information is hidden by the delocalized molecular orbitals (MO) used to construct the wave functions. The transformation of such wave functions into valence bond (VB) wave functions, which are based on localized orbitals, reveals the hidden information; this transformation is called a VB reading of MCSCF wave functions. The two-electron VB wave functions describing the Lewis electron pair that connects two atoms are frequently called covalent or neutral, suggesting that these wave functions describe an electronic situation where two electrons are never located at the same atom; such electronic situations and the wave functions describing them are called ionic. When the distance between two atoms decreases, however, every covalent VB wave function composed of non-orthogonal atomic orbitals changes its character from neutral to ionic. However, this change in the character of conventional VB wave functions is hidden by its mathematical form. Orthogonal VB wave functions composed of orthonormalized orbitals never change their character. When localized fragment orbitals are used instead of atomic orbitals, one can decide which local information is revealed and which remains hidden. In this paper, we analyze four chemical reactions by transforming the MCSCF wave functions into orthogonal VB wave functions; we show how the reactions are influenced by changing the atoms involved or by changing their local symmetry. Using orthogonal instead of non-orthogonal orbitals is not just a technical issue; it also changes the interpretation, revealing the properties of wave functions that remain otherwise undetected. PMID:25906476

125Te NMR and Seebeck Effect in Bi 2Te 3 Synthesized from Stoichiometric and Te-Rich Melts

DOE PAGES

Levin, E. M.; Iowa State Univ., Ames, IA; Riedemann, T. M.; ...

2016-10-14

Bi 2Te 3 is a well-known thermoelectric material and, as a new form of quantum matter, a topological insulator. Variation of local chemical composition in Bi2Te3 results in formation of several types of atomic defects, including Bi and Te vacancies and Bi and Te antisite defects; these defects can strongly affect material functionality via generation of free electrons and/or holes. Nonuniform distribution of atomic defects produces electronic inhomogeneity, which can be detected by 125Te nuclear magnetic resonance (NMR). Here we report on 125Te NMR and Seebeck effect (heat to electrical energy conversion) for two single crystalline samples: (#1) grown frommore » stoichiometric composition by Bridgman technique and (#2) grown out of Te-rich, high temperature flux. The Seebeck coefficients of these samples show p- and n-type conductivity, respectively, arising from different atomic defects. 125Te NMR spectra and spin–lattice relaxation measurements demonstrate that both Bi 2Te 3 samples are electronically inhomogeneous at the atomic scale, which can be attributed to a different Te environment due to spatial variation of the Bi/Te ratio and formation of atomic defects. In conclusion, correlations between 125Te NMR spectra, spin–lattice relaxation times, the Seebeck coefficients, carrier concentrations, and atomic defects are discussed. Our data demonstrate that 125Te NMR is an effective probe to study antisite defects in Bi 2Te 3.« less

125Te NMR and Seebeck Effect in Bi 2Te 3 Synthesized from Stoichiometric and Te-Rich Melts

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

Levin, E. M.; Iowa State Univ., Ames, IA; Riedemann, T. M.

Bi 2Te 3 is a well-known thermoelectric material and, as a new form of quantum matter, a topological insulator. Variation of local chemical composition in Bi2Te3 results in formation of several types of atomic defects, including Bi and Te vacancies and Bi and Te antisite defects; these defects can strongly affect material functionality via generation of free electrons and/or holes. Nonuniform distribution of atomic defects produces electronic inhomogeneity, which can be detected by 125Te nuclear magnetic resonance (NMR). Here we report on 125Te NMR and Seebeck effect (heat to electrical energy conversion) for two single crystalline samples: (#1) grown frommore » stoichiometric composition by Bridgman technique and (#2) grown out of Te-rich, high temperature flux. The Seebeck coefficients of these samples show p- and n-type conductivity, respectively, arising from different atomic defects. 125Te NMR spectra and spin–lattice relaxation measurements demonstrate that both Bi 2Te 3 samples are electronically inhomogeneous at the atomic scale, which can be attributed to a different Te environment due to spatial variation of the Bi/Te ratio and formation of atomic defects. In conclusion, correlations between 125Te NMR spectra, spin–lattice relaxation times, the Seebeck coefficients, carrier concentrations, and atomic defects are discussed. Our data demonstrate that 125Te NMR is an effective probe to study antisite defects in Bi 2Te 3.« less

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

Bowman, Adam J.; Scherrer, Joseph R.; Reiserer, Ronald S., E-mail: ron.reiserer@vanderbilt.edu

We present a simple apparatus for improved surface modification of polydimethylsiloxane (PDMS) microfluidic devices. A single treatment chamber for plasma activation and chemical/physical vapor deposition steps minimizes the time-dependent degradation of surface activation that is inherent in multi-chamber techniques. Contamination and deposition irregularities are also minimized by conducting plasma activation and treatment phases in the same vacuum environment. An inductively coupled plasma driver allows for interchangeable treatment chambers. Atomic force microscopy confirms that silane deposition on PDMS gives much better surface quality than standard deposition methods, which yield a higher local roughness and pronounced irregularities in the surface.

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

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2004-03-01

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

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.

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 1 2014-07-01 2014-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 1 2011-07-01 2011-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 1 2012-07-01 2012-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

40 CFR 23.9 - Timing of Administrator's action under the Atomic Energy Act.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 1 2013-07-01 2013-07-01 false Timing of Administrator's action under the Atomic Energy Act. 23.9 Section 23.9 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Atomic Energy Act. Unless the Administrator otherwise explicitly provides in a particular order, the time...

Atomistic simulation of the trapping capability of He-vacancy defects at Ni {\\sum}^{}3\\left(1\\bar{1}2\\right)[110] grain boundary

NASA Astrophysics Data System (ADS)

Gong, Hengfeng; Wang, Chengbin; Zhang, Wei; Huai, Ping; Lu, Wei; Zhu, Zhiyuan

2016-12-01

He atoms tend to cluster and precipitate into bubbles that prefer to grow in the grain boundaries, resulting in high temperature He embrittlement with significantly degraded material properties. This is a major bottleneck in employing Ni-based alloys for applications such as molten salt reactors (MSRs). This paper focuses on understanding how the local grain boundary structure interacts with He atoms and how the local atomistic environment in the grain boundary influences the binding energy of He defects. Using molecular dynamics simulations, we have investigated the trapping capability of the Ni {\\sum}3≤ft(1 \\bar{1} 2\\right)≤ft[1 1 0\\right] grain boundary to He defects (He N ) and to He-vacancy defects (He N V M ). The two defects in the Ni grain boundary exhibit geometries with high symmetry. The binding energy of an interstitial He atom to He N V M defects is found to be generally larger in pure Ni than that in the grain boundary. We compared the binding energy of He N defects to the Ni vacancy and to the Ni grain boundary, finding that the Ni vacancy possesses a higher trapping strength to He N . We also found that the binding strength of He N to the grain boundary is stronger than that of He N V M to the grain boundary. The He-vacancy ratio in He N V M defects does not significantly affect the binding energy in the grain boundary plane. The current work will provide insight in understanding the experimentally observed He bubble formation in Ni-based alloys and bridge atomic scale events and damage with macroscopic failure.

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.

Doping of Semiconducting Atomic Chains

NASA Technical Reports Server (NTRS)

Toshishige, Yamada; Kutler, Paul (Technical Monitor)

1997-01-01

Due to the rapid progress in atom manipulation technology, atomic chain electronics would not be a dream, where foreign atoms are placed on a substrate to form a chain, and its electronic properties are designed by controlling the lattice constant d. It has been shown theoretically that a Si atomic chain is metallic regardless of d and that a Mg atomic chain is semiconducting or insulating with a band gap modified with d. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along the chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of dopant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Correlation of atomic packing with the boson peak in amorphous alloys

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

Yang, W. M.; Key Laboratory of Magnetic Materials and Devices, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201; School of Materials Science and Engineering, Southeast University, Nanjing 211189

2014-09-28

Boson peaks (BP) have been observed from phonon specific heats in 10 studied amorphous alloys. Two Einstein-type vibration modes were proposed in this work and all data can be fitted well. By measuring and analyzing local atomic structures of studied amorphous alloys and 56 reported amorphous alloys, it is found that (a) the BP originates from local harmonic vibration modes associated with the lengths of short-range order (SRO) and medium-range order (MRO) in amorphous alloys, and (b) the atomic packing in amorphous alloys follows a universal scaling law, i.e., the ratios of SRO and MRO lengths to solvent atomic diametermore » are 3 and 7, respectively, which exact match with length ratios of BP vibration frequencies to Debye frequency for the studied amorphous alloys. This finding provides a new perspective for atomic packing in amorphous materials, and has significant implications for quantitative description of the local atomic orders and understanding the structure-property relationship.« less

First-principles analysis of structural and opto-electronic properties of indium tin oxide

NASA Astrophysics Data System (ADS)

Tripathi, Madhvendra Nath; Shida, Kazuhito; Sahara, Ryoji; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2012-05-01

Density functional theory (DFT) and DFT + U (DFT with on-site Coulomb repulsion corrections) calculations have been carried out to study the structural and opto-electronic properties of indium tin oxide (ITO) for both the oxidized and reduced environment conditions. Some of the results obtained by DFT calculations differ from the experimental observations, such as uncertain indication for the site preference of tin atom to replace indium atom at b-site or d-site, underestimation of local inward relaxation in the first oxygen polyhedra around tin atom, and also the improper estimation of electronic density of states and hence resulting in an inappropriate optical spectra of ITO. These discrepancies of theoretical outcomes with experimental observations in ITO arise mainly due to the underestimation of the cationic 4d levels within standard DFT calculations. Henceforth, the inclusion of on-site corrections within DFT + U framework significantly modifies the theoretical results in better agreement to the experimental observations. Within this framework, our calculations show that the indium b-site is preferential site over d-site for tin atom substitution in indium oxide under both the oxidized and reduced conditions. Moreover, the calculated average inward relaxation value of 0.16 Å around tin atom is in good agreement with the experimental value of 0.18 Å. Furthermore, DFT + U significantly modify the electronic structure and consequently induce modifications in the calculated optical spectra of ITO.

XPS and XANES studies of biomimetic composites based on B-type nano-hydroxyapatite

NASA Astrophysics Data System (ADS)

Goloshchapov, D. L.; Gushchin, M. S.; Kashkarov, V. M.; Seredin, P. V.; Ippolitov, Y. A.; Khmelevsky, N. O.; Aksenenko, A. Yu.

2018-06-01

The paper presents an investigation of the local atomic structure of nanocrystalline carbonate-substituted hydroxyapatite (CHAP) contained in biomimetic composites - analogues of intact human tooth tissues. Using the XPS technique, the presence of impurity Mg and F atoms and structurally bound carbon in CHAP, at the concentrations typical of apatite enamel and dentine was determined. The XANES method was used to study the changes occurring in P L2,3 spectra of biocomposites with CHAP, depending on the percentage of the amino acid matrix. The appearance of maxima in the spectra of XANES P L2,3 near 135.7 eV for the samples with the composition of amino acid complex/hydroxyapatite - 5/95, 25/75 and the splitting of a broad peak of 146.9 eV in the spectrum of a biocomposite with a composition of 40/60 indicates at the interaction of molecular complex of amino acids with atomic environment of phosphorus. This fact can be used in the fundamental medicine for synthesizing of new biomaterials in dentistry.

Mulliken's populations and electron momentum densities of transition metal tungstates using LCAO scheme

NASA Astrophysics Data System (ADS)

Meena, B. S.; Heda, N. L.; Ahuja, B. L.

2018-05-01

We have computed the Mulliken's populations (MP) and electron momentum densities (EMDs) for TMWO4 (TM=Co, Ni, Cu and Zn) using linear combination of atomic orbitals (LCAO) scheme. The latest hybridization of Hartree-Fock (HF) and density functional theory (DFT) under the framework of LCAO approximations (so called WC1LYP and B1WC) have been employed. The theoretical EMDs have been compared with the available experimental data which show that WC1LYP scheme gives slightly better agreement with the experimental data for all the reported tungstates. Such trend shows the applicability of Lee-Yang-Parr (LYP) correlation energies within hybrid approximations in predicting the electronic properties of these compounds. Further, the MP data show the charge transfer from Co/Ni/Cu/Zn and W to O atoms. In addition, we have plotted the total EMDs at the same normalized area which show almost similar type of localization of 3d electrons (in real space) of Cu and Zn, which is lower than that of Ni and Co atoms in their tungstates environment.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

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

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; Giese, Timothy J.

2015-12-21

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom’s local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion andmore » dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the S{sub N}2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.« less

Approaching the theoretical limit in periodic local MP2 calculations with atomic-orbital basis sets: the case of LiH.

PubMed

Usvyat, Denis; Civalleri, Bartolomeo; Maschio, Lorenzo; Dovesi, Roberto; Pisani, Cesare; Schütz, Martin

2011-06-07

The atomic orbital basis set limit is approached in periodic correlated calculations for solid LiH. The valence correlation energy is evaluated at the level of the local periodic second order Møller-Plesset perturbation theory (MP2), using basis sets of progressively increasing size, and also employing "bond"-centered basis functions in addition to the standard atom-centered ones. Extended basis sets, which contain linear dependencies, are processed only at the MP2 stage via a dual basis set scheme. The local approximation (domain) error has been consistently eliminated by expanding the orbital excitation domains. As a final result, it is demonstrated that the complete basis set limit can be reached for both HF and local MP2 periodic calculations, and a general scheme is outlined for the definition of high-quality atomic-orbital basis sets for solids. © 2011 American Institute of Physics

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

PubMed

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

2012-12-01

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

Subwavelength atom localization via coherent manipulation of the Raman gain process

NASA Astrophysics Data System (ADS)

Qamar, Sajid; Mehmood, Asad; Qamar, Shahid

2009-03-01

We present a simple scheme of atom localization in a subwavelength domain via manipulation of Raman gain process. We consider a four-level system with a pump and a weak probe field. In addition, we apply a coherent field to control the gain process. The system is similar to the one used by Agarwal and Dasgupta [Phys. Rev. A 70, 023802 (2004)] for the superluminal pulse propagation through Raman gain medium. For atom localization, we consider both pump and control fields to be the standing-wave fields of the cavity. We show that a much precise position of an atom passing through the standing-wave fields can be determined by measuring the gain spectrum of the probe field.

Interconfigurational energies in transition-metal atoms using gradient-corrected density-functional theory

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

Kutzler, F.W.; Painter, G.S.

1991-03-15

The rapid variation of charge and spin densities in atoms and molecules provides a severe test for local-density-functional theory and for the use of gradient corrections. In the study reported in this paper, we use the Langreth, Mehl, and Hu (LMH) functional and the generalized gradient approximation (GGA) of Perdew and Yue to calculate {ital s}-{ital d} transition energies, 4{ital s} ionization energies, and 3{ital d} ionization energies for the 3{ital d} transition-metal atoms. These calculations are compared with results from the local-density functional of Vosko, Wilk, and Nusair. By comparison with experimental energies, we find that the gradient functionalsmore » are only marginally more successful than the local-density approximation in calculating energy differences between states in transition-metal atoms. The GGA approximation is somewhat better than the LMH functional for most of the atoms studied, although there are several exceptions.« less

Atomic quantum simulation of the lattice gauge-Higgs model: Higgs couplings and emergence of exact local gauge symmetry.

PubMed

Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

2013-09-13

Recently, the possibility of quantum simulation of dynamical gauge fields was pointed out by using a system of cold atoms trapped on each link in an optical lattice. However, to implement exact local gauge invariance, fine-tuning the interaction parameters among atoms is necessary. In the present Letter, we study the effect of violation of the U(1) local gauge invariance by relaxing the fine-tuning of the parameters and showing that a wide variety of cold atoms is still a faithful quantum simulator for a U(1) gauge-Higgs model containing a Higgs field sitting on sites. The clarification of the dynamics of this gauge-Higgs model sheds some light upon various unsolved problems, including the inflation process of the early Universe. We study the phase structure of this model by Monte Carlo simulation and also discuss the atomic characteristics of the Higgs phase in each simulator.

Exotic topological density waves in cold atomic Rydberg-dressed fermions

PubMed Central

Li, Xiaopeng; Sarma, S Das

2015-01-01

Versatile controllability of interactions in ultracold atomic and molecular gases has now reached an era where quantum correlations and unconventional many-body phases can be studied with no corresponding analogues in solid-state systems. Recent experiments in Rydberg atomic gases have achieved exquisite control over non-local interactions, allowing novel quantum phases unreachable with the usual local interactions in atomic systems. Here we study Rydberg-dressed atomic fermions in a three-dimensional optical lattice predicting the existence of hitherto unheard-of exotic mixed topological density wave phases. By varying the spatial range of the non-local interaction, we find various chiral density waves with spontaneous time-reversal symmetry breaking, whose quasiparticles form three-dimensional quantum Hall and Weyl semimetal states. Remarkably, certain density waves even exhibit mixed topologies beyond the existing topological classification. Our results suggest gapless fermionic states could exhibit far richer topology than previously expected. PMID:25972134

Variations on a theme - the evolution of hydrocarbon solids. I. Compositional and spectral modelling - the eRCN and DG models

NASA Astrophysics Data System (ADS)

Jones, A. P.

2012-04-01

Context. The compositional properties of hydrogenated amorphous carbons are known to evolve in response to the local conditions. Aims: We present a model for low-temperature, amorphous hydrocarbon solids, based on the microphysical properties of random and defected networks of carbon and hydrogen atoms, that can be used to study and predict the evolution of their properties in the interstellar medium. Methods: We adopt an adaptable and prescriptive approach to model these materials, which is based on a random covalent network (RCN) model, extended here to a full compositional derivation (the eRCN model), and a defective graphite (DG) model for the hydrogen poorer materials where the eRCN model is no longer valid. Results: We provide simple expressions that enable the determination of the structural, infrared and spectral properties of amorphous hydrocarbon grains as a function of the hydrogen atomic fraction, XH. Structural annealing, resulting from hydrogen atom loss, results in a transition from H-rich, aliphatic-rich to H-poor, aromatic-rich materials. Conclusions: The model predicts changes in the optical properties of hydrogenated amorphous carbon dust in response to the likely UV photon-driven and/or thermal annealing processes resulting, principally, from the radiation field in the environment. We show how this dust component will evolve, compositionally and structurally in the interstellar medium in response to the local conditions. Appendices A and B are available in electronic form at http://www.aanda.org

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

NASA Astrophysics Data System (ADS)

Thompson, A. P.; Swiler, L. P.; Trott, C. R.; Foiles, S. M.; Tucker, G. J.

2015-03-01

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

NASA Astrophysics Data System (ADS)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Ambient atomic resolution atomic force microscopy with qPlus sensors: Part 1.

PubMed

Wastl, Daniel S

2017-01-01

Atomic force microscopy (AFM) is an enormous tool to observe nature in highest resolution and understand fundamental processes like friction and tribology on the nanoscale. Atomic resolution in highest quality was possible only in well-controlled environments like ultrahigh vacuum (UHV) or controlled buffer environments (liquid conditions) and more specified for long-term high-resolution analysis at low temperatures (∼4 K) in UHV where drift is nearly completely absent. Atomic resolution in these environments is possible and is widely used. However, in uncontrolled environments like air, with all its pollutants and aerosols, unspecified thin liquid films as thin as a single molecular water-layer of 200 pm or thicker condensation films with thicknesses up to hundred nanometer, have been a problem for highest resolution since the invention of the AFM. The goal of true atomic resolution on hydrophilic as well as hydrophobic samples was reached recently. In this manuscript we want to review the concept of ambient AFM with atomic resolution. The reader will be introduced to the phenomenology in ambient conditions and the problems will be explained and analyzed while a method for scan parameter optimization will be explained. Recently developed concepts and techniques how to reach atomic resolution in air and ultra-thin liquid films will be shown and explained in detail, using several examples. Microsc. Res. Tech. 80:50-65, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Spatial dispersion in atom-surface quantum friction

DOE PAGES

Reiche, D.; Dalvit, D. A. R.; Busch, K.; ...

2017-04-15

We investigate the influence of spatial dispersion on atom-surface quantum friction. We show that for atom-surface separations shorter than the carrier's mean free path within the material, the frictional force can be several orders of magnitude larger than that predicted by local optics. In addition, when taking into account spatial dispersion effects, we show that the commonly used local thermal equilibrium approximation underestimates by approximately 95% the drag force, obtained by employing the recently reported nonequilibrium fluctuation-dissipation relation for quantum friction. Unlike the treatment based on local optics, spatial dispersion in conjunction with corrections to local thermal equilibrium change notmore » only the magnitude but also the distance scaling of quantum friction.« less

Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

2015-12-01

A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

Precipitates and voids in cubic silicon carbide implanted with 25Mg+ ions

NASA Astrophysics Data System (ADS)

Jiang, Weilin; Spurgeon, Steven R.; Liu, Jia; Schreiber, Daniel K.; Jung, Hee Joon; Devaraj, Arun; Edwards, Danny J.; Henager, Charles H.; Kurtz, Richard J.; Wang, Yongqiang

2018-01-01

Single crystal cubic phase silicon carbide (3C-SiC) films on Si were implanted to 9.6 × 101625Mg+/cm2 at 673 K and annealed at 1073 and 1573 K for 2, 6, and 12 h in an Ar environment. The data from scanning transmission election microscopy (STEM) and electron energy loss spectroscopy (EELS) mapping suggest a possible formation of unidirectionally aligned tetrahedral precipitates of core (MgC2)-shell (Mg2Si) in the implanted sample annealed at 1573 K for 12 h. There are also small spherical voids near the surface and larger faceted voids around the region of maximum vacancy concentration. Atom probe tomography confirms 25Mg segregation dominated by small atomic clusters with local 25Mg concentrations up to 85 at.%. The resulting precipitate size and number density are found to decrease and increase, respectively, probably as a result of the thermal annealing that decomposes the 25Mg-bearing precipitates at the elevated temperatures and subsequent nucleation and growth below 1073 K during the cooling stage. The results from this study provide data needed to fully understand the property degradation of SiC in a high-flux fast neutron environment.

Experimental Observation of Two-Dimensional Anderson Localization with the Atomic Kicked Rotor.

PubMed

Manai, Isam; Clément, Jean-François; Chicireanu, Radu; Hainaut, Clément; Garreau, Jean Claude; Szriftgiser, Pascal; Delande, Dominique

2015-12-11

Dimension 2 is expected to be the lower critical dimension for Anderson localization in a time-reversal-invariant disordered quantum system. Using an atomic quasiperiodic kicked rotor-equivalent to a two-dimensional Anderson-like model-we experimentally study Anderson localization in dimension 2 and we observe localized wave function dynamics. We also show that the localization length depends exponentially on the disorder strength and anisotropy and is in quantitative agreement with the predictions of the self-consistent theory for the 2D Anderson localization.

Femtosecond laser patterning, synthesis, defect formation, and structural modification of atomic layered materials

DOE PAGES

Yoo, Jae-Hyuck; Kim, Eunpa; Hwang, David J.

2016-12-06

This article summarizes recent research on laser-based processing of twodimensional (2D) atomic layered materials, including graphene and transition metal dichalcogenides (TMDCs). Ultrafast lasers offer unique processing routes that take advantage of distinct interaction mechanisms with 2D materials to enable extremely localized energy deposition. Experiments have shown that ablative direct patterning of graphene by ultrafast lasers can achieve resolutions of tens of nanometers, as well as single-step pattern transfer. Ultrafast lasers also induce non-thermal excitation mechanisms that are useful for the thinning of TMDCs to tune the 2D material bandgap. Laser-assisted site-specific doping was recently demonstrated where ultrafast laser radiation undermore » ambient air environment could be used for the direct writing of high-quality graphene patterns on insulating substrates. This article concludes with an outlook towards developing further advanced laser processing with scalability, in situ monitoring strategies and potential applications.« less

Atomic force microscopy – looking at mechanosensors on the cell surface

PubMed Central

Heinisch, Jürgen J.; Lipke, Peter N.; Beaussart, Audrey; El Kirat Chatel, Sofiane; Dupres, Vincent; Alsteens, David; Dufrêne, Yves F.

2012-01-01

Summary Living cells use cell surface proteins, such as mechanosensors, to constantly sense and respond to their environment. However, the way in which these proteins respond to mechanical stimuli and assemble into large complexes remains poorly understood at the molecular level. In the past years, atomic force microscopy (AFM) has revolutionized the way in which biologists analyze cell surface proteins to molecular resolution. In this Commentary, we discuss how the powerful set of advanced AFM techniques (e.g. live-cell imaging and single-molecule manipulation) can be integrated with the modern tools of molecular genetics (i.e. protein design) to study the localization and molecular elasticity of individual mechanosensors on the surface of living cells. Although we emphasize recent studies on cell surface proteins from yeasts, the techniques described are applicable to surface proteins from virtually all organisms, from bacteria to human cells. PMID:23077172

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

Hoffman, A. S.; Debefve, L. M.; Gates, B. C., E-mail: bcgates@ucdavis.edu

X-ray absorption spectroscopy is an element-specific technique for probing the local atomic-scale environment around an absorber atom. It is widely used to investigate the structures of liquids and solids, being especially valuable for characterization of solid-supported catalysts. Reported cell designs are limited in capabilities—to fluorescence or transmission and to static or flowing atmospheres, or to vacuum. Our goal was to design a robust and widely applicable cell for catalyst characterizations under all these conditions—to allow tracking of changes during genesis and during operation, both under vacuum and in reactive atmospheres. Herein, we report the design of such a cell andmore » a demonstration of its operation both with a sample under dynamic vacuum and in the presence of gases flowing at temperatures up to 300 °C, showing data obtained with both fluorescence and transmission detection. The cell allows more flexibility in catalyst characterization than any reported.« less

Dependence of Van-Vleck paramagnetism on the size of nanocrystals in superstoichiometric TiO{sub y}

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

Valeeva, A. A., E-mail: valeeva@ihim.uran.ru; Nazarova, S. Z.; Rempel, A. A.

2016-04-15

In situ measurements of the magnetic susceptibility of titanium monoxide nanocrystals with superstoichiometric composition TiO{sub y} (y > 1) in the 300–1200 K temperature range showed that this value depends not only on the structural state of a sample, but also on the size of crystals. Analysis of data obtained for both ordered and disordered TiO{sub y} showed that the Van-Vleck paramagnetism is inversely proportional to the nanocrystal size because of breakage of the symmetry of local environment of the near-surface atoms of titanium and oxygen. The Van-Vleck paramagnetism contribution due to atomic-vacancy disorder in superstoichiometric titanium monoxide nanocrystals, asmore » well as in the stoichiometric composition, is proportional to a deviation of the degree of long-range order from its maximum value.« less

Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties

NASA Astrophysics Data System (ADS)

Xie, Tian; Grossman, Jeffrey C.

2018-04-01

The use of machine learning methods for accelerating the design of crystalline materials usually requires manually constructed feature vectors or complex transformation of atom coordinates to input the crystal structure, which either constrains the model to certain crystal types or makes it difficult to provide chemical insights. Here, we develop a crystal graph convolutional neural networks framework to directly learn material properties from the connection of atoms in the crystal, providing a universal and interpretable representation of crystalline materials. Our method provides a highly accurate prediction of density functional theory calculated properties for eight different properties of crystals with various structure types and compositions after being trained with 1 04 data points. Further, our framework is interpretable because one can extract the contributions from local chemical environments to global properties. Using an example of perovskites, we show how this information can be utilized to discover empirical rules for materials design.

A structurally driven analysis of thiol reactivity in mammalian albumins.

PubMed

Spiga, Ottavia; Summa, Domenico; Cirri, Simone; Bernini, Andrea; Venditti, Vincenzo; De Chiara, Matteo; Priora, Raffaella; Frosali, Simona; Margaritis, Antonios; Di Giuseppe, Danila; Di Simplicio, Paolo; Niccolai, Neri

2011-04-01

Understanding the structural basis of protein redox activity is still an open question. Hence, by using a structural genomics approach, different albumins have been chosen to correlate protein structural features with the corresponding reaction rates of thiol exchange between albumin and disulfide DTNB. Predicted structures of rat, porcine, and bovine albumins have been compared with the experimentally derived human albumin. High structural similarity among these four albumins can be observed, in spite of their markedly different reactivity with DTNB. Sequence alignments offered preliminary hints on the contributions of sequence-specific local environments modulating albumin reactivity. Molecular dynamics simulations performed on experimental and predicted albumin structures reveal that thiolation rates are influenced by hydrogen bonding pattern and stability of the acceptor C34 sulphur atom with donor groups of nearby residues. Atom depth evolution of albumin C34 thiol groups has been monitored during Molecular Dynamic trajectories. The most reactive albumins appeared also the ones presenting the C34 sulphur atom on the protein surface with the highest accessibility. High C34 sulphur atom reactivity in rat and porcine albumins seems to be determined by the presence of additional positively charged amino acid residues favoring both the C34 S⁻ form and the approach of DTNB. Copyright © 2011 Wiley Periodicals, Inc.

Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

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

Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at

Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy ismore » constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.« less

Ab Initio Molecular Dynamics Simulations and GIPAW NMR Calculations of a Lithium Borate Glass Melt.

PubMed

Ohkubo, Takahiro; Tsuchida, Eiji; Takahashi, Takafumi; Iwadate, Yasuhiko

2016-04-14

The atomic structure of a molten 0.3Li2O-0.7B2O3 glass at 1250 K was investigated using ab initio molecular dynamics (AIMD) simulations. The gauge including projector augmented wave (GIPAW) method was then employed for computing the chemical shift and quadrupolar coupling constant of (11)B, (17)O, and (7)Li from 764 AIMD derived structures. The chemical shift and quadrupolar coupling constant distributions were directly estimated from the dynamical structure of the molten glass. (11)B NMR parameters of well-known structural units such as the three-coordinated ring, nonring, and four-coordinated tetrahedron were found to be in good agreement with the experimental results. In this study, more detailed classification of B units was presented based on the number of O species bonded to the B atoms. This highlights the limitations of (11)B NMR sensitivity for resolving (11)B local environment using the experimentally obtained spectra only. The (17)O NMR parameter distributions can theoretically resolve the bridging and nonbridging O atoms with different structural units such as nonring, single boroxol ring, and double boroxol ring. Slight but clear differences in the number of bridging O atoms surrounding Li that have not been reported experimentally were observed in the theoretically obtained (7)Li NMR parameters.

Path integral Monte Carlo study on the structure and absorption spectra of alkali atoms (Li, Na, K) attached to superfluid helium clusters

NASA Astrophysics Data System (ADS)

Nakayama, Akira; Yamashita, Koichi

2001-01-01

Path integral Monte Carlo calculations have been performed to investigate the microscopic structure and thermodynamic properties of the AkṡHeN (Ak=Li, Na, K,N⩽300) clusters at T=0.5 K. Absorption spectra which correspond to the 2P←2S transitions of alkali atoms are also calculated within a pairwise additive model, which employs diatomic Ak-He potential energy curves. The size dependences of the cluster structure and absorption spectra that show the influence of the helium cluster environment are examined in detail. It is found that alkali atoms are trapped in a dimple on the helium cluster's surface and that, from the asymptotic behavior, the AkṡHe300 cluster, at least semiquantitatively, mimics the local structure of experimentally produced large helium clusters in the vicinity of alkali atoms. We have successfully reproduced the overall shapes of the spectra and explained their features from a static and structural point of view. The positions, relative intensities, and line widths of the absorption maxima are calculated to be in moderate agreement with experiments [F. Stienkemeier, J. Higgins, C. Callegari, S. I. Kanorsky, W. E. Ernst, and G. Scoles, Z. Phys. D 38, 253 (1996)].

Star Formation and Gas Dynamics in Galactic Disks: Physical Processes and Numerical Models

NASA Astrophysics Data System (ADS)

Ostriker, Eve C.

2011-04-01

Star formation depends on the available gaseous ``fuel'' as well as galactic environment, with higher specific star formation rates where gas is predominantly molecular and where stellar (and dark matter) densities are higher. The partition of gas into different thermal components must itself depend on the star formation rate, since a steady state distribution requires a balance between heating (largely from stellar UV for the atomic component) and cooling. In this presentation, I discuss a simple thermal and dynamical equilibrium model for the star formation rate in disk galaxies, where the basic inputs are the total surface density of gas and the volume density of stars and dark matter, averaged over ~kpc scales. Galactic environment is important because the vertical gravity of the stars and dark matter compress gas toward the midplane, helping to establish the pressure, and hence the cooling rate. In equilibrium, the star formation rate must evolve until the gas heating rate is high enough to balance this cooling rate and maintain the pressure imposed by the local gravitational field. In addition to discussing the formulation of this equilibrium model, I review the current status of numerical simulations of multiphase disks, focusing on measurements of quantities that characterize the mean properties of the diffuse ISM. Based on simulations, turbulence levels in the diffuse ISM appear relatively insensitive to local disk conditions and energetic driving rates, consistent with observations. It remains to be determined, both from observations and simulations, how mass exchange processes control the ratio of cold-to-warm gas in the atomic ISM.

77 FR 42483 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

... creating artificial nanoscale structures on an atom-by- atom basis using nascent atom manipulation techniques. The instrument will be used to investigate the amount of force required to move one atom on a materials surface while simultaneously measuring local electronic structural changes during atom movement...

Enhanced one-photon double ionization of atoms and molecules in an environment of different species.

PubMed

Stumpf, V; Kryzhevoi, N V; Gokhberg, K; Cederbaum, L S

2014-05-16

The correlated nature of electronic states in atoms and molecules is manifested in the simultaneous emission of two electrons after absorption of a single photon close to the respective threshold. Numerous observations in atoms and small molecules demonstrate that the double ionization efficiency close to threshold is rather small. In this Letter we show that this efficiency can be dramatically enhanced in the environment. To be specific, we concentrate on the case where the species in question has one or several He atoms as neighbors. The enhancement is achieved by an indirect process, where a He atom of the environment absorbs a photon and the resulting He(+) cation is neutralized fast by a process known as electron transfer mediated decay, producing thereby doubly ionized species. The enhancement of the double ionization is demonstrated in detail for the example of the Mg · He cluster. We show that the double ionization cross section of Mg becomes 3 orders of magnitude larger than the respective cross section of the isolated Mg atom. The impact of more neighbors is discussed and the extension to other species and environments is addressed.

Simulation of the low earth orbital atomic oxygen interaction with materials by means of an oxygen ion beam

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Rutledge, Sharon K.; Paulsen, Phillip E.; Steuber, Thomas J.

1989-01-01

Atomic oxygen is the predominant species in low-Earth orbit between the altitudes of 180 and 650 km. These highly reactive atoms are a result of photodissociation of diatomic oxygen molecules from solar photons having a wavelength less than or equal to 2430A. Spacecraft in low-Earth orbit collide with atomic oxygen in the 3P ground state at impact energies of approximately 4.2 to 4.5 eV. As a consequence, organic materials previously used for high altitude geosynchronous spacecraft are severely oxidized in the low-Earth orbital environment. The evaluation of materials durability to atomic oxygen requires ground simulation of this environment to cost effectively screen materials for durability. Directed broad beam oxygen sources are necessary to evaluate potential spacecraft materials performance before and after exposure to the simulated low-Earth orbital environment. This paper presents a description of a low energy, broad oxygen ion beam source used to simulate the low-Earth orbital atomic oxygen environment. The results of materials interaction with this beam and comparison with actual in-space tests of the same meterials will be discussed. Resulting surface morphologies appear to closely replicate those observed in space tests.

Atomic fountain clock with very high frequency stability employing a pulse-tube-cryocooled sapphire oscillator.

PubMed

Takamizawa, Akifumi; Yanagimachi, Shinya; Tanabe, Takehiko; Hagimoto, Ken; Hirano, Iku; Watabe, Ken-ichi; Ikegami, Takeshi; Hartnett, John G

2014-09-01

The frequency stability of an atomic fountain clock was significantly improved by employing an ultra-stable local oscillator and increasing the number of atoms detected after the Ramsey interrogation, resulting in a measured Allan deviation of 8.3 × 10(-14)τ(-1/2)). A cryogenic sapphire oscillator using an ultra-low-vibration pulse-tube cryocooler and cryostat, without the need for refilling with liquid helium, was applied as a local oscillator and a frequency reference. High atom number was achieved by the high power of the cooling laser beams and optical pumping to the Zeeman sublevel m(F) = 0 employed for a frequency measurement, although vapor-loaded optical molasses with the simple (001) configuration was used for the atomic fountain clock. The resulting stability is not limited by the Dick effect as it is when a BVA quartz oscillator is used as the local oscillator. The stability reached the quantum projection noise limit to within 11%. Using a combination of a cryocooled sapphire oscillator and techniques to enhance the atom number, the frequency stability of any atomic fountain clock, already established as primary frequency standard, may be improved without opening its vacuum chamber.

How localized is ``local?'' Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory

NASA Astrophysics Data System (ADS)

Havu, Vile; Blum, Volker; Scheffler, Matthias

2007-03-01

Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO's can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ˜tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,^1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc<= 3å have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

Origin of the transition voltage in gold-vacuum-gold atomic junctions.

PubMed

Wu, Kunlin; Bai, Meilin; Sanvito, Stefano; Hou, Shimin

2013-01-18

The origin and the distance dependence of the transition voltage of gold-vacuum-gold junctions are investigated by employing first-principles quantum transport simulations. Our calculations show that atomic protrusions always exist on the electrode surface of gold-vacuum-gold junctions fabricated using the mechanically controllable break junction (MCBJ) method. The transition voltage of these gold-vacuum-gold junctions with atomically sharp electrodes is determined by the local density of states (LDOS) of the apex gold atom on the electrode surface rather than by the vacuum barrier shape. More specifically, the absolute value of the transition voltage roughly equals the rising edge of the LDOS peak contributed by the 6p atomic orbitals of the gold atoms protruding from the electrode surface, whose local Fermi level is shifted downwards when a bias voltage is applied. Since the LDOS of the apex gold atom depends strongly on the exact shape of the electrode, the transition voltage is sensitive to the variation of the atomic configuration of the junction. For asymmetric junctions, the transition voltage may also change significantly depending on the bias polarity. Considering that the occurrence of the transition voltage requires the electrode distance to be larger than a critical value, the interaction between the two electrodes is actually rather weak. Consequently, the LDOS of the apex gold atom is mainly determined by its local atomic configuration and the transition voltage only depends weakly on the electrode distance as observed in the MCBJ experiments.

Model-based local density sharpening of cryo-EM maps

PubMed Central

Jakobi, Arjen J; Wilmanns, Matthias

2017-01-01

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

Description of the atomic disorder (local order) in crystals by the mixed-symmetry method

NASA Astrophysics Data System (ADS)

Dudka, A. P.; Novikova, N. E.

2017-11-01

An approach to the description of local atomic disorder (short-range order) in single crystals by the mixed-symmetry method based on Bragg scattering data is proposed, and the corresponding software is developed. In defect-containing crystals, each atom in the unit cell can be described by its own symmetry space group. The expression for the calculated structural factor includes summation over different sets of symmetry operations for different atoms. To facilitate the search for new symmetry elements, an "atomic disorder expert" was developed, which estimates the significance of tested models. It is shown that the symmetry lowering for some atoms correlates with the existence of phase transitions (in langasite family crystals) and the anisotropy of physical properties (in rare-earth dodecaborides RB12).

Unambiguous observation of F-atom core-hole localization in CF 4 through body-frame photoelectron angular distributions

DOE PAGES

McCurdy, C. W.; Rescigno, T. N.; Trevisan, C. S.; ...

2017-01-17

A dramatic symmetry breaking in K-shell photoionization of the CF 4 molecule in which a core-hole vacancy is created in one of four equivalent fluorine atoms is displayed in the molecular frame angular distribution of the photoelectrons. In observing the photoejected electron in coincidence with an F + atomic ion after Auger decay we see how selecting the dissociation path where the core hole was localized was almost exclusively on that atom. A combination of measurements and ab initio calculations of the photoelectron angular distribution in the frame of the recoiling CF 3 + and F + atoms elucidates themore » underlying physics that derives from the Ne-like valence structure of the F(1s -1) core-excited atom.« less

Residue-level global and local ensemble-ensemble comparisons of protein domains.

PubMed

Clark, Sarah A; Tronrud, Dale E; Karplus, P Andrew

2015-09-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a "consistency check" of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. © 2015 The Protein Society.

Residue-level global and local ensemble-ensemble comparisons of protein domains

PubMed Central

Clark, Sarah A; Tronrud, Dale E; Andrew Karplus, P

2015-01-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a “consistency check” of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. PMID:26032515

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

2017-01-27

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

2017-04-01

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

AceDRG: a stereochemical description generator for ligands

PubMed Central

Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas

2017-01-01

The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files. PMID:28177307

Local structure study of (In{sub 0.95−x}Fe{sub x}Cu{sub 0.05}){sub 2}O{sub 3} thin films using x-ray absorption spectroscopy

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

Ren, Yuan; Xing, Yaya; Ma, Guanxiong

2015-07-15

The (In{sub 0.95−x}Fe{sub x}Cu{sub 0.05}){sub 2}O{sub 3} (x = 0.06, 0.08, 0.15, and 0.20) films prepared by RF-magnetron sputtering were investigated by the combination of x-ray absorption spectroscopy (XAS) at Fe, Cu, and O K-edge. Although the Fe and O K-edge XAS spectra show that the Fe atoms substitute for the In sites of In{sub 2}O{sub 3} lattice for all the films, the Cu K-edge XAS spectra reveal that the codoped Cu atoms are separated to form the Cu metal clusters. After being annealed in air, the Fe atoms are still substitutionally incorporated into the In{sub 2}O{sub 3} lattice, while the Cumore » atoms form the CuO secondary phases. With the increase of Fe concentration, the bond length R{sub Fe-O} shortens and the Debye–Waller factor σ{sup 2}{sub Fe-O} increases in the first coordination shell of Fe, which are attributed to the relaxation of oxygen environment around the substitutional Fe ions. The forming of Cu relating secondary phases in the films is due to high ionization energy of Cu atoms, leading that the Cu atoms are energetically much harder to be oxidized to substitute for the In sites of In{sub 2}O{sub 3} lattice than Fe atoms. These results provide new experimental guidance in the preparation of the codoped In{sub 2}O{sub 3} based dilute magnetic oxides.« less

Prediction of conformationally dependent atomic multipole moments in carbohydrates

PubMed Central

Cardamone, Salvatore

2015-01-01

The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an “atom in a molecule,” thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol−1 for open chains and just over 90% an error of maximum 4 kJ mol−1 for rings. © 2015 Wiley Periodicals, Inc. PMID:26547500

Prediction of conformationally dependent atomic multipole moments in carbohydrates.

PubMed

Cardamone, Salvatore; Popelier, Paul L A

2015-12-15

The conformational flexibility of carbohydrates is challenging within the field of computational chemistry. This flexibility causes the electron density to change, which leads to fluctuating atomic multipole moments. Quantum Chemical Topology (QCT) allows for the partitioning of an "atom in a molecule," thus localizing electron density to finite atomic domains, which permits the unambiguous evaluation of atomic multipole moments. By selecting an ensemble of physically realistic conformers of a chemical system, one evaluates the various multipole moments at defined points in configuration space. The subsequent implementation of the machine learning method kriging delivers the evaluation of an analytical function, which smoothly interpolates between these points. This allows for the prediction of atomic multipole moments at new points in conformational space, not trained for but within prediction range. In this work, we demonstrate that the carbohydrates erythrose and threose are amenable to the above methodology. We investigate how kriging models respond when the training ensemble incorporating multiple energy minima and their environment in conformational space. Additionally, we evaluate the gains in predictive capacity of our models as the size of the training ensemble increases. We believe this approach to be entirely novel within the field of carbohydrates. For a modest training set size of 600, more than 90% of the external test configurations have an error in the total (predicted) electrostatic energy (relative to ab initio) of maximum 1 kJ mol(-1) for open chains and just over 90% an error of maximum 4 kJ mol(-1) for rings. © 2015 Wiley Periodicals, Inc.

Synchrotron EXAFS and XANES spectroscopy studies of transition aluminas doped with La and Cr for catalytic applications

NASA Astrophysics Data System (ADS)

Glazoff, Michael V.

2016-04-01

Transition aluminas doped with Cr find widespread application in the dehydrogenation catalysis industry, while La-stabilized transition aluminas are used extensively for high-temperature application as catalytic supports (Wefers and Misra in Oxides and hydroxides of aluminum, Alcoa Laboratories, Pittsburgh, 1987). In this work, detailed synchrotron XAFS spectroscopy studies were conducted to shed light upon the atomic mechanisms of surface and subsurface reconstructions and/or catalytic support stabilization of doped aluminas. It was demonstrated that in four transition aluminas doped with Cr, it is the atoms which are mostly in the state of oxidation Cr3+ and enter nanoparticles of Cr-bearing phases (Cr2O3 in the case of gamma- and chi-alumina). In the transition series aluminas: "gamma- chi- theta- eta-alumina," the change of properties (in particular, the dramatic increase in dehydrogenation catalytic activity and catalyst longevity and the coloration of samples) takes place because of the reduction in the average size of Cr clusters and their appearance on the Al2O3 surface, probably responsible for change in catalytic activity. It was demonstrated that in the samples of gamma-alumina doped with La any substantial change in the local coordination of the La atoms takes place only upon heating up to 1400 °C. This makes the La-stabilized gamma-alumina a perfect catalytic support for the numerous applications, e.g., catalytic three-way conversion of automobile exhaust gases. This change manifested itself in the form of increased La-O bond lengths and the La coordination number (from 8 to 12). Furthermore, it was demonstrated that the local environment of La in this new La-bearing phase cannot be explained in terms of the LaAlO3 formation. The absence of the La atoms in the second coordination sphere favors monoatomic distribution of La atoms on grain boundaries, proving that only very small amount of this rare earth material is required to achieve full stabilization. It is inferred that the tendency of La atoms to get surrounded by oxygen atoms, and also the impossibility of going into the alumina bulk, could be a major reason of the increased thermal stability of gamma-alumina doped with lanthanum.

Proceedings of the NASA Workshop on Atomic Oxygen Effects. [low earth orbital environment

NASA Technical Reports Server (NTRS)

Brinza, David E. (Editor)

1987-01-01

A workshop was held to address the scientific issues concerning the effects of atomic oxygen on materials in the low Earth orbital (LEO) environment. The program included 18 invited speakers plus contributed posters covering topics such as LEO spaceflight experiments, interaction mechanisms, and atomic oxygen source development. Discussion sessions were also held to organize a test program to evaluate atomic oxygen exposure facilities. The key issues raised in the workshop were: (1) the need to develop a reliable predictive model of the effects of long-term exposure of materials to the LEO environment; (2) the ability of ground-based exposure facilities to provide useful data for development of durable materials; and (3) accurate determination of the composition of the LEO environment. These proceedings include the invited papers, the abstracts for the contributed posters, and an account of the test program discussion sessions.

Photon Localization and Dicke Superradiance in Atomic Gases

NASA Astrophysics Data System (ADS)

Akkermans, E.; Gero, A.; Kaiser, R.

2008-09-01

Photon propagation in a gas of N atoms is studied using an effective Hamiltonian describing photon-mediated atomic dipolar interactions. The density P(Γ) of photon escape rates is determined from the spectrum of the N×N random matrix Γij=sin⁡(xij)/xij, where xij is the dimensionless random distance between any two atoms. Varying disorder and system size, a scaling behavior is observed for the escape rates. It is explained using microscopic calculations and a stochastic model which emphasizes the role of cooperative effects in photon localization and provides an interesting relation with statistical properties of “small world networks.”

Hydrogen positions in single nanocrystals revealed by electron diffraction

NASA Astrophysics Data System (ADS)

Palatinus, L.; Brázda, P.; Boullay, P.; Perez, O.; Klementová, M.; Petit, S.; Eigner, V.; Zaarour, M.; Mintova, S.

2017-01-01

The localization of hydrogen atoms is an essential part of crystal structure analysis, but it is difficult because of their small scattering power. We report the direct localization of hydrogen atoms in nanocrystalline materials, achieved using the recently developed approach of dynamical refinement of precession electron diffraction tomography data. We used this method to locate hydrogen atoms in both an organic (paracetamol) and an inorganic (framework cobalt aluminophosphate) material. The results demonstrate that the technique can reliably reveal fine structural details, including the positions of hydrogen atoms in single crystals with micro- to nanosized dimensions.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

NASA Astrophysics Data System (ADS)

Parrish, Robert M.; Sherrill, C. David

2014-07-01

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

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

Parrish, Robert M.; Sherrill, C. David, E-mail: sherrill@gatech.edu

2014-07-28

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work throughmore » the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.« less

Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments.

PubMed Central

Thomas, K A; Smith, G M; Thomas, T B; Feldmann, R J

1982-01-01

The atomic environments of 170 phenylalanine-residue aromatic rings from 28 protein crystal structures are transformed into a common orientation and combined to calculate an average three-dimensional environment. The spatial distribution of atom types in this environment reveals a preferred interaction between oxygen atoms and the edge of the planar aromatic rings. From the difference in frequency of interaction of oxygen atoms with the edge and the top of the ring, an apparent net free energy difference of interaction favoring the edge of the ring is estimated to be about -1 kcal/mol (1 cal = 4.184 J). Ab initio quantum mechanical calculations, performed on a model consisting of benzene and formamide, indicate that the observed geometry is stabilized by a favorable enthalpic interaction. Although benzene rings are considered to be nonpolar, the electron distribution is a complex multipole with no net dipole moment. The observed interaction orientation frequencies demonstrate that these multipolar electron distributions, when occurring at the short distances encountered in densely packed protein molecules, are significant determinants of internal packing geometries. PMID:6956896

Real-time ab initio KMC simulation of the self-assembly and sintering of bimetallic epitaxial nanoclusters: Au + Ag on Ag(100).

PubMed

Han, Yong; Liu, Da-Jiang; Evans, James W

2014-08-13

Far-from-equilibrium shape and structure evolution during formation and post-assembly sintering of bimetallic nanoclusters is extremely sensitive to the periphery diffusion and intermixing kinetics. Precise characterization of the many distinct local-environment-dependent diffusion barriers is achieved for epitaxial nanoclusters using density functional theory to assess interaction energies both with atoms at adsorption sites and at transition states. Kinetic Monte Carlo simulation incorporating these barriers then captures structure evolution on the appropriate time scale for two-dimensional core-ring and intermixed Au-Ag nanoclusters on Ag(100).

Real-Time Ab Initio KMC Simulation of the Self-Assembly and Sintering of Bimetallic Epitaxial Nanoclusters: Au + Ag on Ag(100)

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

Han, Yong; Liu, Da-Jiang; Evans, James W

2014-08-13

Far-from-equilibrium shape and structure evolution during formation and post-assembly sintering of bimetallic nanoclusters is extremely sensitive to the periphery diffusion and intermixing kinetics. Precise characterization of the many distinct local-environment-dependent diffusion barriers is achieved for epitaxial nanoclusters using density functional theory to assess interaction energies both with atoms at adsorption sites and at transition states. Kinetic Monte Carlo simulation incorporating these barriers then captures structure evolution on the appropriate time scale for two-dimensional core-ring and intermixed Au-Ag nanoclusters on Ag(100).

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

PubMed Central

Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

2011-01-01

Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909

Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction

NASA Astrophysics Data System (ADS)

Song, Chenchen; Martínez, Todd J.

2017-01-01

In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N2.5) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction.

PubMed

Song, Chenchen; Martínez, Todd J

2017-01-21

In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N 2.5 ) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

An intrinsic representation of atomic structure: From clusters to periodic systems

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-01

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

An intrinsic representation of atomic structure: From clusters to periodic systems.

PubMed

Li, Xiao-Tian; Xu, Shao-Gang; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-10-14

We have improved our distance matrix and eigen-subspace projection function (EPF) [X.-T. Li et al., J. Chem. Phys. 146, 154108 (2017)] to describe the atomic structure for periodic systems. Depicting the local structure of an atom, the EPF turns out to be invariant with respect to the choices of the unit cell and coordinate frame, leading to an intrinsic representation of the crystal with a set of EPFs of the nontrivial atoms. The difference of EPFs reveals the difference of atoms in local structure, while the accumulated difference between two sets of EPFs can be taken as the distance between configurations. Exemplified with the cases of carbon allotropes and boron sheets, our EPF approach shows exceptional rationality and efficiency to distinguish the atomic structures, which is crucial in structure recognition, comparison, and analysis.

Atomic-Resolution Spectrum Imaging of Semiconductor Nanowires.

PubMed

Zamani, Reza R; Hage, Fredrik S; Lehmann, Sebastian; Ramasse, Quentin M; Dick, Kimberly A

2018-03-14

Over the past decade, III-V heterostructure nanowires have attracted a surge of attention for their application in novel semiconductor devices such as tunneling field-effect transistors (TFETs). The functionality of such devices critically depends on the specific atomic arrangement at the semiconductor heterointerfaces. However, most of the currently available characterization techniques lack sufficient spatial resolution to provide local information on the atomic structure and composition of these interfaces. Atomic-resolution spectrum imaging by means of electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) is a powerful technique with the potential to resolve structure and chemical composition with sub-angstrom spatial resolution and to provide localized information about the physical properties of the material at the atomic scale. Here, we demonstrate the use of atomic-resolution EELS to understand the interface atomic arrangement in three-dimensional heterostructures in semiconductor nanowires. We observed that the radial interfaces of GaSb-InAs heterostructure nanowires are atomically abrupt, while the axial interface in contrast consists of an interfacial region where intermixing of the two compounds occurs over an extended spatial region. The local atomic configuration affects the band alignment at the interface and, hence, the charge transport properties of devices such as GaSb-InAs nanowire TFETs. STEM-EELS thus represents a very promising technique for understanding nanowire physical properties, such as differing electrical behavior across the radial and axial heterointerfaces of GaSb-InAs nanowires for TFET applications.

Resonance interaction energy between two entangled atoms in a photonic bandgap environment.

PubMed

Notararigo, Valentina; Passante, Roberto; Rizzuto, Lucia

2018-03-26

We consider the resonance interaction energy between two identical entangled atoms, where one is in the excited state and the other in the ground state. They interact with the quantum electromagnetic field in the vacuum state and are placed in a photonic-bandgap environment with a dispersion relation quadratic near the gap edge and linear for low frequencies, while the atomic transition frequency is assumed to be inside the photonic gap and near its lower edge. This problem is strictly related to the coherent resonant energy transfer between atoms in external environments. The analysis involves both an isotropic three-dimensional model and the one-dimensional case. The resonance interaction asymptotically decays faster with distance compared to the free-space case, specifically as 1/r 2 compared to the 1/r free-space dependence in the three-dimensional case, and as 1/r compared to the oscillatory dependence in free space for the one-dimensional case. Nonetheless, the interaction energy remains significant and much stronger than dispersion interactions between atoms. On the other hand, spontaneous emission is strongly suppressed by the environment and the correlated state is thus preserved by the spontaneous-decay decoherence effects. We conclude that our configuration is suitable for observing the elusive quantum resonance interaction between entangled atoms.

The structure of K3C60 and the mechanism of superconductivity.

PubMed Central

Pauling, L

1991-01-01

Analysis of the interatomic distances in the superconducting substance K3C60 indicates that each of the K atoms in tetrahedral interstices between C60 spheres accepts three electrons from C60, thus becoming quadricovalent; its four bonds resonate among the 24 adjacent carbon atoms to give a strong framework in which the negative charges are localized on these K atoms. The electric current is carried by the motion of positive charges (holes) through the network of C60 spheres and the K atoms in octahedral holes. Superconductivity is favored by the localization of the negative charges on the tetrahedral K atoms and their noninvolvement in valence-bond resonance, decreasing the rate of mutual extinction of electrons and holes. PMID:11607222

Controlling the delocalization-localization transition of light via electromagnetically induced transparency

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

Cheng Jing; Huang Guoxiang; State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062

2011-05-15

We propose a scheme to realize a transition from delocalization to localization of light waves via electromagnetically induced transparency. The system we suggested is a resonant cold atomic ensemble having N configuration, with a control field consisting of two pairs of laser beams with different cross angles, which produce an electromagnetically induced quasiperiodic waveguide (EIQPW) for the propagation of a signal field. By appropriately tuning the incommensurate rate or relative modulation strength between the two pairs of control-field components, the signal field can exhibit the delocalization-localization transition as it transports inside the atomic ensemble. The delocalization-localization transition point is determinedmore » and the propagation property of the signal field is studied in detail. Our work provides a way of realizing wave localization via atomic coherence, which is quite different from the conventional, off-resonant mechanism-based Aubry-Andre model, and the great controllability of the EIQPW also allows an easy manipulation of the delocalization-localization transition.« less

Identifying local structural states in atomic imaging by computer vision

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

Laanait, Nouamane; Ziatdinov, Maxim; He, Qian

The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both localmore » and non-local information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale-invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect engineered multilayer graphene surface.« less

Identifying local structural states in atomic imaging by computer vision

DOE PAGES

Laanait, Nouamane; Ziatdinov, Maxim; He, Qian; ...

2016-11-02

The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both localmore » and non-local information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale-invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect engineered multilayer graphene surface.« less

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

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

Thompson, Aidan P.; Swiler, Laura P.; Trott, Christian R.

2015-03-15

Here, we present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1].more » The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

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

Thompson, A.P., E-mail: athomps@sandia.gov; Swiler, L.P., E-mail: lpswile@sandia.gov; Trott, C.R., E-mail: crtrott@sandia.gov

2015-03-15

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. Themore » SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less

Theory and Application of Photoelectron Diffraction for Complex Oxide Systems

NASA Astrophysics Data System (ADS)

Chassé, Angelika; Chassé, Thomas

2018-06-01

X-ray photoelectron diffraction (XPD) has been used to investigate film structures and local sites of surface and dopant atoms in complex oxide materials. We have performed angular-resolved measurements of intensity distribution curves (ADCs) and patterns (ADPs) of elemental core level intensities from binary to quaternary mixed oxide samples and compared them to multiple-scattering cluster (MSC) calculations in order to derive information on structural models and related parameters. MSC calculations permitted to describe both bulk diffraction features of binary oxide MnO(001) and the thickness-dependence of the tetragonal distortion of epitaxial MnO films on Ag(001). XPD was further used to investigate the surface termination of perovskite SrTiO3 and BaTiO3 substrates in order to evaluate influence of different ex situ and in situ preparation procedures on the surface layers, which are crucial for quality of following film growth. Despite the similarity of local environments of Sr (Ba) and Ti atoms in the perovskite film structure an angular region in the ADCs was identified as a fingerprint with the help of MSC simulations which provided clear conclusions on the perovskite oxide surfaces. Dopant sites in quaternary perovskite manganites La1-xCaxMnO3, La1-xSrxMnO3, and La1-xCexMnO3 were studied with polar angle scans of the photoemission intensities of host and dopant atoms. Both direct comparison of experimental ADCs and to the simulations within MSC models confirm the occupation of A sites by the dopants and the structural quality of the complex oxide films.

Vibrational dynamics of thiocyanate and selenocyanate bound to horse heart myoglobin

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

Maj, Michał; Oh, Younjun; Park, Kwanghee

2014-06-21

The structure and vibrational dynamics of SCN- and SeCN-bound myoglobin have been investigated using polarization-controlled IR pump-probe measurements and quantum chemistry calculations. The complexes are found to be in low and high spin states, with the dominant contribution from the latter. In addition, the Mb:SCN high spin complex exhibits a doublet feature in the thiocyanate stretch IR absorption spectra, indicating two distinct molecular conformations around the heme pocket. The binding mode of the high spin complexes was assigned to occur through the nitrogen atom, contrary to the binding through the sulfur atom that was observed in myoglobin derived from Aplysiamore » Limacina. The vibrational energy relaxation process has been found to occur substantially faster than those of free SCN{sup −} and SeCN{sup −} ions and neutral SCN- and SeCN-derivatized molecules reported previously. This supports the N-bound configurations of MbNCS and MbNCSe, because S- and Se-bound configurations are expected to have significantly long lifetimes due to the insulation effect by heavy bridge atom like S and Se in such IR probes. Nonetheless, even though their lifetimes are much shorter than those of corresponding free ions in water, the vibrational lifetimes determined for MbNCS and MbNCSe are still fairly long compared to those of azide and cyanide myoglobin systems studied before. Thus, thiocyanate and selenocyanate can be good local probes of local electrostatic environment in the heme pocket. The globin dependence on binding mode and vibrational dynamics is also discussed.« less

Robustness of Many-Body Localization in the Presence of Dissipation

NASA Astrophysics Data System (ADS)

Levi, Emanuele; Heyl, Markus; Lesanovsky, Igor; Garrahan, Juan P.

2016-06-01

Many-body localization (MBL) has emerged as a novel paradigm for robust ergodicity breaking in closed quantum many-body systems. However, it is not yet clear to which extent MBL survives in the presence of dissipative processes induced by the coupling to an environment. Here we study heating and ergodicity for a paradigmatic MBL system—an interacting fermionic chain subject to quenched disorder—in the presence of dephasing. We find that, even though the system is eventually driven into an infinite-temperature state, heating as monitored by the von Neumann entropy can progress logarithmically slowly, implying exponentially large time scales for relaxation. This slow loss of memory of initial conditions makes signatures of nonergodicity visible over a long, but transient, time regime. We point out a potential controlled realization of the considered setup with cold atomic gases held in optical lattices.

The Materials Chemistry of Atomic Oxygen with Applications to Anisotropic Etching of Submicron Structures in Microelectronics and the Surface Chemistry Engineering of Porous Solids

NASA Technical Reports Server (NTRS)

Koontz, Steve L.; Leger, Lubert J.; Wu, Corina; Cross, Jon B.; Jurgensen, Charles W.

1994-01-01

Neutral atomic oxygen is the most abundant component of the ionospheric plasma in the low Earth orbit environment (LEO; 200 to 700 kilometers altitude) and can produce significant degradation of some spacecraft materials. In order to produce a more complete understanding of the materials chemistry of atomic oxygen, the chemistry and physics of O-atom interactions with materials were determined in three radically different environments: (1) The Space Shuttle cargo bay in low Earth orbit (the EOIM-3 space flight experiment), (2) a high-velocity neutral atom beam system (HVAB) at Los Alamos National Laboratory (LANL), and (3) a microwave-plasma flowing-discharge system at JSC. The Space Shuttle and the high velocity atom beam systems produce atom-surface collision energies ranging from 0.1 to 7 eV (hyperthermal atoms) under high-vacuum conditions, while the flowing discharge system produces a 0.065 eV surface collision energy at a total pressure of 2 Torr. Data obtained in the three different O-atom environments referred to above show that the rate of O-atom reaction with polymeric materials is strongly dependent on atom kinetic energy, obeying a reactive scattering law which suggests that atom kinetic energy is directly available for overcoming activation barriers in the reaction. General relationships between polymer reactivity with O atoms and polymer composition and molecular structure have been determined. In addition, vacuum ultraviolet photochemical effects have been shown to dominate the reaction of O atoms with fluorocarbon polymers. Finally, studies of the materials chemistry of O atoms have produced results which may be of interest to technologists outside the aerospace industry. Atomic oxygen 'spin-off' or 'dual use' technologies in the areas of anisotropic etching in microelectronic materials and device processing, as well as surface chemistry engineering of porous solid materials are described.

Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments.

PubMed

Sastry, Madhavi; Lowrie, Jeffrey F; Dixon, Steven L; Sherman, Woody

2010-05-24

A systematic virtual screening study on 11 pharmaceutically relevant targets has been conducted to investigate the interrelation between 8 two-dimensional (2D) fingerprinting methods, 13 atom-typing schemes, 13 bit scaling rules, and 12 similarity metrics using the new cheminformatics package Canvas. In total, 157 872 virtual screens were performed to assess the ability of each combination of parameters to identify actives in a database screen. In general, fingerprint methods, such as MOLPRINT2D, Radial, and Dendritic that encode information about local environment beyond simple linear paths outperformed other fingerprint methods. Atom-typing schemes with more specific information, such as Daylight, Mol2, and Carhart were generally superior to more generic atom-typing schemes. Enrichment factors across all targets were improved considerably with the best settings, although no single set of parameters performed optimally on all targets. The size of the addressable bit space for the fingerprints was also explored, and it was found to have a substantial impact on enrichments. Small bit spaces, such as 1024, resulted in many collisions and in a significant degradation in enrichments compared to larger bit spaces that avoid collisions.

IMPACT OF PLANETARY GRAVITATION ON HIGH-PRECISION NEUTRAL ATOM MEASUREMENTS

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

Kucharek, H.; Möbius, E.; Lee, M. A.

2015-10-15

Measurements of energetic neutral atoms (ENAs) have been extremely successful in providing very important information on the physical processes inside and outside of our heliosphere. For instance, recent Interstellar Boundary Explorer (IBEX) observations have provided new insights into the local interstellar environment and improved measurements of the interstellar He temperature, velocity, and direction of the interstellar flow vector. Since particle collisions are rare, and radiation pressure is negligible for these neutrals, gravitational forces mainly determine the trajectories of neutral He atoms. Depending on the distance of an ENA to the source of a gravitational field and its relative speed andmore » direction, this can result in significant deflection and acceleration. In this paper, we investigate the impact of the gravitational effects of Earth, the Moon, and Jupiter on ENA measurements performed in Earth’s orbit. The results show that current analysis of the interstellar neutral parameters by IBEX is not significantly affected by planetary gravitational effects. We further studied the possibility of whether or not the Helium focusing cone of the Sun and Jupiter could be measured by IBEX and whether or not these cones could be used as an independent measure of the temperature of interstellar Helium.« less

Origin of structural analogies and differences between the atomic structures of GeSe4 and GeS4 glasses: A first principles study.

PubMed

Bouzid, Assil; Le Roux, Sébastien; Ori, Guido; Boero, Mauro; Massobrio, Carlo

2015-07-21

First-principles molecular dynamics simulations based on density functional theory are employed for a comparative study of structural and bonding properties of two stoichiometrically identical chalcogenide glasses, GeSe4 and GeS4. Two periodic cells of 120 and 480 atoms are adopted. Both glasses feature a coexistence of Ge-centered tetrahedra and Se(S) homopolar connections. Results obtained for N = 480 indicate substantial differences at the level of the Se(S) environment, since Ge-Se-Se connections are more frequent than the corresponding Ge-S-S ones. The presence of a more prominent first sharp diffraction peak in the total neutron structure factor of glassy GeS4 is rationalized in terms of a higher number of large size rings, accounting for extended Ge-Se correlations. Both the electronic density of states and appropriate electronic localization tools provide evidence of a higher ionic character of Ge-S bonds when compared to Ge-Se bonds. An interesting byproduct of these investigations is the occurrence of discernible size effects that affect structural motifs involving next nearest neighbor distances, when 120 or 480 atoms are used.

Effective band structure of random III-V alloys

NASA Astrophysics Data System (ADS)

Popescu, Voicu; Zunger, Alex

2010-03-01

Random substitutional alloys have no long range order (LRO) or translational symmetry so rigorously speaking they have no E(k) band structure or manifestations thereof. Yet, many experiments on alloys are interpreted using the language of band theory, e.g. inferring Van Hove singularities, band dispersion and effective masses. Many standard alloy theories (VCA- or CPA-based) have the LRO imposed on the alloy Hamiltonian, assuming only on-site disorder, so they can not be used to judge the extent of LRO that really exists. We adopt the opposite way, by using large (thousand atom) randomly generated supercells in which chemically identical alloy atoms are allowed to have different local environments (a polymorphous representation). This then drives site-dependent atomic relaxation as well as potential fluctuations. The eigenstates from such supercells are then mapped onto the Brillouin zone (BZ) of the primitive cell, producing effective band dispersion. Results for (In,Ga)X show band-like behaviour only near the centre and faces of the BZ but rapidly lose such characteristics away from γ or for higher bands. We further analyse the effects of stoichiometry variation, internal relaxation, and short-range order on the alloy band structure.

Intrinsic differences in atomic ordering of calcium (alumino)silicate hydrates in conventional and alkali-activated cements

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

White, Claire E., E-mail: whitece@princeton.edu; Andlinger Center for Energy and the Environment, Princeton University, Princeton; Lujan Neutron Scattering Center, Los Alamos National Laboratory, Los Alamos

2015-01-15

The atomic structures of calcium silicate hydrate (C–S–H) and calcium (–sodium) aluminosilicate hydrate (C–(N)–A–S–H) gels, and their presence in conventional and blended cement systems, have been the topic of significant debate over recent decades. Previous investigations have revealed that synthetic C–S–H gel is nanocrystalline and due to the chemical similarities between ordinary Portland cement (OPC)-based systems and low-CO{sub 2} alkali-activated slags, researchers have inferred that the atomic ordering in alkali-activated slag is the same as in OPC–slag cements. Here, X-ray total scattering is used to determine the local bonding environment and nanostructure of C(–A)–S–H gels present in hydrated tricalcium silicatemore » (C{sub 3}S), blended C{sub 3}S–slag and alkali-activated slag, revealing the large intrinsic differences in the extent of nanoscale ordering between C–S–H derived from C{sub 3}S and alkali-activated slag systems, which may have a significant influence on thermodynamic stability, and material properties at higher length scales, including long term durability of alkali-activated cements.« less

Comparative investigation of pure and mixed rare gas atoms on coronene molecules.

PubMed

Rodríguez-Cantano, Rocío; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; González-Lezana, Tomás; Villarreal, Pablo; Pérez de Tudela, Ricardo; Pirani, Fernando; Hernández-Rojas, Javier; Bretón, José

2017-01-21

Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr. The observed coexistence of various geometries for Ne suggests the motion of the RG atoms on the multi-well potential energy surface landscape offered by the coronene. Therefore, the investigation of different clusters enables a comparative analysis of localized versus non-localized features. Mixed Ar-He-coronene clusters have also been considered and the competition of the RG atoms to occupy the docking sites on the molecule is discussed. All the obtained information is crucial to assess the behavior of coronene, a prototypical polycyclic aromatic hydrocarbon clustering with RG atoms at a temperature close to that of interstellar medium, which arises from the critical balance of the interactions involved.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

PubMed

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-05

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins

NASA Astrophysics Data System (ADS)

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-01

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

Local Energies and Energy Fluctuations — Applied to the High Entropy Alloy CrFeCoNi

NASA Astrophysics Data System (ADS)

Fukushima, Tetsuya; Katayama-Yoshida, Hiroshi; Sato, Kazunori; Ogura, Masako; Zeller, Rudolf; Dederichs, Peter H.

2017-11-01

High entropy alloys show a variety of fascinating properties like high hardness, wear resistance, corrosion resistance, etc. They are random solid solutions of many components with rather high concentrations. We perform ab-initio calculations for the high entropy alloy CrFeCoNi, which equal concentration of 25% for each element. By the KKRnano program package, which is based on an order-N screened Korringa-Kohn-Rostoker Green's function method, we consider a face-centered cubic (FCC) supercell with 1372 randomly distributed elements, and in addition also smaller supercells with 500 and 256 atoms. It is found from our calculations that the local moments of the Cr atoms show a large environmental variation, ranging from -1.70 μB to +1.01 μB with an average of about -0.51 μB. We present a new method to calculate "local energies" of all atoms. This is based on the partitioning of the whole space into Voronoi cells and allows to calculate the energetic contribution of each atomic cell to the total energy of the supercell. The supercell calculations show very large variations of the local energies, analogous to the variations of the local moments. This shows that the random solid solution is not stable and has a tendency to form an L12-structure with the Cr-atoms ordered at the corner of the cube and the elements Fe, Co, and Ni randomly distributed on the three other FCC sublattices. For this structure the variation of the local moments are much smaller.

Tip Effect of the Tapping Mode of Atomic Force Microscope in Viscous Fluid Environments.

PubMed

Shih, Hua-Ju; Shih, Po-Jen

2015-07-28

Atomic force microscope with applicable types of operation in a liquid environment is widely used to scan the contours of biological specimens. The contact mode of operation allows a tip to touch a specimen directly but sometimes it damages the specimen; thus, a tapping mode of operation may replace the contact mode. The tapping mode triggers the cantilever of the microscope approximately at resonance frequencies, and so the tip periodically knocks the specimen. It is well known that the cantilever induces extra liquid pressure that leads to drift in the resonance frequency. Studies have noted that the heights of protein surfaces measured via the tapping mode of an atomic force microscope are ~25% smaller than those measured by other methods. This discrepancy may be attributable to the induced superficial hydrodynamic pressure, which is worth investigating. In this paper, we introduce a semi-analytical method to analyze the pressure distribution of various tip geometries. According to our analysis, the maximum hydrodynamic pressure on the specimen caused by a cone-shaped tip is ~0.5 Pa, which can, for example, pre-deform a cell by several nanometers in compression before the tip taps it. Moreover, the pressure calculated on the surface of the specimen is 20 times larger than the pressure without considering the tip effect; these results have not been motioned in other papers. Dominating factors, such as surface heights of protein surface, mechanical stiffness of protein increasing with loading velocity, and radius of tip affecting the local pressure of specimen, are also addressed in this study.

Atomic oxygen effects on spacecraft materials: The state of the art of our knowledge

NASA Technical Reports Server (NTRS)

Koontz, Steven L.

1989-01-01

In the flight materials exposure data base extensive quantitative data is available from limited exposures in a narrow range of orbital environments. More data is needed in a wider range of environments as well as longer exposure times. Synergistic effects with other environmental factors; polar orbit and higher altitude environments; and real time materials degradation data is needed to understand degradation kinetics and mechanism. Almost no laboratory data exists from high fidelity simulations of the LEO environment. Simulation and test system are under development, and the data base is scanty. Theoretical understanding of hyperthermal atom surface reactions in the LEO environment is not good enough to support development of reliable accelerated test methods. The laser sustained discharge, atom beam sources are the most promising high fidelity simulation-test systems at this time.

Metal-Insulator Transition Revisited for Cold Atoms in Non-Abelian Gauge Potentials

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

Satija, Indubala I.; National Institute of Standards and Technology, Gaithersburg, Maryland 20899; Dakin, Daniel C.

2006-11-24

We discuss the possibility of realizing metal-insulator transitions with ultracold atoms in two-dimensional optical lattices in the presence of artificial gauge potentials. For Abelian gauges, such transitions occur when the magnetic flux penetrating the lattice plaquette is an irrational multiple of the magnetic flux quantum. Here we present the first study of these transitions for non-Abelian U(2) gauge fields. In contrast to the Abelian case, the spectrum and localization transition in the non-Abelian case is strongly influenced by atomic momenta. In addition to determining the localization boundary, the momentum fragments the spectrum. Other key characteristics of the non-Abelian case includemore » the absence of localization for certain states and satellite fringes around the Bragg peaks in the momentum distribution and an interesting possibility that the transition can be tuned by the atomic momenta.« less

Molecular Self-Assembly in a Poorly Screened Environment: F4TCNQ on Graphene/BN

PubMed Central

2015-01-01

We report a scanning tunneling microscopy and noncontact atomic force microscopy study of close-packed 2D islands of tetrafluorotetracyanoquinodimethane (F4TCNQ) molecules at the surface of a graphene layer supported by boron nitride. While F4TCNQ molecules are known to form cohesive 3D solids, the intermolecular interactions that are attractive for F4TCNQ in 3D are repulsive in 2D. Our experimental observation of cohesive molecular behavior for F4TCNQ on graphene is thus unexpected. This self-assembly behavior can be explained by a novel solid formation mechanism that occurs when charged molecules are placed in a poorly screened environment. As negatively charged molecules coalesce, the local work function increases, causing electrons to flow into the coalescing molecular island and increase its cohesive binding energy. PMID:26482218

Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

NASA Astrophysics Data System (ADS)

Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

2017-11-01

Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

DOE PAGES

Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; ...

2017-11-13

Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify thesemore » basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO 2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.« less

Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

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

Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav

Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify thesemore » basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO 2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.« less

Characterization of the surface charge distribution on kaolinite particles using high resolution atomic force microscopy

NASA Astrophysics Data System (ADS)

Kumar, Naveen; Zhao, Cunlu; Klaassen, Aram; van den Ende, Dirk; Mugele, Frieder; Siretanu, Igor

2016-02-01

Most solid surfaces, in particular clay minerals and rock surfaces, acquire a surface charge upon exposure to an aqueous environment due to adsorption and/or desorption of ionic species. Macroscopic techniques such as titration and electrokinetic measurements are commonly used to determine the surface charge and ζ -potential of these surfaces. However, because of the macroscopic averaging character these techniques cannot do justice to the role of local heterogeneities on the surfaces. In this work, we use dynamic atomic force microscopy (AFM) to determine the distribution of surface charge on the two (gibbsite-like and silica-like) basal planes of kaolinite nanoparticles immersed in aqueous electrolyte with a lateral resolution of approximately 30 nm. The surface charge density is extracted from force-distance curves using DLVO theory in combination with surface complexation modeling. While the gibbsite-like and the silica-like facet display on average positive and negative surface charge values as expected, our measurements reveal lateral variations of more than a factor of two on seemingly atomically smooth terraces, even if high resolution AFM images clearly reveal the atomic lattice on the surface. These results suggest that simple surface complexation models of clays that attribute a unique surface chemistry and hence homogeneous surface charge densities to basal planes may miss important aspects of real clay surfaces.

What We've Learned from IBEX ENA Imaging of the Heliosheath

NASA Astrophysics Data System (ADS)

Zirnstein, E.

2017-12-01

The Interstellar Boundary Explorer (IBEX) is an Earth-orbiting spacecraft equipped with two single-pixel cameras that detect neutral atoms produced by the interaction of the solar wind (SW) with the very local interstellar medium (VLISM), as well as neutral atoms flowing in from the VLISM itself. Since its launch in 2009, IBEX has provided us with over half a solar cycle of measurements of energetic neutral atom (ENA) fluxes produced in the heliosphere. In particular, a large number of these ENAs originate in the inner heliosheath, a region of nearly incompressible SW plasma that is slowed, compressed, and heated at the termination shock. As the heated SW plasma flows through the heliosheath and down the heliotail, charge-exchange with cold neutral atoms from the VLISM generates ENAs that travel on ballistic trajectories. Some of these ENAs travel to Earth and are detected by IBEX. IBEX all-sky observations of these ENAs show a unique energy and spatial dependence, revealing the structural and plasma properties of the heliosheath. One of the prime scientific objectives of the Interstellar Mapping and Acceleration Probe (IMAP) mission is to understand the SW-VLISM interaction, including the properties of the heliosheath and heliotail. This talk will review key IBEX observations of the inner heliosheath environment, the way they have shaped our understanding of the SW-VLISM interaction, and their implications for the upcoming IMAP mission.

MoleCoolQt – a molecule viewer for charge-density research

PubMed Central

Hübschle, Christian B.; Dittrich, Birger

2011-01-01

MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS. PMID:22477783

Observing electron localization in a dissociating H2+ molecule in real time

PubMed Central

Xu, H.; Li, Zhichao; He, Feng; Wang, X.; Atia-Tul-Noor, A.; Kielpinski, D.; Sang, R. T.; Litvinyuk, I. V.

2017-01-01

Dissociation of diatomic molecules with odd number of electrons always causes the unpaired electron to localize on one of the two resulting atomic fragments. In the simplest diatomic molecule H2+ dissociation yields a hydrogen atom and a proton with the sole electron ending up on one of the two nuclei. That is equivalent to breaking of a chemical bond—the most fundamental chemical process. Here we observe such electron localization in real time by performing a pump–probe experiment. We demonstrate that in H2+ electron localization is complete in just 15 fs when the molecule’s internuclear distance reaches 8 atomic units. The measurement is supported by a theoretical simulation based on numerical solution of the time-dependent Schrödinger equation. This observation advances our understanding of detailed dynamics of molecular dissociation. PMID:28621332

Quantum theory of open systems based on stochastic differential equations of generalized Langevin (non-Wiener) type

NASA Astrophysics Data System (ADS)

Basharov, A. M.

2012-09-01

It is shown that the effective Hamiltonian representation, as it is formulated in author's papers, serves as a basis for distinguishing, in a broadband environment of an open quantum system, independent noise sources that determine, in terms of the stationary quantum Wiener and Poisson processes in the Markov approximation, the effective Hamiltonian and the equation for the evolution operator of the open system and its environment. General stochastic differential equations of generalized Langevin (non-Wiener) type for the evolution operator and the kinetic equation for the density matrix of an open system are obtained, which allow one to analyze the dynamics of a wide class of localized open systems in the Markov approximation. The main distinctive features of the dynamics of open quantum systems described in this way are the stabilization of excited states with respect to collective processes and an additional frequency shift of the spectrum of the open system. As an illustration of the general approach developed, the photon dynamics in a single-mode cavity without losses on the mirrors is considered, which contains identical intracavity atoms coupled to the external vacuum electromagnetic field. For some atomic densities, the photons of the cavity mode are "locked" inside the cavity, thus exhibiting a new phenomenon of radiation trapping and non-Wiener dynamics.

Chemically sensitive free-volume study of amorphization of Cu60Zr40 induced by cold rolling and folding

NASA Astrophysics Data System (ADS)

Puff, Werner; Rabitsch, Herbert; Wilde, Gerhard; Dinda, Guru P.; Würschum, Roland

2007-06-01

With the aim to contribute to a microscopical understanding of the processes of solid-state amorphization, the chemically sensitive technique of background—reduced Doppler broadening of positron-electron annihilation radiation in combination with positron lifetime spectroscopy and microstructural characterization is applied to a free volume study of the amorphization of Cu60Zr40 induced by consecutive folding and rolling. Starting from the constituent pure metal foils, a nanosale multilayer structure of elemental layers and amorphous interlayers develops in an intermediate state of folding and rolling, where free volumes with a Zr-rich environment occur presumably located in the hetero-interfaces between the various layers or in grain boundaries of the Cu layers. After complete intermixing and amorphization, the local chemical environment of the free volumes reflects the average chemical alloy composition. In contrast to other processes of amorphization, free volumes of the size of few missing atoms occur in the rolling-induced amorphous state. Self-consistent results from three different methods for analyzing the Doppler broadening spectra, i.e., S-W-parameter correlation, multicomponent fit, and the shape of ratio curves, demonstrate the potential of the background-reduced Doppler technique for chemically sensitive characterization of structurally complex materials on an atomic scale.

Localizing gravitational wave sources with single-baseline atom interferometers

NASA Astrophysics Data System (ADS)

Graham, Peter W.; Jung, Sunghoon

2018-02-01

Localizing sources on the sky is crucial for realizing the full potential of gravitational waves for astronomy, astrophysics, and cosmology. We show that the midfrequency band, roughly 0.03 to 10 Hz, has significant potential for angular localization. The angular location is measured through the changing Doppler shift as the detector orbits the Sun. This band maximizes the effect since these are the highest frequencies in which sources live for several months. Atom interferometer detectors can observe in the midfrequency band, and even with just a single baseline they can exploit this effect for sensitive angular localization. The single-baseline orbits around the Earth and the Sun, causing it to reorient and change position significantly during the lifetime of the source, and making it similar to having multiple baselines/detectors. For example, atomic detectors could predict the location of upcoming black hole or neutron star merger events with sufficient accuracy to allow optical and other electromagnetic telescopes to observe these events simultaneously. Thus, midband atomic detectors are complementary to other gravitational wave detectors and will help complete the observation of a broad range of the gravitational spectrum.

Self-trapping and tunneling of Bose-Einstein condensates in a cavity-mediated triple-well system

NASA Astrophysics Data System (ADS)

Wang, Bin; Zhang, Hui; Chen, Yan; Tan, Lei

2017-03-01

We have investigated tunneling characteristics of Bose-Einstein condensates (BECs) in a triple-well potential coupled to a high finesse optical cavity within a mean field approach. Due to the intrinsic atom-cavity field nonlinearity, several interesting phenomena arise which are the focuses of this work. In the dynamical process, an extensive numerical simulation of localization of the BECs for atoms initially trapped in one-, two-, and three-wells are performed for the symmetric and asymmetric cases in detail. It is shown that the the transition from the oscillation to the localization can be modified by the cavity-mediated potential, which will enlarge the regions of oscillation. With the increasing of the atomic interaction, the oscillation is blocked and the localization emerges. The condensates atoms can be trapped either in one-, two-, or in three wells eventually where they are initially uploaded for certain parameters. In particular, we find that the transition from the oscillation to the localization is accompanied with some irregular regime where tunneling dynamics is dominated by chaos for this cavity-mediated system.

Atomic adsorption on pristine graphene along the Periodic Table of Elements - From PBE to non-local functionals

NASA Astrophysics Data System (ADS)

Pašti, Igor A.; Jovanović, Aleksandar; Dobrota, Ana S.; Mentus, Slavko V.; Johansson, Börje; Skorodumova, Natalia V.

2018-04-01

The understanding of atomic adsorption on graphene is of high importance for many advanced technologies. Here we present a complete database of the atomic adsorption energies for the elements of the Periodic Table up to the atomic number 86 (excluding lanthanides) on pristine graphene. The energies have been calculated using the projector augmented wave (PAW) method with PBE, long-range dispersion interaction corrected PBE (PBE+D2, PBE+D3) as well as non-local vdW-DF2 approach. The inclusion of dispersion interactions leads to an exothermic adsorption for all the investigated elements. Dispersion interactions are found to be of particular importance for the adsorption of low atomic weight earth alkaline metals, coinage and s-metals (11th and 12th groups), high atomic weight p-elements and noble gases. We discuss the observed adsorption trends along the groups and rows of the Periodic Table as well some computational aspects of modelling atomic adsorption on graphene.

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

NASA Astrophysics Data System (ADS)

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

2010-07-01

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

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

PubMed

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

2017-07-18

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

Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

PubMed

Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro

2006-03-02

We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to coexistence of brittle grains and soft amorphous-like grain boundary phases. Simulations predict a crossover from intergranular continuous deformation to intragrain discrete deformation at a critical indentation depth.

KinImmerse: Macromolecular VR for NMR ensembles

PubMed Central

Block, Jeremy N; Zielinski, David J; Chen, Vincent B; Davis, Ian W; Vinson, E Claire; Brady, Rachael; Richardson, Jane S; Richardson, David C

2009-01-01

Background In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. Results In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs). Conclusion The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis. PMID:19222844

Rolf Landauer and Charles H. Bennett Award Talk: Experimental development of spin qubits in silicon

NASA Astrophysics Data System (ADS)

Morello, Andrea

The modern information era is built on silicon nanoelectronic devices. The future quantum information era might be built on silicon too, if we succeed in controlling the interactions between individual spins hosted in silicon nanostructures. Spins in silicon constitute excellent solid-state qubits, because of the weak spin-orbit coupling and the possibility to remove nuclear spins from the environment through 28Si isotopic enrichment. Substitutional 31P atoms in silicon behave approximately like hydrogen in vacuum, providing two spin 1/2 qubits - the donor-bound electron and the 31P nucleus - that can be coherently controlled, read out in single-shot, and are naturally coupled through the hyperfine interaction. In isotopically-enriched 28Si, these single-atom qubits have demonstrated outstanding coherence times, up to 35 seconds for the nuclear spin, and 1-qubit gate fidelities well above 99.9% for both the electron and the nucleus. The hyperfine coupling provides a built-in interaction to entangle the two qubits within one atom. The combined initialization, control and readout fidelities result in a violation of Bell's inequality with S = 2 . 70 , a record value for solid-state qubits. Despite being identical atomic systems, 31P atoms can be addressed individually by locally modifying the hyperfine interaction through electrostatic gating. Multi-qubit logic gates can be mediated either by the exchange interaction or by electric dipole coupling. Scaling up beyond a single atom presents formidable challenges, but provides a pathway to building quantum processors that are compatible with standard semiconductor fabrication, and retain a nanometric footprint, important for truly large-scale quantum computers. Work supported by US Army Research Office (W911NF-13-1-0024) and Australian Research Council (CE110001027).

Investigation on structure, electronic and magnetic properties of Cr doped (ZnO)12 clusters: First-principles calculations

NASA Astrophysics Data System (ADS)

Liu, Huan; Zhang, Jian-Min

2018-05-01

The structural, electronic, and magnetic properties of (ZnO)12 clusters doped with Cr atoms have been investigated by using spin-polarized first-principles calculations. The exohedral a3 isomer is favorable than endohedral a2 isomer. The isomer a1 and a5 respectively have the narrowest and biggest gap between highest unoccupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO) of 0.473 and 1.291 eV among these five monodoped isomers. The magnetic moment may be related to the local environment around the Cr atom that the a2 isomer whose total magnetic moment is 6 μB while the other monodoped isomers which all isomers have nearly total magnetic moments 4 μB . For Cr-doped (ZnO)12 on a1 or a3 isomer, the DOS of spin-up channel cross the Fermi level EF showing a finite magnitude near the Fermi level which might be useful for half metallic character. For the bidoped cases, the exohedral isomers are found to be most favorable. Including all bipoed isomers of substitutional, exohedral and endohedral bidoped clusters, the total magnetic moment of the ferromagnetic (antiferromagnetic) state is 8 (0) μB and the HOMO-LUMO gap of antiferromagnetic state is slightly larger than that of ferromagnetic state. The magnetic coupling between the Cr atoms in bidoped configurations is mainly governed by the competition between direct Cr and Cr atoms antiferromagnetic interaction and the ferromagnetic interaction between two Cr atoms via O atom due to strong p-d hybridization. Most importantly, we show that the exohedral bidoped (ZnO)12 clusters favor the ferromagnetic state, which may have the future applications in spin-dependent magneto-optical and magneto-electrical devices.

Adsorption of Fe(II) and U(VI) to carboxyl-functionalized microspheres: The influence of speciation on uranyl reduction studied by titration and XAFS

NASA Astrophysics Data System (ADS)

Boyanov, Maxim I.; O'Loughlin, Edward J.; Roden, Eric E.; Fein, Jeremy B.; Kemner, Kenneth M.

2007-04-01

The chemical reduction of U(VI) by Fe(II) is a potentially important pathway for immobilization of uranium in subsurface environments. Although the presence of surfaces has been shown to catalyze the reaction between Fe(II) and U(VI) aqueous species, the mechanism(s) responsible for the enhanced reactivity remain ambiguous. To gain further insight into the U-Fe redox process at a complexing, non-conducting surface that is relevant to common organic phases in the environment, we studied suspensions containing combinations of 0.1 mM U(VI), 1.0 mM Fe(II), and 4.2 g/L carboxyl-functionalized polystyrene microspheres. Acid-base titrations were used to monitor protolytic reactions, and Fe K-edge and U L-edge X-ray absorption fine structure spectroscopy was used to determine the valence and atomic environment of the adsorbed Fe and U species. In the Fe + surface carboxyl system, a transition from monomeric to oligomeric Fe(II) surface species was observed between pH 7.5 and pH 8.4. In the U + surface carboxyl system, the U(VI) cation was adsorbed as a mononuclear uranyl-carboxyl complex at both pH 7.5 and 8.4. In the ternary U + Fe + surface carboxyl system, U(VI) was not reduced by the solvated or adsorbed Fe(II) at pH 7.5 over a 4-month period, whereas complete and rapid reduction to U(IV) nanoparticles occurred at pH 8.4. The U(IV) product reoxidized rapidly upon exposure to air, but it was stable over a 4-month period under anoxic conditions. Fe atoms were found in the local environment of the reduced U(IV) atoms at a distance of 3.56 Å. The U(IV)-Fe coordination is consistent with an inner-sphere electron transfer mechanism between the redox centers and involvement of Fe(II) atoms in both steps of the reduction from U(VI) to U(IV). The inability of Fe(II) to reduce U(VI) in solution and at pH 7.5 in the U + Fe + carboxyl system is explained by the formation of a transient, "dead-end" U(V)-Fe(III) complex that blocks the U(V) disproportionation pathway after the first electron transfer. The increased reactivity at pH 8.4 relative to pH 7.5 is explained by the reaction of U(VI) with an Fe(II) oligomer, whereby the bonds between Fe atoms facilitate the transfer of a second electron to the hypothetical U(V)-Fe(III) intermediate. We discuss how this mechanism may explain the commonly observed higher efficiency of uranyl reduction by adsorbed or structural Fe(II) relative to aqueous Fe(II).

77 FR 52683 - UChicago Argonne, LLC, Notice of Decision on Applications for Duty-Free Entry of Scientific...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... science. This instrument is specialized for creating artificial nanoscale structures on an atom-by-atom basis using nascent atom manipulation techniques. The instrument will be used to investigate the amount of force required to move one atom on a materials surface while simultaneously measuring local...

Generation of long-living entanglement between two distant three-level atoms in non-Markovian environments.

PubMed

Li, Chuang; Yang, Sen; Song, Jie; Xia, Yan; Ding, Weiqiang

2017-05-15

In this paper, a scheme for the generation of long-living entanglement between two distant Λ-type three-level atoms separately trapped in two dissipative cavities is proposed. In this scheme, two dissipative cavities are coupled to their own non-Markovian environments and two three-level atoms are driven by the classical fields. The entangled state between the two atoms is produced by performing Bell state measurement (BSM) on photons leaving the dissipative cavities. Using the time-dependent Schördinger equation, we obtain the analytical results for the evolution of the entanglement. It is revealed that, by manipulating the detunings of classical field, the long-living stationary entanglement between two atoms can be generated in the presence of dissipation.

Cytochrome C in a dry trehalose matrix: structural and dynamical effects probed by x-ray absorption spectroscopy.

PubMed

Giachini, Lisa; Francia, Francesco; Cordone, Lorenzo; Boscherini, Federico; Venturoli, Giovanni

2007-02-15

We report on the structure and dynamics of the Fe ligand cluster of reduced horse heart cytochrome c in solution, in a dried polyvinyl alcohol (PVA) film, and in two trehalose matrices characterized by different contents of residual water. The effect of the solvent/matrix environment was studied at room temperature using Fe K-edge x-ray absorption fine structure (XAFS) spectroscopy. XAFS data were analyzed by combining ab initio simulations and multi-parameter fitting in an attempt to disentangle structural from disorder parameters. Essentially the same structural and disorder parameters account adequately for the XAFS spectra measured in solution, both in the absence and in the presence of glycerol, and in the PVA film, showing that this polymer interacts weakly with the embedded protein. Instead, incorporation in trehalose leads to severe structural changes, more prominent in the more dried matrix, consisting of 1), an increase up to 0.2 A of the distance between Fe and the imidazole N atom of the coordinating histidine residue and 2), an elongation up to 0.16 A of the distance between Fe and the fourth-shell C atoms of the heme pyrrolic units. These structural distortions are accompanied by a substantial decrease of the relative mean-square displacements of the first ligands. In the extensively dried trehalose matrix, extremely low values of the Debye Waller factors are obtained for the pyrrolic and for the imidazole N atoms. This finding is interpreted as reflecting a drastic hindering in the relative motions of the Fe ligand cluster atoms and an impressive decrease in the static disorder of the local Fe structure. It appears, therefore, that the dried trehalose matrix dramatically perturbs the energy landscape of cytochrome c, giving rise, at the level of local structure, to well-resolved structural distortions and restricting the ensemble of accessible conformational substates.

Temperature dependent local atomic displacements in ammonia intercalated iron selenide superconductor

NASA Astrophysics Data System (ADS)

Paris, E.; Simonelli, L.; Wakita, T.; Marini, C.; Lee, J.-H.; Olszewski, W.; Terashima, K.; Kakuto, T.; Nishimoto, N.; Kimura, T.; Kudo, K.; Kambe, T.; Nohara, M.; Yokoya, T.; Saini, N. L.

2016-06-01

Recently, ammonia-thermal reaction has been used for molecular intercalation in layered FeSe, resulting a new Lix(NH3)yFe2Se2 superconductor with Tc ~ 45 K. Here, we have used temperature dependent extended x-ray absorption fine structure (EXAFS) to investigate local atomic displacements in single crystals of this new superconductor. Using polarized EXAFS at Fe K-edge we have obtained direct information on the local Fe-Se and Fe-Fe bondlengths and corresponding mean square relative displacements (MSRD). We find that the Se-height in the intercalated system is lower than the one in the binary FeSe, suggesting compressed FeSe4 tetrahedron in the title system. Incidentally, there is hardly any effect of the intercalation on the bondlengths characteristics, revealed by the Einstein temperatures, that are similar to those found in the binary FeSe. Therefore, the molecular intercalation induces an effective compression and decouples the FeSe slabs. Furthermore, the results reveal an anomalous change in the atomic correlations across Tc, appearing as a clear decrease in the MSRD, indicating hardening of the local lattice mode. Similar response of the local lattice has been found in other families of superconductors, e.g., A15-type and cuprates superconductors. This observation suggests that local atomic correlations should have some direct correlation with the superconductivity.

New Insight into the Local Structure of Hydrous Ferric Arsenate Using Full-Potential Multiple Scattering Analysis, Density Functional Theory Calculations, and Vibrational Spectroscopy.

PubMed

Wang, Shaofeng; Ma, Xu; Zhang, Guoqing; Jia, Yongfeng; Hatada, Keisuke

2016-11-15

Hydrous ferric arsenate (HFA) is an important arsenic-bearing precipitate in the mining-impacted environment and hydrometallurgical tailings. However, there is no agreement on its local atomic structure. The local structure of HFA was reprobed by employing a full-potential multiple scattering (FPMS) analysis, density functional theory (DFT) calculations, and vibrational spectroscopy. The FPMS simulations indicated that the coordination number of the As-Fe, Fe-As, or both in HFA was approximately two. The DFT calculations constructed a structure of HFA with the formula of Fe(HAsO 4 ) x (H 2 AsO 4 ) 1-x (OH) y ·zH 2 O. The presence of protonated arsenate in HFA was also evidenced by vibrational spectroscopy. The As and Fe K-edge X-ray absorption near-edge structure spectra of HFA were accurately reproduced by FPMS simulations using the chain structure, which was also a reasonable model for extended X-Ray absorption fine structure fitting. The FPMS refinements indicated that the interatomic Fe-Fe distance was approximately 5.2 Å, consistent with that obtained by Mikutta et al. (Environ. Sci. Technol. 2013, 47 (7), 3122-3131) using wavelet analysis. All of the results suggested that HFA was more likely to occur as a chain with AsO 4 tetrahedra and FeO 6 octahedra connecting alternately in an isolated bidentate-type fashion. This finding is of significance for understanding the fate of arsenic and the formation of ferric arsenate minerals in an acidic environment.

Phonon dispersion and local density of states in NiPd alloy using modified embedded atom method potential

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

Joshi, Subodh, E-mail: subodhssgk@gmail.com; Chand, Manesh, E-mail: maneshchand@gmail.com; Dabral, Krishna, E-mail: kmkrishna.dabral@gmail.com

2016-05-06

A modified embedded atom method (MEAM) potential model up to second neighbours has been used to calculate the phonon dispersions for Ni{sub 0.55}Pd{sub 0.45} alloy in which Pd is introduced as substitutional impurity. Using the force-constants obtained from MEAM potential, the local vibrational density of states in host Ni and substitutional Pd atoms using Green’s function method has been calculated. The calculation of phonon dispersions of NiPd alloy shows a good agreement with the experimental results. Condition of resonance mode has also been investigated and resonance mode in the frequency spectrum of impurity atom at low frequency is observed.

Infrared detection of (H 2O) 20 isomers of exceptional stability: A drop-like and a face-sharing pentagonal prism cluster

DOE PAGES

Pradzynski, Christoph C.; Dierking, Christoph W.; Zurheide, Florian; ...

2014-09-01

Water clusters containing fully coordinated water molecules are model systems that mimic the local environment of the condensed phase. Present knowledge about the water cluster size regime in which the transition from the allsurface to the fully solvated water molecules occurs is mainly based on theoretical predictions in lieu of the absence of precisely size resolved experimental measurements. Here, we report size and isomer selective infrared (IR) spectra of (H 2O) 20 clusters tagged with a sodium atom by employing IR excitation modulated photoionization spectroscopy. The observed absorption patterns in the OH stretching ”fingerprint” region are consistent with the theoreticallymore » predicted spectra of two structurally distinct isomers: A drop-like cluster with a fully coordinated (interior) water and an edge-sharing pentagonal prism cluster in which all atoms are on the surface. The observed isomers show exceptional stability and are predicted to be nearly isoenergetic.« less

Australian Red Dune Sand: A Potential Martian Regolith Analog

NASA Technical Reports Server (NTRS)

Kuhlman, K. R.; Marshall, J.; Evans, N. D.; Luttge, A.

2001-01-01

To demonstrate the potential scientific and technical merits of in situ microscopy on Mars, we analyzed a possible Martian regolith analog - an acolian red dune sand from the central Australian desert (near Mt. Olga). This sand was chosen for its ubiquitous red coating and the desert environment in which is it found. Grains of this sand were analyzed using a variety of microanalytical techniques. A database of detailed studies of such terrestrial analogs would assist the study of geological and astrobiological specimens in future missions to Mars. Potential instrument concepts for in situ deployment on Mars include local electrode atom probe nanoanalysis (LEAP), vertical scanning white light interferometry (VSWLI), scanning electron microscopies, energy dispersive x-ray microanalysis (EDX), atomic force microscopy (AFM) and X-ray diffraction (XRD). While in situ deployment of these techniques is many years away, ground-based studies using these analytical techniques extend our understanding of the data obtained from instruments to be flown in the near future.

Dynamical gauge effects in an open quantum network

NASA Astrophysics Data System (ADS)

Zhao, Jianshi; Price, Craig; Liu, Qi; Gemelke, Nathan

2016-05-01

We describe new experimental techniques for simulation of high-energy field theories based on an analogy between open thermodynamic systems and effective dynamical gauge-fields following SU(2) × U(1) Yang-Mills models. By coupling near-resonant laser-modes to atoms moving in a disordered optical environment, we create an open system which exhibits a non-equilibrium phase transition between two steady-state behaviors, exhibiting scale-invariant behavior near the transition. By measuring transport of atoms through the disordered network, we observe two distinct scaling behaviors, corresponding to the classical and quantum limits for the dynamical gauge field. This behavior is loosely analogous to dynamical gauge effects in quantum chromodynamics, and can mapped onto generalized open problems in theoretical understanding of quantized non-Abelian gauge theories. Additional, the scaling behavior can be understood from the geometric structure of the gauge potential and linked to the measure of information in the local disordered potential, reflecting an underlying holographic principle. We acknowledge support from NSF Award No.1068570, and the Charles E. Kaufman Foundation.

Identification of best particle radiation shielded region through Energetic Neutral Atoms mapping

NASA Astrophysics Data System (ADS)

Milillo, A.; De Angelis, E.; Mura, A.; Orsini, S.; Mangano, V.; Massetti, S.; Rispoli, R.; Lazzarotto, F.; Vertolli, N.; Lavagna, M.; Ferrari, F.; Lunghi, P.; Attinà, P.; Parissenti, G.

2017-09-01

The lunar surface is directly exposed either to direct solar wind, or to Earth's magnetospheric plasma due to the Moon's lack of a magnetosphere or a dense atmosphere. This exposure could create inhospitable conditions for a possible human presence on the Moon, so it is crucial to investigate the close-to-surface environment for establishing the best reliable locations for future human bases. Although it lacks a global magnetic field, the Moon possesses magnetic anomalies that create mini-magnetospheres, where the solar wind is partly deflected. The local protection of the surface from the solar wind radiation inside the mini-magnetospheres could make these sites preferred for future lunar colonization. It is crucial a detailed characterization of these sites. In this paper, an investigation based on the detection of Energetic Neutral Atoms (ENA) from the surface for identifying the best particle radiation shielded region is proposed. A high spatial resolution mapping via ENA is a feasible and it is powerful way for reaching this goal.

Non-thermalization in trapped atomic ion spin chains

NASA Astrophysics Data System (ADS)

Hess, P. W.; Becker, P.; Kaplan, H. B.; Kyprianidis, A.; Lee, A. C.; Neyenhuis, B.; Pagano, G.; Richerme, P.; Senko, C.; Smith, J.; Tan, W. L.; Zhang, J.; Monroe, C.

2017-10-01

Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state. This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'.

Non-thermalization in trapped atomic ion spin chains.

PubMed

Hess, P W; Becker, P; Kaplan, H B; Kyprianidis, A; Lee, A C; Neyenhuis, B; Pagano, G; Richerme, P; Senko, C; Smith, J; Tan, W L; Zhang, J; Monroe, C

2017-12-13

Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state.This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'. © 2017 The Author(s).

An objective alternative to IUPAC's approach to assign oxidation states.

PubMed

Postils, Verònica; Delgado-Alonso, Carlos; Luis, Josep M; Salvador, Pedro

2018-05-22

The IUPAC has recently clarified the term Oxidation State (OS), and provided algorithms for its determination based on the ionic approximation (IA) of the bonds supported by atomic electronegativities (EN). Unfortunately, there are a number of exceptions and ambiguities in IUPAC's algorithms when it comes to practical applications. Our comprehensive study reveals the critical role of the chemical environment on establishing the OS, which cannot always be properly predicted using fix atomic EN values. By identifying what we define here as subsystems of enhanced stability within the molecular system, OS can be safely assigned in many cases without invoking exceptions. New insights about the effect of local aromaticity upon OS are revealed. Moreover, we prove that there are intrinsic limitations of the IA that cannot be overcome. In this context, the effective oxidation state (EOS) analysis arises as a robust and general scheme to derive OS without any external guidance. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Substrate temperature effect on the structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Hellman, F.; Elam, W. T.; Koon, N. C.

1993-05-01

Using extended x-ray absorption fine structures (EXAFS) measurements we have investigated the atomic environment around the Fe atom in a series of amorphous Tb0.26Fe0.74 films having different magnetic anisotropy energies owing to different deposition temperatures. The polarization properties of synchrotron radiation allowed the separate study of structure parallel and perpendicular to the sample plane. An anisotropy between these two structures was observed. Modeling results indicate this anisotropy is due to anisotropic pair correlations where the Fe-Fe pairs are statistically preferred in-plane and the Fe-Tb pairs out-of-plane. The amplitude of this anisotropy scales with both the substrate temperature and the magnetic anisotropy energy. A ≊1% in-plane compression of the Fe-Fe distance was measured between the in-plane and out-of-plane structure of the sample grown at 77 K. This sample had no detectable local chemical anisotropy suggesting that intrinsic stress plays an important role in determining its magnetic anisotropy.

Identifying Atomic Scale Structure in Undoped/Doped Semicrystalline P3HT Using Inelastic Neutron Scattering

DOE PAGES

Harrelson, Thomas F.; Cheng, Yongqiang Q.; Li, Jun; ...

2017-03-07

The greatest advantage of organic materials is the ability to synthetically tune desired properties. However, structural heterogeneity often obfuscates the relationship between chemical structure and functional properties. Inelastic neutron scattering (INS) is sensitive to both local structure and chemical environment and provides atomic level details that cannot be obtained through other spectroscopic or diffraction methods. INS data are composed of a density of vibrational states with no selection rules, which means that every structural configuration is equally weighted in the spectrum. This allows the INS spectrum to be quantitatively decomposed into different structural motifs. Here in this paper we presentmore » INS measurements of the semiconducting polymer P3HT doped with F4TCNQ supported by density functional theory calculations to identify two dominant families of undoped crystalline structures and one dominant doped structural motif, in spite of considerable heterogeneity. The differences between the undoped and doped structures indicate that P3HT side chains flatten upon doping.« less

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

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

Novel rattling of K atoms in aluminium-doped defect pyrochlore tungstate

NASA Astrophysics Data System (ADS)

Shoko, Elvis; Kearley, Gordon J.; Peterson, Vanessa K.; Mutka, Hannu; Koza, Michael M.; Yamaura, Jun-ichi; Hiroi, Zenji; Thorogood, Gordon J.

2014-07-01

Rattling dynamics have been identified as fundamental to superconductivity in defect pyrochlore osmates and aluminium vanadium intermetallics, as well as low thermal conductivity in clathrates and filled skutterudites. Combining inelastic neutron scattering (INS) measurements and ab initio molecular dynamics (MD) simulations, we use a new approach to investigate rattling in the Al-doped defect pyrochlore tungstates: AAl0.33W1.67O6 (A = K, Rb, Cs). We find that although all the alkali metals rattle, the rattling of the K atoms is unique, not only among the tungstates but also among the analogous defect osmates, KOs2O6 and RbOs2O6. Detailed analysis of the MD trajectories reveals that two unique features set the K dynamics apart from the rest, namely, (1) quasi one-dimensional local diffusion within a cage, and (2) vibration at a range of frequencies. The local diffusion is driven by strongly anharmonic local potentials around the K atoms exhibiting a double-well structure in the direction of maximum displacement, which is also the direction of local diffusion. On the other hand, vibration at a range of frequencies is a consequence of the strong anisotropy in the local potentials around the K atoms as revealed by directional magnitude spectra. We present evidence to show that it is the smaller size rather than the smaller mass of the K rattler which leads to the unusual dynamics. Finally, we suggest that the occurrence of local diffusion and vibration at a range of frequencies in the dynamics of a single rattler, as found here for the K atoms, may open new possibilities for phonon engineering in thermoelectric materials.

Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

PubMed Central

Levin, Igor; Vanderah, Terrell

2008-01-01

The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure—a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale—the so-called “nanostructure problem”—at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem—an ultimate frontier in materials characterization—necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed “institute” would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3) developing and maintaining pertinent databases, and (4) providing necessary education and training. PMID:27096131

Iodine-129 measurements in soil samples from Dolon village near the Semipalatinsk nuclear test site.

PubMed

Endo, Satoru; Tomita, Junpei; Tanaka, Kenichi; Yamamoto, Masayoshi; Fukutani, Satoshi; Imanaka, Tetsuji; Sakaguchi, Aya; Amano, Hikaru; Kawamura, Hidehisa; Kawamura, Hisao; Apsalikov, Kazbek N; Gusev, Boris I; Whitehead, Neil E; Shinkarev, Sergey; Hoshi, Masaharu

2008-07-01

Dolon village, located about 60 km from the border of the Semipalatinsk nuclear test site, is known to be heavily contaminated by the first USSR atomic bomb test in August 1949. Soil samples around Dolon were taken in October 2005 in an attempt to evaluate internal thyroid dose arising from incorporation of radioiodine isotopes (mainly (131)I). Iodine-129 in soil was measured by using the technique of accelerator mass spectrometry. The (129)I/(127)I atom ratios measured were in the range from 3.3 x 10(-9) to 3.3 x 10(-7). These values were within the range of the current background level ( approximately 10(-9) to 10(-7)) in the environment, including contributions from the global fallout of atmospheric nuclear tests and local fallout of nuclear facilities. The (129)I atom accumulated level in soil ranged from 1.28 x 10(13) to 1.59 x 10(14) atoms m(-2), the average (8.0 x 10(13)) of which was higher than the background level of (2-5) x 10(13). From the relationship between (129)I and( 137)Cs (corrected for background and decay from 1949 to 2005) accumulated levels, the background level of (129)I and the (129)I/(137)Cs ratio around Dolon were estimated to be (6.4 +/- 0.4) x 10(13) atoms m(-2) and 0.25 +/- 0.16, respectively. This (129)I/(137)Cs ratio is almost similar to the fission yield ratio for (239)Pu fast fission (0.24).

Event-Ready Bell Test Using Entangled Atoms Simultaneously Closing Detection and Locality Loopholes

NASA Astrophysics Data System (ADS)

Rosenfeld, Wenjamin; Burchardt, Daniel; Garthoff, Robert; Redeker, Kai; Ortegel, Norbert; Rau, Markus; Weinfurter, Harald

2017-07-01

An experimental test of Bell's inequality allows ruling out any local-realistic description of nature by measuring correlations between distant systems. While such tests are conceptually simple, there are strict requirements concerning the detection efficiency of the involved measurements, as well as the enforcement of spacelike separation between the measurement events. Only very recently could both loopholes be closed simultaneously. Here we present a statistically significant, event-ready Bell test based on combining heralded entanglement of atoms separated by 398 m with fast and efficient measurements of the atomic spin states closing essential loopholes. We obtain a violation with S =2.221 ±0.033 (compared to the maximal value of 2 achievable with models based on local hidden variables) which allows us to refute the hypothesis of local realism with a significance level P <2.57 ×10-9.

Local Structure and Short-Range Order in a NiCoCr Solid Solution Alloy

DOE PAGES

Zhang, F. X.; Zhao, Shijun; Jin, Ke; ...

2017-05-19

Multi-element solid solution alloys are intrinsically disordered on the atomic scale, and many of their advanced properties originate from the unique local structural characteristics. We measured the local structure of a NiCoCr solid solution alloy with X-ray/neutron total scattering and extended X-ray absorption fine structure (EXAFS) techniques. The atomic pair distribution function analysis (PDF) did not exhibit distinct structural distortion. But, EXAFS analysis suggested that the Cr atoms are favorably bonded with Ni and Co in the solid solution alloys. This short-range order (SRO) plays a role in the distinct low values of electrical and thermal conductivities in Ni-based solidmore » solution alloys when Cr is incorporated. Both the long-range and local structures of the NiCoCr alloy upon Ni ion irradiation were studied and an irradiation-induced enhancement of SRO was found.« less

Effects of atomic oxygen on polymeric materials flown on EOIM-3

NASA Technical Reports Server (NTRS)

Kamenetzky, Rachel R.; Linton, Roger C.; Finckenor, Miria M.; Vaughn, Jason A.

1995-01-01

Diverse polymeric materials, including several variations of Kapton, were flown on STS-46 as part of the Evaluation of Oxygen Interaction with Materials Experiment (EOIM-3). These materials were flown in the cargo bay and exposed to the space environment July 31 - August 8, 1992, including 40 hours of direct atomic oxygen impingement. The atomic oxygen exposure was approximately 2.2 x 10(exp 20) atoms/sq cm. Polymeric materials flown on EOIM-3 include coated and uncoated Kapton, Tefzel ETFE, Lexan, FEP and TFE Teflon, bulk Halar and PEEK, S383 silicone and Viton elastomeric seal material. Analyses performed included thickness measurements using Dektak and eddy current methods, mass loss, resistance, permeability, hardness, and FTIR. The effects of stress and the space environment on Kapton were also evaluated. Previous EOIM missions on STS-5 and STS-8 and the Long Duration Exposure Facility also contained polymeric material samples. Data from these previous flights are shown for comparison, as well as ground simulation of space environment effects using both thermal energy flow tubes and 5 eV neutral atomic oxygen beam facilities. Reaction efficiencies for the various atomic oxygen exposure conditions are discussed.

Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former.

PubMed

Kim, Jeongmin; Sung, Bong June

2015-06-17

The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

Density effects on electronic configurations in dense plasmas

NASA Astrophysics Data System (ADS)

Faussurier, Gérald; Blancard, Christophe

2018-02-01

We present a quantum mechanical model to describe the density effects on electronic configurations inside a plasma environment. Two different approaches are given by starting from a quantum average-atom model. Illustrations are shown for an aluminum plasma in local thermodynamic equilibrium at solid density and at a temperature of 100 eV and in the thermodynamic conditions of a recent experiment designed to characterize the effects of the ionization potential depression treatment. Our approach compares well with experiment and is consistent in that case with the approach of Stewart and Pyatt to describe the ionization potential depression rather than with the method of Ecker and Kröll.

Nanostructure and Dynamics of Ionic and Non-Ionic PEO-Containing Polyureas

NASA Astrophysics Data System (ADS)

Chuayprakong, Sunanta; Runt, James

2013-03-01

A series of polyethylene oxide (PEO) - based diamines with molecular weights ranging from 250 - 6000 g/mol were polymerized in solution with 4,4'-methylene diphenyl diisocyanate (MDI). In addition, PEO soft segment diamines where modified to incorporate ionomeric species and also polymerized with MDI. The role of PEO soft segment molecular weight and the presence of ionic species on nanoscale segregation and cation conductivity were explored. The former was investigated using small-angle X-ray scattering and atomic force microscopy. Dielectric relaxation spectroscopy was used to investigate polymer and ion dynamics. Local environment and hydrogen bonding were identified by using FTIR spectroscopy.

Effect of oxidation on the mechanical properties of a NbAl3 alloy at intermediate temperatures

NASA Technical Reports Server (NTRS)

Raj, S. V.; Hebsur, M.; Locci, I. E.; Doychak, J.

1992-01-01

The effect of environment on the mechanical properties of an Nb-67Al-7Cr-0.25W-0.5Y alloy was investigated experimentally in the temperature range 800-1200 K. It is found that the severity of environmental attack in the alloy is determined by both matrix plasticity and oxidation kinetics. The former determines the ability of the matrix to accommodate the localized stresses generated during deformation and oxidation, while the latter governs the rate of formation of a protective oxide scale. The environmental degradation of the alloy can thus be reduced or eliminated by increasing atomic mobility.

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

The stability of vacancy-like defects in amorphous silicon

NASA Astrophysics Data System (ADS)

Joly, Jean-Francois; Mousseau, Normand

2013-03-01

The contribution of vacancy-like defects to the relaxation of amorphous silicon (a-Si) has been a matter of debate for a long time. Due to their disordered nature, there is a large number local environments in which such a defect can exists. Previous numerical studies the vacancy in a-Si have been limited to small systems and very short timescales. Here we use kinectic ART (k-ART), an off-lattice kinetic Monte-Carlo simulation method with on-the-fly catalog building to study the time evolution of 1000 different single vacancy configurations in a well-relaxed a-Si model. Our results show that most of the vacancies are annihlated quickly. In fact, while 16% of the 1000 isolated vacancies survive for more than 1 ns of simulated time, 0.043% remain after 1 ms and only 6 of them survive longer than 0.1 second. Diffusion of the full vacancy is only seen in 19% of the configurations and diffusion usually leads directly to the annihilation of the defect. The actual annihilation event, in which one of the defective atoms fills the vacancy, is usually similar in all the configurations but local bonding environment heavily influence its activation barrier and relaxation energy.

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

Analog tree-organized multiplexer

NASA Technical Reports Server (NTRS)

Crabbe, J. S.; Smith, D. M.; Turner, W. R.

1971-01-01

An analog tree-organized multiplexer (ATOM) which is intended for use in the telemetry system of an interplanetary spacecraft is designed. The ATOM will be fabricated by a monolithic, dielectric isolation process, and will contain silicon junction field effect transistors (JFET) as the active elements. The effect of the radiation environment on the performance of the ATOM is analyzed. The result indicates that the expected radiation environment will cause only minor changes in the preradiation characteristics of ATOM. The JFET in the ATOM is designed to meet the electrical requirements when fabricated by either the double poly-dielectric isolation process or the raised dielectric isolation process. The effect of the heat treatment required for the dielectric isolation process on the diffusion profile of the JFET is described. The layout of the ATOM circuit for fabrication by either the double poly or raised dielectric isolation process is also given.

Atomistic study on shock behaviour of NiTi shape memory alloy

NASA Astrophysics Data System (ADS)

Yin, Qiuyun; Wu, Xianqian; Huang, Chenguang

2017-06-01

The shock behaviour of NiTi shape memory alloy is investigated by using molecular dynamics simulation. The nano-pillar samples of the alloy are subjected to the impact of a piston with a velocity of 350 m/s at initial environment temperatures of 325 and 500 K. At 325 K, we observe two different pathways of the formation of BCO phase, the gradient twins, and the detwinning phenomena, strongly depending on the local stress and the deformation state. As the initial temperature increases to 500 K, the plasticity is dominated by the dislocation movements rather than the twinning at 325 K. The phase transformation and plasticity result in stress attenuation when the stress wave propagates through the nano-pillar. Furthermore, it is interesting to note that multiple stress peaks occur due to the formation of local complex atomic structures with various wave speeds, leading to the catch up and overlap of the stress waves.

Casimir forces between defects in one-dimensional quantum liquids

NASA Astrophysics Data System (ADS)

Recati, A.; Fuchs, J. N.; Peça, C. S.; Zwerger, W.

2005-08-01

We discuss the effective interactions between two localized perturbations in one-dimensional quantum liquids. For noninteracting fermions, the interactions exhibit Friedel oscillations, giving rise to a Ruderman-Kittel-Kasuya-Yosida-type interaction familiar from impurity spins in metals. In the interacting case, at low energies, a Luttinger-liquid description applies. In the case of repulsive fermions, the Friedel oscillations of the interacting system are replaced, at long distances, by a universal Casimir-type interaction which depends only on the sound velocity and decays inversely with the separation. The Casimir-type interaction between localized perturbations embedded in a fermionic environment gives rise to a long-range coupling between quantum dots in ultracold Fermi gases, opening an alternative to couple qubits with neutral atoms. We also briefly discuss the case of bosonic quantum liquids in which the interaction between weak impurities turns out to be short ranged, decaying exponentially on the scale of the healing length.

Science Goals of the Primary Atomic Reference Clock in Space (PARCS) Experiment

NASA Technical Reports Server (NTRS)

Ashby, N.

2003-01-01

The PARCS (Primary Atomic Reference Clock in Space) experiment will use a laser-cooled Cesium atomic clock operating in the microgravity environment aboard the International Space Station (ISS) to provide both advanced tests of gravitational theory and to demonstrate a new cold-atom clock technology for space. PARCS is a joint project of the National Institute of Standards and Technology (NIST), NASA's Jet Propulsion Laboratory (JPL), and the University of Colorado (CU). This paper concentrates on the scientific goals of the PARCS mission. The microgravity space environment allows laser-cooled Cs atoms to have Ramsey times in excess of those feasible on Earth, resulting in improved clock performance. Clock stabilities of 5x10(exp -14) at one second, and accuracies better than 10(exp -16) are projected.

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

Theoretical prediction of the energy stability of graphene nanoblisters

NASA Astrophysics Data System (ADS)

Glukhova, O. E.; Slepchenkov, M. M.; Barkov, P. V.

2018-04-01

The paper presents the results of a theoretical prediction of the energy stability of graphene nanoblisters with various geometrical parameters. As a criterion for the evaluation of the stability of investigated carbon objects we propose to consider the value of local stress of the nanoblister atomic grid. Numerical evaluation of stresses experienced by atoms of the graphene blister framework was carried out by means of an original method for calculation of local stresses that is based on energy approach. Atomistic models of graphene nanoblisters corresponding to the natural experiment data were built for the first time in this work. New physical regularities of the influence of topology on the thermodynamic stability of nanoblisters were established as a result of the analysis of the numerical experiment data. We built the distribution of local stresses for graphene blister structures, whose atomic grid contains a variety of structural defects. We have shown how the concentration and location of defects affect the picture of the distribution of the maximum stresses experienced by the atoms of the nanoblisters.

Nuclear Power and the Environment, Understanding the Atom Series.

ERIC Educational Resources Information Center

Atomic Energy Commission, Oak Ridge, TN. Div. of Technical Information.

This booklet is one of the booklets in the "Understanding the Atom Series" published by the U. S. Atomic Energy Commission for high school science teachers and their students. Discussion concentrates on the radiological and thermal aspects of the environmental effects of nuclear power plants; on the procedures followed by the Atomic Energy…

Densification and Devitrification of Fused Silica Induced by Ballistic Impact: A Computational Investigation

DTIC Science & Technology

2015-03-25

lime glass, the polyhedron -center atoms are all silicon and each silicon atom is surrounded by four oxygen atoms (while each oxygen atom is connected...of metallic force-field functions (in the pure metallic environment) within the force-field function database used in the present work. Consequently

Molecular Self-Assembly in a Poorly Screened Environment: F 4TCNQ on Graphene/BN

DOE PAGES

Tsai, Hsin-Zon; Omrani, Arash A.; Coh, Sinisa; ...

2015-10-20

Here we report a scanning tunneling microscopy and noncontact atomic force microscopy study of close-packed 2D islands of tetrafluoro-tetracyanoquinodimethane (F 4TCNQ) molecules at the surface of a graphene layer supported by boron nitride. While F 4TCNQ molecules are known to form cohesive 3D solids, the intermolecular interactions that are attractive for F 4TCNQ in 3D are repulsive in 2D. Our experimental observation of cohesive molecular behavior for F 4TCNQ on graphene is thus unexpected. This self-assembly behavior can be explained by a novel solid formation mechanism that occurs when charged molecules are placed in a poorly screened environment. As negativelymore » charged molecules coalesce, the local work function increases, causing electrons to flow into the coalescing molecular island and increase its cohesive binding energy.« less

The photoexcitation of crystalline ice and amorphous solid water: A molecular dynamics study of outcomes at 11 K and 125 K

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

Crouse, J.; Loock, H.-P., E-mail: hploock@chem.queensu.ca; Cann, N. M., E-mail: ncann@chem.queensu.ca

2015-07-21

Photoexcitation of crystalline ice Ih and amorphous solid water at 7-9 eV is examined using molecular dynamics simulations and a fully flexible water model. The probabilities of photofragment desorption, trapping, and recombination are examined for crystalline ice at 11 K and at 125 K and for amorphous solid water at 11 K. For 11 K crystalline ice, a fully rigid water model is also employed for comparison. The kinetic energy of desorbed H atoms and the distance travelled by trapped fragments are correlated to the location and the local environment of the photoexcited water molecule. In all cases, H atommore » desorption is found to be the most likely outcome in the top bilayer while trapping of all photofragments is most probable deeper in the solid where the likelihood for recombination of the fragments into H{sub 2}O molecules also rises. Trajectory analysis indicates that the local hydrogen bonding network in amorphous solid water is more easily distorted by a photodissociation event compared to crystalline ice. Also, simulations indicate that desorption of OH radicals and H{sub 2}O molecules are more probable in amorphous solid water. The kinetic energy distributions for desorbed H atoms show a peak at high energy in crystalline ice, arising from photoexcited water molecules in the top monolayer. This peak is less pronounced in amorphous solid water. H atoms that are trapped may be displaced by up to ∼10 water cages, but migrate on average 3 water cages. Trapped OH fragments tend to stay near the original solvent cage.« less

Application of x-ray absorption fine structure (XAFS) to local-order analysis in Fe-Cr maghemite-like materials

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

Montero-Cabrera, M. E., E-mail: elena.montero@cimav.edu.mx; Fuentes-Cobas, L. E.; Macías-Ríos, E.

2015-07-23

The maghemite-like oxide system γ-Fe{sub 2-x}Cr{sub x}O{sub 3} (x=0.75, 1 and 1.25) was studied by X-ray absorption fine structure (XAFS) and by synchrotron radiation X-ray diffraction (XRD). Measurements were performed at the Stanford Synchrotron Radiation Lightsource at room temperature, at beamlines 2-1, 2-3 and 4-3. High-resolution XRD patterns were processed by means of the Rietveld method. In cases of atoms being neighbors in the Periodic Table, the order/disorder degree of the considered solutions is indiscernible by “normal” (absence of “anomalous scattering”) diffraction experiments. Thus, maghemite-like materials were investigated by XAFS in both Fe and Cr K-edges to clarify, via short-rangemore » structure characterization, the local ordering of the investigated system. Athena and Artemis graphic user interfaces for IFEFFIT and FEFF8.4 codes were employed for XAFS spectra interpretation. Pre-edge decomposition and theoretical modeling of X-ray absorption near edge structure (XANES) transitions were performed. By analysis of the Cr K-edge XANES, it has been confirmed that Cr is located in an octahedral environment. Fitting of the extended X-ray absorption fine structure (EXAFS) spectra was performed under the consideration that the central atom of Fe is allowed to occupy octa- and tetrahedral positions, while Cr occupies only octahedral ones. Coordination number of neighboring atoms, interatomic distances and their quadratic deviation average were determined for x=1, by fitting simultaneously the EXAFS spectra of both Fe and Cr K-edges. The results of fitting the experimental spectra with theoretical standards showed that the cation vacancies tend to follow a regular pattern within the structure of the iron-chromium maghemite (FeCrO{sub 3})« less

Steady bipartite coherence induced by non-equilibrium environment

NASA Astrophysics Data System (ADS)

Huangfu, Yong; Jing, Jun

2018-01-01

We study the steady state of two coupled two-level atoms interacting with a non-equilibrium environment that consists of two heat baths at different temperatures. Specifically, we analyze four cases with respect to the configuration about the interactions between atoms and heat baths. Using secular approximation, the conventional master equation usually neglects steady-state coherence, even when the system is coupled with a non-equilibrium environment. When employing the master equation with no secular approximation, we find that the system coherence in our model, denoted by the off-diagonal terms in the reduced density matrix spanned by the eigenvectors of the system Hamiltonian, would survive after a long-time decoherence evolution. The absolute value of residual coherence in the system relies on different configurations of interaction channels between the system and the heat baths. We find that a large steady quantum coherence term can be achieved when the two atoms are resonant. The absolute value of quantum coherence decreases in the presence of additional atom-bath interaction channels. Our work sheds new light on the mechanism of steady-state coherence in microscopic quantum systems in non-equilibrium environments.

Ultrafast time scale X-rotation of cold atom storage qubit using Rubidium clock states

NASA Astrophysics Data System (ADS)

Song, Yunheung; Lee, Han-Gyeol; Kim, Hyosub; Jo, Hanlae; Ahn, Jaewook

2017-04-01

Ultrafast-time-scale optical interaction is a local operation on the electronic subspace of an atom, thus leaving its nuclear state intact. However, because atomic clock states are maximally entangled states of the electronic and nuclear degrees of freedom, their entire Hilbert space should be accessible only with local operations and classical communications (LOCC). Therefore, it may be possible to achieve hyperfine qubit gates only with electronic transitions. Here we show an experimental implementation of ultrafast X-rotation of atomic hyperfine qubits, in which an optical Rabi oscillation induces a geometric phase between the constituent fine-structure states, thus bringing about the X-rotation between the two ground hyperfine levels. In experiments, cold atoms in a magneto-optical trap were controlled with a femtosecond laser pulse from a Ti:sapphire laser amplifier. Absorption imaging of the as-controlled atoms initially in the ground hyperfine state manifested polarization dependence, strongly agreeing with the theory. The result indicates that single laser pulse implementations of THz clock speed qubit controls are feasible for atomic storage qubits. Samsung Science and Technology Foundation [SSTF-BA1301-12].

Atomic scale imaging of magnetic circular dichroism by achromatic electron microscopy.

PubMed

Wang, Zechao; Tavabi, Amir H; Jin, Lei; Rusz, Ján; Tyutyunnikov, Dmitry; Jiang, Hanbo; Moritomo, Yutaka; Mayer, Joachim; Dunin-Borkowski, Rafal E; Yu, Rong; Zhu, Jing; Zhong, Xiaoyan

2018-03-01

In order to obtain a fundamental understanding of the interplay between charge, spin, orbital and lattice degrees of freedom in magnetic materials and to predict and control their physical properties 1-3 , experimental techniques are required that are capable of accessing local magnetic information with atomic-scale spatial resolution. Here, we show that a combination of electron energy-loss magnetic chiral dichroism 4 and chromatic-aberration-corrected transmission electron microscopy, which reduces the focal spread of inelastically scattered electrons by orders of magnitude when compared with the use of spherical aberration correction alone, can achieve atomic-scale imaging of magnetic circular dichroism and provide element-selective orbital and spin magnetic moments atomic plane by atomic plane. This unique capability, which we demonstrate for Sr 2 FeMoO 6 , opens the door to local atomic-level studies of spin configurations in a multitude of materials that exhibit different types of magnetic coupling, thereby contributing to a detailed understanding of the physical origins of magnetic properties of materials at the highest spatial resolution.

Partitioned key-value store with atomic memory operations

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

Bent, John M.; Faibish, Sorin; Grider, Gary

A partitioned key-value store is provided that supports atomic memory operations. A server performs a memory operation in a partitioned key-value store by receiving a request from an application for at least one atomic memory operation, the atomic memory operation comprising a memory address identifier; and, in response to the atomic memory operation, performing one or more of (i) reading a client-side memory location identified by the memory address identifier and storing one or more key-value pairs from the client-side memory location in a local key-value store of the server; and (ii) obtaining one or more key-value pairs from themore » local key-value store of the server and writing the obtained one or more key-value pairs into the client-side memory location identified by the memory address identifier. The server can perform functions obtained from a client-side memory location and return a result to the client using one or more of the atomic memory operations.« less

Calculations with the quasirelativistic local-spin-density-functional theory for high-Z atoms

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

Guo, Y.; Whitehead, M.A.

1988-10-01

The generalized-exchange local-spin-density-functional theory (LSD-GX) with relativistic corrections of the mass velocity and Darwin terms has been used to calculate statistical total energies for the neutral atoms, the positive ions, and the negative ions for high-Z elements. The effect of the correlation and relaxation correction on the statistical total energy is discussed. Comparing the calculated results for the ionization potentials and electron affinities for the atoms (atomic number Z from 37 to 56 and 72 to 80) with experiment, shows that for the atoms rubidium to barium both the LSD-GX and the quasirelativistic LSD-GX, with self-interaction correction, Gopinathan, Whitehead, andmore » Bogdanovic's Fermi-hole parameters (Phys. Rev. A 14, 1 (1976)), and Vosko, Wilk, and Nusair's correlation correction (Can. J. Phys. 58, 1200 (1980)), are very good methods for calculating ionization potentials and electron affinities. For the atoms hafnium to mercury the relativistic effect has to be considered.« less

Localizing gravitational wave sources with single-baseline atom interferometers

DOE PAGES

Graham, Peter W.; Jung, Sunghoon

2018-01-31

Localizing sources on the sky is crucial for realizing the full potential of gravitational waves for astronomy, astrophysics, and cosmology. Here in this paper, we show that the midfrequency band, roughly 0.03 to 10 Hz, has significant potential for angular localization. The angular location is measured through the changing Doppler shift as the detector orbits the Sun. This band maximizes the effect since these are the highest frequencies in which sources live for several months. Atom interferometer detectors can observe in the midfrequency band, and even with just a single baseline they can exploit this effect for sensitive angular localization.more » The single-baseline orbits around the Earth and the Sun, causing it to reorient and change position significantly during the lifetime of the source, and making it similar to having multiple baselines/detectors. For example, atomic detectors could predict the location of upcoming black hole or neutron star merger events with sufficient accuracy to allow optical and other electromagnetic telescopes to observe these events simultaneously. Thus, midband atomic detectors are complementary to other gravitational wave detectors and will help complete the observation of a broad range of the gravitational spectrum.« less

Localizing gravitational wave sources with single-baseline atom interferometers

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

Graham, Peter W.; Jung, Sunghoon

Localizing sources on the sky is crucial for realizing the full potential of gravitational waves for astronomy, astrophysics, and cosmology. Here in this paper, we show that the midfrequency band, roughly 0.03 to 10 Hz, has significant potential for angular localization. The angular location is measured through the changing Doppler shift as the detector orbits the Sun. This band maximizes the effect since these are the highest frequencies in which sources live for several months. Atom interferometer detectors can observe in the midfrequency band, and even with just a single baseline they can exploit this effect for sensitive angular localization.more » The single-baseline orbits around the Earth and the Sun, causing it to reorient and change position significantly during the lifetime of the source, and making it similar to having multiple baselines/detectors. For example, atomic detectors could predict the location of upcoming black hole or neutron star merger events with sufficient accuracy to allow optical and other electromagnetic telescopes to observe these events simultaneously. Thus, midband atomic detectors are complementary to other gravitational wave detectors and will help complete the observation of a broad range of the gravitational spectrum.« less

In Situ Flow MAS NMR Spectroscopy and Synchrotron PDF Analyses of the Local Response of the Brønsted Acidic Site in SAPO-34 during Hydration at Elevated Temperatures.

PubMed

Kalantzopoulos, Georgios N; Lundvall, Fredrik; Checchia, Stefano; Lind, Anna; Wragg, David S; Fjellvåg, Helmer; Arstad, Bjørnar

2018-02-19

In situ flow magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and synchrotron-based pair distribution function (PDF) analyses were applied to study water's interactions with the Brønsted acidic site and the surrounding framework in the SAPO-34 catalyst at temperatures up to 300 °C for NMR spectroscopy and 700 °C for PDF. 29 Si enrichment of the sample enabled detailed NMR spectroscopy investigations of the T-atom generating the Brønsted site. By NMR spectroscopy, we observed dehydration above 100 °C and a coalescence of Si peaks due to local framework adjustments. Towards 300 °C, the NMR spectroscopy data indicated highly mobile acidic protons. In situ total X-ray scattering measurements analyzed by PDF showed clear changes in the Al local environment in the 250-300 °C region, as the Al-O bond lengths showed a sudden change. This fell within the same temperature range as the increased Brønsted proton mobility. We suggest that the active site in this catalyst under industrial conditions comprises not only the Brønsted proton but also SiO 4 . To the best of our knowledge, this is the first work proposing a structural model of a SAPO catalyst by atomic PDF analysis. The combination of synchrotron PDF analysis with in situ NMR spectroscopy is promising in revealing the dynamic features of a working catalyst. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Local structure of amorphous Ag5In5Sb60Te30 and In3SbTe2 phase change materials revealed by X-ray photoelectron and Raman spectroscopic studies

NASA Astrophysics Data System (ADS)

Sahu, Smriti; Manivannan, Anbarasu; Shaik, Habibuddin; Mohan Rao, G.

2017-07-01

Reversible switching between highly resistive (binary "0") amorphous phase and low resistive (binary "1") crystalline phase of chalcogenide-based Phase Change Materials is accredited for the development of next generation high-speed, non-volatile, data storage applications. The doped Sb-Te based materials have shown enhanced electrical/optical properties, compared to Ge-Sb-Te family for high-speed memory devices. We report here the local atomic structure of as-deposited amorphous Ag5In5Sb60Te30 (AIST) and In3SbTe2 (IST) phase change materials using X-ray photoelectron and Raman spectroscopic studies. Although AIST and IST materials show identical crystallization behavior, they differ distinctly in their crystallization temperatures. Our experimental results demonstrate that the local environment of In remains identical in the amorphous phase of both AIST and IST material, irrespective of its atomic fraction. In bonds with Sb (˜44%) and Te (˜56%), thereby forming the primary matrix in IST with a very few Sb-Te bonds. Sb2Te constructs the base matrix for AIST (˜63%) along with few Sb-Sb bonds. Furthermore, an interesting assimilation of the role of small-scale dopants such as Ag and In in AIST, reveals rare bonds between themselves, while showing selective substitution in the vicinity of Sb and Te. This results in increased electronegativity difference, and consequently, the bond strength is recognized as the factor rendering stability in amorphous AIST.

Doping Scheme in Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Toshishige, Yamada

1997-01-01

Due to the dramatic reduction in MOS size, there appear many unwanted effects. In these small devices, the number of dopant atoms in the channel is not macroscopic and electrons may suffer significantly different scattering from device to device since the spatial distribution of dopant atoms is no longer regarded as continuous. This prohibits integration, while it is impossible to control such dopant positions within atomic scale. A fundamental solution is to create electronics with simple but atomically precise structures, which could be fabricated with recent atom manipulation technology. All the constituent atoms are placed as planned, and then the device characteristics are deviation-free, which is mandatory for integration. Atomic chain electronics belongs to this category. Foreign atom chains or arrays form devices, and they are placed on the atomically flat substrate surface. We can design the band structure and the resultant Fermi energy of these structures by manipulating the lattice constant. Using the tight-binding theory with universal parameters, it has been predicted that isolated Si chains and arrays are metallic, Mg chains are insulating, and Mg arrays have metallic and insulating phases [1]. The transport properties along a metallic chain have been studied, emphasizing the role of the contact to electrodes [2]. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along die chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of pant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Magnitude of pseudopotential localization errors in fixed node diffusion quantum Monte Carlo

DOE PAGES

Kent, Paul R.; Krogel, Jaron T.

2017-06-22

Growth in computational resources has lead to the application of real space diffusion quantum Monte Carlo to increasingly heavy elements. Although generally assumed to be small, we find that when using standard techniques, the pseudopotential localization error can be large, on the order of an electron volt for an isolated cerium atom. We formally show that the localization error can be reduced to zero with improvements to the Jastrow factor alone, and we define a metric of Jastrow sensitivity that may be useful in the design of pseudopotentials. We employ an extrapolation scheme to extract the bare fixed node energymore » and estimate the localization error in both the locality approximation and the T-moves schemes for the Ce atom in charge states 3+/4+. The locality approximation exhibits the lowest Jastrow sensitivity and generally smaller localization errors than T-moves although the locality approximation energy approaches the localization free limit from above/below for the 3+/4+ charge state. We find that energy minimized Jastrow factors including three-body electron-electron-ion terms are the most effective at reducing the localization error for both the locality approximation and T-moves for the case of the Ce atom. Less complex or variance minimized Jastrows are generally less effective. Finally, our results suggest that further improvements to Jastrow factors and trial wavefunction forms may be needed to reduce localization errors to chemical accuracy when medium core pseudopotentials are applied to heavy elements such as Ce.« less

Spin dynamics and Kondo physics in optical tweezers

NASA Astrophysics Data System (ADS)

Lin, Yiheng; Lester, Brian J.; Brown, Mark O.; Kaufman, Adam M.; Long, Junling; Ball, Randall J.; Isaev, Leonid; Wall, Michael L.; Rey, Ana Maria; Regal, Cindy A.

2016-05-01

We propose to use optical tweezers as a toolset for direct observation of the interplay between quantum statistics, kinetic energy and interactions, and thus implement minimum instances of the Kondo lattice model in systems with few bosonic rubidium atoms. By taking advantage of strong local exchange interactions, our ability to tune the spin-dependent potential shifts between the two wells and complete control over spin and motional degrees of freedom, we design an adiabatic tunneling scheme that efficiently creates a spin-singlet state in one well starting from two initially separated atoms (one atom per tweezer) in opposite spin state. For three atoms in a double-well, two localized in the lowest vibrational mode of each tweezer and one atom in an excited delocalized state, we plan to use similar techniques and observe resonant transfer of two-atom singlet-triplet states between the wells in the regime when the exchange coupling exceeds the mobile atom hopping. Moreover, we argue that such three-atom double-tweezers could potentially be used for quantum computation by encoding logical qubits in collective spin and motional degrees of freedom. Current address: Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

Optical Materials with a Genome: Nanophotonics with DNA-Stabilized Silver Clusters

NASA Astrophysics Data System (ADS)

Copp, Stacy M.

Fluorescent silver clusters with unique rod-like geometries are stabilized by DNA. The sizes and colors of these clusters, or AgN-DNA, are selected by DNA base sequence, which can tune peak emission from blue-green into the near-infrared. Combined with DNA nanostructures, AgN-DNA promise exciting applications in nanophotonics and sensing. Until recently, however, a lack of understanding of the mechanisms controlling AgN-DNA fluorescence has challenged such applications. This dissertation discusses progress toward understanding the role of DNA as a "genome" for silver clusters and toward using DNA to achieve atomic-scale precision of silver cluster size and nanometer-scale precision of silver cluster position on a DNA breadboard. We also investigate sensitivity of AgN-DNA to local solvent environment, with an eye toward applications in chemical and biochemical sensing. Using robotic techniques to generate large data sets, we show that fluorescent silver clusters are templated by certain DNA base motifs that select "magic-sized" cluster cores of enhanced stabilities. The linear arrangement of bases on the phosphate backbone imposes a unique rod-like geometry on the clusters. Harnessing machine learning and bioinformatics techniques, we also demonstrate that sequences of DNA templates can be selected to stabilize silver clusters with desired optical properties, including high fluorescence intensity and specific fluorescence wavelengths, with much higher rates of success as compared to current strategies. The discovered base motifs can be also used to design modular DNA host strands that enable individual silver clusters with atomically precise sizes to bind at specific programmed locations on a DNA nanostructure. We show that DNA-mediated nanoscale arrangement enables near-field coupling of distinct clusters, demonstrated by dual-color cluster assemblies exhibiting resonant energy transfer. These results demonstrate a new degree of control over the optical properties and relative positions of nanoparticles, selected almost solely by the sequence of DNA. AgN-DNA are promising chemical and biochemical sensors due to the sensitivity of their fluorescence to local environment. However, the mechanisms behind many sensing schemes are not understood, and the nature of the excited state of the silver cluster itself remains unknown. To probe the fluorescence mechanisms of AgN-DNA, we investigate the behavior of purified solutions of these clusters in various solvents. We find that standard models for fluorophore solvatochromism, including the Lippert-Mataga model, do not describe AgN-DNA fluorescence because such models neglect specific interactions between the cluster and surrounding solvent molecules. Fluorescence colors are well-modeled by Mie-Gans theory, suggesting that the local dielectric environment of the cluster does play a role in fluorescence, although additional specific solvent interactions and cluster shape changes may also determine fluorescence color and intensity. These results suggest that AgN-DNA may be sensitive to changes in local dielectric environment on nanometer length scales and may also act as sensors for small molecules with affinity for DNA.

Simulations of Ground and Space-Based Oxygen Atom Experiments

NASA Technical Reports Server (NTRS)

Minton, T. K.; Cline, J. A.; Braunstein, M.

2002-01-01

Fast, pulsed atomic oxygen sources are a key tool in ground-based investigations of spacecraft contamination and surface erosion effects. These technically challenging ground-based studies provide a before and after picture of materials under low-earth-orbit (LEO) conditions. It would be of great interest to track in real time the pulsed flux from the source to the surface sample target and beyond in order to characterize the population of atoms and molecules that actually impact the surface and those that make it downstream to any coincident detectors. We have performed simulations in order to provide such detailed descriptions of these ground-based measurements and to provide an assessment of their correspondence to the actual LEO environment. Where possible we also make comparisons to measured fluxes and erosion yields. To perform the calculations we use a detailed description of a measurement beam and surface geometry based on the W, pulsed apparatus at Montana State University. In this system, a short pulse (on the order of 10 microseconds) of an O/O2 beam impacts a flat sample about 40 cm downstream and slightly displaced &om the beam s central axis. Past this target, at the end of the beam axis is a quadrupole mass spectrometer that measures the relative in situ flux of 0102 to give an overall normalized erosion yield. In our simulations we use the Direct Simulation Monte Carlo (DSMC) method, and track individual atoms within the atomic oxygen pulse. DSMC techniques are typically used to model rarefied (few collision) gas-flows which occur at altitudes above approximately 110 kilometers. These techniques are well suited for the conditions here, and multi-collision effects that can only be treated by this or a similar technique are included. This simulation includes collisions with the surface and among gas atoms that have scattered from the surface. The simulation also includes descriptions of the velocity spread and spatial profiles of the O/O2 beam obtained from separate measurements. These computations use basic engineering models for the gas-gas and gas-surface scattering and focus on the influence of multi-collision effects. These simulations characterize many important quantities of interest including the actual flux of atoms that reach the surface, the energy distribution of this flux, as well as the direction of the velocity of the flux that strikes the surface. These quantities are important in characterizing the conditions which give rise to measured surface erosion. The calculations also yield time- snapshots of the pulse as it impacts and flows around the surface. These snapshots reveal the local environment of gas near the surface for the duration of the pulse. We are also able to compute the flux of molecules that travel downstream and reach the spectrometer, and we characterize their velocity distribution. The number of atoms that reach the spectrometer can in fact be influenced by the presence of the surface due to gas-gas collisions from atoms scattered h m the surface, and it will generally be less than that with the surface absent. This amounts to an overall normalization factor in computing erosion yields. We discuss these quantities and their relationship to the gas-surf$ce interaction parameters. We have also performed similar calculations corresponding to conditions (number densities, temperatures, and velocities) of low-earth orbit. The steady-state nature and lower overall flux of the actual space environment give rise to differences in the nature of the gas-impacts on the surface from those of the ground-based measurements using a pulsed source.

Spectroscopic imaging of self-organization in high power impulse magnetron sputtering plasmas

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

Andersson, Joakim; Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, 117543 Singapore; Ni, Pavel

Excitation and ionization conditions in traveling ionization zones of high power impulse magnetron sputtering plasmas were investigated using fast camera imaging through interference filters. The images, taken in end-on and side-on views using light of selected gas and target atom and ion spectral lines, suggest that ionization zones are regions of enhanced densities of electrons, and excited atoms and ions. Excited atoms and ions of the target material (Al) are strongly concentrated near the target surface. Images from the highest excitation energies exhibit the most localized regions, suggesting localized Ohmic heating consistent with double layer formation.

Spectroscopic imaging of self-organization in high power impulse magnetron sputtering plasmas

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

Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, 117543 Singapore, Singapore; Andersson, Joakim; Ni, Pavel

Excitation and ionization conditions in traveling ionization zones of high power impulse magnetron sputtering plasmas were investigated using fast camera imaging through interference filters. The images, taken in end-on and side on views using light of selected gas and target atom and ion spectral lines, suggest that ionization zones are regions of enhanced densities of electrons, and excited atoms and ions. Excited atoms and ions of the target material (Al) are strongly concentrated near the target surface. Images from the highest excitation energies exhibit the most localized regions, suggesting localized Ohmic heating consistent with double layer formation.

Partially Oxidized SnS2 Atomic Layers Achieving Efficient Visible-Light-Driven CO2 Reduction.

PubMed

Jiao, Xingchen; Li, Xiaodong; Jin, Xiuyu; Sun, Yongfu; Xu, Jiaqi; Liang, Liang; Ju, Huanxin; Zhu, Junfa; Pan, Yang; Yan, Wensheng; Lin, Yue; Xie, Yi

2017-12-13

Unraveling the role of surface oxide on affecting its native metal disulfide's CO 2 photoreduction remains a grand challenge. Herein, we initially construct metal disulfide atomic layers and hence deliberately create oxidized domains on their surfaces. As an example, SnS 2 atomic layers with different oxidation degrees are successfully synthesized. In situ Fourier transform infrared spectroscopy spectra disclose the COOH* radical is the main intermediate, whereas density-functional-theory calculations reveal the COOH* formation is the rate-limiting step. The locally oxidized domains could serve as the highly catalytically active sites, which not only benefit for charge-carrier separation kinetics, verified by surface photovoltage spectra, but also result in electron localization on Sn atoms near the O atoms, thus lowering the activation energy barrier through stabilizing the COOH* intermediates. As a result, the mildly oxidized SnS 2 atomic layers exhibit the carbon monoxide formation rate of 12.28 μmol g -1 h -1 , roughly 2.3 and 2.6 times higher than those of the poorly oxidized SnS 2 atomic layers and the SnS 2 atomic layers under visible-light illumination. This work uncovers atomic-level insights into the correlation between oxidized sulfides and CO 2 reduction property, paving a new way for obtaining high-efficiency CO 2 photoreduction performances.

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

Kent, Paul R.; Krogel, Jaron T.

Growth in computational resources has lead to the application of real space diffusion quantum Monte Carlo to increasingly heavy elements. Although generally assumed to be small, we find that when using standard techniques, the pseudopotential localization error can be large, on the order of an electron volt for an isolated cerium atom. We formally show that the localization error can be reduced to zero with improvements to the Jastrow factor alone, and we define a metric of Jastrow sensitivity that may be useful in the design of pseudopotentials. We employ an extrapolation scheme to extract the bare fixed node energymore » and estimate the localization error in both the locality approximation and the T-moves schemes for the Ce atom in charge states 3+/4+. The locality approximation exhibits the lowest Jastrow sensitivity and generally smaller localization errors than T-moves although the locality approximation energy approaches the localization free limit from above/below for the 3+/4+ charge state. We find that energy minimized Jastrow factors including three-body electron-electron-ion terms are the most effective at reducing the localization error for both the locality approximation and T-moves for the case of the Ce atom. Less complex or variance minimized Jastrows are generally less effective. Finally, our results suggest that further improvements to Jastrow factors and trial wavefunction forms may be needed to reduce localization errors to chemical accuracy when medium core pseudopotentials are applied to heavy elements such as Ce.« less

Parametric Study of Amorphous High-Entropy Alloys formation from two New Perspectives: Atomic Radius Modification and Crystalline Structure of Alloying Elements

NASA Astrophysics Data System (ADS)

Hu, Q.; Guo, S.; Wang, J. M.; Yan, Y. H.; Chen, S. S.; Lu, D. P.; Liu, K. M.; Zou, J. Z.; Zeng, X. R.

2017-01-01

Chemical and topological parameters have been widely used for predicting the phase selection in high-entropy alloys (HEAs). Nevertheless, previous studies could be faulted due to the small number of available data points, the negligence of kinetic effects, and the insensitivity to small compositional changes. Here in this work, 92 TiZrHfM, TiZrHfMM, TiZrHfMMM (M = Fe, Cr, V, Nb, Al, Ag, Cu, Ni) HEAs were prepared by melt spinning, to build a reliable and sufficiently large material database to inspect the robustness of previously established parameters. Modification of atomic radii by considering the change of local electronic environment in alloys, was critically found out to be superior in distinguishing the formation of amorphous and crystalline alloys, when compared to using atomic radii of pure elements in topological parameters. Moreover, crystal structures of alloying element were found to play an important role in the amorphous phase formation, which was then attributed to how alloying hexagonal-close-packed elements and face-centered-cubic or body-centered-cubic elements can affect the mixing enthalpy. Findings from this work not only provide parametric studies for HEAs with new and important perspectives, but also reveal possibly a hidden connection among some important concepts in various fields.

A molecular dynamics study of the atomic structure of (CaO)x(SiO2)1-x glasses.

PubMed

Mead, Robert N; Mountjoy, Gavin

2006-07-27

The local atomic environment of Ca in (CaO)x(SiO2)1-x glasses is of interest because of the role of Ca in soda-lime glass, the application of calcium silicate glasses as biomaterials, and the previous experimental measurement of the Ca-Ca correlation in CaSiO(3) glass. Molecular dynamics has been used to obtain models of (CaO)x(SiO2)1-x glasses with x = 0, 0.1, 0.2, 0.3, 0.4, and 0.5, and with approximately 1000 atoms and size approximately 25 A. As expected, the models contain a tetrahedral silica network, the connectivity of which decreases as x increases. In the glass-forming region, i.e., x = 0.4 and 0.5, Ca has a mixture of 6- and 7-fold coordination. Bridging oxygen makes an important contribution to the coordination of Ca, with most bridging oxygens coordinated to 2 Si plus 1 Ca. The x = 0.5 model is in reasonable agreement with previous experimental studies, and does not substantiate the previous theory of cation ordering, which predicted Ca arranged in sheets. In the phase-separated region, i.e., x = 0.1 and 0.2, there is marked clustering of Ca.

Energy-efficient quantum frequency estimation

NASA Astrophysics Data System (ADS)

Liuzzo-Scorpo, Pietro; Correa, Luis A.; Pollock, Felix A.; Górecka, Agnieszka; Modi, Kavan; Adesso, Gerardo

2018-06-01

The problem of estimating the frequency of a two-level atom in a noisy environment is studied. Our interest is to minimise both the energetic cost of the protocol and the statistical uncertainty of the estimate. In particular, we prepare a probe in a ‘GHZ-diagonal’ state by means of a sequence of qubit gates applied on an ensemble of n atoms in thermal equilibrium. Noise is introduced via a phenomenological time-non-local quantum master equation, which gives rise to a phase-covariant dissipative dynamics. After an interval of free evolution, the n-atom probe is globally measured at an interrogation time chosen to minimise the error bars of the final estimate. We model explicitly a measurement scheme which becomes optimal in a suitable parameter range, and are thus able to calculate the total energetic expenditure of the protocol. Interestingly, we observe that scaling up our multipartite entangled probes offers no precision enhancement when the total available energy {\\boldsymbol{ \\mathcal E }} is limited. This is at stark contrast with standard frequency estimation, where larger probes—more sensitive but also more ‘expensive’ to prepare—are always preferred. Replacing {\\boldsymbol{ \\mathcal E }} by the resource that places the most stringent limitation on each specific experimental setup, would thus help to formulate more realistic metrological prescriptions.

MoS2 interactions with 1.5 eV atomic oxygen

NASA Technical Reports Server (NTRS)

Martin, J. A.; Cross, J. B.; Pope, L. E.

1989-01-01

Exposures of MoS2 to 1.5-eV atomic oxygen in an anhydrous environment reveal that the degree of oxidation is essentially independent of crystallite orientation, and that the surface-adsorbed reaction products are MoO3 and MoO2. A mixture of oxides and sulfide exists over a depth of about 90 A, and this layer has a low diffusion rate for oxygen. It is concluded that a protective oxide layer forms on MoS2 on exposure to the atomic-oxygen-rich environment of LEO.

Identifying the Distribution of Al 3+ in LiNi 0.8 Co 0.15 Al 0.05 O 2

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

Trease, Nicole M.; Seymour, Ieuan D.; Radin, Maxwell D.

2016-11-22

The doping of Al into layered Li transition metal (TM) oxide cathode materials, LiTMO 2, is known to improve the structural and thermal stability, although the origin of the enhanced properties is not well understood. The effect of aluminum doping on layer stabilization has been investigated using a combination of techniques to measure the aluminum distribution in layered LiNi 0.8Co 0.15Al 0.05O 2 (NCA) over multiple length scales with 27Al and 7Li MAS NMR, local electrode atom probe (APT) tomography, X-ray and neutron diffraction, DFT, and SQUID magnetic susceptibility measurements. APT ion maps show a homogenous distribution of Ni, Co,more » Al and O 2 throughout the structure at the single particle level in agreement with the high-temperature phase diagram. 7Li and 27Al NMR indicates that the Ni 3+ ions undergo a dynamic Jahn-Teller (JT) distortion. 27Al NMR spectra indicate that the Al reduces the strain associated with the JT distortion, by preferential electronic ordering of the JT long bonds directed toward the Al 3+ ion. The ability to understand the complex atomic and orbital ordering around Al 3+ demonstrated in the current method will be useful for studying the local environment of Al 3+ in a range of transition metal oxide battery materials.« less

Identifying the Distribution of Al 3+ in LiNi 0.8 Co 0.15 Al 0.05 O 2

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

Trease, Nicole M.; Seymour, Ieuan D.; Radin, Maxwell D.

2016-10-07

The doping of Al into layered Li transition metal (TM) oxide cathode materials, LiTMO 2, is known to improve the structural and thermal stability, although the origin of the enhanced properties is not well understood. We have investigated the effect of aluminum doping on layer stabilization using a combination of techniques to measure the aluminum distribution in layered LiNi 0.8Co 0.15Al 0.05O 2 (NCA) over multiple length scales with 27Al and 7Li MAS NMR, local electron atom probe (LEAP) tomography, X-ray and neutron diffraction, DFT, and SQUID magnetic susceptibility measurements. LEAP tomographic maps show a homogenous distribution of Ni, Co,more » Al and O 2 throughout the structure at the particle level in agreement with the hightemperature phase diagram. 7Li and 27Al NMR indicates that the Ni 3+ ions undergo a dynamic Jahn-Teller (JT) distortion. 27Al NMR spectra indicate that the Al reduces the strain associated with the JT distortion, by preferential electronic ordering of the JT long bonds directed toward the Al 3+ ion. Our ability to understand the complex atomic and orbital ordering around Al 3+ demonstrated in the current method will be useful for studying the local environment of Al 3+ in a range of transition metal oxide battery materials.« less

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

Reiche, D.; Dalvit, D. A. R.; Busch, K.

We investigate the influence of spatial dispersion on atom-surface quantum friction. We show that for atom-surface separations shorter than the carrier's mean free path within the material, the frictional force can be several orders of magnitude larger than that predicted by local optics. In addition, when taking into account spatial dispersion effects, we show that the commonly used local thermal equilibrium approximation underestimates by approximately 95% the drag force, obtained by employing the recently reported nonequilibrium fluctuation-dissipation relation for quantum friction. Unlike the treatment based on local optics, spatial dispersion in conjunction with corrections to local thermal equilibrium change notmore » only the magnitude but also the distance scaling of quantum friction.« less

Realization of localized Bohr-like wave packets.

PubMed

Mestayer, J J; Wyker, B; Lancaster, J C; Dunning, F B; Reinhold, C O; Yoshida, S; Burgdörfer, J

2008-06-20

We demonstrate a protocol to create localized wave packets in very-high-n Rydberg states which travel in nearly circular orbits around the nucleus. Although these wave packets slowly dephase and eventually lose their localization, their motion can be monitored over several orbital periods. These wave packets represent the closest analog yet achieved to the original Bohr model of the hydrogen atom, i.e., an electron in a circular classical orbit around the nucleus. The possible extension of the approach to create "planetary atoms" in highly correlated stable multiply excited states is discussed.

Phonon localization transition in relaxor ferroelectric PZN-5%PT

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

Manley, Michael E.; Christianson, Andrew D.; Abernathy, Douglas L.

Relaxor ferroelectric behavior occurs in many disordered ferroelectric materials but is not well understood at the atomic level. Recent experiments and theoretical arguments indicate that Anderson localization of phonons instigates relaxor behavior by driving the formation of polar nanoregions (PNRs). Here, we use inelastic neutron scattering to observe phonon localization in relaxor ferroelectric PZN-5%PT (0.95[Pb(Zn 1/3 Nb 2/3)O 3]–0.05PbTiO 3) and detect additional features of the localization process. In the lead, up to phonon localization on cooling, the local resonant modes that drive phonon localization increase in number. The increase in resonant scattering centers is attributed to a known increasemore » in the number of locally off centered Pb atoms on cooling. The transition to phonon localization occurs when these random scattering centers increase to a concentration where the Ioffe-Regel criterion is satisfied for localizing the phonon. Finally, we also model the effects of damped mode coupling on the observed phonons and phonon localization structure.« less

Phonon localization transition in relaxor ferroelectric PZN-5%PT

DOE PAGES

Manley, Michael E.; Christianson, Andrew D.; Abernathy, Douglas L.; ...

2017-03-27

Relaxor ferroelectric behavior occurs in many disordered ferroelectric materials but is not well understood at the atomic level. Recent experiments and theoretical arguments indicate that Anderson localization of phonons instigates relaxor behavior by driving the formation of polar nanoregions (PNRs). Here, we use inelastic neutron scattering to observe phonon localization in relaxor ferroelectric PZN-5%PT (0.95[Pb(Zn 1/3 Nb 2/3)O 3]–0.05PbTiO 3) and detect additional features of the localization process. In the lead, up to phonon localization on cooling, the local resonant modes that drive phonon localization increase in number. The increase in resonant scattering centers is attributed to a known increasemore » in the number of locally off centered Pb atoms on cooling. The transition to phonon localization occurs when these random scattering centers increase to a concentration where the Ioffe-Regel criterion is satisfied for localizing the phonon. Finally, we also model the effects of damped mode coupling on the observed phonons and phonon localization structure.« less

Rationalization of Hubbard U in CeOx from first principles: Unveiling the role of local structure in screening

NASA Astrophysics Data System (ADS)

Lu, Deyu; Liu, Ping

2014-03-01

DFT+U method has been widely employed in theoretical studies on various ceria systems to correct the delocalization bias in local and semi-local DFT functionals with moderate computational cost. To rationalize the Hubbard U of Ce 4f, we employed the first principles linear response method to compute Hubbard U for Ce in ceria clusters, bulks, and surfaces. We found that in contrast to the commonly used approach treating U as a constant, the Hubbard U varies in a wide range from 4.1 eV to 6.7 eV, and exhibits a strong correlation with the Ce coordination numbers and Ce-O bond lengths, rather than the Ce 4f valence state. The variation of the Hubbard U can be explained by the changes in the strength of local screening due to O --> Ce intersite transition. Our study represents a systematic, quantitative investigation of the relationship between the Hubbard U and the local atomic arrangement, enabling a DFT+environment-dependent U scheme that can have potential impact on catalysis research of strongly correlated systems. This work is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886.

The reaction mechanism of SnSb and Sb thin film anodes for Na-ion batteries studied by X-ray diffraction, 119Sn and 121Sb Mössbauer spectroscopies

DOE PAGES

Baggetto, Loïc; Hah, Hien-Yoong; Jumas, Jean-Claude; ...

2014-06-01

The electrochemical reaction of Sb and SnSb anode materials with Na results in the formation of amorphous materials. To understand the resulting phases and electrochemical capacities we studied the reaction products local order using 119Sn and 121Sb Mössbauer spectroscopies in conjunction with measurements performed on model powder compounds of Na-Sn and Na-Sb to further clarify the reactions steps. For pure Sb the discharge (sodiation) starts with the formation of an amorphous phase composed of atomic environments similar to those found in NaSb, and proceeds further by the formation of environments similar to that present in Na 3Sb. The reversible reactionmore » takes place during a large portion of the charge process. At full charge the anode material still contains a substantial fraction of Na, which explains the lack of recrystallization into crystalline Sb. The reaction of SnSb yields Na 3Sb crystalline phase at full discharge at higher temperatures (65 and 95°C) while the room temperature reaction yields amorphous compounds. The electrochemically-driven, solid-state amorphization reaction occurring at room temperature is governed by the simultaneous formation of Na-coordinated Sn and Sb environments, as monitored by the decrease (increase) of the 119Sn ( 121Sb) Mössbauer isomer shifts. Overall, the monitoring of the hyperfine parameters enables to correlate the changes in Na content to the individual Sn and Sb local chemical environments.« less

Focused-ion-beam induced interfacial intermixing of magnetic bilayers for nanoscale control of magnetic properties.

PubMed

Burn, D M; Hase, T P A; Atkinson, D

2014-06-11

Modification of the magnetic properties in a thin-film ferromagnetic/non-magnetic bilayer system by low-dose focused ion-beam (FIB) induced intermixing is demonstrated. The highly localized capability of FIB may be used to locally control magnetic behaviour at the nanoscale. The magnetic, electronic and structural properties of NiFe/Au bilayers were investigated as a function of the interfacial structure that was actively modified using focused Ga(+) ion irradiation. Experimental work used MOKE, SQUID, XMCD as well as magnetoresistance measurements to determine the magnetic behavior and grazing incidence x-ray reflectivity to elucidate the interfacial structure. Interfacial intermixing, induced by low-dose irradiation, is shown to lead to complex changes in the magnetic behavior that are associated with monotonic structural evolution of the interface. This behavior may be explained by changes in the local atomic environment within the interface region resulting in a combination of processes including the loss of moment on Ni and Fe, an induced moment on Au and modifications to the spin-orbit coupling between Au and NiFe.

A first-principles study of As doping at a disordered Si-SiO2 interface.

PubMed

Corsetti, Fabiano; Mostofi, Arash A

2014-02-05

Understanding the interaction between dopants and semiconductor-oxide interfaces is an increasingly important concern in the drive to further miniaturize modern transistors. To this end, using a combination of first-principles density-functional theory and a continuous random network Monte Carlo method, we investigate electrically active arsenic donors at the interface between silicon and its oxide. Using a realistic model of the disordered interface, we find that a small percentage (on the order of ∼10%) of the atomic sites in the first few monolayers on the silicon side of the interface are energetically favourable for segregation, and that this is controlled by the local bonding and local strain of the defect centre. We also find that there is a long-range quantum confinement effect due to the interface, which results in an energy barrier for dopant segregation, but that this barrier is small in comparison to the effect of the local environment. Finally, we consider the extent to which the energetics of segregation can be controlled by the application of strain to the interface.

Introducing Fe 2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity

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

Cai, Zhao; Zhou, Daojin; Wang, Maoyu

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel–iron layered double hydroxides (NiFe–LDHs) by partially substituting Ni 2+ with Fe 2+ to introduce Fe–O–Fe moieties. These Fe 2+–containing NiFe–LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm 2, which is among the best OER catalytic performance reported to date. In–situ X–ray absorption, Raman, and electrochemical analysis jointlymore » reveal that the Fe–O–Fe motifs could stabilize high–valent metal sites at low overpotentials, thereby enhancing the OER activity. Lastly, these results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts.« less

Introducing Fe2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity.

PubMed

Cai, Zhao; Zhou, Daojin; Wang, Maoyu; Bak, Seongmin; Wu, Yueshen; Wu, Zishan; Tian, Yang; Xiong, Xuya; Li, Yaping; Liu, Wen; Siahrostami, Samira; Kuang, Yun; Yang, Xiao-Qing; Duan, Haohong; Feng, Zhenxing; Wang, Hailiang; Sun, Xiaoming

2018-06-11

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel-iron layered double hydroxides (NiFe-LDHs) by partially substituting Ni2+ with Fe2+ to introduce Fe-O-Fe moieties. These Fe2+-containing NiFe-LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm2, which is among the best OER catalytic performance reported to date. In-situ X-ray absorption, Raman, and electrochemical analysis jointly reveal that the Fe-O-Fe motifs could stabilize high-valent metal sites at low overpotentials, thereby enhancing the OER activity. These results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Introducing Fe 2+ into Nickel-Iron Layered Double Hydroxide: Local Structure Modulated Water Oxidation Activity

DOE PAGES

Cai, Zhao; Zhou, Daojin; Wang, Maoyu; ...

2018-06-11

Exploring materials with regulated local structures and understanding how the atomic motifs govern the reactivity and durability of catalysts are a critical challenge for designing advanced catalysts. Here we report the tuning of the local atomic structure of nickel–iron layered double hydroxides (NiFe–LDHs) by partially substituting Ni 2+ with Fe 2+ to introduce Fe–O–Fe moieties. These Fe 2+–containing NiFe–LDHs exhibit enhanced oxygen evolution reaction (OER) activity with an ultralow overpotential of 195 mV at the current density of 10 mA/cm 2, which is among the best OER catalytic performance reported to date. In–situ X–ray absorption, Raman, and electrochemical analysis jointlymore » reveal that the Fe–O–Fe motifs could stabilize high–valent metal sites at low overpotentials, thereby enhancing the OER activity. Lastly, these results reveal the importance of tuning the local atomic structure for designing high efficiency electrocatalysts.« less

Identification of phases, symmetries and defects through local crystallography

DOE PAGES

Belianinov, Alex; He, Qian; Kravchenko, Mikhail; ...

2015-07-20

Here we report that advances in electron and probe microscopies allow 10 pm or higher precision in measurements of atomic positions. This level of fidelity is sufficient to correlate the length (and hence energy) of bonds, as well as bond angles to functional properties of materials. Traditionally, this relied on mapping locally measured parameters to macroscopic variables, for example, average unit cell. This description effectively ignores the information contained in the microscopic degrees of freedom available in a high-resolution image. Here we introduce an approach for local analysis of material structure based on statistical analysis of individual atomic neighbourhoods. Clusteringmore » and multivariate algorithms such as principal component analysis explore the connectivity of lattice and bond structure, as well as identify minute structural distortions, thus allowing for chemical description and identification of phases. This analysis lays the framework for building image genomes and structure–property libraries, based on conjoining structural and spectral realms through local atomic behaviour.« less

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

Finzel, Kati, E-mail: kati.finzel@liu.se

The local conditions for the Pauli potential that are necessary in order to yield self-consistent electron densities from orbital-free calculations are investigated for approximations that are expressed with the help of a local position variable. It is shown that those local conditions also apply when the Pauli potential is given in terms of the electron density. An explicit formula for the Ne atom is given, preserving the local conditions during the iterative procedure. The resulting orbital-free electron density exhibits proper shell structure behavior and is in close agreement with the Kohn-Sham electron density. This study demonstrates that it is possiblemore » to obtain self-consistent orbital-free electron densities with proper atomic shell structure from simple one-point approximations for the Pauli potential at local density level.« less

Reactivity of amino acid anions with nitrogen and oxygen atoms.

PubMed

Wang, Zhe-Chen; Li, Ya-Ke; He, Sheng-Gui; Bierbaum, Veronica M

2018-02-14

For many decades, astronomers have searched for biological molecules, including amino acids, in the interstellar medium; this endeavor is important for investigating the hypothesis of the origin of life from space. The space environment is complex and atomic species, such as nitrogen and oxygen atoms, are widely distributed. In this work, the reactions of eight typical deprotonated amino acids (glycine, alanine, cysteine, proline, aspartic acid, histidine, tyrosine, and tryptophan) with ground state nitrogen and oxygen atoms are studied by experiment and theory. These amino acid anions do not react with nitrogen atoms. However, the reactions of these ions with oxygen atoms show an intriguing variety of ionic products and the reaction rate constants are of the order of 10 -10 cm 3 s -1 . Density functional calculations provide detailed mechanisms of the reactions, and demonstrate that spin conversion is essential for some processes. Our study provides important data and insights for understanding the kinetic and dynamic behavior of amino acids in space environments.

Method and apparatus for atomic imaging

DOEpatents

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

1993-01-01

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

Atomic oxygen durability of solar concentrator materials for Space Station Freedom

NASA Technical Reports Server (NTRS)

Degroh, Kim K.; Terlep, Judith A.; Dever, Therese M.

1990-01-01

The findings are reviewed of atomic oxygen exposure testing of candidate solar concentrator materials containing SiO2 and Al2O3 protective coatings for use on Space Station Freedom solar dynamic power modules. Both continuous and iterative atomic oxygen exposure tests were conducted. Iterative air plasma ashing resulted in larger specular reflectance decreases and solar absorptance increases than continuous ashing to the same fluence, and appears to provide a more severe environment than the continuous atomic oxygen exposure that would occur in the low Earth orbit environment. First generation concentrator fabrication techniques produced surface defects including scratches, macroscopic bumps, dendritic regions, porosity, haziness, and pin hole defects. Several of these defects appear to be preferential sites for atomic oxygen attack leading to erosive undercutting. Extensive undercutting and flaking of reflective and protective coatings were found to be promoted through an undercutting tearing propagation process. Atomic oxygen erosion processes and effects on optical performance is presented.

Atom probe tomographic mapping directly reveals the atomic distribution of phosphorus in resin embedded ferritin

DOE PAGES

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

2016-02-29

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.

Atoms in molecules, an axiomatic approach. I. Maximum transferability

NASA Astrophysics Data System (ADS)

Ayers, Paul W.

2000-12-01

Central to chemistry is the concept of transferability: the idea that atoms and functional groups retain certain characteristic properties in a wide variety of environments. Providing a completely satisfactory mathematical basis for the concept of atoms in molecules, however, has proved difficult. The present article pursues an axiomatic basis for the concept of an atom within a molecule, with particular emphasis devoted to the definition of transferability and the atomic description of Hirshfeld.

Theory of Reactions at a Solid Surface.

DTIC Science & Technology

1983-03-01

vibrational and rotational motions of X2 and X are separable even at small distances away from the surface, and that the lattice vibra- tions do not...volume of the clean surface, and o(X) is the reaction cross section of X atoms with lattice atoms M. Rearranging Eq. (28), we ,can write d[n(M) - an(R...positions of only a small number, n, of local surface atoms. We designate these as the "primary lattice atoms". The remaining N-n solid atoms serve

The study of structures and properties of PdnHm(n=1-10, m=1,2) clusters by density functional theory

NASA Astrophysics Data System (ADS)

Wen, Jun-Qing; Chen, Guo-Xiang; Zhang, Jian-Min; Wu, Hua

2018-04-01

The geometrical evolution, local relative stability, magnetism and charge transfer characteristics of PdnHm(n = 1-10, m = 1,2) have been systematically calculated by using density functional theory. The studied results show that the most stable geometries of PdnH and PdnH2 (n = 1-10) can be got by doping one or two H atoms on the sides of Pdn clusters except Pd6H and Pd6H2. It is found that doping one or two H atoms on Pdn clusters cannot change the basic framework of Pdn. The analysis of stability shows that Pd2H, Pd4H, Pd7H, Pd2H2, Pd4H2 and Pd7H2 clusters have higher local relative stability than neighboring clusters. The analysis of magnetic properties demonstrates that absorption of hydrogen atoms decreases the average atomic magnetic moments compared with pure Pdn clusters. More charges transfer from H atoms to Pd atoms for Pd6H and Pd6H2 clusters, demonstrating the adsorption of hydrogen atoms change from side adsorption to surface adsorption.

Oxidation and protection of fiberglass-epoxy composite masts for photovoltaic arrays in the low Earth orbital environment

NASA Technical Reports Server (NTRS)

Rutledge, Sharon K.; Paulsen, Phillip E.; Brady, Joyce A.; Ciancone, Michael L.

1988-01-01

Fiberglass-epoxy composites are considered for use as structural members for the mast of the space station solar array panel. The low Earth orbital environment in which space station is to operate is composed mainly of atomic oxygen, which has been shown to cause erosion of many organic materials and some metals. Ground based testing in a plasma asher was performed to determine the extent of degradation of fiberglass-epoxy composites when exposed to a simulated atomic oxygen environment. During exposure, the epoxy at the surface of the composite was oxidized, exposing individual glass fibers which could easily be removed. Several methods of protecting the composite were evaluated in an atomic oxygen environment and with thermal cycling and flexing. The protection techniques evaluated to date include an aluminum braid covering, an indium-tin eutectic and a silicone based paint. The open aluminum braid offered little protection while the CV-1144 coating offered some initial protection against atomic oxygen, but appears to develop cracks which accelerate degradation when flexed. Coatings such as the In-Sn eutectic may provide adequate protection by containing the glass fibers even though mass loss still occurs.

SYNCHROTRON RADIATION, FREE ELECTRON LASER, APPLICATION OF NUCLEAR TECHNOLOGY, ETC.: A new cell for X-ray absorption spectroscopy study under high pressure

NASA Astrophysics Data System (ADS)

Zheng, Li-Rong; Che, Rong-Zheng; Liu, Jing; Du, Yong-Hua; Zhou, Ying-Li; Hu, Tian-Dou

2009-08-01

X-ray absorption fine structure (XAFS) spectroscopy is a powerful technique for the investigation of the local environment around selected atoms in condensed matter. XAFS under pressure is an important method for the synchrotron source. We design a cell for a high pressure XAFS experiment. Sintered boron carbide is used as the anvils of this high pressure cell in order to obtain a full XAFS spectrum free from diffraction peaks. In addition, a hydraulic pump was adopted to make in-suit pressure modulation. High quality XAFS spectra of ZrH2 under high pressure (up to 13 GPa) were obtained by this cell.

Local atomic order of a metallic glass made visible by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Luo, Yuansu; Samwer, Konrad

2018-06-01

Exploring the atomic level structure in amorphous materials by STM becomes extremely difficult due to the localized electronic states. Here we carried out STM studies on a quasi-low-dimensional film of metallic glass Zr65Cu27.5Al7.5 which is ‘ultrathin’ compared with the localization length and/or the length scale of short range order. The local electronic structure must appear more inherent, having states at E f available for tip-sample tunneling current. To enhance imaging contrasts between long-range and short-range orders, the highly oriented pyrolytic graphite was chosen as substrate, so that the structural heterogeneity arising from competition between the glass former ability and the epitaxy can be ascertained. A chemical order predicted for this system was observed in atomic ordered regimes (1–2 monolayers), accompanied with a superstructure with the period Zr–Cu(Al)–Zr along three hexagonal axes. The result implies a chemical short range order in disordered regimes, where polyhedral clusters are dominant with the solute atom Cu(Al) in the center. An attempt for the structural modelling was made based on high resolution STM images, giving icosahedral order on the surface and different Voronoi clusters in 3D space.

Anomalous diffusion in a dynamical optical lattice

NASA Astrophysics Data System (ADS)

Zheng, Wei; Cooper, Nigel R.

2018-02-01

Motivated by experimental progress in strongly coupled atom-photon systems in optical cavities, we study theoretically the quantum dynamics of atoms coupled to a one-dimensional dynamical optical lattice. The dynamical lattice is chosen to have a period that is incommensurate with that of an underlying static lattice, leading to a dynamical version of the Aubry-André model which can cause localization of single-particle wave functions. We show that atomic wave packets in this dynamical lattice generically spread via anomalous diffusion, which can be tuned between superdiffusive and subdiffusive regimes. This anomalous diffusion arises from an interplay between Anderson localization and quantum fluctuations of the cavity field.

Si-centered capped trigonal prism ordering in liquid Pd 82Si 18 alloy study by first-principles calculations

DOE PAGES

Dong, F.; Yue, G. Q.; Ames Lab. and Iowa State Univ., Ames, IA; ...

2017-03-24

First-principles molecular dynamic (MD) simulation and X-ray diffraction were employed to study the local structures of Pd–Si liquid at the eutectic composition (Pd 82Si 18). Here, a strong repulsion is found between Si atoms, and Si atoms prefer to be evenly distributed in the liquid. The dominate local structures around Si atoms are found to be with of a trigonal prism capped by three half-octahedra and an archimedean anti-prism. The populations of these clusters increase significantly upon cooling, and may play an important role in the formation of Pd 82Si 18 alloy glass.

Si-centered capped trigonal prism ordering in liquid Pd 82Si 18 alloy study by first-principles calculations

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

Dong, F.; Yue, G. Q.; Ames Lab. and Iowa State Univ., Ames, IA

First-principles molecular dynamic (MD) simulation and X-ray diffraction were employed to study the local structures of Pd–Si liquid at the eutectic composition (Pd 82Si 18). Here, a strong repulsion is found between Si atoms, and Si atoms prefer to be evenly distributed in the liquid. The dominate local structures around Si atoms are found to be with of a trigonal prism capped by three half-octahedra and an archimedean anti-prism. The populations of these clusters increase significantly upon cooling, and may play an important role in the formation of Pd 82Si 18 alloy glass.

Synthesis and structural characterization of two half-sandwich nickel(II) complexes with the scorpionate ligands

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

Wang, G.-F., E-mail: wgf1979@126.com, E-mail: s-shuwen@163.com; Zhang, X., E-mail: zhangx@hit.edu.cn; Sun, S.-W.

The synthesis and characterization of two new halfsandwich mononuclear nickel(II) complexes with the scorpionate ligands, [k{sup 3}-N, N',N''-Tp{sup t-Bu}, {sup Me}NiI] (1) and [k{sup 3}-N,N',N''-Tp{sup t-Bu}, {sup Me}NiNO{sub 3}] (2), are reported. These complexes have been fully characterized by elemental analyses and infrared spectra. Their molecular structures were determined by single crystal X-ray diffraction. The nickel(II) ion of complex 1 is in a four-coordinate environment, in which the donor atoms are provided by three nitrogen atoms of a hydrotris(pyrazolyl) borate ligand and one iodide atom, while that of complex 2 is in a five-coordinate environment with three nitrogen atoms frommore » a hydrotris(pyrazolyl)borate ligand and two oxygen atoms from a nitrate ion.« less

A spectral study of a radio-frequency plasma-generated flux of atomic oxygen

NASA Technical Reports Server (NTRS)

Batten, Carmen E.; Brown, Kenneth G.; Lewis, Beverley W.

1994-01-01

The active environment of a radio-frequency (RF) plasma generator, with and without low-pressure oxygen, has been characterized through the identification of emission lines in the spectral region from 250 to 900 nm. The environment is shown to be dependent on the partial pressure of oxygen and the power applied to the RF generator. Atomic oxygen has been found in significant amounts as well as atomic hydrogen and the molecular oxygen species O2((sup 1)Sigma). The only charged species observed was the singly charged molecular ion O2(+). With a polymer specimen in the plasma chamber, carbon monoxide was also observed. The significance of these observations with respect to previous studies using this type of generator to stimulate material degradation in space is discussed. The possibility of using these generators as atomic oxygen sources in the development of oxygen atom fluorescence sensors is explored.

Defect propagation in one-, two-, and three-dimensional compounds doped by magnetic atoms

DOE PAGES

Furrer, A.; Podlesnyak, A.; Krämer, K. W.; ...

2014-10-29

Inelastic neutron scattering experiments were performed to study manganese(II) dimer excitations in the diluted one-, two-, and three-dimensional compounds CsMn xMg 1-xBr 3, K 2Mn xZn 1-xF 4, and KMn xZn 1-xF 3 (x≤0.10), respectively. The transitions from the ground-state singlet to the excited triplet, split into a doublet and a singlet due to the single-ion anisotropy, exhibit remarkable fine structures. These unusual features are attributed to local structural inhomogeneities induced by the dopant Mn atoms which act like lattice defects. Statistical models support the theoretically predicted decay of atomic displacements according to 1/r 2, 1/r, and constant (for three-,more » two-, and one-dimensional compounds, respectively) where r denotes the distance of the displaced atoms from the defect. In conclusion, the observed fine structures allow a direct determination of the local exchange interactions J, and the local intradimer distances R can be derived through the linear law dJ/dR.« less

Non-local electron transport through normal and topological ladder-like atomic systems

NASA Astrophysics Data System (ADS)

Kurzyna, Marcin; Kwapiński, Tomasz

2018-05-01

We propose a locally protected ladder-like atomic system (nanoconductor) on a substrate that is insensitive to external perturbations. The system corresponds to coupled atomic chains fabricated on different surfaces. Electron transport properties of such conductors are studied theoretically using the model tight-binding Su-Schriffer-Hegger (SSH) Hamiltonian and Green's function formalism. We have found that the conductance of the system is almost insensitive to single adatoms and oscillates as a function of the side chain length with very large periods. Non-local character of the electron transport was observed also for topological SSH chains where nontrivial end states survive in the presence of disturbances as well as for different substrates. We have found that the careful inspection of the density of states or charge waves can provide the information about the atom energy levels and hopping amplitudes. Moreover, the ladder-like geometry allows one to distinguish between normal and topological zero-energy states. It is important that topological chains do not reveal Friedel oscillations which are observed in non-topological chains.

Atomic Spectroscopic Databases at NIST

NASA Technical Reports Server (NTRS)

Reader, J.; Kramida, A. E.; Ralchenko, Yu.

2006-01-01

We describe recent work at NIST to develop and maintain databases for spectra, transition probabilities, and energy levels of atoms that are astrophysically important. Our programs to critically compile these data as well as to develop a new database to compare plasma calculations for atoms that are not in local thermodynamic equilibrium are also summarized.

Sensitive Technique Developed Using Atomic Force Microscopy to Measure the Low-Earth-Orbit Atomic Oxygen Erosion of Polymers

NASA Technical Reports Server (NTRS)

deGroh, Kim D.; Banks, Bruce A.; Clark, Gregory W.; Hammerstrom, Anne; Youngstrom, Erica; Kaminski, Carolyn; Fine, Elizabeth; Marx, Laura

2001-01-01

A recession measurement technique has been developed at the NASA Glenn Research Center to determine the atomic oxygen durability of polymers exposed to the space environment for short durations. Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene, DuPont) are commonly used in spacecraft because of their desirable properties, such as flexibility, low density, and in the case of FEP, low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low- Earth-orbit environment are exposed to energetic atomic oxygen, resulting in erosion and potential structural loss. It is, therefore, important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. Because long-term space exposure data are rare and very costly, short-term exposures, such as on the space shuttles, are often relied on for atomic oxygen erosion determination. The most common technique for determining E is through mass-loss measurements. For limited-duration exposure experiments, such as shuttle flight experiments, the atomic oxygen fluence is often so small that mass-loss measurements are not sensitive enough. Therefore, a recession measurement technique has been developed at Glenn to obtain accurate erosion yields of polymers exposed to low atomic oxygen fluences.

Laser-driven atomic-probe-beam diagnostics

NASA Astrophysics Data System (ADS)

Knyazev, B. A.; Greenly, J. B.; Hammer, D. A.

2000-12-01

A new laser-driven atomic-probe-beam diagnostic (LAD) is proposed for local, time-resolved measurements of electric field and ion dynamics in the accelerating gap of intense ion beam diodes. LAD adds new features to previous Stark-shift diagnostics which have been progressively developed in several laboratories, from passive observation of Stark effect on ion species or fast (charge-exchanged) neutrals present naturally in diodes, to active Stark atomic spectroscopy (ASAS) in which selected probe atoms were injected into the gap and excited to suitable states by resonant laser radiation. The LAD scheme is a further enhancement of ASAS in which the probe atoms are also used as a local (laser-ionized) ion source at an instant of time. Analysis of the ion energy and angular distribution after leaving the gap enables measurement, at the chosen ionization location in the gap, of both electrostatic potential and the development of ion divergence. Calculations show that all of these quantities can be measured with sub-mm and ns resolution. Using lithium or sodium probe atoms, fields from 0.1 to 10 MV/cm can be measured.

Local structure of NiPd solid solution alloys and its response to ion irradiation

DOE PAGES

Zhang, Fuxiang; Ullah, Mohammad Wali; Zhao, Shijun; ...

2018-04-27

The local structure of Ni$-$Pd solid solution alloys with compositions of Ni 80Pd 20 and Ni 50Pd 50 was investigated with anomalous X-ray diffraction, X-ray absorption and theoretical calculation/simulation. The fcc lattice is distorted for both alloys, and the Pd$-$Pd atomic pair distance is +4.4% and +1.4% larger than ideal values in Ni 80Pd 20 and Ni 50Pd 50 alloys, respectively. The corresponding atomic pair distance of Ni$-$Ni is -1.8% and -3.0% less than the ideal values. Different short-range orders in the alloys were quantitatively identified at the atomic level. In Ni 80Pd 20, Pd atoms are likely to formmore » Pd$-$Pd pairs, while Pd atoms are connected with Pd atoms in the second shell in the equiatomic solid solution alloy. Upon ion irradiation, little change of interatomic distance, but modification of chemical short-range order was observed. The number of Pd$-$Pd pairs decreases to the lowest value at 0.1 dpa, and further irradiation make it increase.« less

Local structure of NiPd solid solution alloys and its response to ion irradiation

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

Zhang, Fuxiang; Ullah, Mohammad Wali; Zhao, Shijun

The local structure of Ni$-$Pd solid solution alloys with compositions of Ni 80Pd 20 and Ni 50Pd 50 was investigated with anomalous X-ray diffraction, X-ray absorption and theoretical calculation/simulation. The fcc lattice is distorted for both alloys, and the Pd$-$Pd atomic pair distance is +4.4% and +1.4% larger than ideal values in Ni 80Pd 20 and Ni 50Pd 50 alloys, respectively. The corresponding atomic pair distance of Ni$-$Ni is -1.8% and -3.0% less than the ideal values. Different short-range orders in the alloys were quantitatively identified at the atomic level. In Ni 80Pd 20, Pd atoms are likely to formmore » Pd$-$Pd pairs, while Pd atoms are connected with Pd atoms in the second shell in the equiatomic solid solution alloy. Upon ion irradiation, little change of interatomic distance, but modification of chemical short-range order was observed. The number of Pd$-$Pd pairs decreases to the lowest value at 0.1 dpa, and further irradiation make it increase.« less

Linear indices of the "molecular pseudograph's atom adjacency matrix": definition, significance-interpretation, and application to QSAR analysis of flavone derivatives as HIV-1 integrase inhibitors.

PubMed

Marrero-Ponce, Yovani

2004-01-01

This report describes a new set of molecular descriptors of relevance to QSAR/QSPR studies and drug design, atom linear indices fk(xi). These atomic level chemical descriptors are based on the calculation of linear maps on Rn[fk(xi): Rn--> Rn] in canonical basis. In this context, the kth power of the molecular pseudograph's atom adjacency matrix [Mk(G)] denotes the matrix of fk(xi) with respect to the canonical basis. In addition, a local-fragment (atom-type) formalism was developed. The kth atom-type linear indices are calculated by summing the kth atom linear indices of all atoms of the same atom type in the molecules. Moreover, total (whole-molecule) linear indices are also proposed. This descriptor is a linear functional (linear form) on Rn. That is, the kth total linear indices is a linear map from Rn to the scalar R[ fk(x): Rn --> R]. Thus, the kth total linear indices are calculated by summing the atom linear indices of all atoms in the molecule. The features of the kth total and local linear indices are illustrated by examples of various types of molecular structures, including chain-lengthening, branching, heteroatoms-content, and multiple bonds. Additionally, the linear independence of the local linear indices to other 0D, 1D, 2D, and 3D molecular descriptors is demonstrated by using principal component analysis for 42 very heterogeneous molecules. Much redundancy and overlapping was found among total linear indices and most of the other structural indices presently in use in the QSPR/QSAR practice. On the contrary, the information carried by atom-type linear indices was strikingly different from that codified in most of the 229 0D-3D molecular descriptors used in this study. It is concluded that the local linear indices are an independent indices containing important structural information to be used in QSPR/QSAR and drug design studies. In this sense, atom, atom-type, and total linear indices were used for the prediction of pIC50 values for the cleavage process of a set of flavone derivatives inhibitors of HIV-1 integrase. Quantitative models found are significant from a statistical point of view (R of 0.965, 0.902, and 0.927, respectively) and permit a clear interpretation of the studied properties in terms of the structural features of molecules. A LOO cross-validation procedure revealed that the regression models had a fairly good predictability (q2 of 0.679, 0.543, and 0.721, respectively). The comparison with other approaches reveals good behavior of the method proposed. The approach described in this paper appears to be an excellent alternative or guides for discovery and optimization of new lead compounds.

Voronoi analysis of the short–range atomic structure in iron and iron–carbon melts

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

Sobolev, Andrey; Mirzoev, Alexander

2015-08-17

In this work, we simulated the atomic structure of liquid iron and iron–carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short–range atomic order of iron atoms — it remains effectively the same as in pure iron melts.

Effect of local atomic and electronic structures on thermoelectric properties of chemically substituted CoSi

NASA Astrophysics Data System (ADS)

Hsu, C. C.; Pao, C. W.; Chen, J. L.; Chen, C. L.; Dong, C. L.; Liu, Y. S.; Lee, J. F.; Chan, T. S.; Chang, C. L.; Kuo, Y. K.; Lue, C. S.

2014-05-01

We report the effects of Ge partial substitution for Si on local atomic and electronic structures of thermoelectric materials in binary compound cobalt monosilicides (\\text{CoSi}_{1-x}\\text{Ge}_{x}\\text{:}\\ 0 \\le x \\le 0.15 ). Correlations between local atomic/electronic structure and thermoelectric properties are investigated by means of X-ray absorption spectroscopy. The spectroscopic results indicate that as Ge is partially substituted onto Si sites at x \\le 0.05 , Co in CoSi1-xGex gains a certain amount of charge in its 3d orbitals. Contrarily, upon further replacing Si with Ge at x \\ge 0.05 , the Co 3d orbitals start to lose some of their charge. Notably, thermopower is strongly correlated with charge redistribution in the Co 3d orbital, and the observed charge transfer between Ge and Co is responsible for the variation of Co 3d occupancy number. In addition to Seebeck coefficient, which can be modified by tailoring the Co 3d states, local lattice disorder may also be beneficial in enhancing the thermoelectric properties. Extended X-ray absorption fine structure spectrum results further demonstrate that the lattice phonons can be enhanced by Ge doping, which results in the formation of the disordered Co-Co pair. Improvements in the thermoelectric properties are interpreted based on the variation of local atomic and electronic structure induced by lattice distortion through chemical substitution.

Estimation of chirp rates of music-adapted prolate spheroidal atoms using reassignment

NASA Astrophysics Data System (ADS)

Mesz, Bruno; Serrano, Eduardo

2007-09-01

We introduce a modified Matching Pursuit algorithm for estimating frequency and frequency slope of FM-modulated music signals. The use of Matching Pursuit with constant frequency atoms provides coarse estimates which could be improved with chirped atoms, more suited in principle to this kind of signals. Application of the reassignment method is suggested by its good localization properties for chirps. We start considering a family of atoms generated by modulation and scaling of a prolate spheroidal wave function. These functions are concentrated in frequency on intervals of a semitone centered at the frequencies of the well-tempered scale. At each stage of the pursuit, we search the atom most correlated with the signal. We then consider the spectral peaks at each frame of the spectrogram and calculate a modified frequency and frequency slope using the derivatives of the reassignment operators; this is then used to estimate the parameters of a cubic interpolation polynomial that models local pitch fluctuations. We apply the method both to synthetic and music signals.

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors

PubMed Central

Thorwart, Michael

2018-01-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing. PMID:29756034

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors.

PubMed

Kim, Howon; Palacio-Morales, Alexandra; Posske, Thore; Rózsa, Levente; Palotás, Krisztián; Szunyogh, László; Thorwart, Michael; Wiesendanger, Roland

2018-05-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing.

Heralded entangling quantum gate via cavity-assisted photon scattering

NASA Astrophysics Data System (ADS)

Borges, Halyne S.; Rossatto, Daniel Z.; Luiz, Fabrício S.; Villas-Boas, Celso J.

2018-01-01

We theoretically investigate the generation of heralded entanglement between two identical atoms via cavity-assisted photon scattering in two different configurations, namely, either both atoms confined in the same cavity or trapped into locally separated ones. Our protocols are given by a very simple and elegant single-step process, the key mechanism of which is a controlled-phase-flip gate implemented by impinging a single photon on single-sided cavities. In particular, when the atoms are localized in remote cavities, we introduce a single-step parallel quantum circuit instead of the serial process extensively adopted in the literature. We also show that such parallel circuit can be straightforwardly applied to entangle two macroscopic clouds of atoms. Both protocols proposed here predict a high entanglement degree with a success probability close to unity for state-of-the-art parameters. Among other applications, our proposal and its extension to multiple atom-cavity systems step toward a suitable route for quantum networking, in particular for quantum state transfer, quantum teleportation, and nonlocal quantum memory.

Effects of quantum coherence and interference in atoms near nanoparticles

NASA Astrophysics Data System (ADS)

Dhayal, Suman; Rostovtsev, Yuri V.

2016-04-01

Optical properties of ensembles of realistic quantum emitters coupled to plasmonic systems are studied by using adequate models that can take into account full atomic geometry. In particular, the coherent effects such as forming "dark states," optical pumping, coherent Raman scattering, and the stimulated Raman adiabatic passage (STIRAP) are revisited in the presence of metallic nanoparticles. It is shown that the dark states are still formed but they have more complicated structure, and the optical pumping and the STIRAP cannot be employed in the vicinity of plasmonic nanostructures. Also, there is a huge difference in the behavior of the local atomic polarization and the atomic polarization averaged over an ensemble of atoms homogeneously spread near nanoparticles. The average polarization is strictly related to the polarization induced by the external field, while the local polarization can be very different from the one induced by the external field. This is important for the excitation of single molecules, e.g., different components of scattering from single molecules can be used for their efficient detection.

Disparate ultrafast dynamics of itinerant and localized magnetic moments in gadolinium metal

PubMed Central

Frietsch, B.; Bowlan, J.; Carley, R.; Teichmann, M.; Wienholdt, S.; Hinzke, D.; Nowak, U.; Carva, K.; Oppeneer, P. M.; Weinelt, M.

2015-01-01

The Heisenberg–Dirac intra-atomic exchange coupling is responsible for the formation of the atomic spin moment and thus the strongest interaction in magnetism. Therefore, it is generally assumed that intra-atomic exchange leads to a quasi-instantaneous aligning process in the magnetic moment dynamics of spins in separate, on-site atomic orbitals. Following ultrashort optical excitation of gadolinium metal, we concurrently record in photoemission the 4f magnetic linear dichroism and 5d exchange splitting. Their dynamics differ by one order of magnitude, with decay constants of 14 versus 0.8 ps, respectively. Spin dynamics simulations based on an orbital-resolved Heisenberg Hamiltonian combined with first-principles calculations explain the particular dynamics of 5d and 4f spin moments well, and corroborate that the 5d exchange splitting traces closely the 5d spin-moment dynamics. Thus gadolinium shows disparate dynamics of the localized 4f and the itinerant 5d spin moments, demonstrating a breakdown of their intra-atomic exchange alignment on a picosecond timescale. PMID:26355196

Environmental Impact Specification for Direct Space Weathering of Kuiper Belt and Oort Cloud Objects

NASA Technical Reports Server (NTRS)

Cooper, John F.

2010-01-01

The Direct Space Weathering Project of NASA's Outer Planets Research Program addresses specification of the plasma and energetic particle environments for irradiation and surface chemical processing of icy bodies in the outer solar system and the local interstellar medium. Knowledge of the radiation environments is being expanded by ongoing penetration of the twin Voyager spacecraft into the heliosheath boundary region of the outer heliosphere and expected emergence within the next decade into the very local interstellar medium. The Voyager measurements are being supplemented by remote sensing from Earth orbit of energetic neutral atom emission from this boundary region by NASA's Interstellar Boundary Explorer (IBEX). Although the Voyagers long ago passed the region of the Classical Kuiper Belt, the New Horizons spacecraft will encounter Pluto in 2015 and thereafter explore one or more KBOs, meanwhile providing updated measurements of the heliospheric radiation environment in this region. Modeling of ion transport within the heliosphere allows specification of time-integrated irradiation effects while the combination of Voyager and IBEX data supports projection of the in-situ measurements into interstellar space beyond the heliosheath. Transformation of model ion flux distributions into surface sputtering and volume ionization profiles provides a multi-layer perspective for space weathering impact on the affected icy bodies and may account for some aspects of color and compositional diversity. Other important related factors may include surface erosion and gardening by meteoritic impacts and surface renewal by cryovolcanism. Chemical products of space weathering may contribute to energy resources for the latter.

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

Kaurov, Alexander A., E-mail: kaurov@uchicago.edu

We explore a time-dependent energy dissipation of the energetic electrons in the inhomogeneous intergalactic medium (IGM) during the epoch of cosmic reionization. In addition to the atomic processes, we take into account the inverse Compton (IC) scattering of the electrons on the cosmic microwave background photons, which is the dominant channel of energy loss for electrons with energies above a few MeV. We show that: (1) the effect on the IGM has both local (atomic processes) and non-local (IC radiation) components; (2) the energy distribution between hydrogen and helium ionizations depends on the initial energy of an electron; (3) themore » local baryon overdensity significantly affects the fractions of energy distributed in each channel; and (4) the relativistic effect of the atomic cross-section becomes important during the epoch of cosmic reionization. We release our code as open source for further modification by the community.« less

Advanced concentration analysis of atom probe tomography data: Local proximity histograms and pseudo-2D concentration maps.

PubMed

Felfer, Peter; Cairney, Julie

2018-06-01

Analysing the distribution of selected chemical elements with respect to interfaces is one of the most common tasks in data mining in atom probe tomography. This can be represented by 1D concentration profiles, 2D concentration maps or proximity histograms, which represent concentration, density etc. of selected species as a function of the distance from a reference surface/interface. These are some of the most useful tools for the analysis of solute distributions in atom probe data. In this paper, we present extensions to the proximity histogram in the form of 'local' proximity histograms, calculated for selected parts of a surface, and pseudo-2D concentration maps, which are 2D concentration maps calculated on non-flat surfaces. This way, local concentration changes at interfaces or and other structures can be assessed more effectively. Copyright © 2018 Elsevier B.V. All rights reserved.

Achieving DFT accuracy with a machine-learning interatomic potential: Thermomechanics and defects in bcc ferromagnetic iron

NASA Astrophysics Data System (ADS)

Dragoni, Daniele; Daff, Thomas D.; Csányi, Gábor; Marzari, Nicola

2018-01-01

We show that the Gaussian Approximation Potential (GAP) machine-learning framework can describe complex magnetic potential energy surfaces, taking ferromagnetic iron as a paradigmatic challenging case. The training database includes total energies, forces, and stresses obtained from density-functional theory in the generalized-gradient approximation, and comprises approximately 150,000 local atomic environments, ranging from pristine and defected bulk configurations to surfaces and generalized stacking faults with different crystallographic orientations. We find the structural, vibrational, and thermodynamic properties of the GAP model to be in excellent agreement with those obtained directly from first-principles electronic-structure calculations. There is good transferability to quantities, such as Peierls energy barriers, which are determined to a large extent by atomic configurations that were not part of the training set. We observe the benefit and the need of using highly converged electronic-structure calculations to sample a target potential energy surface. The end result is a systematically improvable potential that can achieve the same accuracy of density-functional theory calculations, but at a fraction of the computational cost.

Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation.

PubMed

Sharma, Anirban; Ghorai, Pradip Kr

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

Effect of water on structure and dynamics of [BMIM][PF{sub 6}] ionic liquid: An all-atom molecular dynamics simulation investigation

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

Sharma, Anirban; Ghorai, Pradip Kr., E-mail: pradip@iiserkol.ac.in

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF{sub 6}]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure ILmore » but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.« less

The influence of water on the nanomechanical behavior of the plant biopolyester cutin as studied by AFM and solid-state NMR.

PubMed

Round, A N; Yan, B; Dang, S; Estephan, R; Stark, R E; Batteas, J D

2000-11-01

Atomic force microscopy and solid-state nuclear magnetic resonance have been used to investigate the effect of water absorption on the nanoscale elastic properties of the biopolyester, cutin, isolated from tomato fruit cuticle. Changes in the humidity and temperature at which fruits are grown or stored can affect the plant surface (cuticle) and modify its susceptibility to pathogenic attack by altering the cuticle's rheological properties. In this work, atomic force microscopy measurements of the surface mechanical properties of isolated plant cutin have been made as a first step to probing the impact of water uptake from the environment on surface flexibility. A dramatic decrease in surface elastic modulus (from approximately 32 to approximately 6 MPa) accompanies increases in water content as small as 2 wt %. Complementary solid-state nuclear magnetic resonance measurements reveal enhanced local mobility of the acyl chain segments with increasing water content, even at molecular sites remote from the covalent cross-links that are likely to play a crucial role in cutin's elastic properties.

125Te NMR Probes of Tellurium Oxide Crystals: Shielding-Structure Correlations.

PubMed

Garaga, Mounesha N; Werner-Zwanziger, Ulrike; Zwanziger, Josef W

2018-01-16

The local environments around tellurium atoms in a series of tellurium oxide crystals were probed by 125 Te solid-state NMR spectroscopy. Crystals with distinct TeO n units (n from 3 to 6), including Na 2 TeO 3 , α-TeO 2 and γ-TeO 2 , Te 2 O(PO 4 ) 2 , K 3 LaTe 2 O 9 , BaZnTe 2 O 7 , and CsYTe 3 O 8 were studied. The latter four were synthesized through a solid-state process. X-ray diffraction was used to confirm the successful syntheses. The 125 Te chemical shift was found to exhibit a strong linear correlation with the Te coordination number. The 125 Te chemical-shift components (δ 11 , δ 22 , and δ 33 ) of the TeO 4 units were further correlated to the O-Te-O-bond angles. With the aid of 125 Te NMR, it is likely that these relations can be used to estimate the coordination states of Te atoms in unknown Te crystals and glasses.

Tuning the Curie temperature of L1{sub 0} ordered FePt thin films through site-specific substitution of Rh

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

Xu, Dongbin, E-mail: dongbin.xu@seagate.com; Department of Materials Science and Engineering, National University of Singapore, Singapore 117576; Sun, Cheng-Jun, E-mail: cjsun@aps.anl.gov, E-mail: msecgm@nus.edu.sg

2014-10-14

In structurally ordered magnetic thin films, the Curie temperature (T{sub C}) of ferromagnetic films depends on the exchange integral of the short range ordered neighboring atoms. The exchange integral may be adjusted by controlling the elemental substitutional concentration at the lattice site of interest. We show how to control the T{sub C} in high anisotropy L1{sub 0} Fe{sub 50}Pt{sub 50} magnetic thin films by substituting Rh into the Pt site. Rh substitution in L1{sub 0} FePt modified the local atomic environment and the corresponding electronic properties, while retaining the ordered L1{sub 0} phase. The analysis of extended x-ray Absorption Finemore » Structure spectra shows that Rh uniformly substitutes for Pt in L1{sub 0} FePt. A model of antiferromagnetic defects caused by controlled Rh substitution of the Pt site, reducing the T{sub C,} is proposed to interpret this phenomenon and its validity is further examined by ab initio density functional calculations.« less

XAS and XMCD studies of magnetic properties modifications of Pt/Co/Au and Pt/Co/Pt trilayers induced by Ga⁺ ions irradiation.

PubMed

Mazalski, Piotr; Sveklo, Iosif; Kurant, Zbigniew; Ollefs, Katharina; Rogalev, Andrei; Wilhelm, Fabrice; Fassbender, Juergen; Baczewski, Lech Tomasz; Wawro, Andrzej; Maziewski, Andrzej

2015-05-01

Magnetic and magneto-optical properties of Pt/Co/Au and Pt/Co/Pt trilayers subjected to 30 keV Ga(+) ion irradiation are compared. In two-dimensional maps of these properties as a function of cobalt thickness and ion fluence, two branches with perpendicular magnetic anisotropy (PMA) for Pt/Co/Pt trilayers are well distinguished. The replacement of the Pt capping layer with Au results in the two branches still being visible but the in-plane anisotropy for the low-fluence branch is suppressed whereas the high-fluence branch displays PMA. The X-ray absorption spectra and X-ray magnetic circular dichroism (XMCD) spectra are discussed and compared with non-irradiated reference samples. The changes of their shapes and peak amplitude, particularly for the high-fluence branch, are related to the modifications of the local environment of Co(Pt) atoms and the etching effects induced by ion irradiation. Additionally, in irradiated trilayers the XMCD measurements at the Pt L2,3-edge reveal an increase of the magnetic moment induced in Pt atoms.

Electric-field-induced local and mesoscale structural changes in polycrystalline dielectrics and ferroelectrics

DOE PAGES

Usher, Tedi -Marie; Levin, Igor; Daniels, John E.; ...

2015-10-01

In this study, the atomic-scale response of dielectrics/ferroelectrics to electric fields is central to their functionality. Here we introduce an in situ characterization method that reveals changes in the local atomic structure in polycrystalline materials under fields. The method employs atomic pair distribution functions (PDFs), determined from X-ray total scattering that depends on orientation relative to the applied field, to probe structural changes over length scales from sub-Ångstrom to several nanometres. The PDF is sensitive to local ionic displacements and their short-range order, a key uniqueness relative to other techniques. The method is applied to representative ferroelectrics, BaTiO 3 andmore » Na ½Bi ½TiO 3, and dielectric SrTiO 3. For Na ½Bi ½TiO 3, the results reveal an abrupt field-induced monoclinic to rhombohedral phase transition, accompanied by ordering of the local Bi displacements and reorientation of the nanoscale ferroelectric domains. For BaTiO 3 and SrTiO 3, the local/nanoscale structural changes observed in the PDFs are dominated by piezoelectric lattice strain and ionic polarizability, respectively.« less

Electronic structure, bonding, charge distribution, and x-ray absorption spectra of the (001) surfaces of fluorapatite and hydroxyapatite from first principles

NASA Astrophysics Data System (ADS)

Rulis, Paul; Yao, Hongzhi; Ouyang, Lizhi; Ching, W. Y.

2007-12-01

Fluorapatite (FAP) and hydroxyapatite (HAP) are two very important bioceramic crystals. The (001) surfaces of FAP and HAP crystals are studied by ab initio density functional calculations using a supercell slab geometry. It is shown that in both crystals, the O-terminated (001) surface is more stable with calculated surface energies of 0.865 and 0.871J/m2 for FAP and HAP, respectively. In FAP, the two surfaces are symmetric. In HAP, the orientation of the OH group along the c axis reduces the symmetry such that the top and bottom surfaces are no longer symmetric. It is revealed that the atoms near the surface and subsurface are significantly relaxed especially in the case of HAP. The largest relaxations occurred via the lateral movements of the O ions at the subsurface level. The electronic structures of the surface models in the form of layer-by-layer resolved partial density of states for all the atoms show systematic variation from the surface region toward the bulk region. The calculated Mulliken effective charge on each type of atom and the bond order values between cations (Ca, P) and anions (O, F) show different charge transfers and bond strength variations from the bulk crystal values. Electron charge density calculations show that the surfaces of both FAP and HAP crystals are mostly positively charged due to the presence of Ca ions at the surface. The positively charged surfaces have implications for the absorption on apatite surfaces of water and other organic molecules in an aqueous environment which are an important part of its bioactivity. The x-ray absorption near-edge structure (XANES) spectra ( Ca-K , O-K , F-K , P-K , and P-L3 edges) of both the surface models and the bulk crystals are calculated and compared. The calculations use a supercell approach which takes into account the electron-core-hole interaction. It is shown that the site-specific XANES spectra show significant differences between atoms near the surface and in the bulk and are very sensitive to the local atomic environment of each atom. This information will be very valuable for characterizing the apatite materials and in the interpretation of experimental data. Comparisons of several sets of experimental data with the weighted sums of the calculated spectra at different sites for the same element show very good agreement.

Traffic information computing platform for big data

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

Duan, Zongtao, E-mail: ztduan@chd.edu.cn; Li, Ying, E-mail: ztduan@chd.edu.cn; Zheng, Xibin, E-mail: ztduan@chd.edu.cn

Big data environment create data conditions for improving the quality of traffic information service. The target of this article is to construct a traffic information computing platform for big data environment. Through in-depth analysis the connotation and technology characteristics of big data and traffic information service, a distributed traffic atomic information computing platform architecture is proposed. Under the big data environment, this type of traffic atomic information computing architecture helps to guarantee the traffic safety and efficient operation, more intelligent and personalized traffic information service can be used for the traffic information users.

An array of correlated atom interferometers to study to study the local fluctuations of the gravitational field and its impact on low fequency gravitational waves observations

NASA Astrophysics Data System (ADS)

Bouyer, P.; Canuel, B.; Pelisson, S.; Harms, J.; Bertoldi, A.; Gaffet, S.; Landragin, A.; Lefevre, G.; Riou, I.; Geiger, R.

2016-12-01

We will present here the Matter-Wave laser Interferometer Gravitation Antenna, MIGA, a hybrid instrument composed of a network of atom interferometers horizontally aligned and interrogated by the resonant field of an optical cavity. This detector will provide measurements of sub Hertz variations of the gravitational strain tensor. MIGA will bring new methods for geophysics for the characterization of spatial and temporal variations of the local gravity field and will also be a demonstrator for future low frequency Gravitational Wave (GW) detections. The recent first direct observation of gravitational radiation opens the way towards a novel astronomy requires a new class of low frequency Gravitational Wave detectors such as MIGA. Nevertheless, the fluctuations of the Earth gravitational field over different baselines are of high relevance for the functioning of such experiments. Indeed, a fluctuating gravity gradient causes a tidal effect that cannot, in principle, be distinguished from Gravitational Waves.This so-called « Newtonian Noise » is therefore considered up to now as a fundamental limit for any ground based detector and the main reason for restricting future low frequency GW detectors to space. Nevertheless, these two contributions may become discernible by the use of a network of test masses. Indeed, both GW and NN effects will have different spatial signatures over the test mass network. While GW has extremely long characteristic length, NN has shorter characteristic lengths going from the meter to a few kilometers.The array of distant Atom Interferometers in MIGA can be used as network of test masses, which can be correlated using a common laser link. Differential measurements between the atom interferometers of the Network enables for a large reduction of the effect of NN and opens the way towards the realization of low frequency GW detectors.In this paper, we will detail the projection of background NN in the underground environment of the LSBB and present GW interferometer geometries enabling its reduction.

Remote preparation of an atomic quantum memory.

PubMed

Rosenfeld, Wenjamin; Berner, Stefan; Volz, Jürgen; Weber, Markus; Weinfurter, Harald

2007-02-02

Storage and distribution of quantum information are key elements of quantum information processing and future quantum communication networks. Here, using atom-photon entanglement as the main physical resource, we experimentally demonstrate the preparation of a distant atomic quantum memory. Applying a quantum teleportation protocol on a locally prepared state of a photonic qubit, we realized this so-called remote state preparation on a single, optically trapped 87Rb atom. We evaluated the performance of this scheme by the full tomography of the prepared atomic state, reaching an average fidelity of 82%.

Evaluating excited state atomic polarizabilities of chromophores† †Electronic supplementary information (ESI) available: Basis set dependence, definition of bond charges, Romberg differentiation, python script to calculate atomic polarizabilities, influence of the cavity radius, atomic polarizabilities of coumarin 153, all tables in atomic units. See DOI: 10.1039/c7cp08549d

PubMed Central

Heid, Esther

2018-01-01

Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered. PMID:29542743

Detecting many-body-localization lengths with cold atoms

NASA Astrophysics Data System (ADS)

Guo, Xuefei; Li, Xiaopeng

2018-03-01

Considering ultracold atoms in optical lattices, we propose experimental protocols to study many-body-localization (MBL) length and criticality in quench dynamics. Through numerical simulations with exact diagonalization, we show that in the MBL phase the perturbed density profile following a local quench remains exponentially localized in postquench dynamics. The size of this density profile after long-time-dynamics defines a localization length, which tends to diverge at the MBL-to-ergodic transition as we increase the system size. The determined localization transition point agrees with previous exact diagonalization calculations using other diagnostics. Our numerical results provide evidence for violation of the Harris-Chayes bound for the MBL criticality. The critical exponent ν can be extracted from our proposed dynamical procedure, which can then be used directly in experiments to determine whether the Harris-Chayes-bound holds for the MBL transition. These proposed protocols to detect localization criticality are justified by benchmarking to the well-established results for the noninteracting three-dimensional Anderson localization.

Identification of F impurities in F-doped ZnO by synchrotron X-ray absorption near edge structures

NASA Astrophysics Data System (ADS)

Na-Phattalung, Sutassana; Limpijumnong, Sukit; Min, Chul-Hee; Cho, Deok-Yong; Lee, Seung-Ran; Char, Kookrin; Yu, Jaejun

2018-04-01

Synchrotron X-ray absorption near edge structure (XANES) measurements of F K-edge in conjunction with first-principles calculations are used to identify the local structure of the fluorine (F) atom in F-doped ZnO. The ZnO film was grown by pulsed laser deposition with an Nd:YAG laser, and an oxyfluoridation method was used to introduce F ions into the ZnO films. The measured XANES spectrum of the sample was compared against the first-principles XANES calculations based on various models for local atomic structures surrounding F atoms. The observed spectral features are attributed to ZnF2 and FO defects in wurtzite bulk ZnO.

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

NASA Astrophysics Data System (ADS)

Reinhardt, Aleks; Doye, Jonathan P. K.; Noya, Eva G.; Vega, Carlos

2012-11-01

We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

Atomic research

NASA Technical Reports Server (NTRS)

Hadaway, James B.; Connatser, Robert; Cothren, Bobby; Johnson, R. B.

1993-01-01

Work performed by the University of Alabama in Huntsville's (UAH) Center for Applied Optics (CAO) entitled Atomic Research is documented. Atomic oxygen (AO) effects on materials have long been a critical concern in designing spacecraft to withstand exposure to the Low Earth Orbit (LEO) environment. The objective of this research effort was to provide technical expertise in the design of instrumentation and experimental techniques for analyzing materials exposed to atomic oxygen in accelerated testing at NASA/MSFC. Such testing was required to answer fundamental questions concerning Space Station Freedom (SSF) candidate materials and materials exposed to atomic oxygen aboard the Long-Duration Exposure Facility (LDEF). The primary UAH task was to provide technical design, review, and analysis to MSFC in the development of a state-of-the-art 5eV atomic oxygen beam facility required to simulate the RAM-induced low earth orbit (LEO) AO environment. This development was to be accomplished primarily at NASA/MSFC. In support of this task, contamination effects and ultraviolet (UV) simulation testing was also to be carried out using NASA/MSFC facilities. Any materials analysis of LDEF samples was to be accomplished at UAH.

Neutral atom imaging at Mercury

NASA Astrophysics Data System (ADS)

Mura, A.; Orsini, S.; Milillo, A.; Di Lellis, A. M.; De Angelis, E.

2006-02-01

The feasibility of neutral atom detection and imaging in the Hermean environment is discussed in this study. In particular, we consider those energetic neutral atoms (ENA) whose emission is directly related to solar wind entrance into Mercury's magnetosphere. In fact, this environment is characterised by a weak magnetic field; thus, cusp regions are extremely large if compared to the Earth's ones, and intense proton fluxes are expected there. Our study includes a model of H + distribution in space, energy and pitch angle, simulated by means of a single-particle, Monte-Carlo simulation. Among processes that could generate neutral atom emission, we focus our attention on charge-exchange and ion sputtering, which, in principle, are able to produce directional ENA fluxes. Simulated neutral atom images are investigated in the frame of the neutral particle analyser-ion spectrometer (NPA-IS) SERENA experiment, proposed to fly on board the ESA mission BepiColombo/MPO. The ELENA (emitted low-energy neutral atoms) unit, which is part of this experiment, will be able to detect such fluxes; instrumental details and predicted count rates are given.

Local atomic structure inheritance in Ag{sub 50}Sn{sub 50} melt

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

Bai, Yanwen; Bian, Xiufang, E-mail: xfbian@sdu.edu.cn; Qin, Jingyu

2014-01-28

Local structure inheritance signatures were observed during the alloying process of the Ag{sub 50}Sn{sub 50} melt, using high-temperature X-ray diffraction and ab initio molecular dynamics simulations. The coordination number N{sub m} around Ag atom is similar in the alloy and in pure Ag melts (N{sub m} ∼ 10), while, during the alloying process, the local structure around Sn atoms rearranges. Sn-Sn covalent bonds were substituted by Ag-Sn chemical bonds, and the total coordination number around Sn increases by about 70% as compared with those in the pure Sn melt. Changes in the electronic structure of the alloy have been studied by Agmore » and Sn K-edge X-ray absorption spectroscopy, as well as by calculations of the partial density of states. We propose that a leading mechanism for local structure inheritance in Ag{sub 50}Sn{sub 50} is due to s-p dehybridization of Sn and to the interplay between Sn-s and Ag-d electrons.« less

Prediction of the electron redundant SinNn fullerenes

NASA Astrophysics Data System (ADS)

Yang, Huihui; Song, Yan; Zhang, Yan; Chen, Hongshan

2018-05-01

The stabilities and electronic structures of SimAln-mNn and SinNn (n = 16, 20, m = 12 and n = 24, m = 16) fullerene-like cages have been investigated using density functional method B3LYP and the second-order perturbation theory MP2. The results show that the SimAln-mNn and SinNn fullerenes are more stable than the AlN counterparts. Comparing with the corresponding AlnNn cages, one silicon atom in each Si2N2 square protrudes and the excess electrons reside as lone pair electrons at the outside of the protrudent Si atoms. Analyses on the electronic structures suggest that the Sisbnd N bonds are covalent bonding with strong polarity. The ELF (electron localization function) shows large electron pair probability between Si and N atoms. The orbital interactions between Si and N are stronger than that between Al and N atoms; the overlap integral is 0.40 per Sisbnd N bond in SinNn and 0.34 per Alsbnd N bond in AlnNn. The AIM (atoms in molecule) charges on the Al atoms in AlnNn and SimAln-mNn are 2.37 and 2.40. The charges on the in-plane and protrudent Si atoms are about 2.88 and 1.50 respectively. Considering the large local dipole moments around the protrudent Si atoms, the electrostatic interactions are also favorable to the SiN cages.

Atom-atom interactions around the band edge of a photonic crystal waveguide.

PubMed

Hood, Jonathan D; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E; Kimble, H J

2016-09-20

Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

Local order study of YFe 2D x (0⩽ x⩽3.5) compounds by X-ray absorption and Mössbauer spectroscopy

NASA Astrophysics Data System (ADS)

Paul-Boncour, V.; Wiesinger, G.; Reichl, Ch.; Latroche, M.; Percheron-Guégan, A.; Cortes, R.

2001-12-01

The local order in YFe 2D x deuterides has been characterized by EXAFS and 57Fe Mössbauer spectroscopy. For all the deuterides several Fe sites and a large distribution of Fe-Fe distances are observed. The Y-Fe and Y-Y distances are close to those calculated for a cubic C15 type structure, but with significant static disorder. These large distance distributions are related to the influence of hydrogen atoms which induce local distortions of the interstitial sites with a displacement of Y and Fe atoms. However, the bulk and mean local magnetic properties remain sensitive to the long range order structure of the deuterides.

High temperature extended x-ray absorption fine structure study of multiferroic BiFeO3

NASA Astrophysics Data System (ADS)

Raghavendra Reddy, V.; Meneghini, Carlo; Kothari, Deepti; Gupta, Ajay; Aquilanti, Giuliana

2012-08-01

Local atomic structure modifications around Fe atoms in polycrystalline multiferroic BiFeO3 are studied by Fe K edge x-ray absorption spectroscopy as a function of temperature across the Néel temperature (TN = 643 K) in order to reveal local structure modifications related to the magnetic transition. This work demonstrates that on crossing TN the local structure around Fe shows peculiar changes: the Fe-O bond lengths get shorter, the ligand symmetry increases and the Fe-O bond length disorder (σ2) deviates from Debye behaviour. These results suggest that the structural transition at the ferroelectric Curie temperature (TC = 1103 K) is anticipated by early local rearrangement of the structure starting already at TN.

Evaluating excited state atomic polarizabilities of chromophores.

PubMed

Heid, Esther; Hunt, Patricia A; Schröder, Christian

2018-03-28

Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered.

Localized spatially nonlinear matter waves in atomic-molecular Bose-Einstein condensates with space-modulated nonlinearity

PubMed Central

Yao, Yu-Qin; Li, Ji; Han, Wei; Wang, Deng-Shan; Liu, Wu-Ming

2016-01-01

The intrinsic nonlinearity is the most remarkable characteristic of the Bose-Einstein condensates (BECs) systems. Many studies have been done on atomic BECs with time- and space- modulated nonlinearities, while there is few work considering the atomic-molecular BECs with space-modulated nonlinearities. Here, we obtain two kinds of Jacobi elliptic solutions and a family of rational solutions of the atomic-molecular BECs with trapping potential and space-modulated nonlinearity and consider the effect of three-body interaction on the localized matter wave solutions. The topological properties of the localized nonlinear matter wave for no coupling are analysed: the parity of nonlinear matter wave functions depends only on the principal quantum number n, and the numbers of the density packets for each quantum state depend on both the principal quantum number n and the secondary quantum number l. When the coupling is not zero, the localized nonlinear matter waves given by the rational function, their topological properties are independent of the principal quantum number n, only depend on the secondary quantum number l. The Raman detuning and the chemical potential can change the number and the shape of the density packets. The stability of the Jacobi elliptic solutions depends on the principal quantum number n, while the stability of the rational solutions depends on the chemical potential and Raman detuning. PMID:27403634

Frequency modulation detection atomic force microscopy in the liquid environment

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Ishida, T.; Uchihashi, T.; Nakayama, Y.; Tokumoto, H.

True atomic resolution imaging using frequency modulation detection is already well established in ultra-high vacuum. In this paper we demonstrate that it also has great potential in the liquid environment. Using a combination of magnetic activation and high-aspect-ratio carbon nanotube probes, we show that imaging can be readily combined with point spectroscopy, revealing both the tip-sample interaction and the structure of the intermediate liquid.

Effectiveness of Modal Decomposition for Tapping Atomic Force Microscopy Microcantilevers in Liquid Environment.

PubMed

Kim, Il Kwang; Lee, Soo Il

2016-05-01

The modal decomposition of tapping mode atomic force microscopy microcantilevers in liquid environments was studied experimentally. Microcantilevers with different lengths and stiffnesses and two sample surfaces with different elastic moduli were used in the experiment. The response modes of the microcantilevers were extracted as proper orthogonal modes through proper orthogonal decomposition. Smooth orthogonal decomposition was used to estimate the resonance frequency directly. The effects of the tapping setpoint and the elastic modulus of the sample under test were examined in terms of their multi-mode responses with proper orthogonal modes, proper orthogonal values, smooth orthogonal modes and smooth orthogonal values. Regardless of the stiffness of the microcantilever under test, the first mode was dominant in tapping mode atomic force microscopy under normal operating conditions. However, at lower tapping setpoints, the flexible microcantilever showed modal distortion and noise near the tip when tapping on a hard sample. The stiff microcantilever had a higher mode effect on a soft sample at lower tapping setpoints. Modal decomposition for tapping mode atomic force microscopy can thus be used to estimate the characteristics of samples in liquid environments.

X-Ray photoelectron diffraction and photoelectron holography as methods for investigating the local atomic structure of the surface of solids

NASA Astrophysics Data System (ADS)

Kuznetsov, M. V.; Ogorodnikov, I. I.; Vorokh, A. S.

2014-01-01

The state-of-the-art theory and experimental applications of X-ray photoelectron diffraction (XPD) and photoelectron holography (PH) are discussed. These methods are rapidly progressing and serve to examine the surface atomic structure of solids, including nanostructures formed on surfaces during adsorption of gases, epitaxial film growth, etc. The depth of analysis by these methods is several nanometres, which makes it possible to characterize the positions of atoms localized both on and beneath the surface. A remarkable feature of the XPD and PH methods is their sensitivity to the type of examined atoms and, in the case of high energy resolution, to the particular chemical form of the element under study. The data on experimental applications of XPD and PH to studies of various surface structures are analyzed and generalized. The bibliography includes 121 references.

How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.

PubMed

Cui, Peixin; Wang, Yu; Chu, Wangsheng; Guo, Xiaoyun; Yang, Feifei; Yu, Meijuan; Zhao, Haifeng; Dong, Yuhui; Xie, Yaning; Gong, Weimin; Wu, Ziyu

2014-12-12

Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.

Electrochemical de-alloying in two dimensions: role of the local atomic environment

NASA Astrophysics Data System (ADS)

Damian, A.; Maroun, F.; Allongue, P.

2016-07-01

We investigate by in situ scanning tunnelling microscopy (STM) the potential dependence of the electrochemical dealloying of NiPd monoatomic layers electrodeposited on Au(111). The dealloying process is achieved by Ni selective dissolution and was studied as a function of NiPd composition: for an alloy with a Ni content >=70%, quasi-complete Ni dissolution is achieved at a potential of -0.9 VMSE whereas for a Ni content <70%, Ni dissolution at the same potential drastically slows down after the removal of small amounts of Ni. The alloy morphology at this ``passivation state'' is characterized by the presence of holes in the alloy monolayer with evidence for the Pd enrichment at the hole edges. These findings are confirmed by Monte Carlo simulations. Further Ni dissolution at passivation was achieved by applying more positive potentials which depend on the alloy composition. These results allowed us to determine the correlation between the Ni dissolution onset potential and the local Pd content.

Evaluation of a locally homogeneous model of spray evaporation

NASA Technical Reports Server (NTRS)

Shearer, A. J.; Faeth, G. M.; Tamura, H.

1978-01-01

Measurements were conducted on an evaporating spray in a stagnant environment. The spray was formed using an air-atomizing injector to yield a Sauter mean diameter of the order of 30 microns. The region where evaporation occurred extended approximately 1 m from the injector for the test conditions. Profiles of mean velocity, temperature, composition, and drop size distribution, as well as velocity fluctuations and Reynolds stress, were measured. The results are compared with a locally homogeneous two-phase flow model which implies no velocity difference and thermodynamic equilibrium between the phases. The flow was represented by a k-epsilon-g turbulence model employing a clipped Gaussian probability density function for mixture fraction fluctuations. The model provides a good representation of earlier single-phase jet measurements, but generally overestimates the rate of development of the spray. Using the model predictions to represent conditions along the centerline of the spray, drop life-history calculations were conducted which indicate that these discrepancies are due to slip and loss of thermodynamic equilibrium between the phases.

Glasslike Membrane Protein Diffusion in a Crowded Membrane.

PubMed

Munguira, Ignacio; Casuso, Ignacio; Takahashi, Hirohide; Rico, Felix; Miyagi, Atsushi; Chami, Mohamed; Scheuring, Simon

2016-02-23

Many functions of the plasma membrane depend critically on its structure and dynamics. Observation of anomalous diffusion in vivo and in vitro using fluorescence microscopy and single particle tracking has advanced our concept of the membrane from a homogeneous fluid bilayer with freely diffusing proteins to a highly organized crowded and clustered mosaic of lipids and proteins. Unfortunately, anomalous diffusion could not be related to local molecular details given the lack of direct and unlabeled molecular observation capabilities. Here, we use high-speed atomic force microscopy and a novel analysis methodology to analyze the pore forming protein lysenin in a highly crowded environment and document coexistence of several diffusion regimes within one membrane. We show the formation of local glassy phases, where proteins are trapped in neighbor-formed cages for time scales up to 10 s, which had not been previously experimentally reported for biological membranes. Furthermore, around solid-like patches and immobile molecules a slower glass phase is detected leading to protein trapping and creating a perimeter of decreased membrane diffusion.

In-situ crystallization of GeTe\\GaSb phase change memory stacked films

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

Velea, A., E-mail: alin.velea@psi.ch; National Institute of Materials Physics, RO-077125 Magurele, Ilfov; Borca, C. N.

2014-12-21

Single and double layer phase change memory structures based on GeTe and GaSb thin films were deposited by pulsed laser deposition (PLD). Their crystallization behavior was studied using in-situ synchrotron techniques. Electrical resistance vs. temperature investigations, using the four points probe method, showed transition temperatures of 138 °C and 198 °C for GeTe and GaSb single films, respectively. It was found that after GeTe crystallization in the stacked films, Ga atoms from the GaSb layer diffused in the vacancies of the GeTe crystalline structure. Therefore, the crystallization temperature of the Sb-rich GaSb layer is decreased by more than 30 °C. Furthermore, at 210 °C,more » the antimony excess from GaSb films crystallizes as a secondary phase. At higher annealing temperatures, the crystalline Sb phase increased on the expense of GaSb crystalline phase which was reduced. Extended X-ray absorption fine structure (EXAFS) measurements at the Ga and Ge K-edges revealed changes in their local atomic environments as a function of the annealing temperature. Simulations unveil a tetrahedral configuration in the amorphous state and octahedral configuration in the crystalline state for Ge atoms, while Ga is four-fold coordinated in both as-deposited and annealed samples.« less

Nanoscale Charge-Balancing Mechanism in Alkali-Substituted Calcium-Silicate-Hydrate Gels.

PubMed

Özçelik, V Ongun; White, Claire E

2016-12-15

Alkali-activated materials and related alternative cementitious systems are sustainable technologies that have the potential to substantially lower the CO 2 emissions associated with the construction industry. However, these systems have augmented chemical compositions as compared to ordinary Portland cement (OPC), which may impact the evolution of the hydrate phases. In particular, calcium-silicate-hydrate (C-S-H) gel, the main hydrate phase in OPC, is likely to be altered at the atomic scale due to changes in the bulk chemical composition, specifically via the addition of alkalis (i.e., Na or K) and aluminum. Here, via density functional theory calculations, we reveal the presence of a charge balancing mechanism at the molecular level in C-S-H gel (as modeled using crystalline 14 Å tobermorite) when alkalis and aluminum atoms are introduced into the structure. Different structural representations are obtained depending on the level of substitution and the degree of charge balancing incorporated in the structures. The impact of these substitutional and charge balancing effects on the structures is assessed by analyzing the formation energies, local bonding environments, diffusion barriers and mechanical properties. The results of this computational study provide information on the phase stability of alkali/aluminum containing C-S-H gels, shedding light on the fundamental atomic level mechanisms that play a crucial role in these complex disordered materials.

Teleportation with insurance of an entangled atomic state via cavity decay

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

Chimczak, Grzegorz; Tanas, Ryszard; Miranowicz, Adam

2005-03-01

We propose a scheme to teleport an entangled state of two {lambda}-type three-level atoms via photons. The teleportation protocol involves the local redundant encoding protecting the initial entangled state and allowing for repeating the detection until quantum information transfer is successful. We also show how to manipulate a state of many {lambda}-type atoms trapped in a cavity.

Influence of attrition milling on nano-grain boundaries

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

Rawers, J.; Cook, D.

1999-03-01

Nanostructured materials have a relatively large proportion of their atoms associated with the grain boundary, and the method used to develop the nano-grains has a strong influence on the resulting grain boundary structure. In this study, attrition milling iron powders and blends of iron powders produced micron-size particles composed of nano-size grains. Mechanical cold-working powder resulted in dislocation generation, multiplication, and congealing that produced grain refinement. As the grain size approached nano-dimensions, dislocations were no longer sustained within the grain and once generated, rapidly diffused to the grain boundary. Dislocations on the grain boundary strained the local lattice structure which,more » as the grain size decreased, became the entire grain. Mechanical alloying of substitutional aluminium atoms into iron powder resulted in the aluminium atoms substituting for iron atoms in the grain boundary cells and providing a grain boundary structure similar to that of the iron powder processed in argon. Attrition milling iron powder in nitrogen gas resulted in nitrogen atoms being adsorbed onto the particle surface. Continued mechanical milling infused the nitrogen atoms into interstitial lattice sites on the grain boundary which also contributed to expanding and straining the local lattice.« less

Atomic scale chemical tomography of human bone

NASA Astrophysics Data System (ADS)

Langelier, Brian; Wang, Xiaoyue; Grandfield, Kathryn

2017-01-01

Human bone is a complex hierarchical material. Understanding bone structure and its corresponding composition at the nanometer scale is critical for elucidating mechanisms of biomineralization under healthy and pathological states. However, the three-dimensional structure and chemical nature of bone remains largely unexplored at the nanometer scale due to the challenges associated with characterizing both the structural and chemical integrity of bone simultaneously. Here, we use correlative transmission electron microscopy and atom probe tomography for the first time, to our knowledge, to reveal structures in human bone at the atomic level. This approach provides an overlaying chemical map of the organic and inorganic constituents of bone on its structure. This first use of atom probe tomography on human bone reveals local gradients, trace element detection of Mg, and the co-localization of Na with the inorganic-organic interface of bone mineral and collagen fibrils, suggesting the important role of Na-rich organics in the structural connection between mineral and collagen. Our findings provide the first insights into the hierarchical organization and chemical heterogeneity in human bone in three-dimensions at its smallest length scale - the atomic level. We demonstrate that atom probe tomography shows potential for new insights in biomineralization research on bone.

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

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE PAGES

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

2015-09-03

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

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

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Scanning tunneling microscopy current from localized basis orbital density functional theory

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Paulsson, Magnus

2016-03-01

We present a method capable of calculating elastic scanning tunneling microscopy (STM) currents from localized atomic orbital density functional theory (DFT). To overcome the poor accuracy of the localized orbital description of the wave functions far away from the atoms, we propagate the wave functions, using the total DFT potential. From the propagated wave functions, the Bardeen's perturbative approach provides the tunneling current. To illustrate the method we investigate carbon monoxide adsorbed on a Cu(111) surface and recover the depression/protrusion observed experimentally with normal/CO-functionalized STM tips. The theory furthermore allows us to discuss the significance of s - and p -wave tips.

Ion energies in high power impulse magnetron sputtering with and without localized ionization zones

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

Yang, Yuchen; Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720; Tanaka, Koichi

2015-03-23

High speed imaging of high power impulse magnetron sputtering discharges has revealed that ionization is localized in moving ionization zones but localization disappears at high currents for high yield targets. This offers an opportunity to study the effect ionization zones have on ion energies. We measure that ions have generally higher energies when ionization zones are present, supporting the concept that these zones are associated with moving potential humps. We propose that the disappearance of ionization zones is caused by an increased supply of atoms from the target which cools electrons and reduces depletion of atoms to be ionized.

Localization in momentum space of ultracold atoms in incommensurate lattices

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

Larcher, M.; Dalfovo, F.; Modugno, M.

2011-01-15

We characterize the disorder-induced localization in momentum space for ultracold atoms in one-dimensional incommensurate lattices, according to the dual Aubry-Andre model. For low disorder the system is localized in momentum space, and the momentum distribution exhibits time-periodic oscillations of the relative intensity of its components. The behavior of these oscillations is explained by means of a simple three-mode approximation. We predict their frequency and visibility by using typical parameters of feasible experiments. Above the transition the system diffuses in momentum space, and the oscillations vanish when averaged over different realizations, offering a clear signature of the transition.

The Star Formation Rate Efficiency of Neutral Atomic-Dominated Hydrogen Gas in the Ooutskirts of Star-Forming Galaxies From z approx. 1 to z approx. 3

NASA Technical Reports Server (NTRS)

Rafelski, Marc; Gardner, Jonathan P.; Fumagalli, Michele; Neeleman, Marcel; Teplitz, Harry I.; Grogin, Norman; Koekemoer, Anton M.; Scarlata, Claudia

2016-01-01

Current observational evidence suggests that the star formation rate (SFR)efficiency of neutral atomic hydrogen gas measured in damped Ly(alpha) systems (DLAs) at z approx. 3 is more than 10 times lower than predicted by the Kennicutt-Schmidt (KS)relation. To understand the origin of this deficit, and to investigate possible evolution with redshift and galaxy properties, we measure the SFR efficiency of atomic gas at z approx. 1, z approx. 2, and z approx. 3 around star-forming galaxies. We use new robust photometric redshifts in the Hubble Ultra Deep Field to create galaxy stacks in these three redshift bins, and measure the SFR efficiency by combining DLA absorber statistics with the observed rest-frame UV emission in the galaxies' outskirts. We find that the SFR efficiency of H I gas at z > 1 is approx. 1%-3% of that predicted by the KS relation. Contrary to simulations and models that predict a reduced SFR efficiency with decreasing metallicity and thus with increasing redshift, we find no significant evolution in the SFR efficiency with redshift. Our analysis instead suggests that the reduced SFR efficiency is driven by the low molecular content of this atomic-dominated phase, with metallicity playing a secondary effect in regulating the conversion between atomic and molecular gas. This interpretation is supported by the similarity between the observed SFR efficiency and that observed in local atomic-dominated gas, such as in the outskirts of local spiral galaxies and local dwarf galaxies.

O-atom degradation mechanisms of materials

NASA Technical Reports Server (NTRS)

Coulter, Daniel R.; Liang, Ranty H.; Chung, Shirley Y.; Smith, Keri Oda; Gupta, Amitava

1987-01-01

The low Earth orbit environment is described and the critical issues relating to oxygen atom degradation are discussed. Some analytic techniques for studying the problem and preliminary results on the underlying degradation mechanisms are presented.

The Development of Directional Decohesion Finite Elements for Multiscale Failure Analysis of Metallic Polycrystals

NASA Technical Reports Server (NTRS)

Saether, Erik; Glaessgen, Edward H.

2009-01-01

Atomistic simulations of intergranular fracture have indicated that grain-scale crack growth in polycrystalline metals can be direction dependent. At these material length scales, the atomic environment greatly influences the nature of intergranular crack propagation, through either brittle or ductile mechanisms, that are a function of adjacent grain orientation and direction of crack propagation. Methods have been developed to obtain cohesive zone models (CZM) directly from molecular dynamics simulations. These CZMs may be incorporated into decohesion finite element formulations to simulate fracture at larger length scales. A new directional decohesion element is presented that calculates the direction of Mode I opening and incorporates a material criterion for dislocation emission based on the local crystallographic environment to automatically select the CZM that best represents crack growth. The simulation of fracture in 2-D and 3-D aluminum polycrystals is used to illustrate the effect of parameterized CZMs and the effectiveness of directional decohesion finite elements.

Curved-line search algorithm for ab initio atomic structure relaxation

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

2017-09-01

Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

Adsorption of O_{2} on Ag(111): Evidence of Local Oxide Formation.

PubMed

Andryushechkin, B V; Shevlyuga, V M; Pavlova, T V; Zhidomirov, G M; Eltsov, K N

2016-07-29

The atomic structure of the disordered phase formed by oxygen on Ag(111) at low coverage is determined by a combination of low-temperature scanning tunneling microscopy and density functional theory. We demonstrate that the previous assignment of the dark objects in STM to chemisorbed oxygen atoms is incorrect and incompatible with trefoil-like structures observed in atomic-resolution images in current work. In our model, each object is an oxidelike ring formed by six oxygen atoms around the vacancy in Ag(111).

Control of single-spin magnetic anisotropy by exchange coupling

NASA Astrophysics Data System (ADS)

Oberg, Jenny C.; Calvo, M. Reyes; Delgado, Fernando; Moro-Lagares, María; Serrate, David; Jacob, David; Fernández-Rossier, Joaquín; Hirjibehedin, Cyrus F.

2014-01-01

The properties of quantum systems interacting with their environment, commonly called open quantum systems, can be affected strongly by this interaction. Although this can lead to unwanted consequences, such as causing decoherence in qubits used for quantum computation, it can also be exploited as a probe of the environment. For example, magnetic resonance imaging is based on the dependence of the spin relaxation times of protons in water molecules in a host's tissue. Here we show that the excitation energy of a single spin, which is determined by magnetocrystalline anisotropy and controls its stability and suitability for use in magnetic data-storage devices, can be modified by varying the exchange coupling of the spin to a nearby conductive electrode. Using scanning tunnelling microscopy and spectroscopy, we observe variations up to a factor of two of the spin excitation energies of individual atoms as the strength of the spin's coupling to the surrounding electronic bath changes. These observations, combined with calculations, show that exchange coupling can strongly modify the magnetic anisotropy. This system is thus one of the few open quantum systems in which the energy levels, and not just the excited-state lifetimes, can be renormalized controllably. Furthermore, we demonstrate that the magnetocrystalline anisotropy, a property normally determined by the local structure around a spin, can be tuned electronically. These effects may play a significant role in the development of spintronic devices in which an individual magnetic atom or molecule is coupled to conducting leads.

Roman coloured and opaque glass: a chemical and spectroscopic study

NASA Astrophysics Data System (ADS)

Arletti, R.; Dalconi, M. C.; Quartieri, S.; Triscari, M.; Vezzalini, G.

2006-05-01

This work reports the results of an archaeometrical investigation of opaque Roman glass and is mainly focussed on the role of configuration and oxidation state of copper on the colour and opacity of red and green opaque finds (mosaic tesserae, game counters, and glass artefacts) from Sicily and Pompeii excavations. The glass fragments were characterised by EMPA, SEM-EDS, TEM, and XRPD analyses and the copper local environment was investigated using X-ray absorption spectroscopy. The analyses of high-resolution Cu-K edge XANES and EXAFS spectra suggest that, in red samples, copper is present as monovalent cations coordinated to the oxygen atoms of the glass framework, accompanied by metallic clusters. In green samples all the copper cations are incorporated in the glass matrix.

Using polarized muons as ultrasensitive spin labels in free radical chemistry

NASA Astrophysics Data System (ADS)

McKenzie, Iain; Roduner, Emil

2009-08-01

In a chemical sense, the positive muon is a light proton. It is obtained at the ports of accelerators in beams with a spin polarization of 100%, which makes it a highly sensitive probe of matter. The muonium atom is a light hydrogen isotope, nine times lighter than H, with a muon as its nucleus. It reacts the same way as H, and by addition to double bonds it is implemented in free radicals in which the muon serves as a fully polarized spin label. It is reviewed here how the muon can be used to obtain information about muonium and radical reaction rates, radical structure, dynamics, and local environments. It can even tell us what a fragrance molecule does in a shampoo.

Soft X-ray spectroscopy of transition metal compounds: a theoretical perspective

NASA Astrophysics Data System (ADS)

Bokarev, S. I.; Hilal, R.; Aziz, S. G.; Kühn, O.

2017-01-01

To date, X-ray spectroscopy has become a routine tool that can reveal highly local and element-specific information on the electronic structure of atoms in complex environments. Here, we report on the development of an efficient and versatile theoretical methodology for the treatment of soft X-ray spectra of transition metal compounds based on the multi-configurational self-consistent field electronic structure theory. A special focus is put on the L-edge photon-in/photon-out and photon-in/electron-out processes, i.e. X-ray absorption, resonant inelastic scattering, partial fluorescence yield, and photoelectron spectroscopy, all treated on the same theoretical footing. The investigated systems range from small prototypical coordination compounds and catalysts to aggregates of biomolecules.

Copper-silver-titanium filler metal for direct brazing of structural ceramics

DOEpatents

Moorhead, Arthur J.

1987-01-01

A method of joining ceramics and metals to themselves and to one another is described using a brazing filler metal consisting essentially of 35 to 50 atomic percent copper, 15 to 50 atomic percent silver and 10 to 45 atomic percent titanium. This method produces strong joints that can withstand high service temperatures and oxidizing environments.

40 CFR Appendix C to Part 136 - Inductively Coupled Plasma-Atomic Emission Spectrometric Method for Trace Element Analysis of...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Inductively Coupled Plasma-Atomic... to Part 136—Inductively Coupled Plasma—Atomic Emission Spectrometric Method for Trace Element... technique. Samples are nebulized and the aerosol that is produced is transported to the plasma torch where...

40 CFR Appendix C to Part 136 - Inductively Coupled Plasma-Atomic Emission Spectrometric Method for Trace Element Analysis of...

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Inductively Coupled Plasma-Atomic... to Part 136—Inductively Coupled Plasma—Atomic Emission Spectrometric Method for Trace Element... technique. Samples are nebulized and the aerosol that is produced is transported to the plasma torch where...

Noncontact atomic force microscopy in liquid environment with quartz tuning fork and carbon nanotube probe

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Jensenius, Henriette; Dienwiebel, Martin; Nakayama, Yoshikazu; Tokumoto, Hiroshi; Jarvis, Suzanne P.; Oosterkamp, Tjerk H.

2002-03-01

A force sensor for noncontact atomic force microscopy in liquid environment was developed by combining a multiwalled carbon nanotube (MWNT) probe with a quartz tuning fork. Solvation shells of octamethylcyclotetrasiloxane on a graphite surface were detected both in the frequency shift and dissipation. Due to the high aspect ratio of the CNT probe, the long-range background force was barely detectable in the solvation region.

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

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

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

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

Method for producing an atomic oxygen beam

NASA Technical Reports Server (NTRS)

Outlaw, Ronald A. (Inventor)

1989-01-01

A method for producing an atomic oxygen beam is provided by the present invention. First, a material 10' is provided which dissociates molecular oxygen and dissolves atomic oxygen into its bulk. Next, molecular oxygen is exposed to entrance surface 11' of material 10'. Next, material 10' is heated by heater 17' to facilitate the permeation of atomic oxygen through material 10' to the UHV side 12'. UHV side 12' is interfaced with an ultra-high vacuum (UHV) environment provided by UHV pump 15'. The atomic oxygen on the UHV side 12' is excited to a non-binding state by exciter 14' thus producing the release of atomic oxygen to form an atomic oxygen beam 35'.

Interfacial Li-ion localization in hierarchical carbon anodes

DOE PAGES

McNutt, Nicholas W.; Rios, Orlando; Maroulas, Vasileios; ...

2016-10-24

An understanding of the nanoscale structure and energetics of carbon composites is critical for their applications in electric energy storage. Here, we study the properties of carbon anodes synthesized from low-cost renewable lignin biopolymers for use in energy storage applications such as Li-ion batteries. The anodes possess both nanoscale and mesoscale order, consisting of carbon nanocrystallites distributed within an amorphous carbon matrix. Molecular dynamics simulations of an experimentally validated model of the anode is used to elucidate the nature of Li-ion storage. We report the discovery of a novel mechanism of Li-ion storage, one in which Li+ is not intercalatedmore » between layers of carbon (as is the case in graphitic anodes), but rather is localized at the interface of crystalline carbon domains. In particular, the effects of Li-ion binding energy on the Li-Li, Li-H, and Li-C pair distribution functions are revealed, along with the effect on charge distribution. As a result, the atomic environments surrounding the Li-ions are grouped on the basis of ion energy and then convolved into archetypal structural motifs that reveal deep insight into the geometry of ion localization in disordered systems.« less

Influence of Plasma Environment on K-Line Emission in Highly Ionized Iron Atoms Evaluated Using a Debye-Huckel Model

NASA Technical Reports Server (NTRS)

Deprince, J.; Fritzsche, S.; Kallman, T. R.; Palmeri, P.; Quinet, P.

2017-01-01

The influence of plasma environment on the atomic parameters associated with the K-vacancy states has been investigated theoretically for several iron ions. To do this, a time-averaged Debye-Huckel potential for both the electron-nucleus and electron-electron interactions has been considered in the framework of relativistic multiconfiguration Dirac-Fock computations. More particularly, the plasma screening effects on ionization potentials, K-thresholds, transition energies, and radiative rates have been estimated in the astrophysical context of accretion disks around black holes. In the present paper, we describe the behavior of those atomic parameters for Ne-, Na-, Ar-, and K-like iron ions.

Big Data in Reciprocal Space: Sliding Fast Fourier Transforms for Determining Periodicity

DOE PAGES

Vasudevan, Rama K.; Belianinov, Alex; Gianfrancesco, Anthony G.; ...

2015-03-03

Significant advances in atomically resolved imaging of crystals and surfaces have occurred in the last decade allowing unprecedented insight into local crystal structures and periodicity. Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a challenge. Here, we introduce a Sliding Fast Fourier Transform (FFT) filter to analyze atomically resolved images of in-situ grown La5/8Ca3/8MnO3 films. We demonstrate the ability of sliding FFT algorithm to differentiate two sub-lattices, resulting from a mixed-terminated surface. Principal Component Analysis (PCA) and Independent Component Analysis (ICA) of themore » Sliding FFT dataset reveal the distinct changes in crystallography, step edges and boundaries between the multiple sub-lattices. The method is universal for images with any periodicity, and is especially amenable to atomically resolved probe and electron-microscopy data for rapid identification of the sub-lattices present.« less

Big Data in Reciprocal Space: Sliding Fast Fourier Transforms for Determining Periodicity

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

Vasudevan, Rama K.; Belianinov, Alex; Gianfrancesco, Anthony G.

Significant advances in atomically resolved imaging of crystals and surfaces have occurred in the last decade allowing unprecedented insight into local crystal structures and periodicity. Yet, the analysis of the long-range periodicity from the local imaging data, critical to correlation of functional properties and chemistry to the local crystallography, remains a challenge. Here, we introduce a Sliding Fast Fourier Transform (FFT) filter to analyze atomically resolved images of in-situ grown La5/8Ca3/8MnO3 films. We demonstrate the ability of sliding FFT algorithm to differentiate two sub-lattices, resulting from a mixed-terminated surface. Principal Component Analysis (PCA) and Independent Component Analysis (ICA) of themore » Sliding FFT dataset reveal the distinct changes in crystallography, step edges and boundaries between the multiple sub-lattices. The method is universal for images with any periodicity, and is especially amenable to atomically resolved probe and electron-microscopy data for rapid identification of the sub-lattices present.« less

Probing density and spin correlations in two-dimensional Hubbard model with ultracold fermions

NASA Astrophysics Data System (ADS)

Chan, Chun Fai; Drewes, Jan Henning; Gall, Marcell; Wurz, Nicola; Cocchi, Eugenio; Miller, Luke; Pertot, Daniel; Brennecke, Ferdinand; Koehl, Michael

2017-04-01

Quantum gases of interacting fermionic atoms in optical lattices is a promising candidate to study strongly correlated quantum phases of the Hubbard model such as the Mott-insulator, spin-ordered phases, or in particular d-wave superconductivity. We experimentally realise the two-dimensional Hubbard model by loading a quantum degenerate Fermi gas of 40 K atoms into a three-dimensional optical lattice geometry. High-resolution absorption imaging in combination with radiofrequency spectroscopy is applied to spatially resolve the atomic distribution in a single 2D layer. We investigate in local measurements of spatial correlations in both the density and spin sector as a function of filling, temperature and interaction strength. In the density sector, we compare the local density fluctuations and the global thermodynamic quantities, and in the spin sector, we observe the onset of non-local spin correlation, signalling the emergence of the anti-ferromagnetic phase. We would report our recent experimental endeavours to investigate further down in temperature in the spin sector.

Structural and electronic properties of isovalent boron atoms in GaAs

NASA Astrophysics Data System (ADS)

Krammel, C. M.; Nattermann, L.; Sterzer, E.; Volz, K.; Koenraad, P. M.

2018-04-01

Boron containing GaAs, which is grown by metal organic vapour phase epitaxy, is studied at the atomic level by cross-sectional scanning tunneling microscopy (X-STM) and spectroscopy (STS). In topographic X-STM images, three classes of B related features are identified, which are attributed to individual B atoms on substitutional Ga sites down to the second layer below the natural {110} cleavage planes. The X-STM contrast of B atoms below the surface reflects primarily the structural modification of the GaAs matrix by the small B atoms. However, B atoms in the cleavage plane have in contrast to conventional isovalent impurities, such as Al and In, a strong influence on the local electronic structure similar to donors or acceptors. STS measurements show that B in the GaAs {110} surfaces gives rise to a localized state short below the conduction band (CB) edge while in bulk GaAs, the B impurity state is resonant with the CB. The analysis of BxGa1-xAs/GaAs quantum wells reveals a good crystal quality and shows that the incorporation of B atoms in GaAs can be controlled along the [001] growth direction at the atomic level. Surprisingly, the formation of the first and fourth nearest neighbor B pairs, which are oriented along the <110 > directions, is strongly suppressed at a B concentration of 1% while the third nearest neighbor B pairs are found more than twice as often than expected for a completely spatially random pattern.

Crossover of Microscopic Dynamics in Metallic Supercooled Liquid Observed by NMR

NASA Astrophysics Data System (ADS)

Wu, Yue; Li, Lilong

2004-03-01

Nuclear magnetic resonance (NMR) is used to characterize local atomic motions in the glassy and supercooled liquid states of the bulk metallic glass system Pd_43Ni_10Cu_27P_20. It is shown that NMR is very effective in detecting local motions such as vibrations in metallic systems. The temperature dependence of the Knight shift reveals that certain local atomic motion decreases rapidly below a crossover temperature T_c. Above Tc as well as below the glass transition temperature Tg the mean-squared amplitude of local motions is shown to depend linearly on the temperature. The observed rapid decrease below Tc cannot be explained by heterogeneity effects. It reveals that qualitative changes of microscopic properties in the supercooled liquid take place at temperatures significantly above T_g. The observed phenomenon can be explained in terms of a rapid disappearance of certain local motions below Tc as suggested by the mode-coupling theory.

Controlling stray electric fields on an atom chip for experiments on Rydberg atoms

NASA Astrophysics Data System (ADS)

Davtyan, D.; Machluf, S.; Soudijn, M. L.; Naber, J. B.; van Druten, N. J.; van Linden van den Heuvell, H. B.; Spreeuw, R. J. C.

2018-02-01

Experiments handling Rydberg atoms near surfaces must necessarily deal with the high sensitivity of Rydberg atoms to (stray) electric fields that typically emanate from adsorbates on the surface. We demonstrate a method to modify and reduce the stray electric field by changing the adsorbate distribution. We use one of the Rydberg excitation lasers to locally affect the adsorbed dipole distribution. By adjusting the averaged exposure time we change the strength (with the minimal value less than 0.2 V /cm at 78 μ m from the chip) and even the sign of the perpendicular field component. This technique is a useful tool for experiments handling Rydberg atoms near surfaces, including atom chips.

Dynamics of atom-atom correlations in the Fermi problem

NASA Astrophysics Data System (ADS)

Borrelli, Massimo; Sabín, Carlos; Adesso, Gerardo; Plastina, Francesco; Maniscalco, Sabrina

2012-10-01

We present a detailed perturbative study of the dynamics of several types of atom-atom correlations in the famous Fermi problem. This is an archetypal model to study micro-causality in the quantum domain, where two atoms, one initially excited and the other prepared in its ground state, interact with the vacuum electromagnetic field. The excitation can be transferred to the second atom via a flying photon, and various kinds of quantum correlations between the two are generated during this process. Among these, prominent examples are given by entanglement, quantum discord and non-local correlations. The aim of this paper is to analyze the role of the light cone in the emergence of such correlations.

On the Usage of Locally Dense Basis Sets in the Calculation of NMR Indirect Nuclear Spin-Spin Coupling Constants

NASA Astrophysics Data System (ADS)

Sanchez, Marina; Provasi, Patricio F.; Aucar, Gustavo A.; Sauer, Stephan P. A.

Locally dense basis sets (

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.

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.

PubMed

Ogata, Koji; Hatakeyama, Makoto; Nakamura, Shinichiro

2018-02-15

The octanol-water partition coefficient (log P ow ) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the log P ow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆ G water values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of log P ow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted log P ow values.

Origin of the periodic structure in the conductance curve of gold nanojunctions in hydrogen environment

NASA Astrophysics Data System (ADS)

Jiang, Zhuoling; Wang, Hao; Sanvito, Stefano; Hou, Shimin

2016-03-01

The evolution of the atomic structure and the vibrational and electronic transport properties of gold atomic junctions incorporating molecular and atomic hydrogen upon elongation have been investigated with the nonequilibrium Green's function formalism combined with density functional theory. Our calculations show that for the case of gold junctions doped with a single H2 molecule the low-bias conductance drops rapidly with the electrodes' separation, while it remains almost constant if a single H atom replaces the molecule. In contrast, when one considers two H atoms adsorbed on a gold monatomic chain forming an Au-H-Au-H-Au double-bridge structure, the low-bias conductance increases first and then shows a plateau upon stretching the junction, in perfect agreement with experiments on gold nanocontacts in hydrogen environment. Furthermore, also the distribution of the calculated vibrational energies of the two H atoms is consistent with the experimental result in the low-conductance region, demonstrating clear evidence that hydrogen molecules can dissociate on stretched gold monatomic chains. These findings are helpful to improve our understanding of the structure-property relation of gold nanocontacts and also provide a new prospect for gold nanowires being used as chemical sensors and catalysts.

Importance of chlorine atom oxidation to tropospheric chemistry in an urban, coastal environment

NASA Astrophysics Data System (ADS)

Young, C. J.; Washenfelder, R. A.; Edwards, P.; Gilman, J. B.; Kuster, W. C.; Brown, S. S.

2012-12-01

Chlorine atom contribution to tropospheric chemistry is considered to be small on a global scale. It has been demonstrated to be significant in a few areas, such as the Arctic, using ratios of volatile organic compounds (VOCs) as tracers. During the CalNex campaign in Los Angeles, CA, Cl was shown to be a significant contributor to the primary radical budget. However, ratios of VOCs during this time period show no evidence of Cl atom oxidation. Using the Master Chemical Mechanism model, we investigate this discrepancy. We observe that the VOC ratios are highly dependent on the presence of secondary radicals through radical propagation, which are dependent on NOx levels. Thus, we suggest that in a high-NOx urban environment, VOC ratios are an unsuitable tracer of the importance of Cl chemistry. During the CalNex campaign, Cl atom reactivity is approximately an order of magnitude larger than OH radical reactivity. Further, Cl atoms react preferentially with unsaturated compounds for which OH reaction rates are small. Using the model, we determine the amount of additional ozone that can be expected in Los Angeles as a result of the presence of Cl atom reactivity.

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.