Light element opacities of astrophysical interest from ATOMIC

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

Colgan, J.; Kilcrease, D. P.; Magee, N. H. Jr.

We present new calculations of local-thermodynamic-equilibrium (LTE) light element opacities from the Los Alamos ATOMIC code for systems of astrophysical interest. ATOMIC is a multi-purpose code that can generate LTE or non-LTE quantities of interest at various levels of approximation. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. The ATOMIC code uses ab-initio atomic structure data computed from the CATS code, which is based on Cowan's atomic structure codes, and photoionization cross section data computed from the Los Alamos ionization code GIPPER. ATOMIC also incorporates a newmore » equation-of-state (EOS) model based on the chemical picture. ATOMIC incorporates some physics packages from LEDCOP and also includes additional physical processes, such as improved free-free cross sections and additional scattering mechanisms. Our new calculations are made for elements of astrophysical interest and for a wide range of temperatures and densities.« less

Formation routes and structural details of the CaF1 layer on Si(111) from high-resolution noncontact atomic force microscopy data

NASA Astrophysics Data System (ADS)

Rahe, Philipp; Smith, Emily F.; Wollschläger, Joachim; Moriarty, Philip J.

2018-03-01

We investigate the CaF1/Si (111 ) interface using a combination of high-resolution scanning tunneling and noncontact atomic force microscopy operated at cryogenic temperature as well as x-ray photoelectron spectroscopy. Submonolayer CaF1 films grown at substrate temperatures between 550 and 600 ∘C on Si (111 ) surfaces reveal the existence of two island types that are distinguished by their edge topology, nucleation position, measured height, and inner defect structure. Our data suggest a growth model where the two island types are the result of two reaction pathways during CaF1 interface formation. A key difference between these two pathways is identified to arise from the excess species during the growth process, which can be either fluorine or silicon. Structural details as a result of this difference are identified by means of high-resolution noncontact atomic force microscopy and add insights into the growth mode of this heteroepitaxial insulator-on-semiconductor system.

Dynamical observation and detailed description of catalysts under strong metal–support interaction

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

Zhang, Shuyi; Plessow, Philipp N.; Willis, Joshua J.

2016-06-09

Understanding the structures of catalysts under realistic conditions with atomic precision is crucial to design better materials for challenging transformations. Under reducing conditions, certain reducible supports migrate onto supported metallic particles and create strong metal–support states that drastically change the reactivity of the systems. The details of this process are still unclear and preclude its thorough exploitation. Here, we report an atomic description of a palladium/titania (Pd/TiO 2) system by combining state-of-the-art in situ transmission electron microscopy and density functional theory (DFT) calculations with structurally defined materials, in which we visualize the formation of the overlayers at the atomic scalemore » under atmospheric pressure and high temperature. We show that an amorphous reduced titania layer is formed at low temperatures, and that crystallization of the layer into either mono- or bilayer structures is dictated by the reaction environment and predicted by theory. Moreover, it occurs in combination with a dramatic reshaping of the metallic surface facets.« less

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

PubMed

Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

2016-09-26

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

Neutron diffraction of acetazolamide-bound human carbonic anhydrase II reveals atomic details of drug binding

PubMed Central

Fisher, S. Zoë; Aggarwal, Mayank; Kovalevsky, Andrey Y.; Silverman, David N.; McKenna, Robert

2012-01-01

Carbonic anhydrases (CAs) catalyze the hydration of CO2 forming HCO3− and a proton, an important reaction for many physiological processes including respiration, fluid secretion, and pH regulation. As such, CA isoforms are prominent clinical targets for treating various diseases. The clinically used acetazolamide (AZM) is a sulfonamide that binds with high affinity to human CA isoform II (HCA II). There are several X-ray structures available of AZM bound to various CA isoforms, but these complexes do not show the charged state of AZM, or hydrogen (H) atom positions of the protein and solvent. Neutron diffraction is a useful technique for directly observing H atoms and the mapping of H-bonding networks that can greatly contribute to rational drug design. To this end the neutron structure of H/D exchanged HCA II crystals in complex with AZM was determined. The structure reveals the molecular details of AZM binding and the charged state of the bound drug. This represents the first determined neutron structure of a clinically used drug bound to its target. PMID:22928733

Probing Atomic Dynamics and Structures Using Optical Patterns

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie L.; Gauthier, Daniel J.

2015-05-01

Pattern formation is a widely studied phenomenon that can provide fundamental insights into nonlinear systems. Emergent patterns in cold atoms are of particular interest in condensed matter physics and quantum information science because one can relate optical patterns to spatial structures in the atoms. In our experimental system, we study multimode optical patterns generated from a sample of cold, thermal atoms. We observe this nonlinear optical phenomenon at record low input powers due to the highly nonlinear nature of the spatial bunching of atoms in an optical lattice. We present a detailed study of the dynamics of these bunched atoms during optical pattern formation. We show how small changes in the atomic density distribution affect the symmetry of the generated patterns as well as the nature of the nonlinearity that describes the light-atom interaction. We gratefully acknowledge the financial support of the National Science Foundation through Grant #PHY-1206040.

An effective introduction to structural crystallography using 1D Gaussian atoms

NASA Astrophysics Data System (ADS)

Smith, Emily; Evans, Gwyndaf; Foadi, James

2017-11-01

The most important quantitative aspects of computational structural crystallography can be introduced in a satisfactory way using 1D truncated and periodic Gaussian functions to represent the atoms in a crystal lattice. This paper describes in detail and demonstrates 1D structural crystallography starting with the definition of such truncated Gaussians. The availability of the computer programme CRONE makes possible the repetition of the examples provided in the paper as well as the creation of new ones.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

A New Generation of Los Alamos Opacity Tables

DOE PAGES

Colgan, James Patrick; Kilcrease, David Parker; Magee, Jr., Norman H.; ...

2016-01-26

We present a new, publicly available, set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation-of-state (EOS) model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations thatmore » we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.« less

Theoretical Study of tip apex electronic structure in Scanning Tunneling Microscope

NASA Astrophysics Data System (ADS)

Choi, Heesung; Huang, Min; Randall, John; Cho, Kyeongjae

2011-03-01

Scanning Tunneling Microscope (STM) has been widely used to explore diverse surface properties with an atomic resolution, and STM tip has played a critical role in controlling surface structures. However, detailed information of atomic and electronic structure of STM tip and the fundamental understanding of STM images are still incomplete. Therefore, it is important to develop a comprehensive understanding of the electronic structure of STM tip. We have studied the atomic and electronic structures of STM tip with various transition metals (TMs) by DFT method. The d-electrons of TM tip apex atoms show different orbital states near the Fermi level. We will present comprehensive data of STM tips from our DFT calculation. Verified quantification of the tip electronic structures will lead to fundamental understanding of STM tip structure-property relationship. This work is supported by the DARPA TBN Program and the Texas ETF. DARPA Tip Based Nanofabrication Program and the Emerging Technology Fund of the State of Texas.

Molecular dynamics simulations of large macromolecular complexes.

PubMed

Perilla, Juan R; Goh, Boon Chong; Cassidy, C Keith; Liu, Bo; Bernardi, Rafael C; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

2015-04-01

Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

On the question of fractal packing structure in metallic glasses

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

Ding, Jun; Asta, Mark; Ritchie, Robert O.

2017-07-25

This work addresses the long-standing debate over fractal models of packing structure in metallic glasses (MGs). Through detailed fractal and percolation analyses of MG structures, derived from simulations spanning a range of compositions and quenching rates, we conclude that there is no fractal atomic-level structure associated with the packing of all atoms or solute-centered clusters. The results are in contradiction with conclusions derived from previous studies based on analyses of shifts in radial distribution function and structure factor peaks associated with volume changes induced by pressure and compositional variations. Here in this paper, the interpretation of such shifts is shownmore » to be challenged by the heterogeneous nature of MG structure and deformation at the atomic scale. Moreover, our analysis in the present work illustrates clearly the percolation theory applied to MGs, for example, the percolation threshold and characteristics of percolation clusters formed by subsets of atoms, which can have important consequences for structure–property relationships in these amorphous materials.« less

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

PubMed

Jain, Swati; Schlick, Tamar

2017-11-24

Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis of two-dimensional TlxBi1−x compounds and Archimedean encoding of their atomic structure

PubMed Central

Gruznev, Dimitry V.; Bondarenko, Leonid V.; Matetskiy, Andrey V.; Mihalyuk, Alexey N.; Tupchaya, Alexandra Y.; Utas, Oleg A.; Eremeev, Sergey V.; Hsing, Cheng-Rong; Chou, Jyh-Pin; Wei, Ching-Ming; Zotov, Andrey V.; Saranin, Alexander A.

2016-01-01

Crystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-thick TlxBi1−x compounds which display quite a different arrangement. It represents a quasi-periodic tiling structures that are built by a set of tiling elements as building blocks. Though the layer is lacking strict periodicity, it shows up as an ideally-packed tiling of basic elements without any skips or halting. The two-dimensional TlxBi1−x compounds were formed by depositing Bi onto the Tl-covered Si(111) surface where Bi atoms substitute appropriate amount of Tl atoms. Atomic structure of each tiling element as well as arrangement of TlxBi1−x compounds were established in a detail. Electronic properties and spin texture of the selected compounds having periodic structures were characterized. The shown example demonstrates possibility for the formation of the exotic low-dimensional materials via unusual growth mechanisms. PMID:26781340

Structure determination of helical filaments by solid-state NMR spectroscopy

PubMed Central

Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

2016-01-01

The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

Ultra-small rhenium clusters supported on graphene.

PubMed

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

2015-03-28

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

Ultra-small rhenium clusters supported on graphene

PubMed Central

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

2015-01-01

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

Ionizing gas breakdown waves in strong electric fields.

NASA Technical Reports Server (NTRS)

Klingbeil, R.; Tidman, D. A.; Fernsler, R. F.

1972-01-01

A previous analysis by Albright and Tidman (1972) of the structure of an ionizing potential wave driven through a dense gas by a strong electric field is extended to include atomic structure details of the background atoms and radiative effects, especially, photoionization. It is found that photoionization plays an important role in avalanche propagation. Velocities, electron densities, and temperatures are presented as a function of electric field for both negative and positive breakdown waves in nitrogen.

CIT-7, a crystalline, molecular sieve with pores bounded by 8 and 10-membered rings† †Electronic supplementary information (ESI) available: Details of the synthesis and characterization of all materials as well as details on the synchrotron and RED data collection and structure determination, including the cif file. See DOI: 10.1039/c4sc03935a Click here for additional data file.

PubMed Central

Schmidt, Joel E.; Xie, Dan; Rea, Thomas

2015-01-01

A new crystalline molecular sieve, denoted CIT-7, is synthesized using an imidazolium-based diquaternary organic structure directing agent (OSDA). The framework structure is determined from a combination of rotation electron diffraction and synchrotron X-ray powder diffraction data. The structure has 10 crystallographically unique tetrahedral atoms (T-atoms) in the unit cell, and can be described as an ordered arrangement of the [425462] mtw building unit and a previously unreported [4452] building unit. The framework contains a 2-dimensional pore system that is bounded by 10 T-atom rings (10-ring, 5.1 Å × 6.2 Å opening) that are connected with oval 8-rings (2.9 Å × 5.5 Å opening) through medium-sized cavities (∼7.9 Å) at the channel intersections. CIT-7 can be synthesized over a broad range of compositions including pure-silica and heteroatom, e.g., aluminosilicate and titanosilicate, containing variants. PMID:29163872

A history of gap junction structure: hexagonal arrays to atomic resolution.

PubMed

Grosely, Rosslyn; Sorgen, Paul L

2013-02-01

Gap junctions are specialized membrane structures that provide an intercellular pathway for the propagation and/or amplification of signaling cascades responsible for impulse propagation, cell growth, and development. Prior to the identification of the proteins that comprise gap junctions, elucidation of channel structure began with initial observations of a hexagonal nexus connecting apposed cellular membranes. Concomitant with technological advancements spanning over 50 years, atomic resolution structures are now available detailing channel architecture and the cytoplasmic domains that have helped to define mechanisms governing the regulation of gap junctions. Highlighted in this review are the seminal structural studies that have led to our current understanding of gap junction biology.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

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.

All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

PubMed

Masso, Majid

2018-09-14

Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Comprehensive Analysis in Terms of Molecule-Intrinsic, Quasi-Atomic Orbitals. III. The Covalent Bonding Structure of Urea.

PubMed

West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

2015-10-15

The analysis of molecular electron density matrices in terms of quasi-atomic orbitals, which was developed in previous investigations, is quantitatively exemplified by a detailed application to the urea molecule. The analysis is found to identify strong and weak covalent bonding interactions as well as intramolecular charge transfers. It yields a qualitative as well as quantitative ab initio description of the bonding structure of this molecule, which raises questions regarding some traditional rationalizations.

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

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

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-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by 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.

Water Oxidation Catalysis via Size-Selected Iridium Clusters

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

Halder, Avik; Liu, Cong; LIU, ZHUN

The detailed mechanism and efficacy of four electron electrochemical water oxidation depend critically upon the detailed atomic structure of each catalytic site, which are numerous and diverse in most metal oxides anodes. In order to limit the diversity of sites, arrays of discrete iridium clusters with identical metal atom number (Ir-2, Ir-4, or Ir-8) were deposited in submonolayer coverage on conductive oxide supports, and the electrochemical properties and activity of each was evaluated. Exceptional electroactivity for the oxygen evolving reaction (OER) was observed for all cluster samples in acidic electrolyte. Reproducible cluster-size-dependent trends in redox behavior were also resolved. First-principlesmore » computational models of the individual discrete-size clusters allow correlation of catalytic-site structure and multiplicity with redox behavior.« less

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

PubMed

Blakeley, Matthew P; Hasnain, Samar S; Antonyuk, Svetlana V

2015-07-01

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

Structural details of Al/Al 2O3 junctions and their role in the formation of electron tunnel barriers

NASA Astrophysics Data System (ADS)

Koberidze, M.; Puska, M. J.; Nieminen, R. M.

2018-05-01

We present a computational study of the adhesive and structural properties of the Al/Al 2O3 interfaces as building blocks of the metal-insulator-metal (MIM) tunnel devices, where electron transport is accomplished via tunneling mechanism through the sandwiched insulating barrier. The main goal of this paper is to understand, on the atomic scale, the role of the geometrical details in the formation of the tunnel barrier profiles. Initially, we concentrate on the adhesive properties of the interfaces. To provide reliable results, we carefully assess the accuracy of the traditional methods used to examine Al/Al 2O3 systems. These are the most widely employed exchange-correlation functionals—local-density approximation and two different generalized gradient approximations; the universal binding-energy relation for predicting equilibrium interfacial distances and adhesion energies; and the ideal work of separation as a measure of junction stability. In addition, we show that the established interpretation of the computed ideal work of separation might be misleading in predicting the optimal interface structures. Finally, we perform a detailed analysis of the atomic and interplanar relaxations in each junction, and identify their contributions to the tunnel barrier parameters. Our results imply that the structural irregularities on the surface of the Al film have a significant contribution to lowering the tunnel barrier height, while atomic relaxations at the interface and interplanar relaxations in Al2O3 may considerably change the width of the barrier and, thus, distort its uniformity. Both the effects may critically influence the performance of the MIM tunnel devices.

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

PubMed

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

How glutamate receptor subunits mix and match: details uncovered.

PubMed

Hansen, Kasper B; Traynelis, Stephen F

2011-07-28

Until now, the atomic details explaining why certain subunits prefer to coassemble has been lacking in our understanding of glutamate receptor biogenesis. In this issue, Kumar et al. describe the structural basis by which preferential subunit assembly occurs for homomeric and heteromeric kainate-type glutamate receptors. Copyright © 2011 Elsevier Inc. All rights reserved.

Electric field imaging of single atoms

PubMed Central

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

2017-01-01

In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures. PMID:28555629

Structural mechanism underlying capsaicin binding and activation of TRPV1 ion channel

PubMed Central

Cheng, Wei; Yang, Wei; Yu, Peilin; Song, Zhenzhen; Yarov-Yarovoy, Vladimir; Zheng, Jie

2015-01-01

Capsaicin bestows spiciness by activating TRPV1 channel with exquisite potency and selectivity. Capsaicin-bound channel structure was previously resolved by cryo-EM at 4.2-to-4.5 Å resolution, however important details required for mechanistic understandings are unavailable: capsaicin was registered as a small electron density, reflecting neither its chemical structure nor specific ligand-channel interactions. We obtained the missing atomic-level details by iterative computation, which were confirmed by systematic site-specific functional tests. We observed that the bound capsaicin takes “tail-up, head-down” configurations. The vanillyl and amide groups form specific interactions to anchor its bound position, while the aliphatic tail may sample a range of conformations, making it invisible in cryo-EM images. Capsaicin stabilizes the open state by “pull-and-contact” interactions between the vanillyl group and the S4-S5 linker. Our study provided a structural mechanism for the agonistic function of capsaicin and its analogs, and demonstrated an effective approach to obtain atomic level information from cryo-EM structures. PMID:26053297

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

PubMed Central

Vallat, Brinda Kizhakke; Pillardy, Jaroslaw; Elber, Ron

2010-01-01

The first step in homology modeling is to identify a template protein for the target sequence. The template structure is used in later phases of the calculation to construct an atomically detailed model for the target. We have built from the Protein Data Bank a large-scale learning set that includes tens of millions of pair matches that can be either a true template or a false one. Discriminatory learning (learning from positive and negative examples) is employed to train a decision tree. Each branch of the tree is a mathematical programming model. The decision tree is tested on an independent set from PDB entries and on the sequences of CASP7. It provides significant enrichment of true templates (between 50-100 percent) when compared to PSI-BLAST. The model is further verified by building atomically detailed structures for each of the tentative true templates with modeller. The probability that a true match does not yield an acceptable structural model (within 6Å RMSD from the native structure), decays linearly as a function of the TM structural-alignment score. PMID:18300226

Entering an era of dynamic structural biology….

PubMed

Orville, Allen M

2018-05-31

A recent paper in BMC Biology presents a general method for mix-and-inject serial crystallography, to facilitate the visualization of enzyme intermediates via time-resolved serial femtosecond crystallography (tr-SFX). They apply their method to resolve in near atomic detail the cleavage and inactivation of the antibiotic ceftriaxone by a β-lactamase enzyme from Mycobacterium tuberculosis. Their work demonstrates the general applicability of time-resolved crystallography, from which dynamic structures, at atomic resolution, can be obtained.See research article: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-018-0524-5 .

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

Short and medium range structures of 80GeSe2–20Ga2Se3 chalcogenide glasses

NASA Astrophysics Data System (ADS)

Petracovschi, Elena; Calvez, Laurent; Cormier, Laurent; Le Coq, David; Du, Jincheng

2018-05-01

The short and medium range structures of 80GeSe2–20Ga2Se3 (or Ge23.5Ga11.8Se64.7) chalcogenide glasses have been studied by combining ab initio molecular dynamics (AIMD) simulations and experimental neutron diffraction studies. The structure factor and total correlation function were calculated from glass structures generated from AIMD simulations and compared with neutron diffraction experiments showing reasonable agreement. The atomic structures of ternary chalcogenide glasses were analyzed in detail, and it was found that gallium atoms are four-fold coordinated by selenium (Se) and form [GaSe4] tetrahedra. Germanium atoms on average also have four-fold coordination, among which Se is 3.5 with the remaining being Ge–Ge homo-nuclear bonds. Ga and Ge tetrahedra link together mainly through corner-sharing and some edge-sharing of Se. No homo-nuclear bonds were observed among Ga atoms or between Ge and Ga. In addition, Se–Se homo-nuclear bonds and Se chains with various lengths were observed. A small fraction of Se atom triclusters that bond to three cations of Ge and Ga were also observed, confirming earlier proposals from 77Se solid state nuclear magnetic resonance studies. Furthermore, the electronic structures of ternary chalcogenide glasses were studied in terms of atomic charge and electronic density of states in order to gain insights into the chemical bonding and electronic properties, as well as to provide an explanation of the observed atomic structures in these ternary chalcogenide glasses.

Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

DOE PAGES

Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

2015-07-28

Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

Atomically precise edge chlorination of nanographenes and its application in graphene nanoribbons

PubMed Central

Tan, Yuan-Zhi; Yang, Bo; Parvez, Khaled; Narita, Akimitsu; Osella, Silvio; Beljonne, David; Feng, Xinliang; Müllen, Klaus

2013-01-01

Chemical functionalization is one of the most powerful and widely used strategies to control the properties of nanomaterials, particularly in the field of graphene. However, the ill-defined structure of the present functionalized graphene inhibits atomically precise structural characterization and structure-correlated property modulation. Here we present a general edge chlorination protocol for atomically precise functionalization of nanographenes at different scales from 1.2 to 3.4 nm and its application in graphene nanoribbons. The well-defined edge chlorination is unambiguously confirmed by X-ray single-crystal analysis, which also discloses the characteristic non-planar molecular shape and detailed bond lengths of chlorinated nanographenes. Chlorinated nanographenes and graphene nanoribbons manifest enhanced solution processability associated with decreases in the optical band gap and frontier molecular orbital energy levels, exemplifying the structure-correlated property modulation by precise edge chlorination. PMID:24212200

Atomic structure of a decagonal Al-Pd-Mn phase

NASA Astrophysics Data System (ADS)

Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

2017-12-01

We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

Exotic objects of atomic physics

NASA Astrophysics Data System (ADS)

Eletskii, A. V.

2017-11-01

There has been presented a short survey of physical properties, methods of production and exploration as well as directions of practical usage of the objects of atomic physics which are not yet described in detail in modern textbooks and manuals intended for students of technical universities. The family of these objects includes negative and multicharged ions, Rydberg atoms, excimer molecules, clusters. Besides of that, in recent decades this family was supplemented with new nanocarbon structures such as fullerenes, carbon nanotubes and graphene. The textbook “Exotic objects of atomic physics” [1] edited recently contains some information on the above-listed objects of the atomic physics. This textbook can be considered as a supplement to classic courses of atomic physics teaching in technical universities.

Identification of light elements in silicon nitride by aberration-corrected scanning transmission electron microscopy.

PubMed

Idrobo, Juan C; Walkosz, Weronika; Klie, Robert F; Oğüt, Serdar

2012-12-01

In silicon nitride structural ceramics, the overall mechanical and thermal properties are controlled by the atomic and electronic structures at the interface between the ceramic grains and the amorphous intergranular films (IGFs) formed by various sintering additives. In the last ten years the atomic arrangements of heavy elements (rare-earths) at the Si(3)N(4)/IGF interfaces have been resolved. However, the atomic position of light elements, without which it is not possible to obtain a complete description of the interfaces, has been lacking. This review article details the authors' efforts to identify the atomic arrangement of light elements such as nitrogen and oxygen at the Si(3)N(4)/SiO(2) interface and in bulk Si(3)N(4) using aberration-corrected scanning transmission electron microscopy. Published by Elsevier B.V.

Free energy landscapes of a highly structured β-hairpin peptide and its single mutant

NASA Astrophysics Data System (ADS)

Kim, Eunae; Yang, Changwon; Jang, Soonmin; Pak, Youngshang

2008-10-01

We investigated the free energy landscapes of a highly structured β-hairpin peptide (MBH12) and a less structured peptide with a single mutation of Tyr6 to Asp6 (MBH10). For the free energy mapping, starting from an extended conformation, the replica exchange molecular dynamic simulations for two β-hairpins were performed using a modified version of an all-atom force field employing an implicit solvation (param99MOD5/GBSA). With the present simulation approach, we demonstrated that detailed stability changes associated with the sequence modification from MBH12 to MBH10 are quantitatively well predicted at the all-atom level.

Unraveling protein catalysis through neutron diffraction

NASA Astrophysics Data System (ADS)

Myles, Dean

Neutron scattering and diffraction are exquisitely sensitive to the location, concentration and dynamics of hydrogen atoms in materials and provide a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, non-destructive suite of instruments for biophysical characterization that provide spatial and dynamic information spanning from Angstroms to microns and from picoseconds to microseconds, respectively. Applications range from atomic-resolution analysis of individual hydrogen atoms in enzymes, through to multi-scale analysis of hierarchical structures and assemblies in biological complexes, membranes and in living cells. Here we describe how the precise location of protein and water hydrogen atoms using neutron diffraction provides a more complete description of the atomic and electronic structures of proteins, enabling key questions concerning enzyme reaction mechanisms, molecular recognition and binding and protein-water interactions to be addressed. Current work is focused on understanding how molecular structure and dynamics control function in photosynthetic, cell signaling and DNA repair proteins. We will highlight recent studies that provide detailed understanding of the physiochemical mechanisms through which proteins recognize ligands and catalyze reactions, and help to define and understand the key principles involved.

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

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

Sachan, Ritesh; Zhang, Yanwen; Ou, Xin

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

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

DOE PAGES

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

2016-12-13

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

Atomically resolved scanning force studies of vicinal Si(111)

NASA Astrophysics Data System (ADS)

Pérez León, Carmen; Drees, Holger; Wippermann, Stefan Martin; Marz, Michael; Hoffmann-Vogel, Regina

2017-06-01

Well-ordered stepped semiconductor surfaces attract intense attention owing to the regular arrangements of their atomic steps that makes them perfect templates for the growth of one-dimensional systems, e.g., nanowires. Here, we report on the atomic structure of the vicinal Si (111 ) surface with 10∘ miscut investigated by a joint frequency-modulation scanning force microscopy (FM-SFM) and ab initio approach. This popular stepped surface contains 7 ×7 -reconstructed terraces oriented along the Si (111 ) direction, separated by a stepped region. Recently, the atomic structure of this triple step based on scanning tunneling microscopy (STM) images has been subject of debate. Unlike STM, SFM atomic resolution capability arises from chemical bonding of the tip apex with the surface atoms. Thus, for surfaces with a corrugated density of states such as semiconductors, SFM provides complementary information to STM and partially removes the dependency of the topography on the electronic structure. Our FM-SFM images with unprecedented spatial resolution on steps coincide with the model based on a (7 7 10 ) orientation of the surface and reveal structural details of this surface. Two different FM-SFM contrasts together with density functional theory calculations explain the presence of defects, buckling, and filling asymmetries on the surface. Our results evidence the important role of charge transfers between adatoms, restatoms, and dimers in the stabilisation of the structure of the vicinal surface.

High-resolution imaging of silicene on an Ag(111) surface by atomic force microscopy

NASA Astrophysics Data System (ADS)

Onoda, Jo; Yabuoshi, Keisuke; Miyazaki, Hiroki; Sugimoto, Yoshiaki

2017-12-01

Silicene, a two-dimensional (2D) honeycomb arrangement of Si atoms, is expected to have better electronic properties than graphene and has been mostly synthesized on Ag surfaces. Although scanning tunneling microscopy (STM) has been used for visualizing its atomic structure in real space, the interpretation of STM contrast is not straightforward and only the topmost Si atoms were observed on the (4 ×4 ) silicene/Ag(111) surface. Here, we demonstrate that high-resolution atomic force microscopy (AFM) can resolve all constituent Si atoms in the buckled honeycomb arrangement of the (4 ×4 ) silicene. Site-specific force spectroscopy attributes the origin of the high-resolution AFM images to chemical bonds between the AFM probe apex and the individual Si atoms on the (4 ×4 ) silicene. A detailed analysis of the geometric parameters suggests that the pulling up of lower-buckled Si atoms by the AFM tip could be a key for high-resolution AFM, implying a weakening of the Si-Ag interactions at the interface. We expect that high-resolution AFM will also unveil atomic structures of edges and defects of silicene, or other emerging 2D materials.

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Perilla, Juan R.; Schulten, Klaus

2017-07-01

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.

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

Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*

NASA Technical Reports Server (NTRS)

Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Garcia, J.; Witthoeft, M. C.; Kallman, T. R.

2012-01-01

Complete data sets of level energies, transition wavelengths, A-values, radiative and Auger widths and fluorescence yields for K-vacancy levels of the F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn isonuclear sequences have been computed by a Hartree-Fock method that includes relativistic corrections as implemented in Cowan's atomic structure computer suite. The atomic parameters for more than 3 million fine-structure K lines have been determined. Ions with electron number N greater than 9 are treated for the first time, and detailed comparisons with available measurements and theoretical data for ions with N less than or equal to 9 are carried out in order to estimate reliable accuracy ratings.

Oxygen deficiency induced deterioration in microstructure and magnetic properties at Y{sub 3}Fe{sub 5}O{sub 12}/Pt interface

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

Song, Dongsheng; Zhu, Jing, E-mail: jzhu@mail.tsinghua.edu.cn; Ma, Li

2015-07-27

Transport efficiency of pure spin current across the ferromagnetic films adjacent with a nonmagnetic metal is strongly dependent on the spin mixing conductance, which is very sensitive to atomic-level interface conditions. Here, by the means of advanced electron microscopy techniques, atomic structure, electronic structure, and magnetic properties at Y{sub 3}Fe{sub 5}O{sub 12} (YIG)/Pt interface are detailed characterized to correlate the microstructure and magnetic properties with interfacial transport properties. It is found that the order-disorder structure transformation at the interface is accompanied with oxygen deficiency, thus the reduced iron valence and the break of magnetic atom-O-magnetic atom bridges, which is responsiblemore » for superexchange interaction and magnetic order. It is also found that the magnetic moment of interfacial iron ions is decreased. The disorder interfacial layer with suppressed magnetism finally contributes to the declined spin transport efficiency. Our results provide the knowledge to control and manipulate the interfacial structure and properties in order to obtain higher spin transport efficiency.« less

Universality and diversity of folding mechanics for three-helix bundle proteins.

PubMed

Yang, Jae Shick; Wallin, Stefan; Shakhnovich, Eugene I

2008-01-22

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo folding simulations using a single transferable all-atom potential. Using these trajectories, we examine the relaxation behavior, secondary structure formation, and transition-state ensembles (TSEs) of the two proteins and compare our results with experimental data and previous computational studies. To obtain a detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Moreover, rigorous p(fold) analysis is used to obtain representative samples of the TSEs and a good quantitative agreement between experimental and simulated Phi values is obtained for protein A. Phi values for Villin also are obtained and left as predictions to be tested by future experiments. Our analysis shows that the two-helix hairpin is a common partially stable structural motif that gets formed before entering the TSE in the studied proteins. These results together with our earlier study of Engrailed Homeodomain and recent experimental studies provide a comprehensive, atomic-level picture of folding mechanics of three-helix bundle proteins.

Hydrogen-impurity complexes in III V semiconductors

NASA Astrophysics Data System (ADS)

Ulrici, W.

2004-12-01

This review summarizes the presently available knowledge concerning hydrogen-impurity complexes in III-V compounds. The impurities form shallow acceptors on group III sites (Be, Zn, Cd) and on group V sites (C, Si, Ge) as well as shallow donors on group V sites (S, Se, Te) and on group III sites (Si, Sn). These complexes are mainly revealed by their hydrogen stretching modes. Therefore, nearly all information about their structure and dynamic properties is derived from vibrational spectroscopy. The complexes of shallow impurities with hydrogen have been most extensively investigated in GaAs, GaP and InP. This holds also for Mg-H in GaN. The complexes exhibit a different microscopic structure, which is discussed in detail. The isoelectronic impurity nitrogen, complexed with one hydrogen atom, is investigated in detail in GaAs and GaP. Those complexes can exist in different charge states. The experimental results such as vibrational frequencies, the microscopic structure and the activation energy for reorientation for many of these complexes are in very good agreement with results of ab initio calculations. Different types of oxygen-hydrogen complexes in GaAs and GaP are described, with one hydrogen atom or two hydrogen atoms bonded to oxygen. Three of these complexes in GaAs were found to be electrically active.

Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting.

PubMed

De Backer, A; Martinez, G T; MacArthur, K E; Jones, L; Béché, A; Nellist, P D; Van Aert, S

2015-04-01

Quantitative annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique to characterise nano-particles on an atomic scale. Because of their limited size and beam sensitivity, the atomic structure of such particles may become extremely challenging to determine. Therefore keeping the incoming electron dose to a minimum is important. However, this may reduce the reliability of quantitative ADF STEM which will here be demonstrated for nano-particle atom-counting. Based on experimental ADF STEM images of a real industrial catalyst, we discuss the limits for counting the number of atoms in a projected atomic column with single atom sensitivity. We diagnose these limits by combining a thorough statistical method and detailed image simulations. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural stability and electronic properties of β-tetragonal boron: A first-principles study

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

Hayami, Wataru, E-mail: hayami.wataru@nims.go.jp

2015-01-15

It is known that elemental boron has five polymorphs: α- and β-rhombohedral, α- and β-tetragonal, and the high-pressure γ phase. β-tetragonal (β-t) boron was first discovered in 1960, but there have been only a few studies since then. We have thoroughly investigated, using first-principles calculations, the atomic and electronic structures of β-t boron, the details of which were not known previously. The difficulty of calculation arises from the fact that β-t boron has a large unit cell that contains between 184 and 196 atoms, with 12 partially-occupied interstitial sites. This makes the number of configurations of interstitial atoms too greatmore » to calculate them all. By introducing assumptions based on symmetry and preliminary calculations, the number of configurations to calculate can be greatly reduced. It was eventually found that β-t boron has the lowest total energy, with 192 atoms (8 interstitial atoms) in an orthorhombic lattice. The total energy per atom was between those of α- and β-rhombohedral boron. Another tetragonal structure with 192 atoms was found to have a very close energy. The valence bands were fully filled and the gaps were about 1.16 to 1.54 eV, making it comparable to that of β-rhombohedral boron. - Graphical abstract: Electronic density distribution for the lowest-energy configuration (N=192) viewed from the 〈1 0 0〉 direction. Left: isosurface (yellow) at d=0.09 electrons/a.u.{sup 3} Right: isosurface (orange) at d=0.12 electrons/a.u.{sup 3}. - Highlights: • β-tetragonal boron was thoroughly investigated using first-principles calculations. • The lowest energy structure contains 192 atoms in an orthorhombic lattice. • Another tetragonal structure with 192 atoms has a very close energy. • The total energy per atom is between those of α- and β-rhombohedral boron. • The band gap of the lowest energy structure is about 1.16 to 1.54 eV.« less

Advanced Kr Atomic Structure and Ionization Kinetics for Pinches on ZR

NASA Astrophysics Data System (ADS)

Dasgupta, Arati; Clark, Robert; Giuliani, John; Ouart, Nick; Davis, Jack; Jones, Brent; Ampleford, Dave; Hansen, Stephanie

2011-10-01

High fluence photon sources above 10 keV are a challenge for HED plasmas. This motivates Kr atomic modeling as its K-shell radiation starts at 13 keV. We have developed atomic structure and collisional-radiatve data for the full K-and L-shell and much of the M-shell using the the state-of-the-art Flexible Atomic Code. All relevant atomic collisional and radiative processes that affect ionization balance and are necessary to accurately model the pinch dynamics and the spectroscopic details of the emitted radiation are included in constructing the model. This non-LTE CRE model will be used to generate synthetic spectra for fixed densities and temperatures relevant for Kr gas-puff simulations in ZR. Work supported by DOE/NNSA. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Surface determination through atomically resolved secondary-electron imaging

PubMed Central

Ciston, J.; Brown, H. G.; D'Alfonso, A. J.; Koirala, P.; Ophus, C.; Lin, Y.; Suzuki, Y.; Inada, H.; Zhu, Y.; Allen, L. J.; Marks, L. D.

2015-01-01

Unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we report a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 × 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our work reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO5 units. Dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals. PMID:26082275

Surface determination through atomically resolved secondary-electron imaging

DOE PAGES

Ciston, J.; Brown, H. G.; D’Alfonso, A. J.; ...

2015-06-17

We report that unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we show a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 x 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our workmore » reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO 5 units. Lastly, dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals.« less

Fundamental quantum noise mapping with tunnelling microscopes tested at surface structures of subatomic lateral size.

PubMed

Herz, Markus; Bouvron, Samuel; Ćavar, Elizabeta; Fonin, Mikhail; Belzig, Wolfgang; Scheer, Elke

2013-10-21

We present a measurement scheme that enables quantitative detection of the shot noise in a scanning tunnelling microscope while scanning the sample. As test objects we study defect structures produced on an iridium single crystal at low temperatures. The defect structures appear in the constant current images as protrusions with curvature radii well below the atomic diameter. The measured power spectral density of the noise is very near to the quantum limit with Fano factor F = 1. While the constant current images show detailed structures expected for tunnelling involving d-atomic orbitals of Ir, we find the current noise to be without pronounced spatial variation as expected for shot noise arising from statistically independent events.

Structure of fluorescent metal clusters on a DNA template.

NASA Astrophysics Data System (ADS)

Vdovichev, A. A.; Sych, T. S.; Reveguk, Z. V.; Smirnova, A. A.; Maksimov, D. A.; Ramazanov, R. R.; Kononov, A. I.

2016-08-01

Luminescent metal clusters are a subject of growing interest in recent years due to their bright emission from visible to near infrared range. Detailed structure of the fluorescent complexes of Ag and other metal clusters with ligands still remains a challenging task. In this joint experimental and theoretical study we synthesized Ag-DNA complexes on a DNA oligonucleotide emitting in violet- green spectral range. The structure of DNA template was determined by means of various spectral measurements (CD, MS, XPS). Comparison of the experimental fluorescent excitation spectra and calculated absorption spectra for different QM/MM optimized structures allowed us to determine the detailed structure of the green cluster containing three silver atoms in the stem of the DNA hairpin structure stabilized by cytosine-Ag+-cytosine bonds.

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

NASA Astrophysics Data System (ADS)

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

2013-01-01

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

Ground-state hyperfine splitting for Rb, Cs, Fr, Ba+, and Ra+

NASA Astrophysics Data System (ADS)

Ginges, J. S. M.; Volotka, A. V.; Fritzsche, S.

2017-12-01

We have systematically investigated the ground-state hyperfine structure for alkali-metal atoms 87Rb,133Cs, and 211Fr and alkali-metal-like ions +135Ba and +225Ra, which are of particular interest for parity violation studies. The quantum electrodynamic one-loop radiative corrections have been rigorously evaluated within an extended Furry picture employing core-Hartree and Kohn-Sham atomic potentials. Moreover, the effect of the nuclear magnetization distribution on the hyperfine structure intervals has been studied in detail and its uncertainty has been estimated. Finally, the theoretical description of the hyperfine structure has been completed with full many-body calculations performed in the all-orders correlation potential method.

Liquid Alumina: Detailed Atomic Coordination Determined from Neutron Diffraction Data Using Empirical Potential Structure Refinement

NASA Astrophysics Data System (ADS)

Landron, C.; Hennet, L.; Jenkins, T. E.; Greaves, G. N.; Coutures, J. P.; Soper, A. K.

2001-05-01

The neutron scattering structure factor SN\\(Q\\) for a 40 mg drop of molten alumina ( Al2O3) held at 2500 K, using a laser-heated aerodynamic levitation furnace, is measured for the first time. A 1700 atom model of liquid alumina is generated from these data using the technique of empirical potential structural refinement. About 62% of the aluminum sites are 4-fold coordinated, matching the mostly triply coordinated oxygen sites, but some 24% of the aluminum sites are 5-fold coordinated. The octahedral aluminum sites found in crystalline α-Al2O3 occur only at the 2% level in liquid alumina.

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

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

Perilla, Juan R.; Schulten, Klaus

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

The application of quasi-steady approximation in atomic kinetics in simulation of hohlraum radiation drive

NASA Astrophysics Data System (ADS)

Ren, Guoli; Pei, Wenbing; Lan, Ke; Gu, Peijun; Li, Xin; Institute of Applied Physics; Computional Mathematics Team

2011-10-01

In current routine 2D simulation of hohlraum physics, we adopt the principal-quantum- number(n-level) average atom model(AAM). However, the experimental frequency-dependant radiative drive differs from our n-level simulated drive, which reminds us the need of a more detailed atomic kinetics description. The orbital-quantum-number(nl-level) AAM is a natural consideration but the in-line calculation consumes much more resources. We use a new method to built up a nl-level bound electron distribution using in-line n-level calculated plasma condition (such as temperature, density, average ionization degree). We name this method ``quasi-steady approximation.'' Using the re-built nl-level bound electron distribution (Pnl) , we acquire a new hohlraum radiative drive by post-processing. Comparison with the n-level post-processed hohlraum drive shows that we get an almost identical radiation flux but with more-detailed frequency-dependant structures.

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

DOE PAGES

Perilla, Juan R.; Schulten, Klaus

2017-07-19

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

Antibacterial properties and atomic resolution X-ray complex crystal structure of a ruthenocene conjugated β-lactam antibiotic

DOE PAGES

Lewandowski, Eric M.; Skiba, Joanna; Torelli, Nicholas J.; ...

2015-03-02

We have determined a 1.18 Å resolution X-ray crystal structure of a novel ruthenocenyle-6-aminopenicillinic acid in complex with CTX-M β-lactamase, showing unprecedented details of interactions between ruthenocene and protein. As the first product complex with an intact catalytic serine, the structure also offers insights into β-lactamase catalysis and inhibitor design.

Structural biologists capture detailed image of gene regulator’s fleeting form | Center for Cancer Research

Cancer.gov

Using an ultrafast, high-intensity radiation source called an X-ray free-electron laser (XFEL), scientists have captured an atomic-level picture of an RNA structure called a riboswitch as it reorganizes itself to regulate protein production. The structure they visualized has never before been seen, and likely exists for only milliseconds after the riboswitch first encounters

A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.

PubMed

Zhou, Weiqiang; Yan, Hong

2010-10-15

Protein-DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein-DNA complex are becoming available, the surface characteristics of the complex become an important research topic. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein-DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of -8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of -7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein-DNA interactions. The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm kenandzhou@hotmail.com.

Raman spectroscopy as a tool to investigate the structure and electronic properties of carbon-atom wires

PubMed Central

Milani, Alberto; Tommasini, Matteo; Russo, Valeria; Li Bassi, Andrea; Lucotti, Andrea; Cataldo, Franco

2015-01-01

Summary Graphene, nanotubes and other carbon nanostructures have shown potential as candidates for advanced technological applications due to the different coordination of carbon atoms and to the possibility of π-conjugation. In this context, atomic-scale wires comprised of sp-hybridized carbon atoms represent ideal 1D systems to potentially downscale devices to the atomic level. Carbon-atom wires (CAWs) can be arranged in two possible structures: a sequence of double bonds (cumulenes), resulting in a 1D metal, or an alternating sequence of single–triple bonds (polyynes), expected to show semiconducting properties. The electronic and optical properties of CAWs can be finely tuned by controlling the wire length (i.e., the number of carbon atoms) and the type of termination (e.g., atom, molecular group or nanostructure). Although linear, sp-hybridized carbon systems are still considered elusive and unstable materials, a number of nanostructures consisting of sp-carbon wires have been produced and characterized to date. In this short review, we present the main CAW synthesis techniques and stabilization strategies and we discuss the current status of the understanding of their structural, electronic and vibrational properties with particular attention to how these properties are related to one another. We focus on the use of vibrational spectroscopy to provide information on the structural and electronic properties of the system (e.g., determination of wire length). Moreover, by employing Raman spectroscopy and surface enhanced Raman scattering in combination with the support of first principles calculations, we show that a detailed understanding of the charge transfer between CAWs and metal nanoparticles may open the possibility to tune the electronic structure from alternating to equalized bonds. PMID:25821689

Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities.

PubMed

Neumann, Piotr; Tittmann, Kai

2014-12-01

Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

Are X-rays the key to integrated computational materials engineering?

DOE PAGES

Ice, Gene E.

2015-11-01

The ultimate dream of materials science is to predict materials behavior from composition and processing history. Owing to the growing power of computers, this long-time dream has recently found expression through worldwide excitement in a number of computation-based thrusts: integrated computational materials engineering, materials by design, computational materials design, three-dimensional materials physics and mesoscale physics. However, real materials have important crystallographic structures at multiple length scales, which evolve during processing and in service. Moreover, real materials properties can depend on the extreme tails in their structural and chemical distributions. This makes it critical to map structural distributions with sufficient resolutionmore » to resolve small structures and with sufficient statistics to capture the tails of distributions. For two-dimensional materials, there are high-resolution nondestructive probes of surface and near-surface structures with atomic or near-atomic resolution that can provide detailed structural, chemical and functional distributions over important length scales. Furthermore, there are no nondestructive three-dimensional probes with atomic resolution over the multiple length scales needed to understand most materials.« less

Programming new geometry restraints: Parallelity of atomic groups

DOE PAGES

Sobolev, Oleg V.; Afonine, Pavel V.; Adams, Paul D.; ...

2015-08-01

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they canmore » be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox( cctbx) are presented.« less

Embedded-atom-method study of structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys

NASA Astrophysics Data System (ADS)

Asta, Mark; Morgan, Dane; Hoyt, J. J.; Sadigh, Babak; Althoff, J. D.; de Fontaine, D.; Foiles, S. M.

1999-06-01

Structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys have been studied by Monte Carlo and molecular-dynamics simulations based upon three different embedded-atom method (EAM) interatomic potentials, namely those due to Foiles and Daw (FD) [J. Mater. Res. 2, 5 (1987)], Voter and Chen (VC) [in Characterization of Defects in Materials, edited by R. W. Siegel et al. MRS Symposia Proceedings. No. 82 (Materials Research Society, Pittsburgh, 1987), p.175] and Ludwig and Gumbsch (LG) [Model. Simul. Mater. Sci. Eng. 3, 533 (1995)]. We present detailed comparisons between calculated results and experimental data for structure factors, atomic volumes, enthalpies of mixing, activities, and viscosities. Calculated partial structure factors are found to be in semiquantitative agreement with published neutron scattering measurements for Ni20Al80 alloys, indicating that short-range order in the liquid phase is qualitatively well described. Calculated thermodynamic properties of mixing are found to agree very well with experimental data for Ni compositions greater than 75 atomic %, while for alloys richer in Al the magnitudes of the enthalpies and entropies of mixing are significantly underestimated. The VC and LG potentials give atomic densities and viscosities in good agreement with experiment for Ni-rich compositions, while FD potentials consistently underestimate both properties at all concentrations. The results of this study demonstrate that VC and LG potentials provide a realistic description of the thermodynamic and atomic transport properties for NixAl1-x liquid alloys with x>=0.75, and point to the limitations of EAM potentials for alloys richer in Al.

Observation of dynamic atom-atom correlation in liquid helium in real space.

PubMed

Dmowski, W; Diallo, S O; Lokshin, K; Ehlers, G; Ferré, G; Boronat, J; Egami, T

2017-05-04

Liquid 4 He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4 He atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.

Structural refinement of vitreous silica bilayers

NASA Astrophysics Data System (ADS)

Sadjadi, Mahdi; Wilson, Mark; Thorpe, M. F.

The importance of glasses resides not only in their applications but in fundamental questions that they put forth. The continuous random network model can successfully describe the glass structure, but determining details, like ring statistics, has always been difficult using only diffraction data. But recent atomic images of 2D vitreous silica bilayers can offer valuable new insights which are hard to be observed directly in 3D silica models/experiments (for references see). However, the experimental results are prone to uncertainty in atomic positions, systematic errors, and being finite. We employ special boundary conditions developed for such networks to refine the experimental structures. We show the best structure can be found by using various potentials to maximize information gained from the experimental samples. We find a range of densities, the so-called flexibility window, in which tetrahedra are perfect. We compare results from simulations using harmonic potentials, MD with atomic polarizabilities included and DFT. We should thank David Drabold and Bishal Bhattarai for useful discussions. Support through NSF Grant # DMS 1564468 is gratefully acknowledged.

Hierarchical structures of amorphous solids characterized by persistent homology

PubMed Central

Hiraoka, Yasuaki; Nakamura, Takenobu; Hirata, Akihiko; Escolar, Emerson G.; Matsue, Kaname; Nishiura, Yasumasa

2016-01-01

This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions such as curves and islands in the PDs identify meaningful shape characteristics of the atomic configuration. Although the method can be applied to a wide variety of disordered systems, it is applied here to silica glass, the Lennard-Jones system, and Cu-Zr metallic glass as standard examples of continuous random network and random packing structures. In silica glass, the method classified the atomic rings as short-range and medium-range orders and unveiled hierarchical ring structures among them. These detailed geometric characterizations clarified a real space origin of the first sharp diffraction peak and also indicated that PDs contain information on elastic response. Even in the Lennard-Jones system and Cu-Zr metallic glass, the hierarchical structures in the atomic configurations were derived in a similar way using PDs, although the glass structures and properties substantially differ from silica glass. These results suggest that the PDs provide a unified method that extracts greater depth of geometric information in amorphous solids than conventional methods. PMID:27298351

Hierarchical Multiscale Modeling of Macromolecules and their Assemblies

PubMed Central

Ortoleva, P.; Singharoy, A.; Pankavich, S.

2013-01-01

Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character of such systems often makes traditional molecular dynamics simulation impractical, a multiscale approach has been presented that allows for long-time simulation with atomic detail based on the co-evolution of slowly-varying order parameters (OPs) with the quasi-equilibrium probability density of atomic configurations. However, this approach breaks down when the structural change is extreme, or when nearest-neighbor connectivity of atoms is not maintained. In the current study, a self-consistent approach is presented wherein OPs and a reference structure co-evolve slowly to yield long-time simulation for dynamical soft-matter phenomena such as structural transitions and self-assembly. The development begins with the Liouville equation for N classical atoms and an ansatz on the form of the associated N-atom probability density. Multiscale techniques are used to derive Langevin equations for the coupled OP-configurational dynamics. The net result is a set of equations for the coupled stochastic dynamics of the OPs and centers of mass of the subsystems that constitute a soft material body. The theory is based on an all-atom methodology and an interatomic force field, and therefore enables calibration-free simulations of soft matter, such as macromolecular assemblies. PMID:23671457

Near-edge X-ray absorption spectra for metallic Cu and Mn

NASA Astrophysics Data System (ADS)

Greaves, G. N.; Durham, P. J.; Diakun, G.; Quinn, P.

1981-11-01

The measurement of X-ray absorption fine structure of metals- both in the extended region (EXAFS) as well as in the near edge region (XANES)-has been widely discussed (see refs 1-6 for Cu and refs 7-9 for Mn). The recent availability of intense X-ray fluxes from storage rings has usually been exploited for EXAFS leaving the XANES often with poorer resolution than earlier work performed on conventional sources (for example, compare the near edge structure for copper in ref. 1 with refs 3 or 6). In addition, whilst the theory and analysis of EXAFS is relatively well-established2,10, a theory for the strong scattering regime near to the absorption edge has only recently been developed11. We report here the first high resolution XANES spectra for Cu and Mn which were performed at the SRS storage ring at Daresbury. Although both metals have close-packed structures consisting of atoms of similar size their local atomic structure is different in detail. Significant differences are found in their respective XANES reflecting the senstivity of this region of the X-ray absorption fine structure to the local atomic structure. Spectra for the two metals have been analysed using the new multiple scattering formalism. This is a real space calculation and unlike a conventional band structure approach it does not require structural periodicity but works from the local arrangement of atoms.

Coherent and radiative couplings through two-dimensional structured environments

NASA Astrophysics Data System (ADS)

Galve, F.; Zambrini, R.

2018-03-01

We study coherent and radiative interactions induced among two or more quantum units by coupling them to two-dimensional (2D) lattices acting as structured environments. This model can be representative of atoms trapped near photonic crystal slabs, trapped ions in Coulomb crystals, or to surface acoustic waves on piezoelectric materials, cold atoms on state-dependent optical lattices, or even circuit QED architectures, to name a few. We compare coherent and radiative contributions for the isotropic and directional regimes of emission into the lattice, for infinite and finite lattices, highlighting their differences and existing pitfalls, e.g., related to long-time or large-lattice limits. We relate the phenomenon of directionality of emission with linear-shaped isofrequency manifolds in the dispersion relation, showing a simple way to disrupt it. For finite lattices, we study further details such as the scaling of resonant number of lattice modes for the isotropic and directional regimes, and relate this behavior with known van Hove singularities in the infinite lattice limit. Furthermore, we export the understanding of emission dynamics with the decay of entanglement for two quantum, atomic or bosonic, units coupled to the 2D lattice. We analyze in some detail completely subradiant configurations of more than two atoms, which can occur in the finite lattice scenario, in contrast with the infinite lattice case. Finally, we demonstrate that induced coherent interactions for dark states are zero for the finite lattice.

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

PubMed

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Structural biologists capture detailed image of gene regulator’s fleeting form | Center for Cancer Research

Cancer.gov

Using an ultrafast, high-intensity radiation source called an X-ray free-electron laser (XFEL), scientists have captured an atomic-level picture of an RNA structure called a riboswitch as it reorganizes itself to regulate protein production. The structure they visualized has never before been seen, and likely exists for only milliseconds after the riboswitch first encounters its activating molecule.  Read more...  

An epistemology on the nature of polymers.

PubMed

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity.

AFM Structural Characterization of Drinking Water Biofilm ...

EPA Pesticide Factsheets

Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

An Epistemology on the Nature of Polymers

PubMed Central

Laridjani, Mortéza; Leboucher, Pierre

2014-01-01

Liquids have neither a periodic structure nor the completely random character of gases therefore the detailed study of their x-ray scattering diagram encounters many difficulties. The idea of periodic regularity in molecules of liquid polymers has been an attractive proposition for the simple interpretation of liquid polymer x-ray diagrams. The categorisation of polymer substances as being between a crystal phase with a perfect order and an amorphous disordered state is an over simplification of the complex reality. For obtaining structural information, during the early stages of the application of x-ray diffraction, a near crystalline model of the molecular arrangements in liquids was utilised. However, the results from these investigations led to just an approximation of the crystalline state. Our studies have analysed the real image of Fourier space of liquid polymers, for the first time, using anomalous diffractometry. The findings show the precise atomic structure of liquid polymers when transformed, by cooling, to solid polymers. We demonstrate that there is an intermediate ordered structure, characterised by the real full image of Fourier space. This prominent state of matter, an intermediate ordered structure, is defined by a regular unit cell with a five-fold symmetry. These structural atomic studies contribute to a more detailed understanding of the properties of polymers than the traditional studies of the degree of crystallinity. PMID:25329440

Advanced Structural Analyses by Third Generation Synchrotron Radiation Powder Diffraction

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

Sakata, M.; Aoyagi, S.; Ogura, T.

2007-01-19

Since the advent of the 3rd generation Synchrotron Radiation (SR) sources, such as SPring-8, the capabilities of SR powder diffraction increased greatly not only in an accurate structure refinement but also ab initio structure determination. In this study, advanced structural analyses by 3rd generation SR powder diffraction based on the Large Debye-Scherrer camera installed at BL02B2, SPring-8 is described. Because of high angular resolution and high counting statistics powder data collected at BL02B2, SPring-8, ab initio structure determination can cope with a molecular crystals with 65 atoms including H atoms. For the structure refinements, it is found that a kindmore » of Maximum Entropy Method in which several atoms are omitted in phase calculation become very important to refine structural details of fairy large molecule in a crystal. It should be emphasized that until the unknown structure is refined very precisely, the obtained structure by Genetic Algorithm (GA) or some other ab initio structure determination method using real space structural knowledge, it is not possible to tell whether the structure obtained by the method is correct or not. In order to determine and/or refine crystal structure of rather complicated molecules, we cannot overemphasize the importance of the 3rd generation SR sources.« less

Structure of shock compressed model basaltic glass: Insights from O K-edge X-ray Raman scattering and high-resolution 27Al NMR spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Sung Keun; Park, Sun Young; Kim, Hyo-Im; Tschauner, Oliver; Asimow, Paul; Bai, Ligang; Xiao, Yuming; Chow, Paul

2012-03-01

The detailed atomic structures of shock compressed basaltic glasses are not well understood. Here, we explore the structures of shock compressed silicate glass with a diopside-anorthite eutectic composition (Di64An36), a common Fe-free model basaltic composition, using oxygen K-edge X-ray Raman scattering and high- resolution 27Al solid-state NMR spectroscopy and report previously unknown details of shock-induced changes in the atomic configurations. A topologically driven densification of the Di64An36 glass is indicated by the increase in oxygen K-edge energy for the glass upon shock compression. The first experimental evidence of the increase in the fraction of highly coordinated Al in shock compressed glass is found in the 27Al NMR spectra. This unambiguous evidence of shock-induced changes in Al coordination environments provides atomistic insights into shock compression in basaltic glasses and allows us to microscopically constrain the magnitude of impact events or relevant processes involving natural basalts on Earth and planetary surfaces.

Multistep modeling of protein structure: application to bungarotoxin

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

An experimental study of air-assist atomizer spray flames

NASA Technical Reports Server (NTRS)

Mao, Chien-Pei; Wang, Geng; Chigier, Norman

1988-01-01

It is noted that air-assisted atomizer spray flames encountered in furnaces, boilers, and gas turbine combustors possess a more complex structure than homogeneous turbulent diffusion flames, due to the swirling motion introduced into the fuel and air flows for the control of flame stability, length, combustion intensity, and efficiency. Detailed comparisons are presented between burning and nonburning condition measurements of these flames obtained by nonintrusive light scattering phase/Doppler detection. Spray structure is found to be drastically changed within the flame reaction zone, with changes in the magnitude and shape of drop number density, liquid flux, mean drop size diameter, and drop mean axial velocity radial distributions.

Advanced Electronic Structure Calculations For Nanoelectronics Using Finite Element Bases and Effective Mass Theory.

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

Gamble, John King; Nielsen, Erik; Baczewski, Andrew David

This paper describes our work over the past few years to use tools from quantum chemistry to describe electronic structure of nanoelectronic devices. These devices, dubbed "artificial atoms", comprise a few electrons, con ned by semiconductor heterostructures, impurities, and patterned electrodes, and are of intense interest due to potential applications in quantum information processing, quantum sensing, and extreme-scale classical logic. We detail two approaches we have employed: nite-element and Gaussian basis sets, exploring the interesting complications that arise when techniques that were intended to apply to atomic systems are instead used for artificial, solid-state devices.

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms

PubMed Central

Olson, Wilma K.

2014-01-01

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides. PMID:24791158

First-Principles Study of the Electronic Structure and Bonding Properties of X8C46 and X8B6C40 (X: Li, Na, Mg, Ca) Carbon Clathrates

NASA Astrophysics Data System (ADS)

KoleŻyński, Andrzej; Szczypka, Wojciech

2016-03-01

Results from theoretical analysis of the crystal structure, electronic structure, and bonding properties of C46 and B6C40 carbon clathrates doped with selected alkali and alkaline earth metals cations (Li, Na, Mg, Ca) are presented. The ab initio calculations were performed by means of the WIEN2k package (full potential linearized augmented plane wave method (FP-LAPW) within density functional theory (DFT)) with PBESol and modified Becke-Johnson exchange-correlation potentials used in geometry optimization and electronic structure calculations, respectively. The bonding properties were analyzed by applying Bader's quantum theory of atoms in molecules formalism to the topological properties of total electron density obtained from ab initio calculations. Analysis of the results obtained (i.a. equilibrium geometry, equation of state, cohesive energy, band structure, density of states—both total and projected on to particular atoms, and topological properties of bond critical points and net charges of topological atoms) is presented in detail.

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)].

Deciphering chemical order/disorder and material properties at the single-atom level.

PubMed

Yang, Yongsoo; Chen, Chien-Chun; Scott, M C; Ophus, Colin; Xu, Rui; Pryor, Alan; Wu, Li; Sun, Fan; Theis, Wolfgang; Zhou, Jihan; Eisenbach, Markus; Kent, Paul R C; Sabirianov, Renat F; Zeng, Hao; Ercius, Peter; Miao, Jianwei

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

Atomic-level characterization of the structural dynamics of proteins.

PubMed

Shaw, David E; Maragakis, Paul; Lindorff-Larsen, Kresten; Piana, Stefano; Dror, Ron O; Eastwood, Michael P; Bank, Joseph A; Jumper, John M; Salmon, John K; Shan, Yibing; Wriggers, Willy

2010-10-15

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.

Three-Dimensional Intercalated Porous Graphene on Si(111)

NASA Astrophysics Data System (ADS)

Pham, Trung T.; Sporken, Robert

2018-02-01

Three-dimensional intercalated porous graphene has been formed on Si(111) by electron beam evaporation under appropriate conditions and its structural and electronic properties investigated in detail by reflection high-energy electron diffraction, x-ray photoemission spectroscopy, Raman spectroscopy, high-resolution scanning electron microscopy, atomic force microscopy, and scanning tunneling microscopy. The results show that the crystalline quality of the porous graphene depended not only on the substrate temperature but also on the SiC layer thickness during carbon atom deposition.

Atomic structure of water/Au, Ag, Cu and Pt atomic junctions.

PubMed

Li, Yu; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

2017-02-08

Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.

Observation of dynamic atom-atom correlation in liquid helium in real space

DOE PAGES

Dmowski, W.; Diallo, S. O.; Lokshin, K.; ...

2017-05-04

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Observation of dynamic atom-atom correlation in liquid helium in real space

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

Dmowski, W.; Diallo, S. O.; Lokshin, K.

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Coherent all-optical control of ultracold atoms arrays in permanent magnetic traps.

PubMed

Abdelrahman, Ahmed; Mukai, Tetsuya; Häffner, Hartmut; Byrnes, Tim

2014-02-10

We propose a hybrid architecture for quantum information processing based on magnetically trapped ultracold atoms coupled via optical fields. The ultracold atoms, which can be either Bose-Einstein condensates or ensembles, are trapped in permanent magnetic traps and are placed in microcavities, connected by silica based waveguides on an atom chip structure. At each trapping center, the ultracold atoms form spin coherent states, serving as a quantum memory. An all-optical scheme is used to initialize, measure and perform a universal set of quantum gates on the single and two spin-coherent states where entanglement can be generated addressably between spatially separated trapped ultracold atoms. This allows for universal quantum operations on the spin coherent state quantum memories. We give detailed derivations of the composite cavity system mediated by a silica waveguide as well as the control scheme. Estimates for the necessary experimental conditions for a working hybrid device are given.

Strongly-correlated crystal-field approach to heavy-fermion compounds and to 3d oxides

NASA Astrophysics Data System (ADS)

Radwanski, Ryszard; Ropka, Zofia

2005-03-01

The description of electronic and magnetic properties of real compounds like LaMnO3, LaCoO3, Na2V3O7, FeO, NdAl2 and ErNi5 as well as heavy-fermion superconductor UPd2Al3 and heavy-fermion metal YbRh2Si2, both zero-temperature ground state properties and thermodynamics, will be presented pointing out the existence of a discrete atomic-like low-energy, in the meV scale, electronic structure. This low-energy many-electron discrete atomic-like electronic structure is governed by very strong electron correlations, predominantly on-site, by the intra-atomic spin-orbit coupling and by details of the local surrounding (crystal-field interactions), but later is modified by inter-site interactions. Our studies indicate that there is the highest time to ``unquench'' the orbital moment in solid state physics in description of 3d-/4f-/5f-atom containing compounds and that heavy-fermion phenomena are of the relativistic origin.

Imaging and manipulation of adatoms on an alumina surface by noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Simon, G. H.; Heyde, M.; Freund, H.-J.

2012-02-01

Noncontact atomic force microscopy (NC-AFM) has been performed on an aluminum oxide film grown on NiAl(110) in ultrahigh vacuum (UHV) at low temperature (5 K). Results reproduce the topography of the structural model, unlike scanning tunnelling microscopy (STM) images. Equipped with this extraordinary contrast the network of extended defects, which stems from domain boundaries intersecting the film surface, can be analysed in atomic detail. The knowledge of occurring surface structures opens up the opportunity to determine adsorption sites of individual adsorbates on the alumina film. The level of difficulty for such imaging depends on the imaging characteristics of the substrate and the interaction which can be maintained above the adsorbate. Positions of single adsorbed gold atoms within the unit cell have been determined despite their easy removal at slightly higher interaction strength. Preliminary manipulation experiments indicate a pick-up process for the vanishing of the gold adatoms from the film surface.

Correlating Atom Probe Tomography with Atomic-Resolved Scanning Transmission Electron Microscopy: Example of Segregation at Silicon Grain Boundaries.

PubMed

Stoffers, Andreas; Barthel, Juri; Liebscher, Christian H; Gault, Baptiste; Cojocaru-Mirédin, Oana; Scheu, Christina; Raabe, Dierk

2017-04-01

In the course of a thorough investigation of the performance-structure-chemistry interdependency at silicon grain boundaries, we successfully developed a method to systematically correlate aberration-corrected scanning transmission electron microscopy and atom probe tomography. The correlative approach is conducted on individual APT and TEM specimens, with the option to perform both investigations on the same specimen in the future. In the present case of a Σ9 grain boundary, joint mapping of the atomistic details of the grain boundary topology, in conjunction with chemical decoration, enables a deeper understanding of the segregation of impurities observed at such grain boundaries.

Atomistic modeling of alternating access of a mitochondrial ADP/ATP membrane transporter with molecular simulations

PubMed Central

Hayashi, Shigehiko

2017-01-01

The mitochondrial ADP/ATP carrier (AAC) is a membrane transporter that exchanges a cytosolic ADP for a matrix ATP. Atomic structures in an outward-facing (OF) form which binds an ADP from the intermembrane space have been solved by X-ray crystallography, and revealed their unique pseudo three-fold symmetry fold which is qualitatively different from pseudo two-fold symmetry of most transporters of which atomic structures have been solved. However, any atomic-level information on an inward-facing (IF) form, which binds an ATP from the matrix side and is fixed by binding of an inhibitor, bongkrekic acid (BA), is not available, and thus its alternating access mechanism for the transport process is unknown. Here, we report an atomic structure of the IF form predicted by atomic-level molecular dynamics (MD) simulations of the alternating access transition with a recently developed accelerating technique. We successfully obtained a significantly stable IF structure characterized by newly formed well-packed and -organized inter-domain interactions through the accelerated simulations of unprecedentedly large conformational changes of the alternating access without a prior knowledge of the target protein structure. The simulation also shed light on an atomistic mechanism of the strict transport selectivity of adenosine nucleotides over guanosine and inosine ones. Furthermore, the IF structure was shown to bind ATP and BA, and thus revealed their binding mechanisms. The present study proposes a qualitatively novel view of the alternating access of transporters having the unique three-fold symmetry in atomic details and opens the way for rational drug design targeting the transporter in the dynamic functional cycle. PMID:28727843

All-atom molecular dynamics of virus capsids as drug targets

DOE PAGES

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

2016-04-29

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

All-atom molecular dynamics of virus capsids as drug targets

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

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

STM study on the surface structures and defects of SnSe

NASA Astrophysics Data System (ADS)

Kim, Jungdae; Duvjir, Ganbat; Ly, Trinh Thi; Min, Taewon; Kim, Taehoon; Kim, Sang Hwa; Duong, Anh-Tuan; Rhim, S. H.; Cho, Sunglae; Lee, Jaekwang

Tin selenide (SnSe) is a IV-VI semiconductor with a band gap of 1.0 eV, and also one of layered chalcogenide materials (LCMs) where each layer is coupled by weak van der Waals interactions. SnSe has been widely studied due to its many potential applications that take advantage of its excellent thermoelectric, photovoltaic, and optoelectronic properties. However, experimental investigations into the microscopic structure of SnSe remain largely unexplored. The atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM). The cleaved surface of SnSe is comprised of covalently bonded Se and Sn atoms in zigzag patterns. However, rectangular periodicity was observed in the atomic images of SnSe surfaces for filled and empty state probing. Detailed atomic structures are analyzed by density functional theory (DFT) calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms. We also report the origin of p-type behavior in SnSe by investigating three dominant intrinsic defects (Sn, Se, and Se-Sn-Se vacancies) using STM and DFT calculations. This work was supported by the National Research Foundation of Korea (NRF-2015R1D1A1A01057271, NRF-2009-0093818, and NRF-2014R1A4A1071686).

The role of atomic level steric effects and attractive forces in protein folding.

PubMed

Lammert, Heiko; Wolynes, Peter G; Onuchic, José N

2012-02-01

Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C(β) atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Copyright © 2011 Wiley Periodicals, Inc.

Development of a force sensor using atom interferometry to constrain theories on dark matter and dark energy

NASA Astrophysics Data System (ADS)

Schlupf, Chandler; Niederriter, Robert; Bohr, Eliot; Khamis, Sami; Park, Youna; Szwed, Erik; Hamilton, Paul

2017-04-01

Atom interferometry has been used in many precision measurements such as Newton's gravitational constant, the fine structure constant, and tests of the equivalence principle. We will perform atom interferometry in an optical lattice to measure the force felt by an atom due to a test mass in search of new forces suggested by dark matter and dark energy theories. We will be developing a new apparatus using laser-cooled ytterbium to continuously measure this force by observing their Bloch oscillations. Interfering atoms in an optical lattice allows continuous measurements in a small volume over a long period of time, enabling our device to be sensitive to time-varying forces while minimizing vibrational noise. We present the details of this experiment and the progress on it thus far.

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

Surface Atomic Structure and Functionality of Metallic Nanoparticles: A Case Study of Au–Pd Nanoalloy Catalysts

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

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit

The surface atomic structure of metallic nanoparticles (NPs) plays a key role in shaping their physicochemical properties and response to external stimuli. Not surprisingly, current research increasingly focuses on exploiting its prime characteristics, including the amount, location, coordination, and electronic configuration of distinct surface atomic species, as tunable parameters for improving the functionality of metallic NPs in practical applications. The effort requires clear understanding of the extent to which changes in each of these characteristics would contribute to achieving the targeted functionality. This, in the first place, requires good knowledge of the actual surface of metallic NPs at atomic level.more » Through a case study on Au–Pd nanoalloy catalysts of industrial and environmental importance, we demonstrate that the surface atomic structure of metallic NPs can be determined in good detail by resonant high-energy X-ray diffraction (HE-XRD). Furthermore, using our experimental surface structure and CO oxidation activity data, we shed new light on the elusive origin of the remarkable catalytic synergy between surface Au and Pd atoms in the nanoalloys. In particular, we show that it arises from the formation of a specific “skin” on top of the nanoalloys that involves as many unlike, i.e., Au–Pd and Pd–Au, atomic pairs as possible given the overall chemical composition of the NPs. Moreover, unlike atoms from the “skin” interact strongly, including both changing their size and electronic structure in inverse proportions. That is, Au atoms shrink and acquire a partial positive charge of 5d-character whereas Pd atoms expand and become somewhat 4d-electron deficient. Accordingly, the reactivity of Au increases whereas Pd atoms become less reactive, as compared to atoms at the surface of pure Au and Pd NPs, respectively. Ultimately, this renders Au–Pd alloy NPs superb catalysts for CO oxidation reaction over a broad range of alloy compositions. Our findings are corroborated by DFT calculations based on a refined version of d-band center theory on the catalytic properties of late transition metals and alloys. Here, we discuss opportunities for improving the accuracy of current theory on surface-controlled properties of metallic NPs through augmenting the theory with surface structure data obtained by resonant XRD.« less

Surface Atomic Structure and Functionality of Metallic Nanoparticles: A Case Study of Au–Pd Nanoalloy Catalysts

DOE PAGES

Petkov, Valeri; Prasai, Binay; Shastri, Sarvjit; ...

2017-03-23

The surface atomic structure of metallic nanoparticles (NPs) plays a key role in shaping their physicochemical properties and response to external stimuli. Not surprisingly, current research increasingly focuses on exploiting its prime characteristics, including the amount, location, coordination, and electronic configuration of distinct surface atomic species, as tunable parameters for improving the functionality of metallic NPs in practical applications. The effort requires clear understanding of the extent to which changes in each of these characteristics would contribute to achieving the targeted functionality. This, in the first place, requires good knowledge of the actual surface of metallic NPs at atomic level.more » Through a case study on Au–Pd nanoalloy catalysts of industrial and environmental importance, we demonstrate that the surface atomic structure of metallic NPs can be determined in good detail by resonant high-energy X-ray diffraction (HE-XRD). Furthermore, using our experimental surface structure and CO oxidation activity data, we shed new light on the elusive origin of the remarkable catalytic synergy between surface Au and Pd atoms in the nanoalloys. In particular, we show that it arises from the formation of a specific “skin” on top of the nanoalloys that involves as many unlike, i.e., Au–Pd and Pd–Au, atomic pairs as possible given the overall chemical composition of the NPs. Moreover, unlike atoms from the “skin” interact strongly, including both changing their size and electronic structure in inverse proportions. That is, Au atoms shrink and acquire a partial positive charge of 5d-character whereas Pd atoms expand and become somewhat 4d-electron deficient. Accordingly, the reactivity of Au increases whereas Pd atoms become less reactive, as compared to atoms at the surface of pure Au and Pd NPs, respectively. Ultimately, this renders Au–Pd alloy NPs superb catalysts for CO oxidation reaction over a broad range of alloy compositions. Our findings are corroborated by DFT calculations based on a refined version of d-band center theory on the catalytic properties of late transition metals and alloys. Here, we discuss opportunities for improving the accuracy of current theory on surface-controlled properties of metallic NPs through augmenting the theory with surface structure data obtained by resonant XRD.« less

First-principles calculations of K-shell X-ray absorption spectra for warm dense nitrogen

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

Li, Zi; Zhang, Shen; Kang, Wei

2016-05-15

X-ray absorption spectrum is a powerful tool for atomic structure detection on warm dense matter. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations on warm dense nitrogen along a Hugoniot curve. From the molecular dynamics trajectory, the detailed atomic structures are examined for each thermodynamical condition. The K-shell X-ray absorption spectrum is calculated, and its changes with temperature and pressure along the Hugoniot curve are discussed. The warm dense nitrogen systems may contain isolated nitrogen atoms, N{sub 2} molecules, and nitrogen clusters, which show quite different contributions to the total X-ray spectrum due to their different electronmore » density of states. The changes of X-ray spectrum along the Hugoniot curve are caused by the different nitrogen structures induced by the temperature and the pressure. Some clear signatures on X-ray spectrum for different thermodynamical conditions are pointed out, which may provide useful data for future X-ray experiments.« less

Symmetry and novelty in the electronic and geometric structure of nanoalloys:. the case of Ag27Cu7

NASA Astrophysics Data System (ADS)

Ortigoza, M. Alcántara; Rahman, T. S.

2008-04-01

Nanoparticles of bimetallic alloys have been shown to possess composition dependent characteristics which distinguish themselves from the corresponding bulk alloys. Taking the 34-atom nanoalloy of Ag and Cu (Ag27Cu7), we show using first principles electronic structure calculations that this core-shell alloy indeed has perfect D5h symmetry and consists of only 6 non-equivalent (2 Cu and 4 Ag) atoms. Analysis of the interatomic bond lengths and detailed electronic structure further reveal that the Cu atoms play a major role in controlling the characteristics of the nanoalloy. The higher cohesive energy, together with shorter bond length for Cu, compared to Ag, conspire to produce a hierarchy in the relative strengths of the Ag - Cu, Ag - Ag, and Cu - Cu bonds and corresponding interatomic bond lengths, point to the uniqueness in the characteristics of this nanoalloy. Charge density plots of Ag27Cu7 provide further insights into the relative strengths of the various interatomic bonds.

The application of 3D Zernike moments for the description of "model-free" molecular structure, functional motion, and structural reliability.

PubMed

Grandison, Scott; Roberts, Carl; Morris, Richard J

2009-03-01

Protein structures are not static entities consisting of equally well-determined atomic coordinates. Proteins undergo continuous motion, and as catalytic machines, these movements can be of high relevance for understanding function. In addition to this strong biological motivation for considering shape changes is the necessity to correctly capture different levels of detail and error in protein structures. Some parts of a structural model are often poorly defined, and the atomic displacement parameters provide an excellent means to characterize the confidence in an atom's spatial coordinates. A mathematical framework for studying these shape changes, and handling positional variance is therefore of high importance. We present an approach for capturing various protein structure properties in a concise mathematical framework that allows us to compare features in a highly efficient manner. We demonstrate how three-dimensional Zernike moments can be employed to describe functions, not only on the surface of a protein but throughout the entire molecule. A number of proof-of-principle examples are given which demonstrate how this approach may be used in practice for the representation of movement and uncertainty.

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

Zarkevich, N. A.; Johnson, D. D.

NiTi is the most used shape-memory alloy, nonetheless, a lack of understanding remains regarding the associated structures and transitions, including their barriers. Using a generalized solid-state nudge elastic band (GSSNEB) method implemented via density-functional theory, we detail the structural transformations in NiTi relevant to shape memory: those between body-centered orthorhombic (BCO) groundstate and a newly identified stable austenite (“glassy” B2-like) structure, including energy barriers (hysteresis) and intermediate structures (observed as a kinetically limited R-phase), and between martensite variants (BCO orientations). All results are in good agreement with available experiment. We contrast the austenite results to those from the often-assumed, butmore » unstable B2. Furthermore, these high- and low-temperature structures and structural transformations provide much needed atomic-scale detail for transitions responsible for NiTi shape-memory effects.« less

Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

PubMed

Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

2011-11-14

The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

Paramagnetic and Diamagnetic Materials

ERIC Educational Resources Information Center

Thompson, Frank

2011-01-01

Paramagnetic and diamagnetic materials are now generally known as the "Cinderella" materials of the magnetic world. However, susceptibility measurements made on these materials in the past have revealed many details about the molecular bonding and the atomic structure of the so-called "transition" elements. Indeed, the magnetic moment of neodymium…

Scanning tunneling microscopy and atomic force microscopy: application to biology and technology.

PubMed

Hansma, P K; Elings, V B; Marti, O; Bracker, C E

1988-10-14

The scanning tunneling microscope (STM) and the atomic force microscope (AFM) are scanning probe microscopes capable of resolving surface detail down to the atomic level. The potential of these microscopes for revealing subtle details of structure is illustrated by atomic resolution images including graphite, an organic conductor, an insulating layered compound, and individual adsorbed oxygen atoms on a semiconductor. Application of the STM for imaging biological materials directly has been hampered by the poor electron conductivity of most biological samples. The use of thin conductive metal coatings and replicas has made it possible to image some biological samples, as indicated by recently obtained images of a recA-DNA complex, a phospholipid bilayer, and an enzyme crystal. The potential of the AFM, which does not require a conductive sample, is shown with molecular resolution images of a nonconducting organic monolayer and an amino acid crystal that reveals individual methyl groups on the ends of the amino acids. Applications of these new microscopes to technology are demonstrated with images of an optical disk stamper, a diffraction grating, a thin-film magnetic recording head, and a diamond cutting tool. The STM has even been used to improve the quality of diffraction gratings and magnetic recording heads.

Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.

PubMed

Howard, E I; Sanishvili, R; Cachau, R E; Mitschler, A; Chevrier, B; Barth, P; Lamour, V; Van Zandt, M; Sibley, E; Bon, C; Moras, D; Schneider, T R; Joachimiak, A; Podjarny, A

2004-06-01

The first subatomic resolution structure of a 36 kDa protein [aldose reductase (AR)] is presented. AR was cocrystallized at pH 5.0 with its cofactor NADP+ and inhibitor IDD 594, a therapeutic candidate for the treatment of diabetic complications. X-ray diffraction data were collected up to 0.62 A resolution and treated up to 0.66 A resolution. Anisotropic refinement followed by a blocked matrix inversion produced low standard deviations (<0.005 A). The model was very well ordered overall (CA atoms' mean B factor is 5.5 A2). The model and the electron-density maps revealed fine features, such as H-atoms, bond densities, and significant deviations from standard stereochemistry. Other features, such as networks of hydrogen bonds (H bonds), a large number of multiple conformations, and solvent structure were also better defined. Most of the atoms in the active site region were extremely well ordered (mean B approximately 3 A2), leading to the identification of the protonation states of the residues involved in catalysis. The electrostatic interactions of the inhibitor's charged carboxylate head with the catalytic residues and the charged coenzyme NADP+ explained the inhibitor's noncompetitive character. Furthermore, a short contact involving the IDD 594 bromine atom explained the selectivity profile of the inhibitor, important feature to avoid toxic effects. The presented structure and the details revealed are instrumental for better understanding of the inhibition mechanism of AR by IDD 594, and hence, for the rational drug design of future inhibitors. This work demonstrates the capabilities of subatomic resolution experiments and stimulates further developments of methods allowing the use of the full potential of these experiments. Copyright 2004 Wiley-Liss, Inc.

Spectroscopic diagnostics of NIF ICF implosions using line ratios of Kr dopant in the ignition capsule

NASA Astrophysics Data System (ADS)

Dasgupta, Arati; Ouart, Nicholas; Giuiani, John; Clark, Robert; Schneider, Marilyn; Scott, Howard; Chen, Hui; Ma, Tammy

2017-10-01

X ray spectroscopy is used on the NIF to diagnose the plasma conditions in the ignition target in indirect drive ICF implosions. A platform is being developed at NIF where small traces of krypton are used as a dopant to the fuel gas for spectroscopic diagnostics using krypton line emissions. The fraction of krypton dopant was varied in the experiments and was selected so as not to perturb the implosion. Our goal is to use X-ray spectroscopy of dopant line ratios produced by the hot core that can provide a precise measurement of electron temperature. Simulations of the krypton spectra using a 1 in 104 atomic fraction of krypton in direct-drive exploding pusher with a range of electron temperatures and densities show discrepancies when different atomic models are used. We use our non-LTE atomic model with a detailed fine-structure level atomic structure and collisional-radiative rates to investigate the krypton spectra at the same conditions. Synthetic spectra are generated with a detailed multi-frequency radiation transport scheme from the emission regions of interest to analyze the experimental data with 0.02% Kr concentration and compare and contrast with the existing simulations at LLNL. Work supported by DOE/NNSA; Part of this work was also done under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.

Solid-state NMR sequential assignment of the β-endorphin peptide in its amyloid form.

PubMed

Seuring, Carolin; Gath, Julia; Verasdonck, Joeri; Cadalbert, Riccardo; Rivier, Jean; Böckmann, Anja; Meier, Beat H; Riek, Roland

2016-10-01

Insights into the three-dimensional structure of hormone fibrils are crucial for a detailed understanding of how an amyloid structure allows the storage of hormones in secretory vesicles prior to hormone secretion into the blood stream. As an example for various hormone amyloids, we have studied the endogenous opioid neuropeptide β-endorphin in one of its fibril forms. We have achieved the sequential assignment of the chemical shifts of the backbone and side-chain heavy atoms of the fibril. The secondary chemical shift analysis revealed that the β-endorphin peptide adopts three β-strands in its fibril state. This finding fosters the amyloid nature of a hormone at the atomic level.

Determination of the fine structure constant based on BLOCH oscillations of ultracold atoms in a vertical optical lattice.

PubMed

Cladé, Pierre; de Mirandes, Estefania; Cadoret, Malo; Guellati-Khélifa, Saïda; Schwob, Catherine; Nez, François; Julien, Lucile; Biraben, François

2006-01-27

We report an accurate measurement of the recoil velocity of 87Rb atoms based on Bloch oscillations in a vertical accelerated optical lattice. We transfer about 900 recoil momenta with an efficiency of 99.97% per recoil. A set of 72 measurements of the recoil velocity, each one with a relative uncertainty of about 33 ppb in 20 min integration time, leads to a determination of the fine structure constant with a statistical relative uncertainty of 4.4 ppb. The detailed analysis of the different systematic errors yields to a relative uncertainty of 6.7 ppb. The deduced value of alpha-1 is 137.035 998 78(91).

On the representation matrices of the spin permutation group. [for atomic and molecular electronic structures

NASA Technical Reports Server (NTRS)

Wilson, S.

1977-01-01

A method is presented for the determination of the representation matrices of the spin permutation group (symmetric group), a detailed knowledge of these matrices being required in the study of the electronic structure of atoms and molecules. The method is characterized by the use of two different coupling schemes. Unlike the Yamanouchi spin algebraic scheme, the method is not recursive. The matrices for the fundamental transpositions can be written down directly in one of the two bases. The method results in a computationally significant reduction in the number of matrix elements that have to be stored when compared with, say, the standard Young tableaux group theoretical approach.

Crystallization of Mitochondrial Respiratory Complex II from Chicken Heart: a Membrane Protein Complex Diffracting to 2.0 Å.

PubMed Central

Huang, Li-shar; Borders, Toni M.; Shen, John T.; Wang, Chung-Jen; Berry, Edward

2006-01-01

Synopsis A multi-subunit mitochondrial membrane protein complex involved in the Krebs Cycle and respiratory chain has been crystallized in a form suitable for near-atomic resolution structure determination. A procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Å with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites. PMID:15805592

Walking Down the Chalcogenic Group of the Periodic Table: From Singlet to Triplet Organic Emitters.

PubMed

Kremer, Adrian; Aurisicchio, Claudia; De Leo, Federica; Ventura, Barbara; Wouters, Johan; Armaroli, Nicola; Barbieri, Andrea; Bonifazi, Davide

2015-10-19

The synthesis, X-ray crystal structures, ground- and excited-state UV/Vis absorption spectra, and luminescence properties of chalcogen-doped organic emitters equipped on both extremities with benzoxa-, benzothia-, benzoselena- and benzotellurazole (1X and 2X ) moieties have been reported for the first time. The insertion of the four different chalcogen atoms within the same molecular skeleton enables the investigation of only the chalcogenic effect on the organisation and photophysical properties of the material. Detailed crystal-structure analyses provide evidence of similar packing for 2O -2Se , in which the benzoazoles are engaged in π-π stacking and, for the heavier atoms, in secondary X⋅⋅⋅X and X⋅⋅⋅N bonding interactions. Detailed computational analysis shows that the arrangement is essentially governed by the interplay of van der Waals and secondary bonding interactions. Progressive quenching of the fluorescence and concomitant onset of phosphorescence features with gradually shorter lifetimes are detected as the atomic weight of the chalcogen heteroatom increases, with the tellurium-doped derivatives exhibiting only emission from the lowest triplet excited state. Notably, the phosphorescence spectra of the selenium and tellurium derivatives can be recorded even at room temperature; this is a very rare finding for fully organic emitters. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Van der Waals interactions and the limits of isolated atom models at interfaces

PubMed Central

Kawai, Shigeki; Foster, Adam S.; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H.; Jung, Thomas A.; Meyer, Ernst

2016-01-01

Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar–Xe, Kr–Xe and Xe–Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal–organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems. PMID:27174162

Structure of liquid tricalcium aluminate

NASA Astrophysics Data System (ADS)

Drewitt, James W. E.; Barnes, Adrian C.; Jahn, Sandro; Kohn, Simon C.; Walter, Michael J.; Novikov, Alexey N.; Neuville, Daniel R.; Fischer, Henry E.; Hennet, Louis

2017-02-01

The atomic-scale structure of aerodynamically levitated and laser-heated liquid tricalcium aluminate (Ca3Al2O6 ) was measured at 2073(30) K by using the method of neutron diffraction with Ca isotope substitution (NDIS). The results enable the detailed resolution of the local coordination environment around calcium and aluminum atoms, including the direct determination of the liquid partial structure factor, SCaCa(Q ) , and partial pair distribution function, gCaCa(r ) . Molecular dynamics (MD) simulation and reverse Monte Carlo (RMC) refinement methods were employed to obtain a detailed atomistic model of the liquid structure. The composition Ca3Al2O6 lies at the CaO-rich limit of the CaO:Al2O3 glass-forming system. Our results show that, although significantly depolymerized, liquid Ca3Al2O6 is largely composed of AlO4 tetrahedra forming an infinite network with a slightly higher fraction of bridging oxygen atoms than expected for the composition. Calcium-centered polyhedra exhibit a wide distribution of four- to sevenfold coordinated sites, with higher coordinated calcium preferentially bonding to bridging oxygens. Analysis of the MD configuration reveals the presence of ˜10 % unconnected AlO4 monomers and Al2O7 dimers in the liquid. As the CaO concentration increases, the number of these isolated units increases, such that the upper value for the glass-forming composition of CaO:Al2O3 liquids could be described in terms of a percolation threshold at which the glass can no longer support the formation of an infinitely connected AlO4 network.

Probing Membrane Order and Topography in Supported Lipid Bilayers by Combined Polarized Total Internal Reflection Fluorescence-Atomic Force Microscopy

PubMed Central

Oreopoulos, John; Yip, Christopher M.

2009-01-01

Determining the local structure, dynamics, and conformational requirements for protein-protein and protein-lipid interactions in membranes is critical to understanding biological processes ranging from signaling to the translocating and membranolytic action of antimicrobial peptides. We report here the application of a combined polarized total internal reflection fluorescence microscopy-in situ atomic force microscopy platform. This platform's ability to image membrane orientational order was demonstrated on DOPC/DSPC/cholesterol model membranes containing the fluorescent membrane probe, DiI-C20 or BODIPY-PC. Spatially resolved order parameters and fluorophore tilt angles extracted from the polarized total internal reflection fluorescence microscopy images were in good agreement with the topographical details resolved by in situ atomic force microscopy, portending use of this technique for high-resolution characterization of membrane domain structures and peptide-membrane interactions. PMID:19254557

Dirac R -matrix calculations for the electron-impact excitation of neutral tungsten providing noninvasive diagnostics for magnetic confinement fusion

NASA Astrophysics Data System (ADS)

Smyth, R. T.; Ballance, C. P.; Ramsbottom, C. A.; Johnson, C. A.; Ennis, D. A.; Loch, S. D.

2018-05-01

Neutral tungsten is the primary candidate as a wall material in the divertor region of the International Thermonuclear Experimental Reactor (ITER). The efficient operation of ITER depends heavily on precise atomic physics calculations for the determination of reliable erosion diagnostics, helping to characterize the influx of tungsten impurities into the core plasma. The following paper presents detailed calculations of the atomic structure of neutral tungsten using the multiconfigurational Dirac-Fock method, drawing comparisons with experimental measurements where available, and includes a critical assessment of existing atomic structure data. We investigate the electron-impact excitation of neutral tungsten using the Dirac R -matrix method, and by employing collisional-radiative models, we benchmark our results with recent Compact Toroidal Hybrid measurements. The resulting comparisons highlight alternative diagnostic lines to the widely used 400.88-nm line.

Atomic sites and stability of Cs+ captured within zeolitic nanocavities

PubMed Central

Yoshida, Kaname; Toyoura, Kazuaki; Matsunaga, Katsuyuki; Nakahira, Atsushi; Kurata, Hiroki; Ikuhara, Yumi H.; Sasaki, Yukichi

2013-01-01

Zeolites have potential application as ion-exchangers, catalysts and molecular sieves. Zeolites are once again drawing attention in Japan as stable adsorbents and solidification materials of fission products, such as 137Cs+ from damaged nuclear-power plants. Although there is a long history of scientific studies on the crystal structures and ion-exchange properties of zeolites for practical application, there are still open questions, at the atomic-level, on the physical and chemical origins of selective ion-exchange abilities of different cations and detailed atomic structures of exchanged cations inside the nanoscale cavities of zeolites. Here, the precise locations of Cs+ ions captured within A-type zeolite were analyzed using high-resolution electron microscopy. Together with theoretical calculations, the stable positions of absorbed Cs+ ions in the nanocavities are identified, and the bonding environment within the zeolitic framework is revealed to be a key factor that influences the locations of absorbed cations. PMID:23949184

Electronic structure of the heavy-fermion caged compound Ce 3 Pd 20 X 6 ( X = Si, Ge ) studied by density functional theory and photoelectron spectroscopy

DOE PAGES

Yamaoka, Hitoshi; Schwier, Eike F.; Arita, Masashi; ...

2015-03-30

The electronic structure of Ce₃Pd₂₀X₆ (X = Si, Ge) has been studied using detailed density functional theory (DFT) calculations and high-resolution photoelectron spectroscopy (PES) measurements. The orbital decomposition of the electronic structure by DFT calculations indicates that Ce atoms at the (8c) site surrounded by 16 Pd atoms have a more localized nature and a tendency to be magnetic. Ce atoms in the (4a) site surrounded by 12 Pd and 6 X atoms, on the other, show only a negligible magnetic moment. In the photoemission valence-band spectra we observe a strong f⁰ (Ce⁴⁺) component with a small fraction of f¹more » (Ce³⁺) component. The spectral weight of f¹ component near the Fermi level Ce₃Pd₂₀Si₆ is stronger than that for Ce₃Pd₂₀Ge₆ at the 4d-4f resonance, suggesting stronger c-f hybridization in the former. This may hint to the origin of the large electronic specific coefficient of Ce₃Pd₂₀Si₆ compared to Ce₃Pd₂₀Ge₆.« less

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

Paulauskas, Tadas; Buurma, Christopher; Colegrove, Eric

Dislocation cores have long dominated the electronic and optical behaviors of semiconductor devices and detailed atomic characterization is required to further explore their effects. Miniaturization of semiconductor devices to nanometre scale also puts emphasis on a material's mechanical properties to withstand failure due to processing or operational stresses. Sessile junctions of dislocations provide barriers to propagation of mobile dislocations and may lead to work-hardening. The sessile Lomer–Cottrell and Hirth lock dislocations, two stable lowest elastic energy stair-rods, are studied in this paper. More specifically, using atomic resolution high-angle annular dark-field imaging and atomic-column-resolved X-ray spectrum imaging in an aberration-corrected scanningmore » transmission electron microscope, dislocation core structures are examined in zinc-blende CdTe. A procedure is outlined for atomic scale analysis of dislocation junctions which allows determination of their identity with specially tailored Burgers circuits and also formation mechanisms of the polar core structures based on Thompson's tetrahedron adapted to reactions of polar dislocations as they appear in CdTe and other zinc-blende solids. Strain fields associated with the dislocations calculatedviageometric phase analysis are found to be diffuse and free of `hot spots' that reflect compact structures and low elastic energy of the pure-edge stair-rods.« less

Atomic Scale Analysis of the Enhanced Electro- and Photo-Catalytic Activity in High-Index Faceted Porous NiO Nanowires

NASA Astrophysics Data System (ADS)

Shen, Meng; Han, Ali; Wang, Xijun; Ro, Yun Goo; Kargar, Alireza; Lin, Yue; Guo, Hua; Du, Pingwu; Jiang, Jun; Zhang, Jingyu; Dayeh, Shadi A.; Xiang, Bin

2015-02-01

Catalysts play a significant role in clean renewable hydrogen fuel generation through water splitting reaction as the surface of most semiconductors proper for water splitting has poor performance for hydrogen gas evolution. The catalytic performance strongly depends on the atomic arrangement at the surface, which necessitates the correlation of the surface structure to the catalytic activity in well-controlled catalyst surfaces. Herein, we report a novel catalytic performance of simple-synthesized porous NiO nanowires (NWs) as catalyst/co-catalyst for the hydrogen evolution reaction (HER). The correlation of catalytic activity and atomic/surface structure is investigated by detailed high resolution transmission electron microscopy (HRTEM) exhibiting a strong dependence of NiO NW photo- and electrocatalytic HER performance on the density of exposed high-index-facet (HIF) atoms, which corroborates with theoretical calculations. Significantly, the optimized porous NiO NWs offer long-term electrocatalytic stability of over one day and 45 times higher photocatalytic hydrogen production compared to commercial NiO nanoparticles. Our results open new perspectives in the search for the development of structurally stable and chemically active semiconductor-based catalysts for cost-effective and efficient hydrogen fuel production at large scale.

Current at Metal-Organic Interfaces

NASA Astrophysics Data System (ADS)

Kern, Klaus

2012-02-01

Charge transport through atomic and molecular constrictions greatly affects the operation and performance of organic electronic devices. Much of our understanding of the charge injection and extraction processes in these systems relays on our knowledge of the electronic structure at the metal-organic interface. Despite significant experimental and theoretical advances in studying charge transport in nanoscale junctions, a microscopic understanding at the single atom/molecule level is missing. In the present talk I will present our recent results to probe directly the nanocontact between single molecules and a metal electrode using scanning probe microscopy and spectroscopy. The experiments provide unprecedented microscopic details of single molecule and atom junctions and open new avenues to study quantum critical and many body phenomena at the atomic scale. Implications for energy conversion devices and carbon based nanoelectronics will also be discussed.

Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation

NASA Astrophysics Data System (ADS)

Schennach, Moritz; Breuker, Kathrin

2015-07-01

The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.

Ni doped Fe3O4 magnetic nanoparticles.

PubMed

Larumbe, S; Gómez-Polo, C; Pérez-Landazábal, J I; García-Prieto, A; Alonso, J; Fdez-Gubieda, M L; Cordero, D; Gómez, J

2012-03-01

In this work, the effect of nickel doping on the structural and magnetic properties of Fe3O4 nanoparticles is analysed. Ni(x)Fe(3-x)O4 nanoparticles (x = 0, 0.04, 0.06 and 0.11) were obtained by chemical co-precipitation method, starting from a mixture of FeCl2 x 4H2O and Ni(AcO)2 x 4H2O salts. The analysis of the structure and composition of the synthesized nanoparticles confirms their nanometer size (main sizes around 10 nm) and the inclusion of the Ni atoms in the characteristic spinel structure of the magnetite Fe3O4 phase. In order to characterize in detail the structure of the samples, X-ray absorption (XANES) measurements were performed on the Ni and Fe K-edges. The results indicate the oxidation of the Ni atoms to the 2+ state and the location of the Ni2+ cations in the Fe2+ octahedral sites. With respect to the magnetic properties, the samples display the characteristic superparamagnetic behaviour, with anhysteretic magnetic response at room temperature. The estimated magnetic moment confirms the partial substitution of the Fe2+ cations by Ni2+ atoms in the octahedral sites of the spinel structure.

Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation

DOE PAGES

Orfield, Noah J.; McBride, James R.; Wang, Feng; ...

2016-02-05

Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. In this paper, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking “giant” CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging,more » rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive “dark” fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be “dark”. Finally and therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.« less

Charge exchange cross sections in slow collisions of Si3+ with Hydrogen atom

NASA Astrophysics Data System (ADS)

Joseph, Dwayne; Quashie, Edwin; Saha, Bidhan

2011-05-01

In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. Work supported by NSF CREST project (grant #0630370).

Close contacts at the interface: Experimental-computational synergies for solving complexity problems

NASA Astrophysics Data System (ADS)

Torras, Juan; Zanuy, David; Bertran, Oscar; Alemán, Carlos; Puiggalí, Jordi; Turón, Pau; Revilla-López, Guillem

2018-02-01

The study of material science has been long devoted to the disentanglement of bulk structures which mainly entails finding the inner structure of materials. That structure is accountable for a major portion of materials' properties. Yet, as our knowledge of these "backbones" enlarged so did the interest for the materials' boundaries properties which means the properties at the frontier with the surrounding environment that is called interface. The interface is thus to be understood as the sum of the material's surface plus the surrounding environment be it in solid, liquid or gas phase. The study of phenomena at this interface requires both the use of experimental and theoretical techniques and, above all, a wise combination of them in order to shed light over the most intimate details at atomic, molecular and mesostructure levels. Here, we report several cases to be used as proof of concept of the results achieved when studying interface phenomena by combining a myriad of experimental and theoretical tools to overcome the usual limitation regardind atomic detail, size and time scales and systems of complex composition. Real world examples of the combined experimental-theoretical work and new tools, software, is offered to the readers.

Diffraction Techniques in Structural Biology

PubMed Central

Egli, Martin

2016-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:27248784

Diffraction Techniques in Structural Biology.

PubMed

Egli, Martin

2016-06-01

A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics.

PubMed

Howard, Rebecca J; Trudell, James R; Harris, R Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.

Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

PubMed Central

Trudell, James R.; Harris, R. Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy. PMID:24515646

High-speed atomic force microscopy coming of age

NASA Astrophysics Data System (ADS)

Ando, Toshio

2012-02-01

High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.

High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

PubMed Central

Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

2017-01-01

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

CG2AA: backmapping protein coarse-grained structures.

PubMed

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

2016-04-15

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

Rotational Spectrum of Saccharine

NASA Astrophysics Data System (ADS)

Alonso, Elena R.; Mata, Santiago; Alonso, José L.

2017-06-01

A significant step forward in the structure-activity relationships of sweeteners was the assignment of the AH-B moiety in sweeteners by Shallenberger and Acree. They proposed that all sweeteners contain an AH-B moiety, known as glucophore, in which A and B are electronegative atoms separated by a distance between 2.5 to 4 Å. H is a hydrogen atom attached to one of the electronegative atom by a covalent bond. For saccharine, one of the oldest artificial sweeteners widely used in food and drinks, two possible B moieties exist ,the carbonyl oxygen atom and the sulfoxide oxygen atom although there is a consensus of opinion among scientists over the assignment of AH-B moieties to HN-SO. In the present work, the solid of saccharine (m.p. 220°C) has been vaporized by laser ablation (LA) and its rotational spectrum has been analyzed by broadband CP-FTMW and narrowband MB-FTMW Fourier transform microwave techniques. The detailed structural information extracted from the rotational constants and ^{14}N nuclear quadrupole coupling constants provided enough information to ascribe the glucophore's AH and B sites of saccharine. R. S. Shallenberger, T. E. Acree. Nature 216, 480-482 Nov 1967. R. S. Shallenberger. Taste Chemistry; Blackie Academic & Professional, London, (1993).

Sulfur Adsorption on the Goethite (110) Surface

NASA Astrophysics Data System (ADS)

Simonetti, S.; Damiani, D.; Brizuela, G.; Juan, A.

The electronic structure of S adsorption on goethite (110) surface has been studied by ASED-MO cluster calculations. For S location, the most exposed surface atoms of goethite surface were selected. The calculations show that the surface offers several places for S adsorption. The most energetically stable system corresponds to S location above H atom. We studied in detail the configurations that correspond to the higher OP values. For these configurations, the H-S and Fe-S computed distances are 2.1 and 3.7 Å, respectively. The H-S and Fe-S are mainly bonding interaction with OP values of 0.156 and 0.034, respectively. The Fe-S interaction mainly involves Fe 3dx2-y2 atomic orbitals with lesser participation of Fe 4py and Fe 3dyz atomic orbitals. The O-S interaction shows the same bonding and antibonding contributions giving a small OP value. The O-S interaction involves O 2p orbitals. There is an electron transfer to the Fe atom from the S atom. On the other hand, there is an electron transfer to S atom from the H and O atoms, respectively.

Experimental evidence and structural modeling of nonstoichiometric (010) surfaces coexisting in hydroxyapatite nano-crystals.

PubMed

Ospina, C A; Terra, J; Ramirez, A J; Farina, M; Ellis, D E; Rossi, A M

2012-01-01

High-resolution transmission electron microscopy (HRTEM) and ab initio quantum-mechanical calculations of electronic structure were combined to investigate the structure of the hydroxyapatite (HA) (010) surface, which plays an important role in HA interactions with biological media. HA was synthesized by in vitro precipitation at 37°C. HRTEM images revealed thin elongated rod nanoparticles with preferential growth along the [001] direction and terminations parallel to the (010) plane. The focal series reconstruction (FSR) technique was applied to develop an atomic-scale structural model of the high-resolution images. The HRTEM simulations identified the coexistence of two structurally distinct terminations for (010) surfaces: a rather flat Ca(II)-terminated surface and a zig-zag structure with open OH channels. Density functional theory (DFT) was applied in a periodic slab plane-wave pseudopotential approach to refine details of atomic coordination and bond lengths of Ca(I) and Ca(II) sites in hydrated HA (010) surfaces, starting from the HRTEM model. Copyright © 2011 Elsevier B.V. All rights reserved.

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

PubMed Central

2011-01-01

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

Interface structure between tetraglyme and graphite

NASA Astrophysics Data System (ADS)

Minato, Taketoshi; Araki, Yuki; Umeda, Kenichi; Yamanaka, Toshiro; Okazaki, Ken-ichi; Onishi, Hiroshi; Abe, Takeshi; Ogumi, Zempachi

2017-09-01

Clarification of the details of the interface structure between liquids and solids is crucial for understanding the fundamental processes of physical functions. Herein, we investigate the structure of the interface between tetraglyme and graphite and propose a model for the interface structure based on the observation of frequency-modulation atomic force microscopy in liquids. The ordering and distorted adsorption of tetraglyme on graphite were observed. It is found that tetraglyme stably adsorbs on graphite. Density functional theory calculations supported the adsorption structure. In the liquid phase, there is a layered structure of the molecular distribution with an average distance of 0.60 nm between layers.

Reflections on the value of electron microscopy in the study of heterogeneous catalysts

PubMed Central

2017-01-01

Electron microscopy (EM) is arguably the single most powerful method of characterizing heterogeneous catalysts. Irrespective of whether they are bulk and multiphasic, or monophasic and monocrystalline, or nanocluster and even single-atom and on a support, their structures in atomic detail can be visualized in two or three dimensions, thanks to high-resolution instruments, with sub-Ångstrom spatial resolutions. Their topography, tomography, phase-purity, composition, as well as the bonding, and valence-states of their constituent atoms and ions and, in favourable circumstances, the short-range and long-range atomic order and dynamics of the catalytically active sites, can all be retrieved by the panoply of variants of modern EM. The latter embrace electron crystallography, rotation and precession electron diffraction, X-ray emission and high-resolution electron energy-loss spectra (EELS). Aberration-corrected (AC) transmission (TEM) and scanning transmission electron microscopy (STEM) have led to a revolution in structure determination. Environmental EM is already playing an increasing role in catalyst characterization, and new advances, involving special cells for the study of solid catalysts in contact with liquid reactants, have recently been deployed. PMID:28265196

Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

PubMed

Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

2010-01-19

Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

Fast flexible modeling of RNA structure using internal coordinates.

PubMed

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

Students' Development and Use of Models to Explain Electrostatic Interactions

NASA Astrophysics Data System (ADS)

Mayer, Kristin Elizabeth

The National Research Council (2012) recently published A Framework for K-12 Science Education that describes a vision for science classrooms where students engage in three dimensions--scientific and engineering practices, crosscutting concepts, and disciplinary core ideas--to explain phenomena or observations they can make about the universe around them. This vision of science instruction is a significant shift from current classroom instruction. This dissertation provides detailed examples of how students developed and used models to build causal explanations of phenomena. I co-taught classes that focused on having students develop and revise models of electric fields and atomic structure using a curriculum that was designed to align with the three-dimensional vision of learning. I developed case studies of eleven students from these classes. I analyzed the students' responses and interviewed the students throughout the school year. By comparing and contrasting the analysis across the analysis of students' interviews, I identified four themes: 1) students could apply their ideas to explain novel and abstract phenomena; 2) students struggled to connect changes in their atomic models to evidence, but ended up with dynamic models of atomic structure that they could apply to explain phenomena; 3) students developed models of atomic structure that they applied to explain phenomena, but they did not use models of electric fields in this way; and 4) too much focus on details interfered with students' ability to apply their models to explain new phenomena. This dissertation highlights the importance of focusing on phenomena in classrooms that aim at aligning with three-dimensional learning. Students struggled to focus on specific content and apply their ideas to explain phenomena at the same time. In order to apply ideas to new context, students had to shift their focus from recalling ideas to applying the ideas they do have. A focus on phenomena allowed students to show their understanding through applying their ideas to new context. During this transition, students struggled, and in particular, had a hard time using evidence from experiments to justify the changes they made to their models of atomic structure. While the changes students made looked unproductive at times, by the end of the semester, students had developed models of atomic structure that incorporated relationships among charged components that they could apply to explain complex phenomena. Asking students to explore and evaluate their own ideas supported their development of models that they could apply to explain new context they experience in their future.

Atomic and Molecular Beam Scattering: Characterizing Structure and Dynamics of Hybrid Organic-Semiconductor Interfaces and Introducing Novel Isotope Separation Techniques

NASA Astrophysics Data System (ADS)

Nihill, Kevin John

This thesis details a range of experiments and techniques that use the scattering of atomic beams from surfaces to both characterize a variety of interfaces and harness mass-specific scattering conditions to separate and enrich isotopic components in a mixture of gases. Helium atom scattering has been used to characterize the surface structure and vibrational dynamics of methyl-terminated Ge(111), thereby elucidating the effects of organic termination on a rigid semiconductor interface. Helium atom scattering was employed as a surface-sensitive, non-destructive probe of the surface. By means of elastic gas-surface diffraction, this technique is capable of providing measurements of atomic spacing, step height, average atomic displacement as a function of surface temperature, gas-surface potential well depth, and surface Debye temperature. Inelastic time-of-flight studies provide highly resolved energy exchange measurements between helium atoms and collective lattice vibrations, or phonons; a collection of these measurements across a range of incident kinematic parameters allowed for a thorough mapping of low-energy phonons (e.g., the Rayleigh wave) across the surface Brillouin zone and subsequent comparison with complementary theoretical calculations. The scattering of molecular beams - here, hydrogen and deuterium from methyl-terminated Si(111) - enables the measurement of the anisotropy of the gas-surface interaction potential through rotationally inelastic diffraction (RID), whereby incident atoms can exchange internal energy between translational and rotational modes and diffract into unique angular channels as a result. The probability of rotational excitations as a function of incident energy and angle were measured and compared with electronic structure and scattering calculations to provide insight into the gas-surface interaction potential and hence the surface charge density distribution, revealing important details regarding the interaction of H2 with an organic-functionalized semiconductor interface. Aside from their use as probes for surface structure and dynamics, atomic beam sources are also demonstrated to enable the efficient separation of gaseous mixtures of isotopes by means of diffraction and differential condensation. In the former method, the kinematic conditions for elastic diffraction result in an incident beam of natural abundance neon diffracting into isotopically distinct angles, resulting in the enrichment of a desired isotope; this purification can be improved by exploiting the difference in arrival times of the two isotopes at a given final angle. In the latter method, the identical incident velocities of coexpanded isotopes lead to minor but important differences in their incident kinetic energies, and thus their probability of adsorbing on a sufficiently cold surface, resulting in preferential condensation of a given isotope that depends on the energy of the incident beam. Both of these isotope separation techniques are made possible by the narrow velocity distribution and velocity seeding effect offered only by high-Mach number supersonic beam sources. These experiments underscore the utility of supersonically expanded atomic and molecular beam sources as both extraordinarily precise probes of surface structure and dynamics and as a means for high-throughput, non-dissociative isotopic enrichment methods.

Numerical study of the defect adamantine compound CuGaGeSe4

NASA Astrophysics Data System (ADS)

Shen, Kesheng; Zhang, Xianzhou; Lu, Hai; Jiao, Zhaoyong

2018-06-01

The electronic structure, elastic and optical properties of the defect adamantine compound CuGaGeSe4 in ? structure are systematically investigated using first-principles calculations. Through detailed calculation and comparison, we obtain three independent atomic arrangements and predict the most stable atomic arrangement according to the lattice constants and enthalpy formation energies. The elastic constants are calculated, which can be used to predict the axial thermal expansion coefficients accurately. The optical properties of compound CuGaGeSe4, including the dielectric function, refractive index and absorption spectrum, are depicted for a more intuitive understanding. Our calculated zero-frequency limits ɛ1(0) and n(0) are very close to the other theoretical values, which proves that our calculations are reliable.

Chemokines and their receptors: insights from molecular modeling and crystallography.

PubMed

Kufareva, Irina

2016-10-01

Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors. Copyright © 2016 Elsevier Ltd. All rights reserved.

High-resolution protein design with backbone freedom.

PubMed

Harbury, P B; Plecs, J J; Tidor, B; Alber, T; Kim, P S

1998-11-20

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

Protein Structure in Context: The Molecular Landscape of Angiogenesis

ERIC Educational Resources Information Center

Span, Elise A.; Goodsell, David S.; Ramchandran, Ramani; Franzen, Margaret A.; Herman, Tim; Sem, Daniel S.

2013-01-01

A team of students, educators, and researchers has developed new materials to teach cell signaling within its cellular context. Two nontraditional modalities are employed: physical models, to explore the atomic details of several of the proteins in the angiogenesis signaling cascade, and illustrations of the proteins in their cellular environment,…

Relativistic opacities for astrophysical applications

DOE PAGES

Fontes, Christopher John; Fryer, Christopher Lee; Hungerford, Aimee L.; ...

2015-06-29

Here, we report on the use of the Los Alamos suite of relativistic atomic physics codes to generate radiative opacities for the modeling of astrophysically relevant plasmas under local thermodynamic equilibrium (LTE) conditions. The atomic structure calculations are carried out in fine-structure detail, including full configuration interaction. Three example applications are considered: iron opacities at conditions relevant to the base of the solar convection zone, nickel opacities for the modeling of stellar envelopes, and samarium opacities for the modeling of light curves produced by neutron star mergers. In the first two examples, comparisons are made between opacities that are generatedmore » with the fully and semi-relativistic capabilities in the Los Alamos suite of codes. As expected for these highly charged, iron-peak ions, the two methods produce reasonably similar results, providing confidence that the numerical methods have been correctly implemented. However, discrepancies greater than 10% are observed for nickel and investigated in detail. In the final application, the relativistic capability is used in a preliminary investigation of the complicated absorption spectrum associated with cold lanthanide elements.« less

10. Architectural Door Details & Plot Plan, 233S, U.S. Atomic ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. Architectural Door Details & Plot Plan, 233-S, U.S. Atomic Energy Commission, Hanford Atomic Products Operations, General Electric Company, Dwg. No. H-2-30469, 1956. - Reduction-Oxidation Complex, Plutonium Concentration Facility, 200 West Area, Richland, Benton County, WA

Stabilizing Rabi oscillation of a charge qubit via the atomic clock technique

NASA Astrophysics Data System (ADS)

Yu, Deshui; Landra, Alessandro; Kwek, Leong Chuan; Amico, Luigi; Dumke, Rainer

2018-02-01

We propose a superconducting circuit-atom hybrid, where the Rabi oscillation of single excess Cooper pair in the island is stabilized via the common atomic clock technique. The noise in the superconducting circuit is mapped onto the voltage source which biases the Cooper-pair box via an inductor and a gate capacitor. The fast fluctuations of the gate charge are significantly suppressed by an inductor-capacitor resonator, leading to a long-relaxation-time Rabi oscillation. More importantly, the residual low-frequency fluctuations are further reduced by using the general feedback-control method, in which the voltage bias is stabilized via continuously measuring the dc-Stark-shift-induced atomic Ramsey signal. The stability and coherence time of the resulting charge-qubit Rabi oscillation are both enhanced. The principal structure of this Cooper-pair-box oscillator is studied in detail.

Nanometer scale atomic structure of zirconium based bulk metallic glass

NASA Astrophysics Data System (ADS)

Hwang, Jinwoo

We have studied the nanometer scale structure of bulk metallic glass (BMG) using fluctuation electron microscopy (FEM). The nanometer scale medium range order (MRO) in BMG is of significant interest because of its possible relationship to the properties, but the experimental study of the MRO is difficult because conventional diffraction techniques are not sensitive to the MRO scale. FEM is a quantitative transmission electron microscopy technique which measures the nanoscale structural fluctuation associated with MRO in amorphous materials, and provides information about the size, distribution, and internal structure of MRO. In this work, we developed an improved method for FEM using energy-filtered STEM nanodiffraction with highly coherent probes with size up to 11nm in a state-of-the-art Cs- corrected STEM. We also developed an effective way to eliminate the effect of sample thickness variation to the FEM data by using Z-contrast images as references. To study the detailed structure of MRO, we developed a hybrid reverse Monte Carlo (H-RMC) simulation which combines an empirical atomic potential and the FEM data. H-RMC generated model structures that match the experimental data at short and medium range. In addition, the subtle rotational symmetries in the FEM nanodiffraction patterns were analyzed by angular correlation function to reveal more details of the internal structure of MRO. Our experiments and simulations show that Zr-based BMG contains pseudo-planar, crystal-like MRO as well as icosahedral clusters in its nanoscale structure. We found that some icosahedral clusters may be connected, and that structural relaxation by annealing increases the population of icosahedral clusters.

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1986-01-01

During this reporting period three investigations were carried out. The first area of research concerned the analysis of the structure-energy relationship in small clusters. This study is very closely related to the improvement of the potential energy functions which are suitable and simple enough to be used in atomistic simulation studies. Parameters obtained from ab initio calculations for dimers and trimers of Al were used to estimate energetics and global minimum energy structures of clusters continuing up to 15 Al atoms. The second research topic addressed modeling of the collision process for atoms impinging on surfaces. In this simulation study qualitative aspects of the O atom collision with a graphite surface were analyzed. Four different O/graphite systems were considered and the aftermath of the impact was analyzed. The final area of investigation was related to the simulation of thin amorphous Si films on crystalline Si substrates. Parameters obtained in an earlier study were used to model an exposed amorphous Si surface and an a-Si/c-Si interface. Structural details for various film thicknesses were investigated at an atomistic level.

Structure of 1-butylpyridinium tetrafluoroborate ionic liquid: quantum chemistry and molecular dynamic simulation studies.

PubMed

Sun, Hui; Qiao, Baofu; Zhang, Dongju; Liu, Chengbu

2010-03-25

Density functional theory (DFT) calculations combined with molecular dynamic (MD) simulations have been performed to show in detail the structure characteristic of 1-butylpyridinium tetrafluoroborate ([BPy(+)][BF(4)(-)]), a representative of pyridinium-based ionic liquids (ILs). It is found that the relative stability for ion pair configurations is synergically determined by the electrostatic attractions and the H-bond interactions between the ions of opposite charge. [BPy(+)][BF(4)(-)] IL possesses strong long-range ordered structure with cations and anions alternately arranging. The spatial distributions of anions and cations around the given cations are clearly shown, and T-shaped orientation is indicated to play a key role in the interaction between two pyridine rings. DFT calculations and MD simulations uniformly suggest that the H-bonds of the fluorine atoms with the hydrogen atoms on the pyridine rings are stronger than those of the fluorine atoms with the butyl chain hydrogens. The present results can offer useful information for understanding the physicochemical properties of [BPy(+)][BF(4)(-)] IL and further designing new pyridinium-based ILs.

Toward a detailed description of the pathways of allosteric communication in the GroEL chaperonin through atomistic simulation.

PubMed

Piggot, Thomas J; Sessions, Richard B; Burston, Steven G

2012-02-28

GroEL, along with its coprotein GroES, is essential for ensuring the correct folding of unfolded or newly synthesized proteins in bacteria. GroEL is a complex, allosteric molecule, composed of two heptameric rings stacked back to back, that undergoes large structural changes during its reaction cycle. These structural changes are driven by the cooperative binding and subsequent hydrolysis of ATP, by GroEL. Despite numerous previous studies, the precise mechanisms of allosteric communication and the associated structural changes remain elusive. In this paper, we describe a series of all-atom, unbiased, molecular dynamics simulations over relatively long (50-100 ns) time scales of a single, isolated GroEL subunit and also a heptameric GroEL ring, in the presence and absence of ATP. Combined with results from a distance restraint-biased simulation of the single ring, the atomistic details of the earliest stages of ATP-driven structural changes within this complex molecule are illuminated. Our results are in broad agreement with previous modeling studies of isolated subunits and with a coarse-grained, forcing simulation of the single ring. These are the first reported all-atom simulations of the GroEL single-ring complex and provide a unique insight into the role of charged residues K80, K277, R284, R285, and E388 at the subunit interface in transmission of the allosteric signal. These simulations also demonstrate the feasibility of performing all-atom simulations of very large systems on sufficiently long time scales on typical high performance computing facilities to show the origins of the earliest events in biologically relevant processes.

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.

Ensemble modeling of very small ZnO nanoparticles.

PubMed

Niederdraenk, Franziska; Seufert, Knud; Stahl, Andreas; Bhalerao-Panajkar, Rohini S; Marathe, Sonali; Kulkarni, Sulabha K; Neder, Reinhard B; Kumpf, Christian

2011-01-14

The detailed structural characterization of nanoparticles is a very important issue since it enables a precise understanding of their electronic, optical and magnetic properties. Here we introduce a new method for modeling the structure of very small particles by means of powder X-ray diffraction. Using thioglycerol-capped ZnO nanoparticles with a diameter of less than 3 nm as an example we demonstrate that our ensemble modeling method is superior to standard XRD methods like, e.g., Rietveld refinement. Besides fundamental properties (size, anisotropic shape and atomic structure) more sophisticated properties like imperfections in the lattice, a size distribution as well as strain and relaxation effects in the particles and-in particular-at their surface (surface relaxation effects) can be obtained. Ensemble properties, i.e., distributions of the particle size and other properties, can also be investigated which makes this method superior to imaging techniques like (high resolution) transmission electron microscopy or atomic force microscopy, in particular for very small nanoparticles. For the particles under study an excellent agreement of calculated and experimental X-ray diffraction patterns could be obtained with an ensemble of anisotropic polyhedral particles of three dominant sizes, wurtzite structure and a significant relaxation of Zn atoms close to the surface.

Probing and Manipulating the Interfacial Defects of InGaAs Dual-Layer Metal Oxides at the Atomic Scale.

PubMed

Wu, Xing; Luo, Chen; Hao, Peng; Sun, Tao; Wang, Runsheng; Wang, Chaolun; Hu, Zhigao; Li, Yawei; Zhang, Jian; Bersuker, Gennadi; Sun, Litao; Pey, Kinleong

2018-01-01

The interface between III-V and metal-oxide-semiconductor materials plays a central role in the operation of high-speed electronic devices, such as transistors and light-emitting diodes. The high-speed property gives the light-emitting diodes a high response speed and low dark current, and they are widely used in communications, infrared remote sensing, optical detection, and other fields. The rational design of high-performance devices requires a detailed understanding of the electronic structure at this interface; however, this understanding remains a challenge, given the complex nature of surface interactions and the dynamic relationship between the morphology evolution and electronic structures. Herein, in situ transmission electron microscopy is used to probe and manipulate the structural and electrical properties of ZrO 2 films on Al 2 O 3 and InGaAs substrate at the atomic scale. Interfacial defects resulting from the spillover of the oxygen-atom conduction-band wavefunctions are resolved. This study unearths the fundamental defect-driven interfacial electric structure of III-V semiconductor materials and paves the way to future high-speed and high-reliability devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids

NASA Astrophysics Data System (ADS)

Dykeman, Eric C.; Sankey, Otto F.

2010-02-01

We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.

Detailed numerical simulations of laser cooling processes

NASA Technical Reports Server (NTRS)

Ramirez-Serrano, J.; Kohel, J.; Thompson, R.; Yu, N.

2001-01-01

We developed a detailed semiclassical numerical code of the forces applied on atoms in optical and magnetic fields to increase the understanding of the different roles that light, atomic collisions, background pressure, and number of particles play in experiments with laser cooled and trapped atoms.

Nanodisc-Targeted STD NMR Spectroscopy Reveals Atomic Details of Ligand Binding to Lipid Environments.

PubMed

Muñoz-García, Juan C; Inacio Dos Reis, Rosana; Taylor, Richard J; Henry, Alistair J; Watts, Anthony

2018-05-18

Saturation transfer difference (STD) NMR spectroscopy is one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. This is due to its robustness and the fact that it is focused on the signals of the ligand, without any need for NMR information on the macromolecular target. This technique is most commonly applied to systems involving different types of ligands (e.g., small organic molecules, carbohydrates or lipids) and a protein as the target, in which the latter is selectively saturated. However, only a few examples have been reported where membrane mimetics are the macromolecular binding partners. Here, we have employed STD NMR spectroscopy to investigate the interactions of the neurotransmitter dopamine with mimetics of lipid bilayers, such as nanodiscs, by saturation of the latter. In particular, the interactions between dopamine and model lipid nanodiscs formed either from charged or zwitterionic lipids have been resolved at the atomic level. The results, in agreement with previous isothermal titration calorimetry studies, show that dopamine preferentially binds to negatively charged model membranes, but also provide detailed atomic insights into the mode of interaction of dopamine with membrane mimetics. Our findings provide relevant structural information for the design of lipid-based drug carriers of dopamine and its structural analogues and are of general applicability to other systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction-induced conducting-non-conducting transition of ultra-cold atoms in one-dimensional optical lattices

NASA Astrophysics Data System (ADS)

Chien, Chih-Chun; Gruss, Daniel; Di Ventra, Massimiliano; Zwolak, Michael

2013-06-01

The study of time-dependent, many-body transport phenomena is increasingly within reach of ultra-cold atom experiments. We show that the introduction of spatially inhomogeneous interactions, e.g., generated by optically controlled collisions, induce negative differential conductance in the transport of atoms in one-dimensional optical lattices. Specifically, we simulate the dynamics of interacting fermionic atoms via a micro-canonical transport formalism within both a mean-field and a higher-order approximation, as well as with a time-dependent density-matrix renormalization group (DMRG). For weakly repulsive interactions, a quasi-steady-state atomic current develops that is similar to the situation occurring for electronic systems subject to an external voltage bias. At the mean-field level, we find that this atomic current is robust against the details of how the interaction is switched on. Further, a conducting-non-conducting transition exists when the interaction imbalance exceeds some threshold from both our approximate and time-dependent DMRG simulations. This transition is preceded by the atomic equivalent of negative differential conductivity observed in transport across solid-state structures.

Dynamics of entanglement of a three-level atom in motion interacting with two coupled modes including parametric down conversion

NASA Astrophysics Data System (ADS)

Faghihi, M. J.; Tavassoly, M. K.; Hatami, M.

In this paper, a model by which we study the interaction between a motional three-level atom and two-mode field injected simultaneously in a bichromatic cavity is considered; the three-level atom is assumed to be in a Λ-type configuration. As a result, the atom-field and the field-field interaction (parametric down conversion) will be appeared. It is shown that, by applying a canonical transformation, the introduced model can be reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions, which may be prepared for the atom and the field, the time evolution of state vector of the entire system is analytically evaluated. Then, the dynamics of atom by considering ‘atomic population inversion’ and two different measures of entanglement, i.e., ‘von Neumann entropy’ and ‘idempotency defect’ is discussed, in detail. It is deduced from the numerical results that, the duration and the maximum amount of the considered physical quantities can be suitably tuned by selecting the proper field-mode structure parameter p and the detuning parameters.

Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

NASA Astrophysics Data System (ADS)

McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

2009-03-01

Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

Structural ordering at solid-liquid interfaces in Al-Sm system: A molecular-dynamics study

DOE PAGES

Sun, Yang; Zhang, Feng; Ye, Zhuo; ...

2016-07-12

The structural ordering at solid-liquid interfaces far from equilibrium is studied with molecular dynamics simulations for the Al-Sm system. Using the van-Hove self-correlation function as the criterion to identify attachment/detachment events that occur at the interface, we are able to determine the time-dependent interface position, and characterize the detailed interfacial structure ordering surrounding the attached atoms. For the interface between an undercooled Al90Sm10 liquid and a metastable cubic structure, the solid induces the crystalline order of the cubic phase in the liquid layers, promoting the continuous growth of the crystal phase. When the same liquid is put in contact withmore » f.c.c. Al, Sm from the liquid can still attach to the solid interface despite its insolubility in the Al lattice. Non-f.c.c. order is revealed surrounding the attached Sm atoms. Lastly, we show that the local structure ordering at interface is highly correlated to solid packing and liquid ordering.« less

Atomic and electronic structures of an extremely fragile liquid.

PubMed

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-12-18

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.

Atomic and electronic structures of an extremely fragile liquid

PubMed Central

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-01-01

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

Potential-specific structure at the hematite-electrolyte interface

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

McBriarty, Martin E.; Stubbs, Joanne; Eng, Peter

The atomic-scale structure of interfaces between metal oxides and aqueous electrolytes controls their catalytic, geochemical, and corrosion behavior. Measurements that probe these interfaces in situ provide important details of ion and solvent arrangements, but atomically precise structural models do not exist for common oxide-electrolyte interfaces far from equilibrium. Using a novel cell, we measured the structure of the hematite (a-Fe 2O 3) (110more » $$\\bar{2}$$)-electrolyte interface under controlled electrochemical bias using synchrotron crystal truncation rod X ray scattering. At increasingly cathodic potentials, charge-compensating protonation of surface oxygen groups increases the coverage of specifically bound water while adjacent water layers displace outwardly and became disordered. Returning to open circuit potential leaves the surface in a persistent metastable protonation state. The flux of current and ions at applied potential is thus regulated by a unique interfacial electrolyte environment, suggesting that electrical double layer models should be adapted to the dynamically changing interfacial structure far from equilibrium.« less

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

PubMed

Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

2014-11-01

Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

Mechanisms of heterogeneous crystal growth in atomic systems: insights from computer simulations.

PubMed

Gulam Razul, M S; Hendry, J G; Kusalik, P G

2005-11-22

In this paper we analyze the atomic-level structure of solid/liquid interfaces of Lennard-Jones fcc systems. The 001, 011, and 111 faces are examined during steady-state growth and melting of these crystals. The mechanisms of crystallization and melting are explored using averaged configurations generated during these steady-state runs, where subsequent tagging and labeling of particles at the interface provide many insights into the detailed atomic behavior at the freezing and melting interfaces. The interfaces are generally found to be rough and we observe the structure of freezing and melting interfaces to be very similar. Large structural fluctuations with solidlike and liquidlike characteristics are apparent in both the freezing and melting interfaces. The behavior at the interface observed under either growth or melting conditions reflects a competition between ordering and disordering processes. In addition, we observe atom hopping that imparts liquidlike characteristics to the solid side of the interfaces for all three crystal faces. Solid order is observed to extend as rough, three-dimensional protuberances through the interface, particularly for the 001 and 011 faces. We are also able to reconcile our different measures for the interfacial width and address the onset of asymmetry in the growth rates at high rates of crystal growth/melting.

Lamb shift and fine structure at n =2 in a hydrogenlike muonic atom with the nuclear spin I =0

NASA Astrophysics Data System (ADS)

Korzinin, Evgeny Yu.; Shelyuto, Valery A.; Ivanov, Vladimir G.; Karshenboim, Savely G.

2018-01-01

The paper is devoted to the Lamb shift and fine structure in a hydrogenlike muonic atom with a spinless nucleus up to the order α5m with all the recoil corrections included. Enhanced contributions of a higher order are also considered. We present the results on the pure QED contribution and on the finite-nuclear-size contribution, proportional to RN2, with the higher-order corrections included. We also consider the consistency of the pure QED theory and the evaluation of the nuclear-structure effects. Most of the QED theory is the same as the theory for the case of the nuclear spin 1/2. Additional nuclear-spin-dependent terms are considered in detail. The issue of the difference for the theories with a spinor nucleus and a scalar one is discussed for the recoil contributions in the order (Zα ) 4m ,α (Zα ) 4m , and (Zα ) 5m . The numerical results are presented for the muonic atoms with two lightest scalar nuclei, helium-4 and beryllium-10. We compare the theory of those muonic atoms with theory for the muonic hydrogen. Some higher-order finite-nuclear-size corrections for the Lamb shift in muonic hydrogen are revisited.

Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations.

PubMed

Sangwan, Smriti; Sawaya, Michael R; Murray, Kevin A; Hughes, Michael P; Eisenberg, David S

2018-02-17

The aggregation cascade of disease-related amyloidogenic proteins, terminating in insoluble amyloid fibrils, involves intermediate oligomeric states. The structural and biochemical details of these oligomers have been largely unknown. Here we report crystal structures of variants of the cytotoxic oligomer-forming segment residues 28-38 of the ALS-linked protein, SOD1. The crystal structures reveal three different architectures: corkscrew oligomeric structure, nontwisting curved sheet structure and a steric zipper proto-filament structure. Our work highlights the polymorphism of the segment 28-38 of SOD1 and identifies the molecular features of amyloidogenic entities. © 2018 The Protein Society.

Hierarchical Coarse-Graining Via a Generalized Yvon-Born Green Framework: Many-Body Correlations, Mappings, and Structural Accuracy

NASA Astrophysics Data System (ADS)

Rudzinski, Joseph F.

Atomically-detailed molecular dynamics simulations have emerged as one of the most powerful theoretic tools for studying complex, condensed-phase systems. Despite their ability to provide incredible molecular insight, these simulations are insufficient for investigating complex biological processes, e.g., protein folding or molecular aggregation, on relevant length and time scales. The increasing scope and sophistication of atomically-detailed models has motivated the development of "hierarchical" approaches, which parameterize a low resolution, coarse-grained (CG) model based on simulations of an atomically-detailed model. The utility of hierarchical CG models depends on their ability to accurately incorporate the correct physics of the underlying model. One approach for ensuring this "consistency" between the models is to parameterize the CG model to reproduce the structural ensemble generated by the high resolution model. The many-body potential of mean force is the proper CG energy function for reproducing all structural distributions of the atomically-detailed model, at the CG level of resolution. However, this CG potential is a configuration-dependent free energy function that is generally too complicated to represent or simulate. The multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to directly determine a variationally optimal approximation to the many-body potential of mean force. The MS-CG/g-YBG method provides a convenient and transparent framework for investigating the equilibrium structure of the system, at the CG level of resolution. In this work, we investigate the fundamental limitations and approximations of the MS-CG/g-YBG method. Throughout the work, we propose several theoretic constructs to directly relate the MS-CG/g-YBG method to other popular structure-based CG approaches. We investigate the physical interpretation of the MS-CG/g-YBG correlation matrix, the quantity responsible for disentangling the various contributions to the average force on a CG site. We then employ an iterative extension of the MS-CG/g-YBG method that improves the accuracy of a particular set of low order correlation functions relative to the original MS-CG/g-YBG model. We demonstrate that this method provides a powerful framework for identifying the precise source of error in an MS-CG/g-YBG model. We then propose a method for identifying an optimal CG representation, prior to the development of the CG model. We employ these techniques together to demonstrate that in the cases where the MS-CG/g-YBG method fails to determine an accurate model, a fundamental problem likely exists with the chosen CG representation or interaction set. Additionally, we explicitly demonstrate that while the iterative model successfully improves the accuracy of the low order structure, it does so by distorting the higher order structural correlations relative to the underlying model. Finally, we apply these methods to investigate the utility of the MS-CG/g- YBG method for developing models for systems with complex intramolecular structure. Overall, our results demonstrate the power of the g-YBG framework for developing accurate CG models and for investigating the driving forces of equilibrium structures for complex condensed-phase systems. This work also explicitly motivates future development of bottom-up CG methods and highlights some outstanding problems in the field. iii.

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

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

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

2014-03-26

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

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

PubMed Central

Nasica-Labouze, Jessica; Meli, Massimiliano; Derreumaux, Philippe; Colombo, Giorgio; Mousseau, Normand

2011-01-01

The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided. PMID:21625573

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

PubMed

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

2015-10-07

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Designing Superhard Materials by Incorporating Boron Into Heavy Transition Metals

NASA Astrophysics Data System (ADS)

Liang, Yongcheng; Li, Anhu; Zhao, Jianzhi; Zhang, Wenqing

First-principles calculations on the incompressibility, elasticity and hardness of the Os, OsB2, Re, and ReB2 materials have systematically been performed by the plane-wave basis pseudopotential method. Transition metals Os and Re, which have high bulk modulus but low hardness, can be converted into hard materials by combining them with small B atoms. Moreover, electronic and structural mechanisms of ReB2 and OsB2 are analyzed in detail and compared. It is shown that incorporating small B atoms into heavy transition metals should be a valid pathway to obtain new superhard materials.

How to Connect Cardiac Excitation to the Atomic Interactions of Ion Channels.

PubMed

Silva, Jonathan R

2018-01-23

Many have worked to create cardiac action potential models that explicitly represent atomic-level details of ion channel structure. Such models have the potential to define new therapeutic directions and to show how nanoscale perturbations to channel function predispose patients to deadly cardiac arrhythmia. However, there have been significant experimental and theoretical barriers that have limited model usefulness. Recently, many of these barriers have come down, suggesting that considerable progress toward creating these long-sought models may be possible in the near term. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

FI-STM study of hydrogen adsorption on Si(100) surface

NASA Astrophysics Data System (ADS)

Hua, Lu; Xiang-dong, Wang; Motai, K.; Hashizume, T.; Sakurai, T.

1992-11-01

Chemisorption of atomic hydrogen on the Si(100)2 × 1 surface has been investigated in detail by using a field ion-scanning tunneling microscope (FI-STM). The results showed that the adsorption geometry changed from the 2 × 1 monohydride phase to the 1 × 1 dihydride phase with increasing exposure of hydrogen. The data of desorption of the hydrogen-saturated Si surface showed that on annealing at 670 K the surface becomes highly disordered: the 1 × 1 dihydride structure is eliminated and the 2 × 1 reconstructed monohydride is also hardly to identify. When the temperature rises to as high as 730 K, the surface is dominated by the 2 × 1 structure with missing dimer rows, and some adatom chains occur on the Si substrate terraces. We attribute the formation of these atomic chains to an epitaxial growth of Si atoms which are formed by the dissociation of SiHx (x = 1, 2, 3 or 4) compounds on the Si surface.

Impact of stoichiometry and disorder on the electronic structure of the PbBi2Te4 -xSex topological insulator

NASA Astrophysics Data System (ADS)

Shvets, I. A.; Klimovskikh, I. I.; Aliev, Z. S.; Babanly, M. B.; Sánchez-Barriga, J.; Krivenkov, M.; Shikin, A. M.; Chulkov, E. V.

2017-12-01

Detailed comparative theoretical and experimental study of electronic properties and spin structure was carried out for a series of Pb-based quaternary compounds PbBi2Te4 -xSex . For all values of x , these compounds are theoretically predicted to be topological insulators, possessing at high Se content a remarkably large band gap and a Dirac point isolated from bulk states. Using spin- and angle-resolved photoemission spectroscopy, it was shown that the PbBi2Te2Se2 and PbBi2Te1.4Se2.6 compounds are characterized by well-defined spin-polarized topological surface state in the bulk gap. To define the probable distribution of atoms over the atomic sites for these samples, we performed ab initio calculations in ordered and disordered configurations of the unit cell. We found that theoretical calculations better reproduce photoemission data when Te atoms are placed in the outermost layers of the septuple layer block.

Atomic and electronic properties of quasi-one-dimensional MOS2 nanowires

PubMed Central

Seivane, Lucas Fernandez; Barron, Hector; Botti, Silvana; Marques, Miguel Alexandre Lopes; Rubio, Ángel; López-Lozano, Xóchitl

2013-01-01

The structural, electronic and magnetic properties of quasi-one-dimensional MoS2 nanowires, passivated by extra sulfur, have been determined using ab initio density-functional theory. The nanostructures were simulated using several different models based on experimental electron microscopy images. It is found that independently of the geometrical details and the coverage of extra sulfur at the Mo-edge, quasi-one-dimensional metallic states are predominant in all the low-energy model structures despite their reduced dimensionality. These metallic states are localized mainly at the edges. However, the electronic and magnetic character of the NWs does not depend only on the S saturation but also on the symmetry configuration of the S edge atoms. Our results show that for the same S saturation the magnetization can be decreased by increasing the pairing of the S and Mo edge atoms. In spite of the observed pairing of S dimers at the Mo-edge, the nanowires do not experience a Peierls-like metal-insulator transition PMID:25429189

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

PubMed

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

Magneto-structural correlations in dirhenium(iv) complexes possessing magnetic pathways with even or odd numbers of atoms.

PubMed

Pedersen, Anders H; Julve, Miguel; Martínez-Lillo, José; Cano, Joan; Brechin, Euan K

2017-09-12

The employment of pyrazine (pyz), pyrimidine (pym) and s-triazine (triz) ligands in Re IV chemistry leads to the isolation of a family of complexes of general formula (NBu 4 ) 2 [(ReX 5 ) 2 (μ-L)] (L = pyz, X = Cl (1) or Br (2); L = pym, X = Br (3); L = triz, X = Br (4)). 1-4 are dinuclear compounds where two pentahalorhenium(iv) fragments are connected by bidentate pyz, pym and triz ligands. Variable-temperature magnetic measurements, in combination with detailed theoretical studies, uncover the underlying magneto-structural correlation whereby the nature of the exchange between the metal ions is dictated by the number of intervening atoms. That is, the spin-polarization mechanism present dictates that odd and even numbers of atoms favour ferromagnetic (F) and antiferromagnetic (AF) exchange interactions, respectively. Hence, while the pyz ligand in 1 and 2 mediates AF coupling, the pym and triz ligands in 3 and 4 promote F interactions.

A coarse-grained model for DNA origami.

PubMed

Reshetnikov, Roman V; Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

2018-02-16

Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.

Atomic-Level Structural Dynamics of Polyoxoniobates during DMMP Decomposition

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

Wang, Qi; Chapleski, Robert C.; Plonka, Anna M.

Ambient pressure in situ synchrotron-based spectroscopic techniques have been correlated to illuminate atomic-level details of bond breaking and formation during the hydrolysis of a chemical warfare nerve agent simulant over a polyoxometalate catalyst. Specifically, a Cs 8[Nb 6O 19] polyoxoniobate catalyst has been shown to react readily with dimethyl methylphosphonate (DMMP). The atomic-level transformations of all reactant moieties, the [Nb 6O 19] 8- polyanion, its Cs + counterions, and the DMMP substrate, were tracked under ambient conditions by a combination of X-ray absorption fine structure spectroscopy, Raman spectroscopy, and X-ray diffraction. Results reveal that the reaction mechanism follows general basemore » (in contrast to specific base) hydrolysis. Together with computational results, the work demonstrates that the ultimate fate of DMMP hydrolysis at the Cs 8[Nb 6O 19] catalyst is strong binding of the (methyl) methylphosphonic acid ((M)MPA) product to the polyanions, which ultimately inhibits catalytic turnover.« less

Atomic-Level Structural Dynamics of Polyoxoniobates during DMMP Decomposition

DOE PAGES

Wang, Qi; Chapleski, Robert C.; Plonka, Anna M.; ...

2017-04-10

Ambient pressure in situ synchrotron-based spectroscopic techniques have been correlated to illuminate atomic-level details of bond breaking and formation during the hydrolysis of a chemical warfare nerve agent simulant over a polyoxometalate catalyst. Specifically, a Cs 8[Nb 6O 19] polyoxoniobate catalyst has been shown to react readily with dimethyl methylphosphonate (DMMP). The atomic-level transformations of all reactant moieties, the [Nb 6O 19] 8- polyanion, its Cs + counterions, and the DMMP substrate, were tracked under ambient conditions by a combination of X-ray absorption fine structure spectroscopy, Raman spectroscopy, and X-ray diffraction. Results reveal that the reaction mechanism follows general basemore » (in contrast to specific base) hydrolysis. Together with computational results, the work demonstrates that the ultimate fate of DMMP hydrolysis at the Cs 8[Nb 6O 19] catalyst is strong binding of the (methyl) methylphosphonic acid ((M)MPA) product to the polyanions, which ultimately inhibits catalytic turnover.« less

A coarse-grained model for DNA origami

PubMed Central

Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

2018-01-01

Abstract Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version. PMID:29267876

Toward understanding the chloroquine action at the molecular level in antimalarial therapy--X-ray absorption studies in acetic acid solution.

PubMed

Walczak, Monika S; Lawniczak-Jablonska, Krystyna; Wolska, Anna; Sikora, Marcin; Sienkiewicz, Andrzej; Suárez, Liliana; Kosar, Aaron J; Bellemare, Marie-Josee; Bohle, D Scott

2011-04-21

The local atomic structure around the central iron of the synthetic soluble analog of malarial pigment in acetic acid solution and with addition of chloroquine as found by X-ray absorption spectroscopy is reported. The special interest was drawn to the axial linkage between the central iron atom of the ferriprotoporphyrin IX (FePPIX) coordinated axially to the propionate group of the adjacent FePPIX. This kind of bonding is typical for hematin anhydride. Detailed analysis revealed differences in oxygen coordination sphere (part of dimer linkage bond) between synthetic equivalent of hemozoin in the powder state and dissolved in acetic acid and water at different concentrations mimicking the physiological condition of the parasite's food vacuole. The results of performed studies suggest that the molecular structure of synthetic analogue of hemozoin is no longer dimer-like in acidic solution. Further changes in atomic order around Fe are seen after addition of the antimalarial drug chloroquine.

Yong-Ki Kim — His Life and Recent Work

NASA Astrophysics Data System (ADS)

Stone, Philip M.

2007-08-01

Dr. Kim made internationally recognized contributions in many areas of atomic physics research and applications, and was still very active when he was killed in an automobile accident. He joined NIST in 1983 after 17 years at the Argonne National Laboratory following his Ph.D. work at the University of Chicago. Much of his early work at Argonne and especially at NIST was the elucidation and detailed analysis of the structure of highly charged ions. He developed a sophisticated, fully relativistic atomic structure theory that accurately predicts atomic energy levels, transition wavelengths, lifetimes, and transition probabilities for a large number of ions. This information has been vital to model the properties of the hot interior of fusion research plasmas, where atomic ions must be described with relativistic atomic structure calculations. In recent years, Dr. Kim worked on the precise calculation of ionization and excitation cross sections of numerous atoms, ions, and molecules that are important in fusion research and in plasma processing for manufacturing semiconductor chips. Dr. Kim greatly advanced the state-of-the-art of calculations for these cross sections through development and implementation of highly innovative methods, including his Binary-Encounter-Bethe (BEB) theory and a scaled plane wave Born (scaled PWB) theory. His methods, using closed quantum mechanical formulas and no adjustable parameters, avoid tedious large-scale computations with main-frame computers. His calculations closely reproduce the results of benchmark experiments as well as large-scale calculations requiring hours of computer time. This recent work on BEB and scaled PWB is reviewed and examples of its capabilities are shown.

Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group.

PubMed

Brouwer, Darren H

2013-01-01

An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state (29)Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with Si-O-Si connectivity information, symmetry restraints, and fits to (29)Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in "NMR crystallography" is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information. Copyright © 2013 Elsevier Inc. All rights reserved.

Inhibition of d-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography

PubMed Central

Kovalevsky, Andrey; Hanson, B. Leif; Mason, Sax A.; Forsyth, V. Trevor; Fisher, Zoe; Mustyakimov, Marat; Blakeley, Matthew P.; Keen, David A.; Langan, Paul

2012-01-01

d-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni2+ cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg2+ ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni2+ ions occupying the catalytic metal site (M2) were found at two locations, while Mg2+ in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH. PMID:22948921

On the influence of tetrahedral covalent-hybridization on electronic band structure of topological insulators from first principles

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

Zhang, X. M.; Xu, G. Z.; Liu, E. K.

Based on first-principles calculations, we investigate the influence of tetrahedral covalent-hybridization between main-group and transition-metal atoms on the topological band structures of binary HgTe and ternary half-Heusler compounds, respectively. Results show that, for the binary HgTe, when its zinc-blend structure is artificially changed to rock-salt one, the tetrahedral covalent-hybridization will be removed and correspondingly the topologically insulating band character lost. While for the ternary half-Heusler system, the strength of covalent-hybridization can be tuned by varying both chemical compositions and atomic arrangements, and the competition between tetrahedral and octahedral covalent-hybridization has been discussed in details. As a result, we found thatmore » a proper strength of tetrahedral covalent-hybridization is probably in favor to realizing the topologically insulating state with band inversion occurring at the Γ point of the Brillouin zone.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

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

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

DOE PAGES

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

2017-03-08

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

On the use of big-bang method to generate low-energy structures of atomic clusters modeled with pair potentials of different ranges.

PubMed

Marques, J M C; Pais, A A C C; Abreu, P E

2012-02-05

The efficiency of the so-called big-bang method for the optimization of atomic clusters is analysed in detail for Morse pair potentials with different ranges; here, we have used Morse potentials with four different ranges, from long- ρ = 3) to short-ranged ρ = 14) interactions. Specifically, we study the efficacy of the method in discovering low-energy structures, including the putative global minimum, as a function of the potential range and the cluster size. A new global minimum structure for long-ranged ρ = 3) Morse potential at the cluster size of n= 240 is reported. The present results are useful to assess the maximum cluster size for each type of interaction where the global minimum can be discovered with a limited number of big-bang trials. Copyright © 2011 Wiley Periodicals, Inc.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

NASA Astrophysics Data System (ADS)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Coarse-grained mechanics of viral shells

NASA Astrophysics Data System (ADS)

Klug, William S.; Gibbons, Melissa M.

2008-03-01

We present an approach for creating three-dimensional finite element models of viral capsids from atomic-level structural data (X-ray or cryo-EM). The models capture heterogeneous geometric features and are used in conjunction with three-dimensional nonlinear continuum elasticity to simulate nanoindentation experiments as performed using atomic force microscopy. The method is extremely flexible; able to capture varying levels of detail in the three-dimensional structure. Nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and φ29. In addition to purely continuum elastic models a multiscale technique is developed that combines finite-element kinematics with MD energetics such that large-scale deformations are facilitated by a reduction in degrees of freedom. Simulations of these capsid deformation experiments provide a testing ground for the techniques, as well as insight into the strength-determining mechanisms of capsid deformation. These methods can be extended as a framework for modeling other proteins and macromolecular structures in cell biology.

Theoretical study of some nitrososulfamide compounds with antitumor activity.

PubMed

Djameleddine, Khatmi; Soumeya, Seridi; Fatiha, Madi

2004-09-30

The lowest-energy conformations of four 2-chloroethylnitrososulfamides were determined using the MM+ molecular mechanics method as implemented in Hyperchem 6.0. Some of the calculated structural parameters, angles and bonds lengths were compared with the crystal structure data of N-nitroso-N-(2-chloroethyl)-N'-sulfamoyl- proline. Using MM+, AM1 and PM3 the anti conformation was predicted to be more stable than the syn conformation in each of these compounds. With these methods we found that the relative energy of the transition state (TS) was considerably higher, but with the ab initio method using RHF with minimal basic function STO-3G we found that the syn conformation is predicted to be slightly more stable. The determination of some atomic charges of a selection of atoms on the syn, anti and TS structures of the various compounds provided some details about the nature of the transition state.

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

PubMed Central

Noh, Hanaul; Diaz, Alfredo J

2017-01-01

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, and is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules. PMID:28382247

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

PubMed

Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-16

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics

PubMed Central

Parker, David; Bryant, Zev; Delp, Scott L.

2010-01-01

Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org. PMID:20428469

Bimolecular dynamics by computer analysis

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

Eilbeck, J.C.; Lomdahl, P.S.; Scott, A.C.

1984-01-01

As numerical tools (computers and display equipment) become more powerful and the atomic structures of important biological molecules become known, the importance of detailed computation of nonequilibrium biomolecular dynamics increases. In this manuscript we report results from a well developed study of the hydrogen bonded polypeptide crystal acetanilide, a model protein. Directions for future research are suggested. 9 references, 6 figures.

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane.

PubMed

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-15

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

NASA Astrophysics Data System (ADS)

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-01

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Triple coupling and parameter resonance in quantum optomechanics with a single atom

NASA Astrophysics Data System (ADS)

Chang, Yue; Ian, H.; Sun, C. P.

2009-11-01

We study the energy level structure and quantum dynamics for a cavity optomechanical system assisted by a single atom. It is found that a triple coupling involving a photon, a phonon and an atom cannot be described only by the quasi-orbital angular momentum at frequency resonance, there also exists the phenomenon of parameter resonance, namely, when the system parameters are matched in some way, the evolution of the end mirror of the cavity is conditioned by the dressed states of the photon-atom subsystem. The quantum decoherence due to this conditional dynamics is studied in detail. In the quasi-classical limit of very large angular momentum, this system will behave like a standard cavity-QED system described by the Jaynes-Cummings (J-C) model when the angular momentum operators are transformed to bosonic operators of a single mode. We test this observation with an experimentally accessible parameter.

Atomic Structure of Interface States in Silicon Heterojunction Solar Cells

NASA Astrophysics Data System (ADS)

George, B. M.; Behrends, J.; Schnegg, A.; Schulze, T. F.; Fehr, M.; Korte, L.; Rech, B.; Lips, K.; Rohrmüller, M.; Rauls, E.; Schmidt, W. G.; Gerstmann, U.

2013-03-01

Combining orientation dependent electrically detected magnetic resonance and g tensor calculations based on density functional theory we assign microscopic structures to paramagnetic states involved in spin-dependent recombination at the interface of hydrogenated amorphous silicon crystalline silicon (a-Si:H/c-Si) heterojunction solar cells. We find that (i) the interface exhibits microscopic roughness, (ii) the electronic structure of the interface defects is mainly determined by c-Si, (iii) we identify the microscopic origin of the conduction band tail state in the a-Si:H layer, and (iv) present a detailed recombination mechanism.

High-Speed Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Ando, Toshio; Uchihashi, Takayuki; Kodera, Noriyuki

2012-08-01

The technology of high-speed atomic force microscopy (HS-AFM) has reached maturity. HS-AFM enables us to directly visualize the structure and dynamics of biological molecules in physiological solutions at subsecond to sub-100 ms temporal resolution. By this microscopy, dynamically acting molecules such as myosin V walking on an actin filament and bacteriorhodopsin in response to light are successfully visualized. High-resolution molecular movies reveal the dynamic behavior of molecules in action in great detail. Inferences no longer have to be made from static snapshots of molecular structures and from the dynamic behavior of optical markers attached to biomolecules. In this review, we first describe theoretical considerations for the highest possible imaging rate, then summarize techniques involved in HS-AFM and highlight recent imaging studies. Finally, we briefly discuss future challenges to explore.

Ab initio effective core potentials including relativistic effects and their application to the electronic structure calculations of heavy atoms and molecules

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

Lee, Y.S.

1977-11-01

The effects of the 4f shell of electrons and the relativity of valence electrons are compared. The effect of 4f shell (lanthanide contraction) is estimated from the numerical Hartree-Fock (HF) calculations of pseudo-atoms corresponding to Hf, Re, Au, Hg, Tl, Pb and Bi without 4f electrons and with atomic numbers reduced by 14. The relativistic effect estimated from the numerical Dirac-Hartree-Fock (DHF) calculations of those atoms is comparable in the magnitude with that of the 4f shell of electrons. Both are larger for 6s than for 5d or 6p electrons. The various relativistic effects on valence electrons are discussed inmore » detail to determine the proper level of the approximation for the valence electron calculations of systems with heavy elements. An effective core potential system has been developed for heavy atoms in which relativistic effects are included in the effective potentials.« less

Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography.

PubMed

Prosa, Ty J; Larson, David J

2017-04-01

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

Spatially resolved In and As distributions in InGaAs/GaP and InGaAs/GaAs quantum dot systems.

PubMed

Shen, J; Song, Y; Lee, M L; Cha, J J

2014-11-21

InGaAs quantum dots (QDs) on GaP are promising for monolithic integration of optoelectronics with Si technology. To understand and improve the optical properties of InGaAs/GaP QD systems, detailed measurements of the QD atomic structure as well as the spatial distributions of each element at high resolution are crucial. This is because the QD band structure, band alignment, and optical properties are determined by the atomic structure and elemental composition. Here, we directly measure the inhomogeneous distributions of In and As in InGaAs QDs grown on GaAs and GaP substrates at the nanoscale using energy dispersive x-ray spectral mapping in a scanning transmission electron microscope. We find that the In distribution is broader on GaP than on GaAs, and as a result, the QDs appear to be In-poor using a GaP matrix. Our findings challenge some of the assumptions made for the concentrations and distributions of In within InGaAs/GaAs or InGaAs/GaP QD systems and provide detailed structural and elemental information to modify the current band structure understanding. In particular, the findings of In deficiency and inhomogeneous distribution in InGaAs/GaP QD systems help to explain photoluminescence spectral differences between InGaAs/GaAs and InGaAs/GaP QD systems.

Electrostatic Levitation Technique for Investigations of Physical Properties of Liquid States

NASA Astrophysics Data System (ADS)

Okada, Junpei; Ishikawa, Takehiko; Paradis, Paul-Francois; Yoda, Shinichi

Electrostatic levitator (ESL) levitates a charged sample in a high vacuum using computer con-trolled electrostatic fields [1]. It can levitate materials such as metals, semiconductors, and some insulators. Sample temperature can be varied over a wide range, and samples can be deeply undercooled. We have been engaged in the research and development of the electro-static levitation technique with the aim of performing levitation dissolution experiments in the International Space Station (ISS). Our device for the electrostatic levitation dissolution test has been developed for experiments on the ISS. To this end, the system is designed to be compact and portable so that it can be launched by rocket and used for experiments in the limited space on the ISS. Accordingly, the device can be installed not just on the ISS or our research laboratory, but also in various external sites. We devised a plan to install the electrostatic levitation system in a site other than the ISS to study atomic structure and electron structure of ultra-high-temperature liquids. We mounted our system on third generation synchrotron radiation facility "SPring-8" in Japan, to investigate the atomic and electron structures of high-temperature liquids. The SPring-8 is an experimental facility that allows use of the most powerful X-rays in the world. We conducted a variety of experiments on ultra-high-temperature liquids using SPring-8. The X-ray is ideal for exploring atomic structure and electron structure. Since the X-ray is an electromagnetic wave, it interacts with electrons. In addition, most electrons gather around the atomic nucleus. By close analysis of the scattered x-rays, we can determine its atomic structure and electron structure in detail. In this talk, we introduce an x-ray Compton scattering and x-ray Raman scattering measurements on liquid aluminum and silicon. [1] W. -K. Rhim, et al, Rev. Sci. Instrum. (1985) 56 307.

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

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

Quantifying the Hierarchical Order in Self-Aligned Carbon Nanotubes from Atomic to Micrometer Scale.

PubMed

Meshot, Eric R; Zwissler, Darwin W; Bui, Ngoc; Kuykendall, Tevye R; Wang, Cheng; Hexemer, Alexander; Wu, Kuang Jen J; Fornasiero, Francesco

2017-06-27

Fundamental understanding of structure-property relationships in hierarchically organized nanostructures is crucial for the development of new functionality, yet quantifying structure across multiple length scales is challenging. In this work, we used nondestructive X-ray scattering to quantitatively map the multiscale structure of hierarchically self-organized carbon nanotube (CNT) "forests" across 4 orders of magnitude in length scale, from 2.0 Å to 1.5 μm. Fully resolved structural features include the graphitic honeycomb lattice and interlayer walls (atomic), CNT diameter (nano), as well as the greater CNT ensemble (meso) and large corrugations (micro). Correlating orientational order across hierarchical levels revealed a cascading decrease as we probed finer structural feature sizes with enhanced sensitivity to small-scale disorder. Furthermore, we established qualitative relationships for single-, few-, and multiwall CNT forest characteristics, showing that multiscale orientational order is directly correlated with number density spanning 10 9 -10 12 cm -2 , yet order is inversely proportional to CNT diameter, number of walls, and atomic defects. Lastly, we captured and quantified ultralow-q meridional scattering features and built a phenomenological model of the large-scale CNT forest morphology, which predicted and confirmed that these features arise due to microscale corrugations along the vertical forest direction. Providing detailed structural information at multiple length scales is important for design and synthesis of CNT materials as well as other hierarchically organized nanostructures.

Atomistic simulation of cubic and tetragonal phases of U-Mo alloy: Structure and thermodynamic properties

NASA Astrophysics Data System (ADS)

Starikov, S. V.; Kolotova, L. N.; Kuksin, A. Yu.; Smirnova, D. E.; Tseplyaev, V. I.

2018-02-01

We studied structure and thermodynamic properties of cubic and tetragonal phases of pure uranium and U-Mo alloys using atomistic simulations: molecular dynamics and density functional theory. The main attention was paid to the metastable γ0 -phase that is formed in U-Mo alloys at low temperature. Structure of γ0 -phase is similar to body-centered tetragonal (bct) lattice with displacement of a central atom in the basic cell along [ 001 ] direction. Such displacements have opposite orientations for part of the neighbouring basic cells. In this case, such ordering of the displacements can be designated as antiferro-displacement. Formation of such complex structure may be interpreted through forming of short U-U bonds. At heating, the tetragonal structure transforms into cubic γs -phase, still showing ordering of central atom displacements. With rise in temperature, γs -phase transforms to γ-phase with a quasi body-centered cubic (q-bcc) lattice. The local positions of uranium atoms in γ-phase correspond to γs -phase, however, orientations of the central atom displacements become disordered. Transition from γ0 to γ can be considered as antiferro-to paraelastic transition of order-disorder type. This approach to the structure description of uranium alloy allows to explain a number of unusual features found in the experiments: anisotropy of lattice at low temperature; remarkably high self-diffusion mobility in γ-phase; decreasing of electrical resistivity at heating for some alloys. In addition, important part of this work is the development of new interatomic potential for U-Mo system made with taking into account details of studied structures.

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

The formation of periodic micro/nano structured on stainless steel by femtosecond laser irradiation

NASA Astrophysics Data System (ADS)

Yao, Caizhen; Gao, Wei; Ye, Yayun; Jiang, Yong; Xu, Shizhen; Yuan, Xiaodong

2017-07-01

Stainless steel surface was irradiated by linear polarized laser (800 nm, 35 fs, 4 Hz and 0.7 J/cm2) with different pulse numbers. Environmental scanning electron microscope (ESEM/EDS) was used for detailed morphology, microstructure and composition studies. The wettability of irradiated steel surface was tested by Interface Tensiometer JC-2000X and compared with untreated stainless steel. Results showed that micro/nanostripes with different periods were formed. The period increased with the increasing pulse numbers from 450 nm for 90 pulses to 500 nm for 180 pulses. The orientation of those stripes was parallel with the laser beam polarization. Nanoparticles were observed on those periodic structures. EDS indicated that the atomic ratio of Cr increased and the atomic ratios of Fe and Ni decreased after laser irradiation, which may enhance the corrosion resistance due to the Cr-rich layer. The prepared structure exhibited hydrophobic property without further treatment. The formation mechanism of micro/nanoperiodic structures was also explored.

Systematic Validation of Protein Force Fields against Experimental Data

PubMed Central

Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

2012-01-01

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins. PMID:22384157

Atomic resolution chemical bond analysis of oxygen in La2CuO4

NASA Astrophysics Data System (ADS)

Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

2013-08-01

The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

Giant dielectric constant dominated by Maxwell-Wagner relaxation in Al{sub 2}O{sub 3}/TiO{sub 2} nanolaminates synthesized by atomic layer deposition.

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

Li, W.; Auciello, O.; Premnath, R. N.

2010-01-01

Nanolaminates consisting of Al{sub 2}O{sub 3} and TiO{sub 2} oxide sublayers were synthesized by using atomic layer deposition to produce individual layers with atomic scale thickness control. The sublayer thicknesses were kept constant for each multilayer structure, and were changed from 50 to 0.2 nm for a series of different samples. Giant dielectric constant ({approx}1000) was observed when the sublayer thickness is less than 0.5 nm, which is significantly larger than that of Al{sub 2}O{sub 3} and TiO{sub 2} dielectrics. Detailed investigation revealed that the observed giant dielectric constant is originated from the Maxwell-Wagner type dielectric relaxation.

A generative, probabilistic model of local protein structure.

PubMed

Boomsma, Wouter; Mardia, Kanti V; Taylor, Charles C; Ferkinghoff-Borg, Jesper; Krogh, Anders; Hamelryck, Thomas

2008-07-01

Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence-structure correlations in the native state. Our method represents a significant theoretical and practical improvement over the widely used fragment assembly technique by avoiding the drawbacks associated with a discrete and nonprobabilistic approach.

Bringing diffuse X-ray scattering into focus

DOE PAGES

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

2018-02-16

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Bringing diffuse X-ray scattering into focus

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

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Brownian dynamics simulation of protein diffusion in crowded environments

NASA Astrophysics Data System (ADS)

Mereghetti, Paolo; Wade, Rebecca C.

2013-02-01

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. We first describe the development of a Brownian dynamics simulation methodology to investigate the dynamic and structural properties of protein solutions using atomic-detail protein structures. We then discuss insights obtained from applying this approach to simulation of solutions of a range of types of proteins.

Electronic structure study of Ce1-xAxO2 (A = Zr & Hf) nanoparticles: NEXAFS and EXAFS investigations.

PubMed

Sharma, Aditya; Varshney, Mayora; Shin, Hyun-Joon; Park, Yong Jun; Kim, Min-Gyu; Ha, Tae-Kyun; Chae, Keun Hwa; Gautam, Sanjeev

2014-10-07

Single phase nanoparticles (NPs) of CeO2, Ce0.5Zr0.5O2, Ce0.5Hf0.5O2 and Ce0.5Hf0.25Zr0.25O2 were successfully synthesized by co-precipitation method at constant pH and temperature. The X-ray diffraction results revealed that the additive atoms did not segregate to form secondary phases but led to grain size variation in the NPs. The 10 Dq values in the near edge X-ray absorption fine structure (NEXAFS) spectra at the O K-edge did not vary in the same way as the average grain size was changed for the doped CeO2 NPs. The deconvolution of Ce M5-edge and detailed analysis of O K pre-edge peak have shown the higher Ce(+3)/(Ce(+3) + Ce(+4)) ratio in the Zr- and Hf-doped samples. The local atomic structure around the Ce, Zr and Hf atoms was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy at Ce K-edge, Zr K-edge and Hf L3-edge, respectively, and the EXAFS data were fitted with the theoretical calculations. The 4f occupancy, Ce(+3)/(Ce(+3) + Ce(+4)) ratio of Ce ions, coordination number of Ce and Ce-Ce/Ce-O bond distances were sensitive to the additive atoms but not explicitly changed according to the grain size variation in the NPs.

Deciphering chemical order/disorder and material properties at the single-atom level

DOE PAGES

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.; ...

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

1-D Metal Nanobead Arrays within Encapsulated Nanowires via a Red-Ox-Induced Dewetting: Mechanism Study by Atom-Probe Tomography.

PubMed

Sun, Zhiyuan; Tzaguy, Avra; Hazut, Ori; Lauhon, Lincoln J; Yerushalmi, Roie; Seidman, David N

2017-12-13

Metal nanoparticle arrays are excellent candidates for a variety of applications due to the versatility of their morphology and structure at the nanoscale. Bottom-up self-assembly of metal nanoparticles provides an important complementary alternative to the traditional top-down lithography method and makes it possible to assemble structures with higher-order complexity, for example, nanospheres, nanocubes, and core-shell nanostructures. Here we present a mechanism study of the self-assembly process of 1-D noble metal nanoparticles arrays, composed of Au, Ag, and AuAg alloy nanoparticles. These are prepared within an encapsulated germanium nanowire, obtained by the oxidation of a metal-germanium nanowire hybrid structure. The resulting structure is a 1-D array of equidistant metal nanoparticles with the same diameter, the so-called nanobead (NB) array structure. Atom-probe tomography and transmission electron microscopy were utilized to investigate the details of the morphological and chemical evolution during the oxidation of the encapsulated metal-germanium nanowire hybrid-structures. The self-assembly of nanoparticles relies on the formation of a metal-germanium liquid alloy and the migration of the liquid alloy into the nanowire, followed by dewetting of the liquid during shape-confined oxidation where the liquid column breaks-up into nanoparticles due to the Plateau-Rayleigh instability. Our results demonstrate that the encapsulating oxide layer serves as a structural scaffold, retaining the overall shape during the eutectic liquid formation and demonstrates the relationship between the oxide mechanical properties and the final structural characteristics of the 1-D arrays. The mechanistic details revealed here provide a versatile tool-box for the bottom-up fabrication of 1-D arrays nanopatterning that can be modified for multiple applications according to the RedOx properties of the material system components.

Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody.

PubMed

Brandt, J Paul; Patapoff, Thomas W; Aragon, Sergio R

2010-08-04

At 150 kDa, antibodies of the IgG class are too large for their structure to be determined with current NMR methodologies. Because of hinge-region flexibility, it is difficult to obtain atomic-level structural information from the crystal, and questions regarding antibody structure and dynamics in solution remain unaddressed. Here we describe the construction of a model of a human IgG1 monoclonal antibody (trastuzumab) from the crystal structures of fragments. We use a combination of molecular-dynamics (MD) simulation, continuum hydrodynamics modeling, and experimental diffusion measurements to explore antibody behavior in aqueous solution. Hydrodynamic modeling provides a link between the atomic-level details of MD simulation and the size- and shape-dependent data provided by hydrodynamic measurements. Eight independent 40 ns MD trajectories were obtained with the AMBER program suite. The ensemble average of the computed transport properties over all of the MD trajectories agrees remarkably well with the value of the translational diffusion coefficient obtained with dynamic light scattering at 20 degrees C and 27 degrees C, and the intrinsic viscosity measured at 20 degrees C. Therefore, our MD results likely represent a realistic sampling of the conformational space that an antibody explores in aqueous solution. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Atoms and Molecules Interacting with Light

NASA Astrophysics Data System (ADS)

van der Straten, Peter; Metcalf, Harold

2016-02-01

Part I. Atom-Light Interaction: 1. The classical physics pathway; Appendix 1.A. Damping force on an accelerating charge; Appendix 1.B. Hanle effect; Appendix 1.C. Optical tweezers; 2. Interaction of two-level atoms and light; Appendix 2.A. Pauli matrices for motion of the bloch vector; Appendix 2.B. The Ramsey method; Appendix 2.C. Echoes and interferometry; Appendix 2.D. Adiabatic rapid passage; Appendix 2.E Superposition and entanglement; 3. The atom-light interaction; Appendix 3.A. Proof of the oscillator strength theorem; Appendix 3.B. Electromagnetic fields; Appendix 3.C. The dipole approximation; Appendix 3.D. Time resolved fluorescence from multi-level atoms; 4. 'Forbidden' transitions; Appendix 4.A. Higher order approximations; 5. Spontaneous emission; Appendix 5.A. The quantum mechanical harmonic oscillator; Appendix 5.B. Field quantization; Appendix 5.C. Alternative theories to QED; 6. The density matrix; Appendix 6.A. The Liouville-von Neumann equation; Part II. Internal Structure: 7. The hydrogen atom; Appendix 7.A. Center-of-mass motion; Appendix 7.B. Coordinate systems; Appendix 7.C. Commuting operators; Appendix 7.D. Matrix elements of the radial wavefunctions; 8. Fine structure; Appendix 8.A. The Sommerfeld fine-structure constant; Appendix 8.B. Measurements of the fine structure 9. Effects of the nucleus; Appendix 9.A. Interacting magnetic dipoles; Appendix 9.B. Hyperfine structure for two spin =2 particles; Appendix 9.C. The hydrogen maser; 10. The alkali-metal atoms; Appendix 10.A. Quantum defects for the alkalis; Appendix 10.B. Numerov method; 11. Atoms in magnetic fields; Appendix 11.A. The ground state of atomic hydrogen; Appendix 11.B. Positronium; Appendix 11.C. The non-crossing theorem; Appendix 11.D. Passage through an anticrossing: Landau-Zener transitions; 12. Atoms in electric fields; 13. Rydberg atoms; 14. The helium atom; Appendix 14.A. Variational calculations; Appendix 14.B. Detail on the variational calculations of the ground state; 15. The periodic system of the elements; Appendix 15. A paramagnetism; Appendix 15.B. The color of gold; 16. Molecules; Appendix 16.A. Morse potential; 17. Binding in the hydrogen molecule; Appendix 17.A. Confocal elliptical coordinates; Appendix 17.B. One-electron two-center integrals; Appendix 17.C. Electron-electron interaction in molecular hydrogen; 18. Ultra-cold chemistry; Part III. Applications: 19. Optical forces and laser cooling; 20. Confinement of neutral atoms; 21. Bose-Einstein condensation; Appendix 21.A. Distribution functions; Appendix 21.B. Density of states; 22. Cold molecules; 23. Three level systems; Appendix 23.A. General Case for _1 , _2; 24. Fundamental physics; Part IV. Appendices: Appendix A. Notation and definitions; Appendix B. Units and notation; Appendix C. Angular momentum in quantum mechanics; Appendix D. Transition strengths; References; Index.

Uncovering the Connection Between Low-Frequency Dynamics and Phase Transformation Phenomena in Molecular Solids

NASA Astrophysics Data System (ADS)

Ruggiero, Michael T.; Zhang, Wei; Bond, Andrew D.; Mittleman, Daniel M.; Zeitler, J. Axel

2018-05-01

The low-frequency motions of molecules in the condensed phase have been shown to be vital to a large number of physical properties and processes. However, in the case of disordered systems, it is often difficult to elucidate the atomic-level details surrounding these phenomena. In this work, we have performed an extensive experimental and computational study on the molecular solid camphor, which exhibits a rich and complex structure-dynamics relationship, and undergoes an order-disorder transition near ambient conditions. The combination of x-ray diffraction, variable temperature and pressure terahertz time-domain spectroscopy, ab initio molecular dynamics, and periodic density functional theory calculations enables a complete picture of the phase transition to be obtained, inclusive of mechanistic, structural, and thermodynamic phenomena. Additionally, the low-frequency vibrations of a disordered solid are characterized for the first time with atomic-level precision, uncovering a clear link between such motions and the phase transformation. Overall, this combination of methods allows for significant details to be obtained for disordered solids and the associated transformations, providing a framework that can be directly applied for a wide range of similar systems.

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

PubMed Central

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

2010-01-01

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

Uncovering the Connection Between Low-Frequency Dynamics and Phase Transformation Phenomena in Molecular Solids.

PubMed

Ruggiero, Michael T; Zhang, Wei; Bond, Andrew D; Mittleman, Daniel M; Zeitler, J Axel

2018-05-11

The low-frequency motions of molecules in the condensed phase have been shown to be vital to a large number of physical properties and processes. However, in the case of disordered systems, it is often difficult to elucidate the atomic-level details surrounding these phenomena. In this work, we have performed an extensive experimental and computational study on the molecular solid camphor, which exhibits a rich and complex structure-dynamics relationship, and undergoes an order-disorder transition near ambient conditions. The combination of x-ray diffraction, variable temperature and pressure terahertz time-domain spectroscopy, ab initio molecular dynamics, and periodic density functional theory calculations enables a complete picture of the phase transition to be obtained, inclusive of mechanistic, structural, and thermodynamic phenomena. Additionally, the low-frequency vibrations of a disordered solid are characterized for the first time with atomic-level precision, uncovering a clear link between such motions and the phase transformation. Overall, this combination of methods allows for significant details to be obtained for disordered solids and the associated transformations, providing a framework that can be directly applied for a wide range of similar systems.

The Complete Heavy-Atom Structure of a Cp-Ftmw Chiral Tag Precursor, Verbenone

NASA Astrophysics Data System (ADS)

Marshall, Frank E.; West, Channing; Sedo, Galen; Pate, Brooks; Grubbs, G. S., II

2017-06-01

The microwave spectrum of the chiral molecule verbenone has been recorded from 2-18 GHz using two CP-FTMW spectrometers. 2-8 GHz data has been acquired on a 2-8 GHz CP-FTMW located at the University of Virginia and 8-18 data has been acquired on a 6-18 GHz spectrometer located at Missouri S&T. From the experiments the authors were able to assign and fit isotopologues corresponding to each heavy atom position (either ^{13}C or ^{18}O), providing for the heavy-atom structure. Previous studies by Evans and coworkers have been added to these measurements in a global fit of the parent species. The measurement and assignment of these transitions provide preliminary information needed for enatiomeric excess experiments using CP-FTMW van der Waals-type chiral tagging processes already being performed at UVa. Details of the experiment, fits, and structure will be discussed. C. J. Evans, S. M. Allpress, P. D. Godfrey, D. McNaughton, 67th International Symposium on Molecular Spectroscopy, 2012, RH13 S. M. Allpress, Spectroscopic and Computational Chemistry Studies on Terpene Related Compounds, University of Leicester, 2015, Chapter 6: Microwave Spectroscopy of Verbenone

Atomic and molecular physics in the gas phase

NASA Astrophysics Data System (ADS)

Toburen, L. H.

1990-09-01

The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets.

Nature of adsorption on TiC(111) investigated with density-functional calculations

NASA Astrophysics Data System (ADS)

Ruberto, Carlo; Lundqvist, Bengt I.

2007-06-01

Extensive density-functional calculations are performed for chemisorption of atoms in the three first periods (H, B, C, N, O, F, Al, Si, P, S, and Cl) on the polar TiC(111) surface. Calculations are also performed for O on TiC(001), for full O(1×1) monolayer on TiC(111), as well as for bulk TiC and for the clean TiC(111) and (001) surfaces. Detailed results concerning atomic structures, energetics, and electronic structures are presented. For the bulk and the clean surfaces, previous results are confirmed. In addition, detailed results are given on the presence of C-C bonds in the bulk and at the surface, as well as on the presence of a Ti-based surface resonance (TiSR) at the Fermi level and of C-based surface resonances (CSR’s) in the lower part of the surface upper valence band. For the adsorption, adsorption energies Eads and relaxed geometries are presented, showing great variations characterized by pyramid-shaped Eads trends within each period. An extraordinarily strong chemisorption is found for the O atom, 8.8eV /adatom. On the basis of the calculated electronic structures, a concerted-coupling model for the chemisorption is proposed, in which two different types of adatom-substrate interactions work together to provide the obtained strong chemisorption: (i) adatom-TiSR and (ii) adatom-CSR’s. This model is used to successfully describe the essential features of the calculated Eads trends. The fundamental nature of this model, based on the Newns-Anderson model, should make it apt for general application to transition-metal carbides and nitrides and for predictive purposes in technological applications, such as cutting-tool multilayer coatings and MAX phases.

Structure of a Clostridium botulinum C143S thiaminase I/thiamin complex reveals active site architecture .

PubMed

Sikowitz, Megan D; Shome, Brateen; Zhang, Yang; Begley, Tadhg P; Ealick, Steven E

2013-11-05

Thiaminases are responsible for the degradation of thiamin and its metabolites. Two classes of thiaminases have been identified based on their three-dimensional structures and their requirements for a nucleophilic second substrate. Although the reactions of several thiaminases have been characterized, the physiological role of thiamin degradation is not fully understood. We have determined the three-dimensional X-ray structure of an inactive C143S mutant of Clostridium botulinum (Cb) thiaminase I with bound thiamin at 2.2 Å resolution. The C143S/thiamin complex provides atomic level details of the orientation of thiamin upon binding to Cb-thiaminase I and the identity of active site residues involved in substrate binding and catalysis. The specific roles of active site residues were probed by using site directed mutagenesis and kinetic analyses, leading to a detailed mechanism for Cb-thiaminase I. The structure of Cb-thiaminase I is also compared to the functionally similar but structurally distinct thiaminase II.

Atomic Structures of Minor Proteins VI and VII in the Human Adenovirus.

PubMed

Dai, Xinghong; Wu, Lily; Sun, Ren; Zhou, Z Hong

2017-10-04

Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts towards more effective applications. Since 2010, atomic models of human Ad5 have been independently derived from photographic film cryoEM and X-ray crystallography, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII and IX. To clarify these discrepancies, here we have employed the technology of direct electron-counting to obtain a cryoEM structure of human Ad5 at 3.2 Å resolution. Our improved structure unambiguously confirmed our previous cryoEM models of proteins IIIa, VIII and IX and explained the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavities of hexons - the cleaved N-terminus of precursor protein VI (pVIn), the cleaved N-terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2--by extension that of genome-condensing pVII--to hexons is consistent with the previously proposed dsDNA genome-capsid co-assembly for adenoviruses, which resembles that of ssRNA viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid, as exemplified by tailed bacteriophages and herpesviruses. IMPORTANCE Adenovirus is a double-edged sword to humans - as a widespread pathogen and a bioengineering tool for anti-cancer and gene therapy. Atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models from conventional/film cryoEM and X-ray crystallography for important cement proteins IIIa, VIII, and IX have caused confusion. Using the cutting-edge cryoEM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid co-assembly mechanism for adenoviruses. Copyright © 2017 American Society for Microbiology.

Final Technical Report of Project DE-FG02-96ER14647

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

Lundeen, Stephen R.

This is the final technical report of work completed under DOE support over the period Sept. 1, 1996 until May 31, 2015. The title of the project was "Ion/Excited Atom Collision Studies with a Rydberg Target and a CO2 Laser" from 9/1/96 to 10/31/06, and "Properties of Actinide Ions from Measurements of Rydberg Ion Fine Structure" from 11/1/06 until 5/31/15. The primary technical results were a detailed experimental study of resonant charge transfer between Rydberg atoms and highly-charged ions, and unique measurements of many properties of multiply-charged Thorium ions.

Low energy electron-impact ionization of hydrogen atom for coplanar equal-energy-sharing kinematics in Debye plasmas

NASA Astrophysics Data System (ADS)

Li, Jun; Zhang, Song Bin; Ye, Bang Jiao; Wang, Jian Guo; Janev, R. K.

2016-12-01

Low energy electron-impact ionization of hydrogen atom in Debye plasmas has been investigated by employing the exterior complex scaling method. The interactions between the charged particles in the plasma have been represented by Debye-Hückel potentials. Triple differential cross sections (TDCS) in the coplanar equal-energy-sharing geometry at an incident energy of 15.6 eV for different screening lengths are reported. As the screening strength increases, TDCS change significantly. The evolutions of dominant typical peak structures of the TDCS are studied in detail for different screening lengths and for different coplanar equal-energy-sharing geometries.

Single atom catalysts on amorphous supports: A quenched disorder perspective

NASA Astrophysics Data System (ADS)

Peters, Baron; Scott, Susannah L.

2015-03-01

Phenomenological models that invoke catalyst sites with different adsorption constants and rate constants are well-established, but computational and experimental methods are just beginning to provide atomically resolved details about amorphous surfaces and their active sites. This letter develops a statistical transformation from the quenched disorder distribution of site structures to the distribution of activation energies for sites on amorphous supports. We show that the overall kinetics are highly sensitive to the precise nature of the low energy tail in the activation energy distribution. Our analysis motivates further development of systematic methods to identify and understand the most reactive members of the active site distribution.

Electronic structure and chemical bonding of the electron-poor II-V semiconductors ZnSb and ZnAs

NASA Astrophysics Data System (ADS)

Benson, Daryn; Sankey, Otto F.; Häussermann, Ulrich

2011-09-01

The binary compounds ZnSb and ZnAs with the CdSb structure are semiconductors (II-V), although the average electron concentration (3.5 per atom) is lower than that of the tetrahedrally bonded III-V and II-VI archetype systems (four per atom). We report a detailed electronic structure and chemical bonding analysis for ZnSb and ZnAs based on first-principles calculations. ZnSb and ZnAs are compared to the zinc blende-type semiconductors GaSb, ZnTe, GaAs, and ZnSe, as well as the more ionic, hypothetical, II-V systems MgSb and MgAs. We establish a clearly covalent bonding scenario for ZnSb and ZnAs where multicenter bonded structural entities (rhomboid rings Zn2Sb2 and Zn2As2) are connected to each other by classical two-center, two-electron bonds. This bonding scenario is only compatible with a weak ionicity in II-V semiconductor systems, and weak ionicity appears as a necessary condition for the stability of the CdSb structure type. It is argued that a chemical bonding scenario with mixed multicenter and two-center bonding resembles that of boron and boron-rich compounds and is typical of electron-poor sp-bonded semiconductors with average valence electron concentrations below four per atom.

Watching Silica's Dance: Imaging the Structure and Dynamics of the Atomic (Re-) Arrangements in 2D Glass

NASA Astrophysics Data System (ADS)

Muller, David

2014-03-01

Even though glasses are almost ubiquitous--in our windows, on our iPhones, even on our faces--they are also mysterious. Because glasses are notoriously difficult to study, basic questions like: ``How are the atoms arranged? Where and how do glasses break?'' are still under contention. We use aberration corrected transmission electron microscopy (TEM) to image the atoms in a new two-dimensional phase of silica glass - freestanding it becomes the world's thinnest pane of glass at only 3-atoms thick, and take a unique look into these questions. Using atom-by-atom imaging and spectroscopy, we are able to reconstruct the full structure and bonding of this 2D glass and identify it as a bi-tetrahedral layer of SiO2. Our images also strikingly resemble Zachariasen's original cartoon models of glasses, drawn in 1932. As such, our work realizes an 80-year-old vision for easily understandable glassy systems and introduces promising methods to test theoretical predictions against experimental data. We image atoms in the disordered solid and track their motions in response to local strain. We directly obtain ring statistics and pair distribution functions that span short-, medium-, and long-range order, and test these against long-standing theoretical predictions of glass structure and dynamics. We use the electron beam to excite atomic rearrangements, producing surprisingly rich and beautiful videos of how a glass bends and breaks, as well as the exchange of atoms at a solid/liquid interface. Detailed analyses of these videos reveal a complex dance of elastic and plastic deformations, phase transitions, and their interplay. These examples illustrate the wide-ranging and fundamental materials physics that can now be studied at atomic-resolution via transmission electron microscopy of two-dimensional glasses. Work in collaboration with: S. Kurasch, U. Kaiser, R. Hovden, Q. Mao, J. Kotakoski, J. S. Alden, A. Shekhawat, A. A. Alemi, J. P. Sethna, P. L. McEuen, A.V. Krasheninnikov, A. Srivastava, V. Skakalova, J. C. Meyer, and J.H. Smet. This work was supported by the NSF through the Cornell Center for Materials Research (NSF DMR-1120296).

Never at rest: insights into the conformational dynamics of ion channels from cryo-electron microscopy.

PubMed

Lau, Carus; Hunter, Mark J; Stewart, Alastair; Perozo, Eduardo; Vandenberg, Jamie I

2018-04-01

The tightly regulated opening and closure of ion channels underlies the electrical signals that are vital for a wide range of physiological processes. Two decades ago the first atomic level view of ion channel structures led to a detailed understanding of ion selectivity and conduction. In recent years, spectacular developments in the field of cryo-electron microscopy have resulted in cryo-EM superseding crystallography as the technique of choice for determining near-atomic resolution structures of ion channels. Here, we will review the recent developments in cryo-EM and its specific application to the study of ion channel gating. We will highlight the advantages and disadvantages of the current technology and where the field is likely to head in the next few years. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

PubMed

Chavent, Matthieu; Duncan, Anna L; Sansom, Mark Sp

2016-10-01

Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Biological water-oxidizing complex: a nano-sized manganese-calcium oxide in a protein environment.

PubMed

Najafpour, Mohammad Mahdi; Moghaddam, Atefeh Nemati; Yang, Young Nam; Aro, Eva-Mari; Carpentier, Robert; Eaton-Rye, Julian J; Lee, Choon-Hwan; Allakhverdiev, Suleyman I

2012-10-01

The resolution of Photosystem II (PS II) crystals has been improved using isolated PS II from the thermophilic cyanobacterium Thermosynechococcus vulcanus. The new 1.9 Å resolution data have provided detailed information on the structure of the water-oxidizing complex (Umena et al. Nature 473: 55-61, 2011). The atomic level structure of the manganese-calcium cluster is important for understanding the mechanism of water oxidation and to design an efficient catalyst for water oxidation in artificial photosynthetic systems. Here, we have briefly reviewed our knowledge of the structure and function of the cluster.

Toward structural elucidation of the gamma-secretase complex

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

Li, H.; Wolfe, M. S.; Selkoe, D. J.

2009-03-11

{gamma}-Secretase is an intramembrane protease complex that mediates the Notch signaling pathway and the production of amyloid {beta}-proteins. As such, this enzyme has emerged as an important target for development of novel therapeutics for Alzheimer disease and cancer. Great progress has been made in the identification and characterization of the membrane complex and its biological functions. One major challenge now is to illuminate the structure of this fascinating and important protease at atomic resolution. Here, we review recent progress on biochemical and biophysical probing of the structure of the four-component complex and discuss obstacles and potential pathways toward elucidating itsmore » detailed structure.« less

Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis.

PubMed

Tagami, Uno; Takahashi, Kazutoshi; Igarashi, Shunsuke; Ejima, Chieko; Yoshida, Tomomi; Takeshita, Sen; Miyanaga, Wataru; Sugiki, Masayuki; Tokumasu, Munetaka; Hatanaka, Toshihiro; Kashiwagi, Tatsuki; Ishikawa, Kohki; Miyano, Hiroshi; Mizukoshi, Toshimi

2016-04-14

X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure-activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the K i value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors.

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

PubMed

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

DGDFT: A massively parallel method for large scale density functional theory calculations.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align/. njyudj@njust.edu.cn or zhng@umich.edu. Supplementary data are available at Bioinformatics online.

Scanning tunneling microscopy of atomically precise graphene nanoribbons exfoliated onto H:Si(100)

NASA Astrophysics Data System (ADS)

Radocea, Adrian; Mehdi Pour, Mohammad; Vo, Timothy; Shekhirev, Mikhail; Sinitskii, Alexander; Lyding, Joseph

Atomically precise graphene nanoribbons (GNRs) are promising materials for next generation transistors due to their well-controlled bandgaps and the high thermal conductivity of graphene. The solution synthesis of graphene nanoribbons offers a pathway towards scalable manufacturing. While scanning tunneling microscopy (STM) can access size scales required for characterization, solvent residue increases experimental difficulty and precludes band-gap determination via scanning tunneling spectroscopy (STS). Our work addresses this challenge through a dry contact transfer method that cleanly transfers solution-synthesized GNRs onto H:Si(100) under UHV using a fiberglass applicator. The semiconducting silicon surface avoids problems with image charge screening enabling intrinsic bandgap measurements. We characterize the nanoribbons using STM and STS. For chevron GNRs, we find a 1.6 eV bandgap, in agreement with computational modeling, and map the electronic structure spatially with detailed spectra lines and current imaging tunneling spectroscopy. Mapping the electronic structure of graphene nanoribbons is an important step towards taking advantage of the ability to form atomically precise nanoribbons and finely tune their properties.

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

PubMed Central

Davis, Ian W.; Leaver-Fay, Andrew; Chen, Vincent B.; Block, Jeremy N.; Kapral, Gary J.; Wang, Xueyi; Murray, Laura W.; Arendall, W. Bryan; Snoeyink, Jack; Richardson, Jane S.; Richardson, David C.

2007-01-01

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu. PMID:17452350

Geometries and properties of bimetallic phosphido-bridged complex Cp(CO) 2W(μ-PPh 2)W(CO) 5 and Cp(CO) 3W(μ-PPh 2)W(CO) 5

NASA Astrophysics Data System (ADS)

Wang, Fang; Yang, Hongmei; Yang, Zuoyin; Zhang, Jingchang; Cao, Weiliang

2007-01-01

Complete geometry optimizations were carried out by HF and DFT methods to study the molecular structure of binuclear transition-metal compounds (Cp(CO) 3W(μ-PPh 2)W(CO) 5) (I) and (Cp(CO) 2W(μ-PPh 2)W(CO) 5) (II). A comparison of the experimental data and calculated structural parameters demonstrates that the most accurate geometry parameters are predicted by the MPW1PW91/LANL2DZ among the three DFT methods. Topological properties of molecular charge distributions were analyzed with the theory of atoms in molecules. (3, -1) critical points, namely bond critical point, were found between the two tungsten atoms, and between W1 and C10 in complex II, which confirms the existence of the metal-metal bond and a semi-bridging CO between the two tungsten atoms. The result provided a theoretical guidance of detailed study on the binuclear phosphido-bridged complex containing transition metal-metal bond, which could be useful in the further study of the heterobimetallic phosphido-bridged complexes.

Large-Area WS2 Film with Big Single Domains Grown by Chemical Vapor Deposition

NASA Astrophysics Data System (ADS)

Liu, Pengyu; Luo, Tao; Xing, Jie; Xu, Hong; Hao, Huiying; Liu, Hao; Dong, Jingjing

2017-10-01

High-quality WS2 film with the single domain size up to 400 μm was grown on Si/SiO2 wafer by atmospheric pressure chemical vapor deposition. The effects of some important fabrication parameters on the controlled growth of WS2 film have been investigated in detail, including the choice of precursors, tube pressure, growing temperature, holding time, the amount of sulfur powder, and gas flow rate. By optimizing the growth conditions at one atmospheric pressure, we obtained tungsten disulfide single domains with an average size over 100 μm. Raman spectra, atomic force microscopy, and transmission electron microscopy provided direct evidence that the WS2 film had an atomic layer thickness and a single-domain hexagonal structure with a high crystal quality. And the photoluminescence spectra indicated that the tungsten disulfide films showed an evident layer-number-dependent fluorescence efficiency, depending on their energy band structure. Our study provides an important experimental basis for large-area, controllable preparation of atom-thick tungsten disulfide thin film and can also expedite the development of scalable high-performance optoelectronic devices based on WS2 film.

Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy.

PubMed

Fang, Chong; Frontiera, Renee R; Tran, Rosalie; Mathies, Richard A

2009-11-12

Tracing the transient atomic motions that lie at the heart of chemical reactions requires high-resolution multidimensional structural information on the timescale of molecular vibrations, which commonly range from 10 fs to 1 ps. For simple chemical systems, it has been possible to map out in considerable detail the reactive potential-energy surfaces describing atomic motions and resultant reaction dynamics, but such studies remain challenging for complex chemical and biological transformations. A case in point is the green fluorescent protein (GFP) from the jellyfish Aequorea victoria, which is a widely used gene expression marker owing to its efficient bioluminescence. This feature is known to arise from excited-state proton transfer (ESPT), yet the atomistic details of the process are still not fully understood. Here we show that femtosecond stimulated Raman spectroscopy provides sufficiently detailed and time-resolved vibrational spectra of the electronically excited chromophore of GFP to reveal skeletal motions involved in the proton transfer that produces the fluorescent form of the protein. In particular, we observe that the frequencies and intensities of two marker bands, the C-O and C = N stretching modes at opposite ends of the conjugated chromophore, oscillate out of phase with a period of 280 fs; we attribute these oscillations to impulsively excited low-frequency phenoxyl-ring motions, which optimize the geometry of the chromophore for ESPT. Our findings illustrate that femtosecond simulated Raman spectroscopy is a powerful approach to revealing the real-time nuclear dynamics that make up a multidimensional polyatomic reaction coordinate.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

PubMed

Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

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

Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it; Jackson, Bret; Hughes, Keith H.

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theorymore » for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.« less

Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

NASA Astrophysics Data System (ADS)

Angelié, C.; Soudan, J.-M.

2017-05-01

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat -1 /3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve.

Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin.

PubMed

Leung, Carl; Dudkina, Natalya V; Lukoyanova, Natalya; Hodel, Adrian W; Farabella, Irene; Pandurangan, Arun P; Jahan, Nasrin; Pires Damaso, Mafalda; Osmanović, Dino; Reboul, Cyril F; Dunstone, Michelle A; Andrew, Peter W; Lonnen, Rana; Topf, Maya; Saibil, Helen R; Hoogenboom, Bart W

2014-12-02

Membrane attack complex/perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins constitute a major superfamily of pore-forming proteins that act as bacterial virulence factors and effectors in immune defence. Upon binding to the membrane, they convert from the soluble monomeric form to oligomeric, membrane-inserted pores. Using real-time atomic force microscopy (AFM), electron microscopy (EM), and atomic structure fitting, we have mapped the structure and assembly pathways of a bacterial CDC in unprecedented detail and accuracy, focussing on suilysin from Streptococcus suis. We show that suilysin assembly is a noncooperative process that is terminated before the protein inserts into the membrane. The resulting ring-shaped pores and kinetically trapped arc-shaped assemblies are all seen to perforate the membrane, as also visible by the ejection of its lipids. Membrane insertion requires a concerted conformational change of the monomeric subunits, with a marked expansion in pore diameter due to large changes in subunit structure and packing.

Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin

PubMed Central

Lukoyanova, Natalya; Hodel, Adrian W; Farabella, Irene; Pandurangan, Arun P; Jahan, Nasrin; Pires Damaso, Mafalda; Osmanović, Dino; Reboul, Cyril F; Dunstone, Michelle A; Andrew, Peter W; Lonnen, Rana; Topf, Maya

2014-01-01

Membrane attack complex/perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins constitute a major superfamily of pore-forming proteins that act as bacterial virulence factors and effectors in immune defence. Upon binding to the membrane, they convert from the soluble monomeric form to oligomeric, membrane-inserted pores. Using real-time atomic force microscopy (AFM), electron microscopy (EM), and atomic structure fitting, we have mapped the structure and assembly pathways of a bacterial CDC in unprecedented detail and accuracy, focussing on suilysin from Streptococcus suis. We show that suilysin assembly is a noncooperative process that is terminated before the protein inserts into the membrane. The resulting ring-shaped pores and kinetically trapped arc-shaped assemblies are all seen to perforate the membrane, as also visible by the ejection of its lipids. Membrane insertion requires a concerted conformational change of the monomeric subunits, with a marked expansion in pore diameter due to large changes in subunit structure and packing. DOI: http://dx.doi.org/10.7554/eLife.04247.001 PMID:25457051

MgCu metallic glass

NASA Astrophysics Data System (ADS)

Durandurdu, Murat

2018-03-01

We generate an amorphous MgCu model using the rapid solidification of the melt through a first-principles molecular dynamics approach within a generalised gradient approximation and reveal, for the first time, its structural features and mechanical properties in details. The liquid and glassy MgCu are found to acquire slightly distinct local structures. Yet in both forms of MgCu, most Cu atoms have a tendency to form the ideal and defective icosahedrons while Mg atoms are arranged in complex configurations. The mean coordination number of Cu and Mg at 300 K is 11.31 and 13.73, respectively. The short-range order of MgCu glass is projected to be different than the known crystalline MgCu and Mg2Cu phases. The mechanical properties of MgCu glass and the CsCl-type MgCu crystal are computed and compared. On the basis of the enthalpy analyses, a possible pressure-induced crystallisation of the MgCu glass into a CsCl-type structure is proposed to occur at around 11 GPa.

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

DOE PAGES

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.; ...

2018-04-19

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

Atomic Resolution Cryo-EM Structure of β-Galactosidase.

PubMed

Bartesaghi, Alberto; Aguerrebere, Cecilia; Falconieri, Veronica; Banerjee, Soojay; Earl, Lesley A; Zhu, Xing; Grigorieff, Nikolaus; Milne, Jacqueline L S; Sapiro, Guillermo; Wu, Xiongwu; Subramaniam, Sriram

2018-05-10

The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at ∼ 1.5 Å resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design. Published by Elsevier Ltd.

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

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

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

The electronic structure of Au25 clusters: between discrete and continuous

NASA Astrophysics Data System (ADS)

Katsiev, Khabiboulakh; Lozova, Nataliya; Wang, Lu; Sai Krishna, Katla; Li, Ruipeng; Mei, Wai-Ning; Skrabalak, Sara E.; Kumar, Challa S. S. R.; Losovyj, Yaroslav

2016-08-01

Here, an approach based on synchrotron resonant photoemission is employed to explore the transition between quantization and hybridization of the electronic structure in atomically precise ligand-stabilized nanoparticles. While the presence of ligands maintains quantization in Au25 clusters, their removal renders increased hybridization of the electronic states in the vicinity of the Fermi level. These observations are supported by DFT studies.Here, an approach based on synchrotron resonant photoemission is employed to explore the transition between quantization and hybridization of the electronic structure in atomically precise ligand-stabilized nanoparticles. While the presence of ligands maintains quantization in Au25 clusters, their removal renders increased hybridization of the electronic states in the vicinity of the Fermi level. These observations are supported by DFT studies. Electronic supplementary information (ESI) available: Experimental details including chemicals, sample preparation, and characterization methods. Computation techniques, SV-AUC, GIWAXS, XPS, UPS, MALDI-TOF, ESI data of Au25 clusters. See DOI: 10.1039/c6nr02374f

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Predicting Catalytic Activity of Nanoparticles by a DFT-Aided Machine-Learning Algorithm.

PubMed

Jinnouchi, Ryosuke; Asahi, Ryoji

2017-09-07

Catalytic activities are often dominated by a few specific surface sites, and designing active sites is the key to realize high-performance heterogeneous catalysts. The great triumphs of modern surface science lead to reproduce catalytic reaction rates by modeling the arrangement of surface atoms with well-defined single-crystal surfaces. However, this method has limitations in the case for highly inhomogeneous atomic configurations such as on alloy nanoparticles with atomic-scale defects, where the arrangement cannot be decomposed into single crystals. Here, we propose a universal machine-learning scheme using a local similarity kernel, which allows interrogation of catalytic activities based on local atomic configurations. We then apply it to direct NO decomposition on RhAu alloy nanoparticles. The proposed method can efficiently predict energetics of catalytic reactions on nanoparticles using DFT data on single crystals, and its combination with kinetic analysis can provide detailed information on structures of active sites and size- and composition-dependent catalytic activities.

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

PubMed

Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

2017-01-01

This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, ProSMART and LORESTR, which are available as part of the CCP4 software suite.

Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

PubMed

Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

2014-09-01

Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.

Positive and negative contribution to birefringence in a family of carbonates: A Born effective charges analysis

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

Jing, Qun; Yang, Guang; Hou, Juan

It is an important topic to investigate the birefringence and reveal the contribution from ions to birefringence because it plays an important role in nonlinear optical materials. In this paper, the birefringence of carbonates with coplanar CO{sub 3} groups were investigated using the first-principles method. The results show that the lead carbonates exhibit relative large birefringence. After detailed investigate the electronic structures, and Born effective charges, the authors find out that anisotropic electron distribution in the CO{sub 3} groups and Pb atoms give positive contribution, while the negative contribution was found from fluorine atoms, meanwhile the Ca, Mg, and Cdmore » atoms give very small contribution to birefringence. - Graphical abstract: Using the DFT and Born effective charges, the birefringence and the contribution of ions were investigated, the positive and negative contribution was found from Pb and F ions, respectively. - Highlights: • Optical properties and Born effective charges of carbonates are investigated. • Lead carbonates exhibit relative large birefringence. • Coplanar CO{sub 3} groups and Pb atoms give positive contribution. • F atoms give negative contribution. • Ca, Mg, and Cd atoms give very small contribution.« less

Functional Properties at Domain Walls in BiFeO3: Electrical, Magnetic, and Structural investigations

NASA Astrophysics Data System (ADS)

He, Qing; Yang, C.-H.; Yu, P.; Gajek, M.; Seidel, J.; Ramesh, R.; Wang, F.; Chu, Y.-H.; Martin, L. W.; Spaldin, N.; Rother, A.

2009-03-01

BiFeO3 (BFO) is a widely studied robust ferroelectric, antiferromagnetic multiferroic. Conducting-atomic force microscopy studies reveal the presence of enhanced conductivity at certain types of domain walls in BFO. We have completed detailed TEM studies of the physical structure at these domain walls as well as in-depth DFT calculations of the evolution of electronic structure at these domain walls. These studies reveal two major contributions to the observed conduction: the formation of an electrostatic potential at the domain walls as well as a structurally-driven change in the electronic structure (i.e., a lower band gap locally) at the domain walls. We will discuss the use of optical characterization techniques as a way of probing this change in electronic structure at domain walls as well as detailed IV characterization both in atmospheric and UHV environments. Finally, the evolution of magnetism at these domain walls has been studied through the use of photoemission measurements. Initial findings point to a significant change in the magnetic order at these domain walls in BFO.

Diffraction Techniques in Structural Biology

PubMed Central

Egli, Martin

2010-01-01

A detailed understanding of chemical and biological function and the mechanisms underlying the activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy and neutron diffraction are well established and have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches and high-speed computing and visualization, now provide specialists and non-specialists alike with a steady flow of molecular images of unprecedented detail. The present chapter combines a general overview of diffraction methods with a step-by-step description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:20517991

Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy*

PubMed Central

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R.; Gerwert, Klaus; Kötting, Carsten

2015-01-01

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg2+ coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg2+ in GTPases. The Mg2+ coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. PMID:26272610

Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental, and theoretical IR spectroscopy.

PubMed

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R; Gerwert, Klaus; Kötting, Carsten

2015-10-02

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg(2+) coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg(2+) in GTPases. The Mg(2+) coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

AFD: an application for bi-molecular interaction using axial frequency distribution.

PubMed

Raza, Saad; Azam, Syed Sikander

2018-03-06

Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented. AFD can profoundly represent distribution and density of ligand atom around a particular atom or set of atoms. It enabled us to obtain an explanation of local movements and rotations, which are not significantly highlighted by any other structural and dynamical parameters. AFD can be implemented on biological models representing ligand and protein interactions. It shows a comprehensive view of the binding pattern of ligand by exploring the distribution of atoms relative to the x-y plane of the system. By taking a relative centroid on protein or ligand, molecular interactions like hydrogen bonds, van der Waals, polar or ionic interaction can be analyzed to cater the ligand movement, stabilization or flexibility with respect to the protein. The AFD graph resulted in the residual depiction of bi-molecular interaction in gradient form which can yield specific information depending upon the system of interest.

Atomic-Scale Theoretical Studies of Fundamental Properties and Processes in CHNO Plastic-Bonded Explosive Constituent Materials under Static and Dynamic Compression

NASA Astrophysics Data System (ADS)

Sewell, Thomas

2013-06-01

The results of recent theoretical atomic-scale studies of CHNO plastic-bonded explosive constituent materials will be presented, emphasizing the effects of static and dynamic compression on structure, vibrational spectroscopy, energy redistribution, and dynamic deformation processes. Among the chemical compounds to be discussed are pentaerythritol tetranitrate (PETN), hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX), nitromethane, and hydroxyl-terminated polybutadiene (HTPB). Specific topics to be discussed include pressure-dependent terahertz IR absorption spectra in crystalline PETN and RDX, microscopic material flow characteristics and energy localization during and after pore collapse in shocked (100)-oriented RDX, establishment of local thermodynamic temperature and the approach to thermal equilibrium in shocked (100)-oriented nitromethane, and structural changes and relaxation phenomena that occur in shocked amorphous cis-HTPB. In the case of shocked HTPB, comparisons will be made between results obtained using fully-atomic and coarse-grained (united atom) molecular dynamics force field models. Rather than attempting to discuss any given topic in extended detail, 3-4 vignettes will be presented that highlight outstanding scientific questions and the predictive methods and tools we are developing to answer them. The U.S. Defense Threat Reduction Agency and Office of Naval Research supported this research.

Arguments, contradictions, resistances, and conceptual change in students' understanding of atomic structure

NASA Astrophysics Data System (ADS)

Niaz, Mansoor; Aguilera, Damarys; Maza, Arelys; Liendo, Gustavo

2002-07-01

Most general chemistry courses and textbooks emphasize experimental details and lack a history and philosophy of science perspective. The objective of this study is to facilitate freshman general chemistry students' understanding of atomic structure based on the work of Thomson, Rutherford, and Bohr. It is hypothesized that classroom discussions based on arguments/counterarguments of the heuristic principles, on which these scientists based their atomic models, can facilitate students' conceptual understanding. This study is based on 160 freshman students enrolled in six sections of General Chemistry I (three sections formed part of the experimental group). All three models (Thomson, Rutherford, and Bohr) were presented to the experimental and control group students in the traditional manner, as found in most textbooks. After this, the three sections of the experimental group participated in the discussion of six items with alternative responses. Students were first asked to select a response and then participate in classroom discussions leading to arguments in favor or against the selected response and finally select a new response. Three weeks after having discussed the six items, both the experimental and control groups presented a monthly exam (based on the three models) and after another 3 weeks a semester exam. Results obtained show that given the opportunity to argue and discuss, students' understanding can go beyond the simple regurgitation of experimental details. Performance of the experimental group showed contradictions, resistances, and progressive conceptual change with considerable and consistent improvement in the last item. It is concluded that if we want our students to understand scientific progress and practice, then it is important that we include the experimental details not as a rhetoric of conclusions (Schwab, 1962, The teaching of science as enquiry, Cambridge, MA, Harward University Press; Schwab, 1974, Conflicting conceptions of curriculum, Berkeley, CA, McCutchan) but as heuristic principles (Lakatos, 1970, Criticism and the growth of knowledge, Cambridge, UK, Cambridge University Press, pp. 91-195), which were based on arguments, controversies, and interpretations of the scientists.

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

Orfield, Noah J.; McBride, James R.; Wang, Feng

Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. In this paper, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking “giant” CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging,more » rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive “dark” fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be “dark”. Finally and therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.« less

The neuronal porosome complex in health and disease

PubMed Central

Naik, Akshata R; Lewis, Kenneth T

2015-01-01

Cup-shaped secretory portals at the cell plasma membrane called porosomes mediate the precision release of intravesicular material from cells. Membrane-bound secretory vesicles transiently dock and fuse at the base of porosomes facing the cytosol to expel pressurized intravesicular contents from the cell during secretion. The structure, isolation, composition, and functional reconstitution of the neuronal porosome complex have greatly progressed, providing a molecular understanding of its function in health and disease. Neuronal porosomes are 15 nm cup-shaped lipoprotein structures composed of nearly 40 proteins, compared to the 120 nm nuclear pore complex composed of >500 protein molecules. Membrane proteins compose the porosome complex, making it practically impossible to solve its atomic structure. However, atomic force microscopy and small-angle X-ray solution scattering studies have provided three-dimensional structural details of the native neuronal porosome at sub-nanometer resolution, providing insights into the molecular mechanism of its function. The participation of several porosome proteins previously implicated in neurotransmission and neurological disorders, further attest to the crosstalk between porosome proteins and their coordinated involvement in release of neurotransmitter at the synapse. PMID:26264442

Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

NASA Astrophysics Data System (ADS)

McBriarty, Martin E.

Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

I Situ Surface X-Ray Diffraction Studies of Electrochemically Deposited Monolayers

NASA Astrophysics Data System (ADS)

Yee, Dennis

1995-01-01

In situ x-ray diffraction has been used to determine the detailed atomic structure of electrochemically deposited lead, thallium, and bismuth monolayers on the silver (111) electrode surface. A review of our previously published lead and thallium monolayer results and the first in situ surface x-ray crystallographic study of the bismuth monolayer structure is presented. The crystallographic analysis of the bismuth Bragg rod intensities and the interference between the bismuth Bragg rod and silver crystal truncation rod scattering were used to determine the detailed atomic structure of the bismuth on silver (111) system at the liquid-solid interface. Our previous in situ x-ray diffraction studies showed that the bismuth monolayer lattice is rectangular and uniaxially incommensurate with the underlying hexagonal silver surface. A crystallographic analysis of the measured structure factor magnitudes reveals that the monolayer forms chains of atoms on the silver surface, similar to the bulk Bi(110)_{rh} plane, with a near neighbor distance of 3.12 +/- 0.01 A and a bond angle of 93 +/- 1^circ, consistent with the bulk Bi(110) _{rh} plane values. The crystallographic refinement also shows that the bismuth monolayer atoms are anisotropically disordered with a rms disorder of 0.25 +/- 0.03 A in the incommensurate direction and 0.09 +/- 0.03 A rms in the commnensurate direction. The interference between the Bi(20) Bragg rod and the Ag(10L)_ {h} crystal truncation rod scattering reveals that one set of bismuth atoms is registered near the bridge sites of the silver (111) surface while another set is registered near the 3-fold hollow sites. In addition, the Bi-Ag d-spacing (3.1 +/- 0.1 A) is found to be consistent with the bulk bismuth near neighbor distance. The bismuth z-direction rms disorder (1.01 +/- 0.08 A) is found to be dominated by the roughness of the underlying silver (sigma_{Ag} = 0.9 +/- 0.1 A rms). Using the estimated bismuth-bismuth spring constant of 1.41 +/- 0.07 eV/A^2 from our measured bismuth two-dimensional compressibility, two simple models are used to try and understand the origin of the anisotropic disorder. A simple two-dimensional isotropic thermal fluctuation model shows that thermal fluctuations are not large enough to account for all of the measured excess disorder in the incommensurate direction. A simple one-dimensional Frenkel-Kontorova model shows that the substrate-induced disorder can account for the anisotropic disorder, assuming a substrate sinusoidal potential strength of 0.35 +/- 0.02 eV.

Capping Ligand Vortices as “Atomic Orbitals” in Nanocrystal Self-Assembly

DOE PAGES

Waltmann, Curt; Horst, Nathan; Travesset, Alex

2017-10-27

In this work, we present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation.more » We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.« less

Capping Ligand Vortices as "Atomic Orbitals" in Nanocrystal Self-Assembly.

PubMed

Waltmann, Curt; Horst, Nathan; Travesset, Alex

2017-11-28

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation. We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.

DNA Free Energy Landscapes and RNA Nano-Self-Assembly Using Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Frey, Eric William

There is an important conceptual lesson which has long been appreciated by those who work in biophysics and related interdisciplinary fields. While the extraordinary behavior of biological matter is governed by its detailed atomic structure and random fluctuations, and is therefore difficult to predict, it can nevertheless be understood within simplified frameworks. Such frameworks model the system as consisting of only one or a few components, and model the behavior of the system as the occupation of a single state out of a small number of states available. The emerging widespread application of nanotechnology, such as atomic force microscopy (AFM), has expanded this understanding in eye-opening new levels of detail by enabling nano-scale control, measurement, and visualization of biological molecules. This thesis describes two independent projects, both of which illuminate this understanding using AFM, but which do so from very different perspectives. The organization of this thesis is as follows. Chapter 1 begins with an experimental background and introduction to AFM, and then describes our setup in both single-molecule manipulation and imaging modes. In Chapter 2, we describe the first project, the motivation for which is to extend methods for the experimental determination of the free energy landscape of a molecule. This chapter relies on the analysis of single-molecule manipulation data. Chapter 3 describes the second project, the motivation for which is to create RNA-based nano-structures suitable for future applications in living mammalian cells. This chapter relies mainly on imaging. Chapters 2 and 3 can thus be read and understood separately.

Surface control of epitaxial manganite films via oxygen pressure

DOE PAGES

Tselev, Alexander; Vasudevan, Rama K.; Gianfrancesco, Anthony G.; ...

2015-03-11

The trend to reduce device dimensions demands increasing attention to atomic-scale details of structure of thin films as well as to pathways to control it. We found that this is of special importance in the systems with multiple competing interactions. We have used in situ scanning tunneling microscopy to image surfaces of La 5/8Ca 3/8MnO 3 films grown by pulsed laser deposition. The atomically resolved imaging was combined with in situ angle-resolved X-ray photoelectron spectroscopy. We find a strong effect of the background oxygen pressure during deposition on structural and chemical features of the film surface. Deposition at 50 mTorrmore » of O 2 leads to mixed-terminated film surfaces, with B-site (MnO 2) termination being structurally imperfect at the atomic scale. Moreover, a relatively small reduction of the oxygen pressure to 20 mTorr results in a dramatic change of the surface structure leading to a nearly perfectly ordered B-site terminated surface with only a small fraction of A-site (La,Ca)O termination. This is accompanied, however, by surface roughening at a mesoscopic length scale. The results suggest that oxygen has a strong link to the adatom mobility during growth. The effect of the oxygen pressure on dopant surface segregation is also pronounced: Ca surface segregation is decreased with oxygen pressure reduction.« less

Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

PubMed

Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

2015-01-01

Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

Laser-induced transformation of graphitic materials to two-dimensional graphene-like structures at ambient conditions.

PubMed

Antonelou, Aspasia; Benekou, Vasiliki; Dracopoulos, Vasileios; Kollia, Mary; Yannopoulos, Spyros N

2018-06-27

Laser processing of carbon containing compounds towards the formation of graphene-based structures gains ground over the last years in view of the practicality that lasers offer against other conventional graphene preparation methods. The current work explores the viability of low-cost lasers, operating at ambient conditions, for the transformation of various graphitic materials to structures with graphene-like atomic arrangement. Starting materials are at two opposing sides. On one side stand typical graphite powder with Bernal stacking and strong sp2 character, while nanocrystalline or quasi-amorphous graphitic powders such as carbon black and activated carbon are also investigated. Electron microscopies are employed to observe post-irradiation morphological changes while Raman scattering identifies details on atomic arrangement. It is demonstrated that graphene-like structures can be prepared either by starting from a well-organized Bernal-stacked network or by irradiating the quasi-amorphous forms of nanocrystalline carbon. Mild structural changes in the former case pertain to increase of the interlayer spacing, which could possibly be rationalized by considering a mechanism based on Coulomb expansion. For less organized carbon structures, reorganization of the atomic arrangement with an appreciable sp3 to sp2 transformation is observed. The findings of this work confirm that laser processing at minimal chamber conditions demonstrate high potential for preparing high-quality graphene-based structures starting from low cost materials. The proposed method being easily scalable adaptable to current technological platforms is expected to be transformed to a viable and eco-friendly graphene production technology. © 2018 IOP Publishing Ltd.

All-atom ab initio native structure prediction of a mixed fold (1FME): A comparison of structural and folding characteristics of various ββα miniproteins

NASA Astrophysics Data System (ADS)

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2009-11-01

We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold ββα miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other ββα miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue ββα miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1→Glu1 and Ile7→Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I' turn (1FME) was well reproduced with the present simulation.

Insight into the Dzyaloshinskii-Moriya interaction through first-principles study of chiral magnetic structures

NASA Astrophysics Data System (ADS)

Sandratskii, L. M.

2017-07-01

The purpose of the paper is to gain deeper insight into microscopic formation of the Dzyaloshinskii-Moriya interaction (DMI). The paper aims at the development of the physical picture able to address apparently contradicting conclusions of recent studies concerning the location of the DMI energy in the real and reciprocal spaces as well as the relation between values of the atomic moments and the DMI strength. The main tools of our study are the first-principles calculations of the energies of the spiral magnetic states with opposite chiralities. We suggest a method of the calculation of the spiral structures with account for the spin-orbit coupling (SOC). It is based on the application of the generalized Bloch theorem and generalized Bloch functions and allows to reduce the consideration of arbitrary incommensurate spiral to small chemical unit cell. The method neglects the anisotropy in the plane orthogonal to the rotation axis of the spirals that does not influence importantly the DMI energy. For comparison, the supercell calculation with full account for the SOC is performed. The concrete calculations are performed for the Co/Pt bilayer. We consider the distribution of the DMI energy in both real and reciprocal spaces and the dependence of the DMI on the number of electrons. The results of the calculations reveal a number of energy compensations in the formation of the DMI. Thus, the partial atomic contributions as functions of the spiral wave vector q are nonmonotonic and have strongly varying slopes. However, in the total DMI energy these atom-related features compensate each other, resulting in a smooth q dependence. The reason for the peculiar form of the partial DMI contributions is a q -dependent difference in the charge distribution between q and -q spirals. The strongly q -dependent relation between atomic contributions shows that the real-space distribution of the DMI energy obtained for a selected q value cannot be considered as a general characteristic of a given material. Our study shows that it is physically most consistent to consider the electronic hybridization as a primary effect reflecting the nature of the DMI whereas the q -dependent real-space distribution of the DMI energy is a consequence of the complex processes in the electronic structure including the charge transfer process. The physical process of the DMI formation is connected with the difference in the hybridization of the Co and Pt states for q and -q spirals under the influence of the SOC and broken spatial inversion. It depends sensitively on details of the electronic structure. The calculations with constraints on the values of the Co and Pt atomic moments show that there is no direct relation between these atomic quantities and the DMI strength since the details of the electronic structure crucial for the DMI are not reflected in these integral characteristics. The application of the method to the calculation of the magnon energies in systems with DMI is briefly addressed.

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

PubMed

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

2015-10-01

The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.

25. Plutonium Recovery From Contaminated Materials, Architectural Plans & Details, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

25. Plutonium Recovery From Contaminated Materials, Architectural Plans & Details, Building 232-Z, U.S. Atomic Energy Commission, Hanford Atomic Products Operation, General Electric Company, Dwg. No. H-2-23105, 1959. - Plutonium Finishing Plant, Waste Incinerator Facility, 200 West Area, Richland, Benton County, WA

24. Plutonium Recovery From Contaminated Materials, Architectural Details, Building 232z, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

24. Plutonium Recovery From Contaminated Materials, Architectural Details, Building 232-z, U.S. Atomic Energy Commission, Hanford Atomic Products Operation, General Electric Company, Dwg. No. H-2-23106, 1959. - Plutonium Finishing Plant, Waste Incinerator Facility, 200 West Area, Richland, Benton County, WA

First principles calculations of the magnetic and hyperfine properties of Fe/N/Fe and Fe/O/Fe multilayers in the ground state of cohesive energy

NASA Astrophysics Data System (ADS)

dos Santos, A. V.; Samudio Pérez, C. A.; Muenchen, D.; Anibele, T. P.

2015-01-01

The ground state properties of Fe/N/Fe and Fe/O/Fe multilayers were investigated using the first principles calculations. The calculations were performed using the Linearized Augmented Plane Wave (LAPW) method implemented in the Wien2k code. A supercell consisting of one layer of nitride (or oxide) between two layers of Fe in the bcc structure was used to model the structure of the multilayer. The research in new materials also stimulated theoretical and experimental studies of iron-based nitrides due to their variety of structural and magnetic properties for the potential applications as in high strength steels and for high corrosion resistance. It is obvious from many reports that magnetic iron nitrides such as γ-Fe4N and α-Fe16N2 have interesting magnetic properties, among these a high magnetisation saturation and a high density crimp. However, although Fe-N films and multilayers have many potential applications, they can be produced in many ways and are being extensively studied from the theoretical point of view there is no detailed knowledge of their electronic structure. Clearly, efforts to understand the influence of the nitrogen atoms on the entire electronic structure are needed as to correctly interpret the observed changes in the magnetic properties when going from Fe-N bulk compounds to multilayer structures. Nevertheless, the N atoms are not solely responsible for electronics alterations in solid compounds. Theoretical results showed that Fe4X bulk compounds, where X is a variable atom with increasing atomic number (Z), the nature of bonding between X and adjacent Fe atoms changes from more covalent to more ionic and the magnetic moments of Fe also increase for Z=7, i.e. N. This is an indicative that atoms with a Z number higher than 7, i.e., O, can produce several new alterations in the entire magnetic properties of Fe multilayers. This paper presents the first results of an ab-initio electronic structure calculations, performed for Fe-N and Fe-O multilayers. Firstly, the formation energy and the cohesive energy of the multilayers are discussed. For optimised values, the cohesive energy of the multilayers to obtain the lattice parameters at the equilibrium ground state was used, i.e. a new methodology for this calculus was applied. Secondly, the magnetic properties and hyperfine interactions (magnetic field, electric field gradient and the isomer shift) of the iron atoms of the multilayers are discussed.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

PubMed Central

Yang, Shengfeng; Chen, Youping

2015-01-01

In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress–strain responses, the GB–crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB–crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation. PMID:25792957

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

PubMed

Yang, Shengfeng; Chen, Youping

2015-03-08

In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

Theory versus experiment for a family of single-layer compounds with a similar atomic arrangement: (Tl,X )/Si(111 )√{3 }×√{3 }(X =Pb,Sn,Bi,Sb,Te,Se)

NASA Astrophysics Data System (ADS)

Matetskiy, A. V.; Kibirev, I. A.; Mihalyuk, A. N.; Eremeev, S. V.; Gruznev, D. V.; Bondarenko, L. V.; Tupchaya, A. Y.; Zotov, A. V.; Saranin, A. A.

2017-08-01

Two-dimensional compounds made of one monolayer of Tl and one-third monolayer of Pb, Bi, Te, or Se (but not of Sn or Sb) on Si(111) have been found to have a similar atomic arrangement which can be visualized as a √{3 }×√{3 } -periodic honeycomb network of chained Tl trimers with atoms of the second adsorbate occupying the centers of the honeycomb units. Structural and electronic properties of the compounds have been examined in detail theoretically using density functional theory (DFT) calculations and experimentally using low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), and angle-resolved photoelectron spectroscopy (ARPES) observations. It has been found that though structural parameters of the compounds are very similar for all species, the only common feature of their band structure is a considerable spin-splitting of the surface-state bands, while other basic electronic properties vary greatly with a change of species. The Tl-Pb compound is strongly metallic with two metallic surface-state bands; the Tl-Bi compound is also metallic but with a single metallic band; the Tl-Te and Tl-Se compounds appear to be insulators.

Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters

PubMed Central

Singharoy, Abhishek; Sereda, Yuriy

2012-01-01

Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure. PMID:22661911

Multi-million atom electronic structure calculations for quantum dots

NASA Astrophysics Data System (ADS)

Usman, Muhammad

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

A simple atomic-level hydrophobicity scale reveals protein interfacial structure.

PubMed

Kapcha, Lauren H; Rossky, Peter J

2014-01-23

Many amino acid residue hydrophobicity scales have been created in an effort to better understand and rapidly characterize water-protein interactions based only on protein structure and sequence. There is surprisingly low consistency in the ranking of residue hydrophobicity between scales, and their ability to provide insightful characterization varies substantially across subject proteins. All current scales characterize hydrophobicity based on entire amino acid residue units. We introduce a simple binary but atomic-level hydrophobicity scale that allows for the classification of polar and non-polar moieties within single residues, including backbone atoms. This simple scale is first shown to capture the anticipated hydrophobic character for those whole residues that align in classification among most scales. Examination of a set of protein binding interfaces establishes good agreement between residue-based and atomic-level descriptions of hydrophobicity for five residues, while the remaining residues produce discrepancies. We then show that the atomistic scale properly classifies the hydrophobicity of functionally important regions where residue-based scales fail. To illustrate the utility of the new approach, we show that the atomic-level scale rationalizes the hydration of two hydrophobic pockets and the presence of a void in a third pocket within a single protein and that it appropriately classifies all of the functionally important hydrophilic sites within two otherwise hydrophobic pores. We suggest that an atomic level of detail is, in general, necessary for the reliable depiction of hydrophobicity for all protein surfaces. The present formulation can be implemented simply in a manner no more complex than current residue-based approaches. © 2013.

Atomistic Method Applied to Computational Modeling of Surface Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo H.; Abel, Phillip B.

2000-01-01

The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of the energetics, consists of a small number of simple PCbased computer codes that deal with the different aspects of surface alloy formation. Two analysis modes are available within this package. The first mode provides an atom-by-atom description of real and virtual stages 1. during the process of surface alloying, based on the construction of catalogues of configurations where each configuration describes one possible atomic distribution. BFS analysis of this catalogue provides information on accessible states, possible ordering patterns, and details of island formation or film growth. More importantly, it provides insight into the evolution of the system. Software developed by the Computational Materials Group allows for the study of an arbitrary number of elements forming surface alloys, including an arbitrary number of surface atomic layers. The second mode involves large-scale temperature-dependent computer 2. simulations that use the BFS method for the energetics and provide information on the dynamic processes during surface alloying. These simulations require the implementation of Monte-Carlo-based codes with high efficiency within current workstation environments. This methodology capitalizes on the advantages of the BFS method: there are no restrictions on the number or type of elements or on the type of crystallographic structure considered. This removes any restrictions in the definition of the configuration catalogues used in the analytical calculations, thus allowing for the study of arbitrary ordering patterns, ultimately leading to the actual surface alloy structure. Moreover, the Monte Carlo numerical technique used for the large-scale simulations allows for a detailed visualization of the simulated process, the main advantage of this type of analysis being the ability to understand the underlying features that drive these processes. Because of the simplicity of the BFS method for e energetics used in these calculations, a detailed atom-by-atom analysis can be performed at any point in the simulation, providing necessary insight on the details of the process. The main objective of this research program is to develop a tool to guide experimenters in understanding and interpreting often unexpected results in alloy formation experiments. By reducing the computational effort without losing physical accuracy, we expect that powerful simulation tools will be developed in the immediate future, which will allow material scientists to easily visualize and analyze processes at a level not achievable experimentally.

Studies of Atomic Free Radicals Stored in a Cryogenic Environment

NASA Technical Reports Server (NTRS)

Lee, David M.; Hubbard, Dorthy (Technical Monitor); Alexander, Glen (Technical Monitor)

2003-01-01

Impurity-Helium Solids are porous gel-like solids consisting of impurity atoms and molecules surrounded by thin layers of solid helium. They provide an ideal medium for matrix isolation of free radicals to prevent recombination and store chemical energy. In this work electron spin resonance, nuclear magnetic resonance, X-ray diffraction, and ultrasound techniques have all been employed to study the properties of these substances. Detailed studies via electron spin resonance of exchange tunneling chemical reactions involving hydrogen and deuterium molecular and atomic impurities in these solids have been performed and compared with theory. Concentrations of hydrogen approaching the quantum solid criterion have been produced. Structured studies involving X ray diffraction, ultrasound, and electron spin resonance have shown that the impurities in impurity helium solids are predominantly contained in impurity clusters, with each cluster being surrounded by thin layers of solid helium.

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

Gaussian approximation potential modeling of lithium intercalation in carbon nanostructures

NASA Astrophysics Data System (ADS)

Fujikake, So; Deringer, Volker L.; Lee, Tae Hoon; Krynski, Marcin; Elliott, Stephen R.; Csányi, Gábor

2018-06-01

We demonstrate how machine-learning based interatomic potentials can be used to model guest atoms in host structures. Specifically, we generate Gaussian approximation potential (GAP) models for the interaction of lithium atoms with graphene, graphite, and disordered carbon nanostructures, based on reference density functional theory data. Rather than treating the full Li-C system, we demonstrate how the energy and force differences arising from Li intercalation can be modeled and then added to a (prexisting and unmodified) GAP model of pure elemental carbon. Furthermore, we show the benefit of using an explicit pair potential fit to capture "effective" Li-Li interactions and to improve the performance of the GAP model. This provides proof-of-concept for modeling guest atoms in host frameworks with machine-learning based potentials and in the longer run is promising for carrying out detailed atomistic studies of battery materials.

Analysis of STM images with pure and CO-functionalized tips: A first-principles and experimental study

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Okabayashi, Norio; Peronio, Angelo; Giessibl, Franz J.; Paulsson, Magnus

2017-08-01

We describe a first-principles method to calculate scanning tunneling microscopy (STM) images, and compare the results to well-characterized experiments combining STM with atomic force microscopy (AFM). The theory is based on density functional theory with a localized basis set, where the wave functions in the vacuum gap are computed by propagating the localized-basis wave functions into the gap using a real-space grid. Constant-height STM images are computed using Bardeen's approximation method, including averaging over the reciprocal space. We consider copper adatoms and single CO molecules adsorbed on Cu(111), scanned with a single-atom copper tip with and without CO functionalization. The calculated images agree with state-of-the-art experiments, where the atomic structure of the tip apex is determined by AFM. The comparison further allows for detailed interpretation of the STM images.

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

PubMed Central

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

2013-01-01

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

A Hybrid Density Functional Study of Atomic Hydrogen and Oxygen Adsorptions on the (0001) Surface of Non-Magnetic DHCP Americium

NASA Astrophysics Data System (ADS)

Amdani-Moten, Shafaq; Atta-Fynn, Raymond; Ray, Asok

2010-03-01

As our group have recently shown^+, hybrid density functional theory (HDFT) which replaces a fraction (40%) of approximate DFT exchange with exact Hartree-Fock exchange yield structural, magnetic, and electronic properties for Americium-I that are in excellent agreement with experimental data. As a natural progression, ab initio calculations for atomic adsorptions on the (0001) surface of non-magnetic americium have been performed using HDFT. The americium surface is modeled by a seven-layer slab using inversion symmetry consisting of one atom per layer and non-magnetic ABAC stacking arrangement of these layers. Top, bridge, hcp and fcc chemisorption sites have been investigated with energies optimized with respect to the adatom distance from the surface. Details of the chemisorptions processes as well as comparisons of different sites will be presented. ^+ R. Atta-Fynn and A. K. Ray, Chemical Physics Letters, 482, 223-227 (2009).

Structural mechanism of the ATP-induced dissociation of rigor myosin from actin

PubMed Central

Kühner, Sebastian; Fischer, Stefan

2011-01-01

Myosin is a true nanomachine, which produces mechanical force from ATP hydrolysis by cyclically interacting with actin filaments in a four-step cycle. The principle underlying each step is that structural changes in separate regions of the protein must be mechanically coupled. The step in which myosin dissociates from tightly bound actin (the rigor state) is triggered by the 30 Å distant binding of ATP. Large conformational differences between the crystal structures make it difficult to perceive the coupling mechanism. Energetically accessible transition pathways computed at atomic detail reveal a simple coupling mechanism for the reciprocal binding of ATP and actin. PMID:21518908

Atomic-scale analysis of deposition and characterization of a-Si:H thin films grown from SiH radical precursor

NASA Astrophysics Data System (ADS)

Sriraman, Saravanapriyan; Aydil, Eray S.; Maroudas, Dimitrios

2002-07-01

Growth of hydrogenated amorphous silicon films (a-Si:H) on an initial H-terminated Si(001)(2 x1) substrate at T=500 K was studied through molecular-dynamics (MD) simulations of repeated impingement of SiH radicals to elucidate the effects of reactive minority species on the structural quality of the deposited films. The important reactions contributing to film growth were identified through detailed visualization of radical-surface interaction trajectories. These reactions include (i) insertion of SiH into Si-Si bonds, (ii) adsorption onto surface dangling bonds, (iii) surface H abstraction by impinging SiH radicals through an Eley-Rideal mechanism, (iv) surface adsorption by penetration into subsurface layers or dissociation leading to interstitial atomic hydrogen, (v) desorption of interstitial hydrogen into the gas phase, (vi) formation of higher surface hydrides through the exchange of hydrogen, and (vii) dangling-bond-mediated dissociation of surface hydrides into monohydrides. The MD simulations of a-Si:H film growth predict an overall surface reaction probability of 95% for the SiH radical that is in good agreement with experimental measurements. Structural and chemical characterization of the deposited films was based on the detailed analysis of evolution of the films' structure, surface morphology and roughness, surface reactivity, and surface composition. The analysis revealed that the deposited films exhibit high dangling bond densities and rough surface morphologies. In addition, the films are abundant in voids and columnar structures that are detrimental to producing device-quality a-Si:H thin films.

Ablation plume structure and dynamics in ambient gas observed by laser-induced fluorescence imaging spectroscopy

NASA Astrophysics Data System (ADS)

Miyabe, M.; Oba, M.; Iimura, H.; Akaoka, K.; Khumaeni, A.; Kato, M.; Wakaida, I.

2015-08-01

The dynamic behavior of an ablation plume in ambient gas has been investigated by laser-induced fluorescence imaging spectroscopy. The second harmonic beam from an Nd:YAG laser (0.5-6 J/cm2) was focused on a sintered oxide pellet or a metal chip of gadolinium. The produced plume was subsequently intersected with a sheet-shaped UV beam from a dye laser so that time-resolved fluorescence images were acquired with an intensified CCD camera at various delay times. The obtained cross-sectional images of the plume indicate that the ablated ground state atoms and ions of gadolinium accumulate in a hemispherical contact layer between the plume and the ambient gas, and a cavity containing a smaller density of ablated species is formed near the center of the plume. At earlier expansion stage, another luminous component also expands in the cavity so that it coalesces into the hemispherical layer. The splitting and coalescence for atomic plume occur later than those for ionic plume. Furthermore, the hemispherical layer of neutral atoms appears later than that of ions; however, the locations of the layers are nearly identical. This coincidence of the appearance locations of the layers strongly suggests that the neutral atoms in the hemispherical layer are produced as a consequence of three-body recombination of ions through collisions with gas atoms. The obtained knowledge regarding plume expansion dynamics and detailed plume structure is useful for optimizing the experimental conditions for ablation-based spectroscopic analysis.

Atomic-scale structural signature of dynamic heterogeneities in metallic liquids

NASA Astrophysics Data System (ADS)

Pasturel, Alain; Jakse, Noel

2017-08-01

With sufficiently high cooling rates, liquids will cross their equilibrium melting temperatures and can be maintained in a metastable undercooled state before solidifying. Studies of undercooled liquids reveal several intriguing dynamic phenomena and because explicit connections between liquid structure and liquids dynamics are difficult to identify, it remains a major challenge to capture the underlying structural link to these phenomena. Ab initio molecular dynamics (AIMD) simulations are yet especially powerful in providing atomic-scale details otherwise not accessible in experiments. Through the AIMD-based study of Cr additions in Al-based liquids, we evidence for the first time a close relationship between the decoupling of component diffusion and the emergence of dynamic heterogeneities in the undercooling regime. In addition, we demonstrate that the origin of both phenomena is related to a structural heterogeneity caused by a strong interplay between chemical short-range order (CSRO) and local fivefold topology (ISRO) at the short-range scale in the liquid phase that develops into an icosahedral-based medium-range order (IMRO) upon undercooling. Finally, our findings reveal that this structural signature is also captured in the temperature dependence of partial pair-distribution functions which opens up the route to more elaborated experimental studies.

Structural expansions for the ground state energy of a simple metal

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1973-01-01

A structural expansion for the static ground state energy of a simple metal is derived. An approach based on single particle band structure which treats the electron gas as a non-linear dielectric is presented, along with a more general many particle analysis using finite temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi surface distortions, and chemical potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron ion interaction, and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero temperature thermodynamic functions of atomic hydrogen are reported.

A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations

PubMed Central

Alberini, Giulio; Benfenati, Fabio

2017-01-01

Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains. Successively, a structural model of claudin-15-based paracellular channels has been proposed, suggesting a putative assembly that illustrates how claudins associate in the same cell (via cis interactions) and across adjacent cells (via trans interactions). Although very promising, the model offers only a static conformation, with residues missing in the most important extracellular regions and potential steric clashes. Here we present detailed atomic models of paracellular single and double pore architectures, obtained from the putative assembly and refined via structural modeling and all-atom molecular dynamics simulations in double membrane bilayer and water environment. Our results show an overall stable configuration of the complex with a fluctuating pore size. Extracellular residue loops in trans interaction are able to form stable contacts and regulate the size of the pore, which displays a stationary radius of 2.5–3.0 Å at the narrowest region. The side-by-side interactions of the cis configuration are preserved via stable hydrogen bonds, already predicted by cysteine crosslinking experiments. Overall, this work introduces an improved version of the claudin-15-based paracellular channel model that strengthens its validity and that can be used in further computational studies to understand the structural features of tight-junctions regulation. PMID:28863193

Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling.

PubMed

Jarzembska, Katarzyna N; Řlepokura, Katarzyna; Kamiński, Radosław; Gutmann, Matthias J; Dominiak, Paulina M; Woźniak, Krzysztof

2017-08-01

Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH - anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.

An atomic model of the tropomyosin cable on F-actin.

PubMed

Orzechowski, Marek; Li, Xiaochuan Edward; Fischer, Stefan; Lehman, William

2014-08-05

Tropomyosin regulates a wide variety of actin filament functions and is best known for the role that it plays together with troponin in controlling muscle activity. For effective performance on actin filaments, adjacent 42-nm-long tropomyosin molecules are joined together by a 9- to 10-residue head-to-tail overlapping domain to form a continuous cable that wraps around the F-actin helix. Yet, despite the apparent simplicity of tropomyosin's coiled-coil structure and its well-known periodic association with successive actin subunits along F-actin, the structure of the tropomyosin cable on actin is uncertain. This is because the conformation of the overlap region that joins neighboring molecules is poorly understood, thus leaving a significant gap in our understanding of thin-filament structure and regulation. However, recent molecular-dynamics simulations of overlap segments defined their overall shape and provided unique and sufficient cues to model the whole actin-tropomyosin filament assembly in atomic detail. In this study, we show that these MD structures merge seamlessly onto the ends of tropomyosin coiled-coils. Adjacent tropomyosin molecules can then be joined together to provide a comprehensive model of the tropomyosin cable running continuously on F-actin. The resulting complete model presented here describes for the first time (to our knowledge) an atomic-level structure of αα-striated muscle tropomyosin bound to an actin filament that includes the critical overlap domain. Thus, the model provides a structural correlate to evaluate thin-filament mechanics, self-assembly mechanisms, and the effect of disease-causing mutations. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Coupled grain boundary motion in aluminium: the effect of structural multiplicity

NASA Astrophysics Data System (ADS)

Cheng, Kuiyu; Zhang, Liang; Lu, Cheng; Tieu, Kiet

2016-05-01

The shear-induced coupled grain boundary motion plays an important role in the deformation of nanocrystalline (NC) materials. It has been known that the atomic structure of the grain boundary (GB) is not necessarily unique for a given set of misorientation and inclination of the boundary plane. However, the effect of the structural multiplicity of the GB on its coupled motion has not been reported. In the present study we investigated the structural multiplicity of the symmetric tilt Σ5(310) boundary in aluminium and its influence on the GB behaviour at a temperature range of 300 K-600 K using molecular dynamic simulations. Two starting atomic configurations were adopted in the simulations which resulted in three different GB structures at different temperatures. Under the applied shear deformation each GB structure exhibited its unique GB behaviour. A dual GB behaviour, namely the transformation of one GB behaviour to another during deformation, was observed for the second starting configuration at a temperature of 500 K. The atomistic mechanisms responsible for these behaviour were analysed in detail. The result of this study implicates a strong relationship between GB structures and their behaviour, and provides a further information of the grain boundary mediated plasticity in nanocrystalline materials.

Extended Graph-Based Models for Enhanced Similarity Search in Cavbase.

PubMed

Krotzky, Timo; Fober, Thomas; Hüllermeier, Eyke; Klebe, Gerhard

2014-01-01

To calculate similarities between molecular structures, measures based on the maximum common subgraph are frequently applied. For the comparison of protein binding sites, these measures are not fully appropriate since graphs representing binding sites on a detailed atomic level tend to get very large. In combination with an NP-hard problem, a large graph leads to a computationally demanding task. Therefore, for the comparison of binding sites, a less detailed coarse graph model is used building upon so-called pseudocenters. Consistently, a loss of structural data is caused since many atoms are discarded and no information about the shape of the binding site is considered. This is usually resolved by performing subsequent calculations based on additional information. These steps are usually quite expensive, making the whole approach very slow. The main drawback of a graph-based model solely based on pseudocenters, however, is the loss of information about the shape of the protein surface. In this study, we propose a novel and efficient modeling formalism that does not increase the size of the graph model compared to the original approach, but leads to graphs containing considerably more information assigned to the nodes. More specifically, additional descriptors considering surface characteristics are extracted from the local surface and attributed to the pseudocenters stored in Cavbase. These properties are evaluated as additional node labels, which lead to a gain of information and allow for much faster but still very accurate comparisons between different structures.

Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus

2015-12-01

Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and 3J(HNHCα)-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

High precision optical spectroscopy and quantum state selected photodissociation of ultracold 88Sr2 molecules in an optical lattice

NASA Astrophysics Data System (ADS)

McDonald, Mickey Patrick

Over the past several decades, rapid progress has been made toward the accurate characterization and control of atoms, made possible largely by the development of narrow-linewidth lasers and techniques for trapping and cooling at ultracold temperatures. Extending this progress to molecules will have exciting implications for chemistry, condensed matter physics, and precision tests of physics beyond the Standard Model. These possibilities are all consequences of the richness of molecular structure, which is governed by physics substantially different from that characterizing atomic structure. This same richness of structure, however, increases the complexity of any molecular experiment manyfold over its atomic counterpart, magnifying the difficulty of everything from trapping and cooling to the comparison of theory with experiment. This thesis describes work performed over the past six years to establish the state of the art in manipulation and quantum control of ultracold molecules. Our molecules are produced via photoassociation of ultracold strontium atoms followed by spontaneous decay to a stable ground state. We describe a thorough set of measurements characterizing the rovibrational structure of very weakly bound (and therefore very large) 88Sr2 molecules from several different perspectives, including determinations of binding energies; linear, quadratic, and higher order Zeeman shifts; transition strengths between bound states; and lifetimes of narrow subradiant states. The physical intuition gained in these experiments applies generally to weakly bound diatomic molecules, and suggests extensive applications in precision measurement and metrology. In addition, we present a detailed analysis of the thermally broadened spectroscopic lineshape of molecules in a non-magic optical lattice trap, showing how such lineshapes can be used to directly determine the temperature of atoms or molecules in situ, addressing a long-standing problem in ultracold physics. Finally, we discuss the measurement of photofragment angular distributions produced by photodissociation, leading to an exploration of quantum-state-resolved ultracold chemistry.

Mechanism for amorphization of boron carbide B{sub 4}C under uniaxial compression

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

Aryal, Sitaram; Rulis, Paul; Ching, W. Y.

2011-11-01

Boron carbide undergoes an amorphization transition under high-velocity impacts, causing it to suffer a catastrophic loss in strength. The failure mechanism is not clear and this limits the ways to improve its resistance to impact. To help uncover the failure mechanism, we used ab initio methods to carry out large-scale uniaxial compression simulations on two polytypes of stoichiometric boron carbide (B{sub 4}C), B{sub 11}C-CBC, and B{sub 12}-CCC, where B{sub 11}C or B{sub 12} is the 12-atom icosahedron and CBC or CCC is the three-atom chain. The simulations were performed on large supercells of 180 atoms. Our results indicate that themore » B{sub 11}C-CBC (B{sub 12}-CCC) polytype becomes amorphous at a uniaxial strain s = 0.23 (0.22) and with a maximum stress of 168 (151) GPa. In both cases, the amorphous state is the consequence of structural collapse associated with the bending of the three-atom chain. Careful analysis of the structures after amorphization shows that the B{sub 11}C and B{sub 12} icosahedra are highly distorted but still identifiable. Calculations of the elastic coefficients (C{sub ij}) at different uniaxial strains indicate that both polytypes may collapse under a much smaller shear strain (stress) than the uniaxial strain (stress). On the other hand, separate simulations of both models under hydrostatic compression up to a pressure of 180 GPa show no signs of amorphization, in agreement with experimental observation. The amorphized nature of both models is confirmed by detailed analysis of the evolution of the radial pair distribution function, total density of states, and distribution of effective charges on atoms. The electronic structure and bonding of the boron carbide structures before and after amorphization are calculated to further elucidate the mechanism of amorphization and to help form the proper rationalization of experimental observations.« less

The application of quasi-steady approximation in atomic kinetics in simulation of hohlraum radiation drive

NASA Astrophysics Data System (ADS)

Ren, Guoli; Pei, Wenbing; Lan, Ke; Li, Xin; Hohlraum Physics Team

2014-10-01

In current routine 2D simulation of hohlraum physics, we adopt the principal-quantum-number (n-level) average atom model (AAM) in NLTE plasma description. The more sophisticated atomic kinetics description is better choice, but the in-line calculation consumes much more resource. By distinguishing the much more fast bound-bound atomic processes from the relative slow bound-free atomic processes, we found a method to built up a bound electron distribution (n-level or nl-level) using in-line n-level calculated plasma condition (such as temperature, density, average ionization degree). We name this method ``quasi-steady approximation.'' Using this method and the plasma condition calculated under n-level, we re-build the nl-level bound electron distribution (Pnl), and acquire a new hohlraum radiative drive by post-processing. Comparison with the n-level post-processed hohlraum drive shows that we get an almost identical radiation flux but with more-detailed frequency-dependant structures. Also we use this method in the benchmark gold sphere experiment, the constructed nl-level radiation drive resembles the experimental results and DCA results, while the n-level raditation does not.

Widths of atomic 4s and 4p vacancy states, 46 less than or equal to Z less than or equal to 50

NASA Technical Reports Server (NTRS)

Hsiungchen, M.; Crasemann, B.; Yin, L. I.; Tsang, T.; Adler, I.

1975-01-01

Auger and X-ray photoelectron spectra involving N1, N2, and N3 vacancy states of Pd, Ag, Cd, In, and Sn were measured and compared with results of free atom calculations. As previously observed in Cu and Zn Auger spectra that involve 3d-band electrons, free-atom characteristics with regard to widths and structure were found in the Ag and Cd M4-N4,5N4,5 and M5-N4,5N4,5 Auger spectra that arise from transitions of 4d-band electrons. Theoretical N1 widths computed with calculated free-atom Auger energies agree well with measurements. Theory however predicts wider N2 than N3 vacancy states (as observed for Xe), while the measured N2 and N3 widths are nearly equal to each other and to the average of the calculated N2 and N3 widths. The calculations are made difficult by the exceedingly short lifetime of some 4p vacancies and by the extreme sensitivity of super-Coster-Kronig rates, which dominate the deexcitation, to the transition energy and to the fine details of the atomic potential.

ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution

PubMed Central

Kurkcuoglu, Zeynep; Bahar, Ivet; Doruker, Pemra

2016-01-01

Accurate sampling of conformational space and, in particular, the transitions between functional substates has been a challenge in molecular dynamic (MD) simulations of large biomolecular systems. We developed an Elastic Network Model (ENM)-based computational method, ClustENM, for sampling large conformational changes of biomolecules with various sizes and oligomerization states. ClustENM is an iterative method that combines ENM with energy minimization and clustering steps. It is an unbiased technique, which requires only an initial structure as input, and no information about the target conformation. To test the performance of ClustENM, we applied it to six biomolecular systems: adenylate kinase (AK), calmodulin, p38 MAP kinase, HIV-1 reverse transcriptase (RT), triosephosphate isomerase (TIM), and the 70S ribosomal complex. The generated ensembles of conformers determined at atomic resolution show good agreement with experimental data (979 structures resolved by X-ray and/or NMR) and encompass the subspaces covered in independent MD simulations for TIM, p38, and RT. ClustENM emerges as a computationally efficient tool for characterizing the conformational space of large systems at atomic detail, in addition to generating a representative ensemble of conformers that can be advantageously used in simulating substrate/ligand-binding events. PMID:27494296

m1A Post-Transcriptional Modification in tRNAs.

PubMed

Oerum, Stephanie; Dégut, Clément; Barraud, Pierre; Tisné, Carine

2017-02-21

To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2'-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs. In some cases, these modifications have been shown to increase tRNA structural stability and induce correct tRNA folding. This review provides an overview of the currently known m1A modifications, the different m1A modification sites, the biological role of each modification, and the enzyme responsible for each methylation in different species. The review further describes, in detail, two enzyme families responsible for formation of m1A at nucleotide position 9 and 58 in tRNA with a focus on the tRNA binding, m1A mechanism, protein domain organisation and overall structures.

Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside Sn2 Reactions: a Reaction Force and Atomic Contribution Analysis.

PubMed

Pedraza-González, Laura Milena; Galindo, Johan Fabian; Gonzalez, Ronald; Reyes, Andrés

2016-10-09

The solvent effect on the nucleophile and leaving group atoms of the prototypical F - + CH 3 Cl → CH 3 F + Cl - backside bimolecular nucleophilic substitution reaction (S N 2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing eleven dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveals that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ΔE 0 and ΔE ↕ of Y - + CH 3 X → YCH 3 + X - (X,Y= F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.

The engine of microtubule dynamics comes into focus.

PubMed

Mitchison, T J

2014-05-22

In this issue, Alushin et al. report high-resolution structures of three states of the microtubule lattice: GTP-bound, which is stable to depolymerization; unstable GDP-bound; and stable Taxol and GDP-bound. By comparing these structures at near-atomic resolution, they are able to propose a detailed model for how GTP hydrolysis destabilizes the microtubule and thus powers dynamic instability and chromosome movement. Destabilization of cytoskeleton filaments by nucleotide hydrolysis is an important general principle in cell dynamics, and this work represents a major step forward on a problem with a long history. Copyright © 2014 Elsevier Inc. All rights reserved.

On-surface synthesis on a bulk insulator surface

NASA Astrophysics Data System (ADS)

Richter, Antje; Floris, Andrea; Bechstein, Ralf; Kantorovich, Lev; Kühnle, Angelika

2018-04-01

On-surface synthesis has rapidly emerged as a most promising approach to prepare functional molecular structures directly on a support surface. Compared to solution synthesis, performing chemical reactions on a surface offers several exciting new options: due to the absence of a solvent, reactions can be envisioned that are otherwise not feasible due to the insolubility of the reaction product. Perhaps even more important, the confinement to a two-dimensional surface might enable reaction pathways that are not accessible otherwise. Consequently, on-surface synthesis has attracted great attention in the last decade, with an impressive number of classical reactions transferred to a surface as well as new reactions demonstrated that have no classical analogue. So far, the majority of the work has been carried out on conducting surfaces. However, when aiming for electronic decoupling of the resulting structures, e.g. for the use in future molecular electronic devices, non-conducting surfaces are highly desired. Here, we review the current status of on-surface reactions demonstrated on the (10.4) surface of the bulk insulator calcite. Besides thermally induced C-C coupling of halogen-substituted aryls, photochemically induced [2  +  2] cycloaddition has been proven possible on this surface. Moreover, experimental evidence exists for coupling of terminal alkynes as well as diacetylene polymerization. While imaging of the resulting structures with dynamic atomic force microscopy provides a direct means of reaction verification, the detailed reaction pathway often remains unclear. Especially in cases where the presence of metal atoms is known to catalyze the corresponding solution chemistry reaction (e.g. in the case of the Ullmann reaction), disclosing the precise reaction pathway is of importance to understand and generalize on-surface reactivity on a bulk insulator surface. To this end, density-functional theory calculations have proven to provide atomic-scale insights that have greatly contributed to unravelling the details of on-surface synthesis on a bulk insulator surface.

Growth mechanism of isolated indium nanowires formed on Si(5 5 12)-2 × 1 templates

NASA Astrophysics Data System (ADS)

Zhu, Yong-Zhe; Kim, Hidong; Seo, Jae M.

2012-08-01

Through self-assembly of In atoms on a reconstructed Si(5 5 12)-2×1 surface, nanowires of a width less than 5 nm have been formed. One specific site of the one-dimensional structure of the substrate turns out to be inert to arriving In atoms so that the self-assembled nanowires are well-isolated from each other, resulting in a high aspect ratio. In addition to such an isolation, keeping the same periodicity as the substrate ( i.e., 5.35 nm) during such self-assembly is another interesting point of the present system. In the present study, the detailed growth mechanism has been disclosed by using scanning tunneling microscopy.

Numerical optimization of a picosecond pulse driven Ni-like Nb x-ray laser at 20.3 nm

NASA Astrophysics Data System (ADS)

Lu, X.; Zhong, J. Y.; Li, Y. J.; Zhang, J.

2003-07-01

Detailed simulations of a Ni-like Nb x-ray laser pumped by a nanosecond prepulse followed by a picosecond main pulse are presented. The atomic physics data are obtained using the Cowan code [R. D. Cowan, The Theory of Atomic Structure and Spectra (University of California Press, Berkeley, CA, 1981)]. The optimization calculations are performed in terms of the intensity of prepulse and the time delay between the prepulse and the main pulse. A high gain over 150 cm-1 is obtained for the optimized drive pulse configuration. The ray-tracing calculations suggest that the total pump energy for a saturated x-ray laser can be reduced to less than 1 J.

Deformation in Metallic Glass: Connecting Atoms to Continua

NASA Astrophysics Data System (ADS)

Hinkle, Adam R.; Falk, Michael L.; Rycroft, Chris H.; Shields, Michael D.

Metallic glasses like other amorphous solids experience strain localization as the primary mode of failure. However, the development of continuum constitutive laws which provide a quantitative description of disorder and mechanical deformation remains an open challenge. Recent progress has shown the necessity of accurately capturing fluctuations in material structure, in particular the statistical changes in potential energy of the atomic constituents during the non-equilibrium process of applied shear. Here we directly cross-compare molecular dynamics shear simulations of a ZrCu glass with continuum shear transformation zone (STZ) theory representations. We present preliminary results for a methodology to coarse-grain detailed molecular dynamics data with the goal of initializing a continuum representation in the STZ theory. NSF Grants Awards 1107838, 1408685, and 0801471.

Tidbits for the synthesis of bis(2-sulfanylethyl)amido (SEA) polystyrene resin, SEA peptides and peptide thioesters.

PubMed

Ollivier, Nathalie; Raibaut, Laurent; Blanpain, Annick; Desmet, Rémi; Dheur, Julien; Mhidia, Reda; Boll, Emmanuelle; Drobecq, Hervé; Pira, Silvain L; Melnyk, Oleg

2014-02-01

Protein total chemical synthesis enables the atom-by-atom control of the protein structure and therefore has a great potential for studying protein function. Native chemical ligation of C-terminal peptide thioesters with N-terminal cysteinyl peptides and related methodologies are central to the field of protein total synthesis. Consequently, methods enabling the facile synthesis of peptide thioesters using Fmoc-SPPS are of great value. Herein, we provide a detailed protocol for the preparation of bis(2-sulfanylethyl)amino polystyrene resin as a starting point for the synthesis of C-terminal bis(2-sulfanylethyl)amido peptides and of peptide thioesters derived from 3-mercaptopropionic acid. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.

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

Schafer, Marion; Bobev, Svilen

This paper presents results from our exploratory work in the systems K-Cd-Ge, Rb-Cd-Ge, and Cs-Cd-Ge, which yielded the novel type-I clathrates with refined compositions K 8Cd 3.77(7)Ge 42.23, Rb 8Cd 3.65(7)Ge 42.35, and Cs 7.80(1)Cd 3.65(6)Ge 42.35. The three compounds represent rare examples of clathrates of germanium with the alkali metals, where a d 10 element substitutes a group 14 element. The three structures, established by single-crystal X-ray diffraction, indicate that the framework-building Ge atoms are randomly substituted by Cd atoms on only one of the three possible crystallographic sites. Furthermore, this and several other details of the crystal chemistrymore » are elaborated.« less

Molecular dynamics simulation of temperature effects on deposition of Cu film on Si by magnetron sputtering

NASA Astrophysics Data System (ADS)

Zhu, Guo; Sun, Jiangping; Zhang, Libin; Gan, Zhiyin

2018-06-01

The temperature effects on the growth of Cu thin film on Si (0 0 1) in the context of magnetron sputtering deposition were systematically studied using molecular dynamics (MD) method. To improve the comparability of simulation results at varying temperatures, the initial status data of incident Cu atoms used in all simulations were read from an identical file via LAMMPS-Python interface. In particular, crystalline microstructure, interface mixing and internal stress of Cu thin film deposited at different temperatures were investigated in detail. With raising the substrate temperature, the interspecies mixed volume and the proportion of face-centered cubic (fcc) structure in the deposited film both increased, while the internal compressive stress decreased. It was found that the fcc structure in the deposited Cu thin films was 〈1 1 1〉 oriented, which was reasonably explained by surface energy minimization and the selectivity of bombardment energy to the crystalline planes. The quantified analysis of interface mixing revealed that the diffusion of Cu atoms dominated the interface mixing, and the injection of incident Cu atoms resulted in the densification of phase near the film-substrate interface. More important, the distribution of atomic stress indicated that the compressive stress was mainly originated from the film-substrate interface, which might be attributed to the densification of interfacial phase at the initial stage of film deposition.

X-ray photoelectron spectrum and electronic properties of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4): LDA, GGA, and EV-GGA.

PubMed

Reshak, Ali Hussain; Khenata, R; Kityk, I V; Plucinski, K J; Auluck, S

2009-04-30

An all electron full potential linearized augmented plane wave method has been applied for a theoretical study of the band structure, density of states, and electron charge density of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4) using three different approximations for the exchange correlation potential. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma resulting in a direct energy gap of about 2.0, 2.2, and 2.8 eV for local density approximation (LDA), generalized gradient approximation (GGA), and Engel-Vosko (EVGGA) compared to the experimental value of 2.84 eV. We notice that EVGGA shows excellent agreement with the experimental data. This agreement is attributed to the fact that the Engel-Vosko GGA formalism optimizes the corresponding potential for band structure calculations. We make a detailed comparison of the density of states deduced from the X-ray photoelectron spectra with our calculations. We find that there is a strong covalent bond between the Hg and S atoms and Ga and S atoms. The Hg-Hg, Ga-Ga, and S-S bonds are found to be weaker than the Hg-S and Ga-S bonds showing that a covalent bond exists between Hg and S atoms and Ga and S atoms.

The atomic level structure of the TiO(2)-NiTi interface.

PubMed

Nolan, M; Tofail, S A M

2010-09-07

The biocompatibility of NiTi shape memory alloys (SMA) has made possible applications in invasive and minimally invasive biomedical devices. The NiTi intermetallic alloy spontaneously forms a thin passive layer of TiO(2), which provides its biocompatibility. The oxide layer is thought to form as Ti in the alloy reacts with oxygen. In this paper, we study the details of the oxide-alloy interface. The atomic model is the (110) NiTi surface interfaced with the (100) rutile TiO(2) surface; this combination provides the best lattice match of alloy and oxide. When the interface forms, static minimisations and molecular dynamics show that there is no migration of atoms between the alloy and the oxide. In the alloy there are some notable structural relaxations. We find that a columnar structure appears in which alternating long and short Ni-Ti bonds are present in each surface and subsurface plane into the fourth subsurface layer. The oxide undergoes some structural changes as a result of terminal oxygen coordinating to Ti in the NiTi surface. The electronic structure shows that Ti(3+) species are present at the interface, with Ti(4+) in the bulk of the oxide layer and that the metallic character of the alloy is unaffected by the interaction with oxygen, all of which is consistent with experiment. A thermodynamic analysis is used to examine the stability of different possible structures-a perfect interface and one with Ti and O vacancies. We find that under conditions typical of oxidation and shape memory treatments, the most stable interface structure is that with Ti vacancies in the alloy surface, leaving an Ni-rich layer, consistent with the experimental findings for this interface.

Multi-scale predictive modeling of nano-material and realistic electron devices

NASA Astrophysics Data System (ADS)

Palaria, Amritanshu

Among the challenges faced in further miniaturization of electronic devices, heavy influence of the detailed atomic configuration of the material(s) involved, which often differs significantly from that of the bulk material(s), is prominent. Device design has therefore become highly interrelated with material engineering at the atomic level. This thesis aims at outlining, with examples, a multi-scale simulation procedure that allows one to integrate material and device aspects of nano-electronic design to predict behavior of novel devices with novel material. This is followed in four parts: (1) An approach that combines a higher time scale reactive force field analysis with density functional theory to predict structure of new material is demonstrated for the first time for nanowires. Novel stable structures for very small diameter silicon nanowires are predicted. (2) Density functional theory is used to show that the new nanowire structures derived in 1 above have properties different from diamond core wires even though the surface bonds in some may be similar to the surface of bulk silicon. (3) Electronic structure of relatively large-scale germanium sections of realistically strained Si/strained Ge/ strained Si nanowire heterostructures is computed using empirical tight binding and it is shown that the average non-homogeneous strain in these structures drives their interesting non-conventional electronic characteristics such as hole effective masses which decrease as the wire cross-section is reduced. (4) It is shown that tight binding, though empirical in nature, is not necessarily limited to the material and atomic structure for which the parameters have been empirically derived, but that simple changes may adapt the derived parameters to new bond environments. Si (100) surface electronic structure is obtained from bulk Si parameters.

Experimental and theoretical studies of metal vapor atoms

NASA Astrophysics Data System (ADS)

Whitfield, Scott B.; Wehlitz, Ralf; Martins, Michael

2004-05-01

Employing electron spectrometry in conjunction with tuneable synchrotron radiation, we will present a detailed examination of the photoionization dynamics of selected metal vapor atoms. In particular, this paper will focus on the relative partial cross sections of the atomic Li K-shell main and satellite (ionization with excitation) photoelectron lines in the region of the strong 1 snℓ n'ℓ' autoionizing transitions, the atomic Sc 3 d, 4 s main and satellite photoelectron lines in the region of the 3 p→3 d giant resonance, and also the atomic Fe 3 d, 4 s main and satellite photoelectron lines in the same resonance region. Our experimental data for Sc and Fe will be compared to our state-of-the-art calculations based on the superposition of configuration method developed by Cowan (The Theory of Atomic Structure and Spectra. University of California Berkeley Press, Berkeley and Los Angeles, 1981). Our partial cross section measurements for Li and Sc will be complemented with measurements of the angular distribution parameter, β. In addition, our Li data will also be compared with recent R-matrix calculations (Phys. Rev. 57 (1998) 1045). In the case of Fe, we will also address the term dependent behavior of the partial cross sections on resonance. These results will highlight what can be achieved with today's technology and point the way towards future endeavors in the study of the photoionization dynamics of open-shell metal vapor atoms.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

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.

Near-Resonant Imaging of Trapped Cold Atomic Samples

PubMed Central

You, L.; Lewenstein, Maciej

1996-01-01

We study the formation of diffraction patterns in the near-resonant imaging of trapped cold atomic samples. We show that the spatial imaging can provide detailed information on the trapped atomic clouds. PMID:27805110

Chaperone-client complexes: A dynamic liaison

NASA Astrophysics Data System (ADS)

Hiller, Sebastian; Burmann, Björn M.

2018-04-01

Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.

Structure of LiPs ground and excited states

NASA Astrophysics Data System (ADS)

Bressanini, Dario

2018-01-01

The lithium atom in its ground state can bind positronium (Ps) forming LiPs, an electronically stable system. In this study we use the fixed node diffusion Monte Carlo method to perform a detailed investigation of the internal structure of LiPs, establishing to what extent it could be described by smaller interacting subsystems. To study the internal structure of positronic systems we propose a way to analyze the particle distribution functions: We first order the particle-nucleus distances, from the closest to the farthest. We then bin the ordered distances obtaining, for LiPs, five distribution functions that we call sorted distribution functions. We used them to show that Ps is a quite well-defined entity inside LiPs: The positron is forming positronium not only when it is far away from the nucleus, but also when it is in the same region of space occupied by the 2 s electrons. Hence, it is not correct to describe LiPs as positronium "orbiting" around a lithium atom, as sometimes has been done, since the positron penetrates the electronic distribution and can be found close to the nucleus.

Advanced electron microscopy characterization of tri-layer rare-earth oxide superlattices

NASA Astrophysics Data System (ADS)

Phillips, Patrick; Disa, Ankit; Ismail-Beigi, Sohrab; Klie, Robert; University of Illinois-Chicago Team; Yale University Team

2015-03-01

Rare-earth nickelates are known to display complex electronic and magnetic behaviors owed to a very localized and sensitive Ni-site atomic and electronic structure. Toward realizing the goal of manipulating of the energetic ordering of Ni d orbitals and 2D conduction, the present work focuses on the experimental characterization of thin film superlattice structures consisting of alternating layers of LaTiO3 and LaNiO3 sandwiched between a dull insulator, LaAlO3. Using advanced scanning transmission electron microscopy (STEM)-based methods, properties such as interfacial sharpness, electron transfer, O presence, and local electronic structure can be probed at the atomic scale, and will be discussed at length. By combining both energy dispersive X-ray (EDX) and electronic energy loss (EEL) spectroscopies in an aberration-corrected STEM, it is possible to attain energy and spatial resolutions of 0.35 eV and 100 pm, respectively. Focus of the talk will remain not only on the aforementioned properties, but will also include details and parameters of the acquisitions to facilitate future characterization at this level.

Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Largo, Antonio; Vega-Vega, Álvaro; Barrientos, Carmen

2015-05-01

The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader's quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN (1Σ) and hydrideisocyanidezinc HZnNC (1Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn]+ composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn+ (2Σ) and HCNZn+ (2Σ).

Domain motions of Argonaute, the catalytic engine of RNA interference

PubMed Central

Ming, Dengming; Wall, Michael E; Sanbonmatsu, Kevin Y

2007-01-01

Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. Results The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes – an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different. Conclusion Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference. PMID:18053142

Domain motions of Argonaute, the catalytic engine of RNA interference.

PubMed

Ming, Dengming; Wall, Michael E; Sanbonmatsu, Kevin Y

2007-11-30

The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference. We have taken the next step by performing an all-atom normal mode analysis of the Pyrococcus furiosus and Aquifex aeolicus Argonaute crystal structures, allowing us to quantitatively assess the feasibility of these conformational changes. To perform the analysis, we begin with the energy-minimized X-ray structures. Normal modes are then calculated using an all-atom molecular mechanics force field. The analysis reveals low-frequency vibrations that facilitate the accommodation of RNA duplexes - an essential step in target recognition. The Pyrococcus furiosus and Aquifex aeolicus Argonaute proteins both exhibit low-frequency torsion and hinge motions; however, differences in the overall architecture of the proteins cause the detailed dynamics to be significantly different. Overall, low-frequency vibrations of Argonaute are consistent with mechanisms within the current reaction cycle model for RNA interference.

IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection

PubMed Central

Moal, Iain H.; Barradas-Bautista, Didier; Jiménez-García, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A.; Fernández-Recio, Juan

2018-01-01

Motivation In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. Results Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. Availability IRaPPA has been implemented in the SwarmDock server (http://bmm.crick.ac.uk/~SwarmDock/), pyDock server (http://life.bsc.es/pid/pydockrescoring/) and ZDOCK server (http://zdock.umassmed.edu/), with code available on request. PMID:28200016

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

Laskowski, Lukasz, E-mail: lukasz.laskowski@kik.pcz.pl; Laskowska, Magdalena, E-mail: magdalena.laskowska@onet.pl; Jelonkiewicz, Jerzy, E-mail: jerzy.jelonkiewicz@kik.pcz.pl

The SBA-15 silica thin films containing copper ions anchored inside channels via propyl phosphonate groups are investigated. Such materials were prepared in the form of thin films, with hexagonally arranged pores, laying rectilinear to the substrate surface. However, in the case of our thin films, their free standing form allowed for additional research possibilities, that are not obtainable for typical thin films on a substrate. The structural properties of the samples were investigated by X-ray reflectometry, atomic force microscopy (AFM) and transmission electron microscopy (TEM). The molecular structure was examined by Raman spectroscopy supported by numerical simulations. Magnetic measurements (SQUIDmore » magnetometry and EPR spectroscopy) showed weak antiferromagnetic interactions between active units inside silica channels. Consequently, the pores arrangement was determined and the process of copper ions anchoring by propyl phosphonate groups was verified in unambiguous way. Moreover, the type of interactions between magnetic atoms was determined. - Highlights: • Functionalized free-standing SBA-15 thin films were synthesized for a first time. • Thin films synthesis procedure was described in details. • Structural properties of the films were thoroughly investigated and presented. • Magnetic properties of the novel material was investigated and presented.« less

Mechanisms of amyloid formation revealed by solution NMR

PubMed Central

Karamanos, Theodoros K.; Kalverda, Arnout P.; Thompson, Gary S.; Radford, Sheena E.

2015-01-01

Amyloid fibrils are proteinaceous elongated aggregates involved in more than fifty human diseases. Recent advances in electron microscopy and solid state NMR have allowed the characterization of fibril structures to different extents of refinement. However, structural details about the mechanism of fibril formation remain relatively poorly defined. This is mainly due to the complex, heterogeneous and transient nature of the species responsible for assembly; properties that make them difficult to detect and characterize in structural detail using biophysical techniques. The ability of solution NMR spectroscopy to investigate exchange between multiple protein states, to characterize transient and low-population species, and to study high molecular weight assemblies, render NMR an invaluable technique for studies of amyloid assembly. In this article we review state-of-the-art solution NMR methods for investigations of: (a) protein dynamics that lead to the formation of aggregation-prone species; (b) amyloidogenic intrinsically disordered proteins; and (c) protein–protein interactions on pathway to fibril formation. Together, these topics highlight the power and potential of NMR to provide atomic level information about the molecular mechanisms of one of the most fascinating problems in structural biology. PMID:26282197

Ground-state energies of simple metals

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1974-01-01

A structural expansion for the static ground-state energy of a simple metal is derived. Two methods are presented, one an approach based on single-particle band structure which treats the electron gas as a nonlinear dielectric, the other a more general many-particle analysis using finite-temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi-surface distortions, and chemical-potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron-ion interaction and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero-temperature thermodynamic functions of atomic hydrogen are reported.

AFM imaging of milk casein micelles: evidence for structural rearrangement upon acidification.

PubMed

Ouanezar, Mustapha; Guyomarc'h, Fanny; Bouchoux, Antoine

2012-03-20

Milk casein micelles are natural association colloids that we all encounter in everyday life, yet we still lack an accurate description of their internal structure and the interactions that stabilize it. In this letter, we provide for the first time detailed images of intact casein micelles as obtained through atomic force microscopy under liquid conditions close to physiological. The micelles appear as heterogeneous raspberry-like particles, which is consistent with a hierarchical/spongelike structure made of connected 10-40 nm dense casein regions. Upon in situ acidification to pH 5, the micelles decrease in size and lose their surface heterogeneities, indicating that this structure is highly sensitive to variations in mineral content and caseins net charge.

Automatic hammering of nano-patterns on special polymer film by using a vibrating AFM tip

PubMed Central

2012-01-01

Complicated nano-patterns with linewidth less than 18 nm can be automatically hammered by using atomic force microscopy (AFM) tip in tapping mode with high speed. In this study, the special sample was thin poly(styrene-ethylene/butylenes-styrene) (SEBS) block copolymer film with hexagonal spherical microstructures. An ordinary silicon tip was used as a nano-hammer, and the entire hammering process is controlled by a computer program. Experimental results demonstrate that such structure-tailored thin films enable AFM tip hammering to be performed on their surfaces. Both imprinted and embossed nano-patterns can be generated by using a vibrating tip with a larger tapping load and by using a predefined program to control the route of tip movement as it passes over the sample’s surface. Specific details for the fabrication of structure-tailored SEBS film and the theory for auto-hammering patterns were presented in detail. PMID:22889045

Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis

PubMed Central

2016-01-01

X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure–activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the Ki value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors. PMID:27096055

Collisional-radiative modeling of tungsten at temperatures of 1200–2400 eV

DOE PAGES

Colgan, James; Fontes, Christopher; Zhang, Honglin; ...

2015-04-30

We discuss new collisional-radiative modeling calculations of tungsten at moderate temperatures of 1200 to 2400 eV. Such plasma conditions are relevant to ongoing experimental work at ASDEX Upgrade and are expected to be relevant for ITER. Our calculations are made using the Los Alamos National Laboratory (LANL) collisional-radiative modeling ATOMIC code. These calculations formed part of a submission to the recent NLTE-8 workshop that was held in November 2013. This series of workshops provides a forum for detailed comparison of plasma and spectral quantities from NLTE collisional-radiative modeling codes. We focus on the LANL ATOMIC calculations for tungsten that weremore » submitted to the NLTE-8 workshop and discuss different models that were constructed to predict the tungsten emission. In particular, we discuss comparisons between semi-relativistic configuration-average and fully relativistic configuration-average calculations. As a result, we also present semi-relativistic calculations that include fine-structure detail, and discuss the difficult problem of ensuring completeness with respect to the number of configurations included in a CR calculation.« less

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Magnetic anisotropy of heteronuclear dimers in the gas phase and supported on graphene: relativistic density-functional calculations.

PubMed

Błoński, Piotr; Hafner, Jürgen

2014-04-09

The structural and magnetic properties of mixed PtCo, PtFe, and IrCo dimers in the gas phase and supported on a free-standing graphene layer have been calculated using density-functional theory, both in the scalar-relativistic limit and self-consistently including spin-orbit coupling. The influence of the strong magnetic moments of the 3d atoms on the spin and orbital moments of the 5d atoms, and the influence of the strong spin-orbit coupling contributed by the 5d atom on the orbital moments of the 3d atoms have been studied in detail. The magnetic anisotropy energy is found to depend very sensitively on the nature of the eigenstates in the vicinity of the Fermi level, as determined by band filling, exchange splitting and spin-orbit coupling. The large magnetic anisotropy energy of free PtCo and IrCo dimers relative to the easy direction parallel to the dimer axis is coupled to a strong anisotropy of the orbital magnetic moments of the Co atom for both dimers, and also on the Ir atom in IrCo. In contrast the PtFe dimer shows a weak perpendicular anisotropy and only small spin and orbital anisotropies of opposite sign on the two atoms. For dimers supported on graphene, the strong binding within the dimer and the stronger interaction of the 3d atom with the substrate stabilizes an upright geometry. Spin and orbital moments on the 3d atom are strongly quenched, but due to the weaker binding within the dimer the properties of the 5d atom are more free-atom-like with increased spin and orbital moments. The changes in the magnetic moment are reflected in the structure of the electronic eigenstates near the Fermi level, for all three dimers the easy magnetic direction is now parallel to the dimer axis and perpendicular to the graphene layer. The already very large magnetic anisotropy energy (MAE) of IrCo is further enhanced by the interaction with the support, the MAE of PtFe changes sign, and that of the PtCo dimer is reduced. These changes are discussed in relation to the relativistic electronic structure of free and supported dimers and it is demonstrated that the existence of a partially occupied quasi-degenerate state at the Fermi level favors the formation of a large magnetic anisotropy.

Structural modeling of djenkolic acid with sulfur replaced by selenium and tellurium.

PubMed

Melnikov, Petr; Nascimento, Valter A; Silva, Anderson F; Consolo, Lourdes Z Z

2014-04-17

The comparative structural modeling of djenkolic acid and its derivatives containing selenium and tellurium in chalcogen sites (Ch=Se, Te) has provided detailed information about the bond lengths and bond angles, filling the gap in what we know about the structural characteristics of these aminoacids. The investigation using the molecular mechanics technique with good approximation confirmed the available information on X-ray refinements for the related compounds methionine and selenomethionine, as well as for an estimate made earlier for telluromethionine. It was shown that the Ch-C(3) and Ch-C(4) bond lengths grow in parallel with the increasing anionic radii. Although the distances C-C, C-O, and C-N are very similar, the geometry of conformers is quite different owing to the possibility of rotation about four carbon atoms, hence the remarkable variability observed in dihedral angles. It was shown that the compounds contain a rigid block with two Ch atoms connected through a methylene group. The standard program Gaussian 03 with graphical interface Gaussview 4.1.2 has proved to be satisfactory tool for the structural description of less-common bioactive compositions when direct X-ray results are absent.

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

PubMed Central

2016-01-01

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results. PMID:27983843

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.

PubMed

Hayatshahi, Hamed S; Roe, Daniel R; Galindo-Murillo, Rodrigo; Hall, Kathleen B; Cheatham, Thomas E

2017-01-26

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results.

Correlative STED and Atomic Force Microscopy on Live Astrocytes Reveals Plasticity of Cytoskeletal Structure and Membrane Physical Properties during Polarized Migration

PubMed Central

Curry, Nathan; Ghézali, Grégory; Kaminski Schierle, Gabriele S.; Rouach, Nathalie; Kaminski, Clemens F.

2017-01-01

The plasticity of the cytoskeleton architecture and membrane properties is important for the establishment of cell polarity, adhesion and migration. Here, we present a method which combines stimulated emission depletion (STED) super-resolution imaging and atomic force microscopy (AFM) to correlate cytoskeletal structural information with membrane physical properties in live astrocytes. Using STED compatible dyes for live cell imaging of the cytoskeleton, and simultaneously mapping the cell surface topology with AFM, we obtain unprecedented detail of highly organized networks of actin and microtubules in astrocytes. Combining mechanical data from AFM with optical imaging of actin and tubulin further reveals links between cytoskeleton organization and membrane properties. Using this methodology we illustrate that scratch-induced migration induces cytoskeleton remodeling. The latter is caused by a polarization of actin and microtubule elements within astroglial cell processes, which correlates strongly with changes in cell stiffness. The method opens new avenues for the dynamic probing of the membrane structural and functional plasticity of living brain cells. It is a powerful tool for providing new insights into mechanisms of cell structural remodeling during physiological or pathological processes, such as brain development or tumorigenesis. PMID:28469559

Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs.

PubMed

Vögeli, Beat; Orts, Julien; Strotz, Dean; Chi, Celestine; Minges, Martina; Wälti, Marielle Aulikki; Güntert, Peter; Riek, Roland

2014-04-01

Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein's function, its entire structural landscape at atomic resolution and insight into the interconversion between all the structural states (i.e. dynamics) are required. Whereas dedicated trickery with NMR relaxation provides aspects of local dynamics, and 3D structure determination by NMR is well established, only recently have several attempts been made to formulate a more comprehensive description of the dynamics and the structural landscape of a protein. Here, a perspective is given on the use of exact NOEs (eNOEs) for the elucidation of structural ensembles of a protein describing the covered conformational space. Copyright © 2013 Elsevier Inc. All rights reserved.

Study on structures and properties of ammonia clusters (NH3)n (n=1-5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model.

PubMed

Yu, Ling; Yang, Zhong-Zhi

2010-05-07

Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.

Coexisting stable conformations of gaseous protein ions.

PubMed Central

Suckau, D; Shi, Y; Beu, S C; Senko, M W; Quinn, J P; Wampler, F M; McLafferty, F W

1993-01-01

For further insight into the role of solvent in protein conformer stabilization, the structural and dynamic properties of protein ions in vacuo have been probed by hydrogen-deuterium exchange in a Fourier-transform mass spectrometer. Multiply charged ions generated by electrospray ionization of five proteins show exchange reactions with 2H2O at 10(-7) torr (1 torr = 133.3 Pa) exhibiting pseudo-first-order kinetics. Gas-phase compactness of the S-S cross-linked RNase A relative to denatured S-derivatized RNase A is indicated by exchange of 35 and 135 hydrogen atoms, respectively. For pure cytochrome c ions, the existence of at least three distinct gaseous conformers is indicated by the substantially different values--52, 113, and 74--of reactive H atoms; the observation of these same values for ions of a number--2, 7, and 5, respectively--of different charge states indicates conformational insensitivity to coulombic forces. For each of these conformers, the compactness in vacuo indicated by these values corresponds directly to that of a known conformer structure in the solution from which the conformer ions are produced by electrospray. S-derivatized RNase A ions also exist as at least two gaseous conformers exchanging 50-140 H atoms. Gaseous conformer ions are isometrically stable for hours; removal of solvent greatly increases conformational rigidity. More specific ion-molecule reactions could provide further details of conformer structures. Images PMID:8381533

SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

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

Khabibullin, A.R.; Woods, L.M.; Karolak, A.

2016-06-15

Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis setmore » in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA-based-radiopharmaceuticals and will enhance our understanding of processes occurring at subatomic levels.« less

In situ formation of the first proteinogenically functionalized [TeW6O24O2(Glu)]7– structure reveals unprecedented chemical and geometrical features of the Anderson-type cluster† †Electronic supplementary information (ESI) available: Full experimental details and additional figures are provided. See DOI: 10.1039/c6cc07004c Click here for additional data file. Click here for additional data file. Click here for additional data file.

PubMed Central

Molitor, Christian; Bijelic, Aleksandar

2016-01-01

The chemistry of polyoxometalates (POMs) in a protein environment is an almost unexplored but highly relevant research field as important biological and pharmacological attributes of certain POMs are based on their interactions with proteins. We report on the A-type Anderson–Evans polyoxotungstate, [TeW6O24]6– (TEW), mediated crystallization of Coreopsis grandiflora aurone synthase (cgAUS1) using ∼0.24 mM protein and 1.0 mM TEW. The 1.78 Å crystal structure reveals the covalent binding of TEW to the protein under the formation of an unprecedented polyoxotungstate cluster, [TeW6O24O2(Glu)]7– (GluTEW). The polyoxotungstate–protein complex exhibits the first covalent bond between a protein and the A-type Anderson–Evans cluster, an archetype where up to now no hybrid structures exist. The polyoxotungstate is modified at two of its six addenda tungsten atoms, which covalently bind to the carboxylic oxygen atoms of glutamic acid (Glu157), leading to W–O distances of ∼2.35 Å. This ligand substitution reaction is accompanied by a reduction of the coordination number of two μ3 polyoxotungstate oxygen atoms. This is so far unique since all known hybridizations of the Anderson–Evans POM with organic units have been obtained via the functionalization of the B-type Anderson–Evans structure through its bridging oxygen atoms. The structure reported here proves the reactivity of this POM archetype's addenda atoms as it has been administered into the protein solution as a pre-assembled cluster. Moreover, the novel cluster [TeW6O24O2(Glu)]7– displays the great versatility of the Anderson–Evans POM class. PMID:27722437

Detailed Balance of Thermalization Dynamics in Rydberg-Atom Quantum Simulators.

PubMed

Kim, Hyosub; Park, YeJe; Kim, Kyungtae; Sim, H-S; Ahn, Jaewook

2018-05-04

Dynamics of large complex systems, such as relaxation towards equilibrium in classical statistical mechanics, often obeys a master equation that captures essential information from the complexities. Here, we find that thermalization of an isolated many-body quantum state can be described by a master equation. We observe sudden quench dynamics of quantum Ising-like models implemented in our quantum simulator, defect-free single-atom tweezers in conjunction with Rydberg-atom interaction. Saturation of their local observables, a thermalization signature, obeys a master equation experimentally constructed by monitoring the occupation probabilities of prequench states and imposing the principle of the detailed balance. Our experiment agrees with theories and demonstrates the detailed balance in a thermalization dynamics that does not require coupling to baths or postulated randomness.

Detailed Balance of Thermalization Dynamics in Rydberg-Atom Quantum Simulators

NASA Astrophysics Data System (ADS)

Kim, Hyosub; Park, YeJe; Kim, Kyungtae; Sim, H.-S.; Ahn, Jaewook

2018-05-01

Dynamics of large complex systems, such as relaxation towards equilibrium in classical statistical mechanics, often obeys a master equation that captures essential information from the complexities. Here, we find that thermalization of an isolated many-body quantum state can be described by a master equation. We observe sudden quench dynamics of quantum Ising-like models implemented in our quantum simulator, defect-free single-atom tweezers in conjunction with Rydberg-atom interaction. Saturation of their local observables, a thermalization signature, obeys a master equation experimentally constructed by monitoring the occupation probabilities of prequench states and imposing the principle of the detailed balance. Our experiment agrees with theories and demonstrates the detailed balance in a thermalization dynamics that does not require coupling to baths or postulated randomness.

Energetic electron processes fluorescence effects for structured nanoparticles X-ray analysis and nuclear medicine applications

NASA Astrophysics Data System (ADS)

Taborda, A.; Desbrée, A.; Carvalho, A.; Chaves, P. C.; Reis, M. A.

2016-08-01

Superparamagnetic iron oxide (SPIO) nanoparticles are widely used as contrast agents for nuclear magnetic resonance imaging (MRI), and can be modified for improved imaging or to become tissue-specific or even protein-specific. The knowledge of their detailed elemental composition characterisation and potential use in nuclear medicine applications, is, therefore, an important issue. X-ray fluorescence techniques such as particle induced X-ray emission (PIXE) or X-ray fluorescence spectrometry (XRF), can be used for elemental characterisation even in problematic situations where very little sample volume is available. Still, the fluorescence coefficient of Fe is such that, during the decay of the inner-shell ionised atomic structure, keV Auger electrons are produced in excess to X-rays. Since cross-sections for ionisation induced by keV electrons, for low atomic number atoms, are of the order of 103 barn, care should be taken to account for possible fluorescence effects caused by Auger electrons, which may lead to the wrong quantification of elements having atomic number lower than the atomic number of Fe. Furthermore, the same electron processes will occur in iron oxide nanoparticles containing 57Co, which may be used for nuclear medicine therapy purposes. In the present work, simple approximation algorithms are proposed for the quantitative description of radiative and non-radiative processes associated with Auger electrons cascades. The effects on analytical processes and nuclear medicine applications are quantified for the case of iron oxide nanoparticles, by calculating both electron fluorescence emissions and energy deposition on cell tissues where the nanoparticles may be embedded.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

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

Zhou, X. Edward; Gao, Xiang; Barty, Anton

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE PAGES

Zhou, X. Edward; Gao, Xiang; Barty, Anton; ...

2016-04-12

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

Effect of Fe incorporation on the optical behavior of ZnO thin films prepared by sol-gel derived spin coating techniques

NASA Astrophysics Data System (ADS)

Rakkesh, R. Ajay; Malathi, R.; Balakumar, S.

2013-02-01

In this work, Fe doped Zinc Oxide (ZnO) thin films were fabricated on the glass substrate by sol-gel derived spin coating technique. X-ray Diffraction studies revealed that the obtained pure and Fe doped ZnO thin films were in the wurtzite and spinel phase respectively. The three well defined Raman lines at 432, 543 and 1091 cm-1 also confirmed the lattice structure of the ZnO thin film has wurtzite symmetry. While doping Fe atoms in the ZnO, there was a significant change in the phase from wurtzite to spinel structure; owing to Fe (III) ions being incorporated into the lattice through substitution of Zn (II) ions. Room temperature PL spectra showed that the role of defect mediated red emissions at 612 nm was due to radial recombination of a photogenerated hole with an electron that belongs to the Fe atoms, which were discussed in detail.

Solution-Synthesized Chevron Graphene Nanoribbons Exfoliated onto H:Si(100).

PubMed

Radocea, Adrian; Sun, Tao; Vo, Timothy H; Sinitskii, Alexander; Aluru, Narayana R; Lyding, Joseph W

2017-01-11

There has been tremendous progress in designing and synthesizing graphene nanoribbons (GNRs). The ability to control the width, edge structure, and dopant level with atomic precision has created a large class of accessible electronic landscapes for use in logic applications. One of the major limitations preventing the realization of GNR devices is the difficulty of transferring GNRs onto nonmetallic substrates. In this work, we developed a new approach for clean deposition of solution-synthesized atomically precise chevron GNRs onto H:Si(100) under ultrahigh vacuum. A clean transfer allowed ultrahigh-vacuum scanning tunneling microscopy (STM) to provide high-resolution imaging and spectroscopy and reveal details of the electronic structure of chevron nanoribbons that have not been previously reported. We also demonstrate STM nanomanipulation of GNRs, characterization of multilayer GNR cross-junctions, and STM nanolithography for local depassivation of H:Si(100), which allowed us to probe GNR-Si interactions and revealed a semiconducting-to-metallic transition. The results of STM measurements were shown to be in good agreement with first-principles computational modeling.

Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

PubMed

Radoux, Chris J; Olsson, Tjelvar S G; Pitt, Will R; Groom, Colin R; Blundell, Tom L

2016-05-12

Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.

Simulation of FRET dyes allows quantitative comparison against experimental data

NASA Astrophysics Data System (ADS)

Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

2018-03-01

Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse.

PubMed

Agarwal, Vinayak; Miles, Zachary D; Winter, Jaclyn M; Eustáquio, Alessandra S; El Gamal, Abrahim A; Moore, Bradley S

2017-04-26

Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.

Subtle Monte Carlo Updates in Dense Molecular Systems.

PubMed

Bottaro, Sandro; Boomsma, Wouter; E Johansson, Kristoffer; Andreetta, Christian; Hamelryck, Thomas; Ferkinghoff-Borg, Jesper

2012-02-14

Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.

A national facility for biological cryo-electron microscopy

PubMed Central

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

2015-01-01

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

Structural, magnetic, and transport properties of Permalloy for spintronic experiments

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

Nahrwold, Gesche; Scholtyssek, Jan M.; Motl-Ziegler, Sandra

2010-07-15

Permalloy (Ni{sub 80}Fe{sub 20}) is broadly used to prepare magnetic nanostructures for high-frequency experiments where the magnetization is either excited by electrical currents or magnetic fields. Detailed knowledge of the material properties is mandatory for thorough understanding its magnetization dynamics. In this work, thin Permalloy films are grown by dc-magnetron sputtering on heated substrates and by thermal evaporation with subsequent annealing. The specific resistance is determined by van der Pauw methods. Point-contact Andreev reflection is employed to determine the spin polarization of the films. The topography is imaged by atomic-force microscopy, and the magnetic microstructure by magnetic-force microscopy. Transmission-electron microscopymore » and transmission-electron diffraction are performed to determine atomic composition, crystal structure, and morphology. From ferromagnetic resonance absorption spectra the saturation magnetization, the anisotropy, and the Gilbert damping parameter are determined. Coercive fields and anisotropy are measured by magneto-optical Kerr magnetometry. The sum of the findings enables optimization of Permalloy for spintronic experiments.« less

Oxygen-induced high diffusion rate of magnesium dopants in GaN/AlGaN based UV LED heterostructures.

PubMed

Michałowski, Paweł Piotr; Złotnik, Sebastian; Sitek, Jakub; Rosiński, Krzysztof; Rudziński, Mariusz

2018-05-23

Further development of GaN/AlGaN based optoelectronic devices requires optimization of the p-type material growth process. In particular, uncontrolled diffusion of Mg dopants may decrease the performance of a device. Thus it is meaningful to study the behavior of Mg and the origins of its diffusion in detail. In this work we have employed secondary ion mass spectrometry to study the diffusion of magnesium in GaN/AlGaN structures. We show that magnesium has a strong tendency to form Mg-H complexes which immobilize Mg atoms and restrain their diffusion. However, these complexes are not present in samples post-growth annealed in an oxygen atmosphere or Al-rich AlGaN structures which naturally have a high oxygen concentration. In these samples, more Mg atoms are free to diffuse and thus the average diffusion length is considerably larger than for a sample annealed in an inert atmosphere.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

Gas adsorption/separation properties of metal directed self-assembly of two coordination polymers with 5-nitroisophthalate

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

Arıcı, Mürsel; Yeşilel, Okan Zafer, E-mail: yesilel@ogu.edu.tr; Keskin, Seda

2014-02-15

Two new coordination polymers, namely, [Co(µ-nip)(µ-bpe)]{sub n} (1) and [Zn(µ-nip)(µ-bpe)]{sub n} (2) (nip: 5-nitroisophthalate, bpe: 1,2-bis(4-pyridyl)ethane) were hydrothermally synthesized and structurally characterized by single crystal X-ray diffraction, IR spectroscopy, elemental analysis and thermal analysis. Moreover, atomically detailed simulation studies of complex 2 for CO{sub 2}/CH{sub 4} adsorption and separation were performed. Complex 1 consists of two dimensional (2D) (4,4) grid networks with the point symbol of 4{sup 4}.6{sup 2}. Complex 2 exhibits a 3-fold interpenetrating 3D framework with 6{sup 5}.8-dmp topology. Thermal properties of the complexes showed that both complexes were stable over 320 °C. Simulation studies demonstrated that complexmore » 2 can separate CO{sub 2} from CH{sub 4} at low pressures at 273 K. - Graphical abstract: In this study, two new coordination polymers, namely, [Co(µ-nip)(µ-bpe)]{sub n} (1) and [Zn(µ-nip)(µ-bpe)]{sub n} (2) (nip: 5-nitroisophthalate, bpe: 1,2-bis(4-pyridyl)ethane) were hydrothermally synthesized and structurally characterized by single crystal X-ray diffraction, IR spectroscopy, elemental analysis and thermal analysis. Moreover, atomically detailed simulation studies of complex 2 for CO{sub 2}/CH{sub 4} adsorption and separation were performed. Complex 1 consists of two dimensional (2D) (4,4) grid networks with the point symbol of 4{sup 4}.6{sup 2}. Complex 2 exhibits a 3-fold interpenetrating 3D framework with 6{sup 5}.8-dmp topology. Simulation studies demonstrated that complex 2 can separate CO{sub 2} from CH{sub 4} at low pressures at 273 K. Display Omitted - Highlights: • Two new coordination polymers with 5-nitroisophthalate and 1,2-bis(4-pyridyl)ethane. • Atomically detailed simulation studies of the complexes. • Complex 2 can be proposed as molecular sieve to separate CO{sub 2} from CH{sub 4} at low pressures.« less

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

NASA Astrophysics Data System (ADS)

Susan, Anju; Joshi, Kavita

2014-04-01

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

Subatomic and atomic crystallographic studies of aldose reductase: implications for inhibitor binding.

PubMed

Podjarny, A; Cachau, R E; Schneider, T; Van Zandt, M; Joachimiak, A

2004-04-01

The determination of several of aldose reductase-inhibitor complexes at subatomic resolution has revealed new structural details, including the specific interatomic contacts involved in inhibitor binding. In this article, we review the structures of the complexes of ALR2 with IDD 594 (resolution: 0.66 angstrom, IC50 (concentration of the inhibitor that produced half-maximal effect): 30 nM, space group: P2(1)), IDD 393 (resolution: 0.90 angstrom, IC50: 6 nM, space group: P1), fidarestat (resolution: 0.92 angstrom, IC50: 9 nM, space group: P2(1)) and minalrestat (resolution: 1.10 angstrom, IC50: 73 nM, space group: P1). The structures are compared and found to be highly reproductible within the same space group (root mean square (RMS) deviations: 0.15 approximately 0.3 angstrom). The mode of binding of the carboxylate inhibitors IDD 594 and IDD 393 is analysed. The binding of the carboxylate head can be accurately determined by the subatomic resolution structures, since both the protonation states and the positions of the atoms are very precisely known. The differences appear in the binding in the specificity pocket. The high-resolution structures explain the differences in IC50, which are confirmed both experimentally by mass spectrometry measures of VC50 and theoretically by free energy perturbation calculations. The binding of the cyclic imide inhibitors fidarestat and minalrestat is also described, focusing on the observation of a Cl(-) ion which binds simultaneously with fidarestat. The presence of this anion, binding also to the active site residue His110, leads to a mechanism in which the inhibitor can bind in a neutral state and then become charged inside the active site pocket. This mechanism can explain the excellent in vivo properties of cyclic imide inhibitors. In summary, the complete and detailed information supplied by the subatomic resolution structures can explain the differences in binding energy of the different inhibitors.

Carboplatin binding to histidine

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

Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.

An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the brominemore » form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.« less

From Structural Complexity to Structure-Property Relationships in Intermetallics: Development of Density Functional Theory-Chemical Pressure Analysis

NASA Astrophysics Data System (ADS)

Engelkemier, Joshua

The unparalleled structural diversity of intermetallic compounds provides nearly unlimited potential for the discovery and optimization of materials with useful properties, such as thermoelectricity, superconductivity, magnetism, hydrogen storage, superelasticity, and catalysis. This same diversity, however, creates challenges for understanding and controlling the unpredictable structure of intermetallic phases. Moreover, the fundamental design principles that have proven so powerful in molecular chemistry do not have simple analogues for metallic, solid state materials. One of these basic principles is the concept of atomic size effects. Especially in densely packed crystal structures where the need to fill space is in competition with the atoms' preferences for ideal interatomic distances, substitution of one element in a compound for another with similar chemical properties yet different atomic size can have dramatic effects on the ordering of the atoms (which in turn affects the electronic structure, vibrational properties, and materials properties). But because the forces that hold metallic phases together are less easily understood from a local perspective than covalent or ionic interactions in other kinds of materials, it is usually unclear whether the atoms are organized to optimize stabilizing, bonding interactions or rather forced to be close together despite repulsive, steric interactions. This dissertation details the development of a theoretical method, called Density Functional Theory-Chemical Pressure (DFT-CP) analysis, to address this issue. It works by converting the distribution of total energy density from a DFT calculation into a map of chemical pressure through a numerical approximation of the first derivative of energy with respect to voxel volume. The CP distribution is then carefully divided into contact volumes between neighboring atoms, from which it is possible to determine whether atoms are too close together (positive CP) or too far away from each other (negative CP). This technique is used in combination with the concept of structural plasticity (Berns, 2014) to demonstrate how complex intermetallic phases can be understood as a response of simpler structure types to the destabilizing buildup of CP. From this point of view, interfaces created in complex structures relieve the CP manifest in the more basic, parent structures. This is shown specifically for Ca36Sn23 relative to a hypothetical W5Si3-type Ca5Sn3 phase, LnMn xGa3 (Ln = Ho-Tm, x < 0.15) compared to unstuffed AuCu3-type LnGa3 structures, and structural derivatives of CaCu5- and HoCoGa5-type compounds. As a direct result of the technical developments necessitated by these analyses on structural complexity in intermetallics, a further connection is made in this thesis between the calculated CP schemes and the frequencies of vibrational modes in MgCu2-type CaPd2, the Cr 3Si-type superconductor Nb3Ge, and CaCu5-type CaPd5. Local chemical interactions revealed by DFT-CP analysis are used to identify structure-property relationships for the pseudogap in the phonon density of states (DOS) of CaPd2, the higher critical temperature of Nb3Ge vs. Nb3Sn, and the wide diversity of structures based on the CaCu5 type.

Neutral atom traps of rare isotopes

NASA Astrophysics Data System (ADS)

Mueller, Peter

2016-09-01

Laser cooling and trapping techniques offer exquisite control of an atom's external and internal degrees of freedom. The species of interest can be selectively captured, cooled close to absolute zero temperatures, and observed with high signal-to-noise ratio. Moreover, the atom's electronic and magnetic state populations can be precisely manipulated and interrogated. Applied in nuclear physics, these techniques are ideal for precision measurements in the fields of fundamental interactions and symmetries, nuclear structure studies, and isotopic trace analysis. In particular, they offer unique opportunities in the quest for physics beyond the standard model. I will shortly review the basics of this approach and the state of the field and then cover in more details recent results from two such efforts: the search for a permanent electric dipole moment in 225Ra and the beta-neutrino angular correlation measurement with laser trapped 6He. This work is supported by the U.S. DOE, Office of Science, Office of Nuclear Physics, under Contract DE-AC02-06CH11357.

Multiscale multiphysics and multidomain models—Flexibility and rigidity

PubMed Central

Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei

2013-01-01

The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomic charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of \\documentclass[12pt]{minimal}\\begin{document}${\\cal O}(N^2)$\\end{document}O(N2) at most, where N is the number of atoms or residues, in contrast to \\documentclass[12pt]{minimal}\\begin{document}${\\cal O}(N^3)$\\end{document}O(N3) for Hamiltonian based methods. We demonstrate that the proposed FRI gives rise to accurate prediction of protein B-Factor for a set of 263 proteins. We show that a parameter free FRI is able to achieve about 95% accuracy of the parameter optimized FRI. An interpolation algorithm is developed to construct continuous atomic flexibility functions for visualization and use with CEWAR. PMID:24320318

Microscopic Analysis of Current and Mechanical Properties of Nafion® Studied by Atomic Force Microscopy

PubMed Central

Hiesgen, Renate; Helmly, Stefan; Galm, Ines; Morawietz, Tobias; Handl, Michael; Friedrich, K. Andreas

2012-01-01

The conductivity of fuel cell membranes as well as their mechanical properties at the nanometer scale were characterized using advanced tapping mode atomic force microscopy (AFM) techniques. AFM produces high-resolution images under continuous current flow of the conductive structure at the membrane surface and provides some insight into the bulk conducting network in Nafion membranes. The correlation of conductivity with other mechanical properties, such as adhesion force, deformation and stiffness, were simultaneously measured with the current and provided an indication of subsurface phase separations and phase distribution at the surface of the membrane. The distribution of conductive pores at the surface was identified by the formation of water droplets. A comparison of nanostructure models with high-resolution current images is discussed in detail. PMID:24958429

Mechanism of Phosphine Dissociation on the Si(001) Surface

NASA Astrophysics Data System (ADS)

Warschkow, Oliver; Schofield, Steven R.; Smith, Phil V.

2005-03-01

The continued down-scaling of electronic devices to the atomic scale increasingly requires an atomic-level understanding of the elementary processes of semiconductor doping. We present a combined experimental and theoretical investigation into the dissociation mechanism of phosphine (PH3) on the Si(001) surface. As reported by us elsewhere in this conference, a number of prominent intermediate species of PH3 dissociation observed in STM experiments have been structurally characterized as PH2+H, PH+2H and P+3H species respectively. In this poster we present detailed quantum chemical calculations of these and other short-lived intermediates as well as the transition (kinetic) barriers between them. This leads us to formulate a step-by-step mechanism for the complete dissociation of PH3 on the Si(001) surface.

N(+)-N and O(+)-O interaction energies, dipole transition moments, and transport cross sections

NASA Technical Reports Server (NTRS)

Partridge, H.; Stallcop, J. R.

1986-01-01

Complete sets of ion-atom interaction energies have been computed for nitrogen and oxygen with accurate large scale structure calculations. The computed energies agree well with the accurate potential curves available from spectroscopic measurement. The state functions from the nitrogen calculations have been applied to determine the transition moment for all allowed dipole transitions. These results can be combined to compute a detailed radiation spectrum such as that required to define the highly nonequilibrium environment of aeroassisted orbital transfer vehicle (AOTV). The long-range interaction energies have been used to determine the ion-atom resonance charge exchange cross sections that are important for transport processes such as diffusion. A calculation to determine reliable transport properties for energies that include the AOTV temperature range from these computed properties is described.

Physics-based simulation of EM and SM in TSV-based 3D IC structures

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

Kteyan, Armen; Sukharev, Valeriy; Zschech, Ehrenfried

2014-06-19

Evolution of stresses in through-silicon-vias (TSVs) and in the TSV landing pad due to the stress migration (SM) and electromigration (EM) phenomena are considered. It is shown that an initial stress distribution existing in a TSV depends on its architecture and copper fill technology. We demonstrate that in the case of proper copper annealing the SM-induced redistribution of atoms results in uniform distributions of the hydrostatic stress and concentration of vacancies along each segment. In this case, applied EM stressing generates atom migration that is characterized by kinetics depending on the preexisting equilibrium concentration of vacancies. Stress-induced voiding in TSVmore » is considered. EM induced voiding in TSV landing pad is analyzed in details.« less

Titanium embedded cage structure formation in Al{sub n}Ti{sup +} clusters and their interaction with Ar

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

Torres, M. B., E-mail: begonia@ubu.es; Vega, A.; Balbás, L. C.

2014-05-07

Recently, Ar physisorption was used as a structural probe for the location of the Ti dopant atom in aluminium cluster cations, Al{sub n}Ti{sup +} [Lang et al., J. Am. Soc. Mass Spectrom. 22, 1508 (2011)]. As an experiment result, the lack of Ar complexes for n > n{sub c} determines the cluster size for which the Ti atom is located inside of an Al cage. To elucidate the decisive factors for the formation of endohedrally Al{sub n}Ti{sup +}, experimentalists proposed detailed computational studies as indispensable. In this work, we investigated, using the density functional theory, the structural and electronic propertiesmore » of singly titanium doped cationic clusters, Al{sub n}Ti{sup +} (n = 16–21) as well as the adsorption of an Ar atom on them. The first endohedral doped cluster, with Ti encapsulated in a fcc-like cage skeleton, appears at n{sub c} = 21, which is the critical number consistent with the exohedral-endohedral transition experimentally observed. At this critical size the non-crystalline icosahedral growth pattern, related to the pure aluminium clusters, with the Ti atom in the surface, changes into a endohedral fcc-like pattern. The map of structural isomers, relative energy differences, second energy differences, and structural parameters were determined and analyzed. Moreover, we show the critical size depends on the net charge of the cluster, being different for the cationic clusters (n{sub c} = 21) and their neutral counterparts (n{sub c} = 20). For the Al {sub n} Ti {sup +} · Ar complexes, and for n < 21, the preferred Ar adsorption site is on top of the exohedral Ti atom, with adsorption energy in very good agreement with the experimental value. Instead, for n = 21, the Ar adsorption occurs on the top an Al atom with very low absorption energy. For all sizes the geometry of the Al{sub n}Ti{sup +} clusters keeps unaltered in the Ar-cluster complexes. This fact indicates that Ar adsorption does not influence the cluster structure, providing support to the experimental technique used. For n{sub c} = 21, the smallest size of endohedral Ti doped cationic clusters, the Ar binding energy decreases drastically, whereas the Ar-cluster distance increases substantially, point to Ar physisorption, as assumed by the experimentalists. Calculated Ar adsorption energies agree well with available experimental binding energies.« less

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

PubMed

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

2017-09-26

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

Fast Atomic-Scale Elemental Mapping of Crystalline Materials by STEM Energy-Dispersive X-Ray Spectroscopy Achieved with Thin Specimens.

PubMed

Lu, Ping; Yuan, Renliang; Zuo, Jian Min

2017-02-01

Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm2 with the acquisition time of ~2 s or less. Here we report the details of this method, and, in particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO3 in [001] projection for 200 keV electrons.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Using simulation to interpret experimental data in terms of protein conformational ensembles.

PubMed

Allison, Jane R

2017-04-01

In their biological environment, proteins are dynamic molecules, necessitating an ensemble structural description. Molecular dynamics simulations and solution-state experiments provide complimentary information in the form of atomically detailed coordinates and averaged or distributions of structural properties or related quantities. Recently, increases in the temporal and spatial scale of conformational sampling and comparison of the more diverse conformational ensembles thus generated have revealed the importance of sampling rare events. Excitingly, new methods based on maximum entropy and Bayesian inference are promising to provide a statistically sound mechanism for combining experimental data with molecular dynamics simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

The gj factor of a bound electron and the hyperfine structure splitting in hydrogenlike ions

NASA Astrophysics Data System (ADS)

Beier, Thomas

2000-12-01

The comparison between theory and experiment of the hyperfine structure splitting and the electronic gj factor in heavy highly charged ions provides a unique testing ground for quantum electrodynamics in the presence of strong electric and magnetic fields. A theoretical evaluation is presented of all quantum electrodynamical contributions to the ground-state hfs splitting in hydrogenlike and lithiumlike atoms as well as to the gj factor. Binding and nuclear effects are discussed as well. A comparison with the available experimental data is performed, and a detailed discussion of theoretical sources of uncertainty is included which is mainly due to insufficiently known nuclear properties.

Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

PubMed

Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

2017-10-01

Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp 2 -H...F-Csp 2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp 2 -F...F-Csp 2 contacts.

Binding of dinitrogen to an iron-sulfur-carbon site

NASA Astrophysics Data System (ADS)

Čorić, Ilija; Mercado, Brandon Q.; Bill, Eckhard; Vinyard, David J.; Holland, Patrick L.

2015-10-01

Nitrogenases are the enzymes by which certain microorganisms convert atmospheric dinitrogen (N2) to ammonia, thereby providing essential nitrogen atoms for higher organisms. The most common nitrogenases reduce atmospheric N2 at the FeMo cofactor, a sulfur-rich iron-molybdenum cluster (FeMoco). The central iron sites that are coordinated to sulfur and carbon atoms in FeMoco have been proposed to be the substrate binding sites, on the basis of kinetic and spectroscopic studies. In the resting state, the central iron sites each have bonds to three sulfur atoms and one carbon atom. Addition of electrons to the resting state causes the FeMoco to react with N2, but the geometry and bonding environment of N2-bound species remain unknown. Here we describe a synthetic complex with a sulfur-rich coordination sphere that, upon reduction, breaks an Fe-S bond and binds N2. The product is the first synthetic Fe-N2 complex in which iron has bonds to sulfur and carbon atoms, providing a model for N2 coordination in the FeMoco. Our results demonstrate that breaking an Fe-S bond is a chemically reasonable route to N2 binding in the FeMoco, and show structural and spectroscopic details for weakened N2 on a sulfur-rich iron site.

Fast Atomic-Scale Elemental Mapping of Crystalline Materials by STEM Energy-Dispersive X-Ray Spectroscopy Achieved with Thin Specimens [Fast Atomic-Scale Chemical Imaging of Crystalline Materials by STEM Energy-Dispersive X-ray Spectroscopy Achieved with Thin Specimens].

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

Lu, Ping; Yuan, Renliang; Zuo, Jian Min

Abstract Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm 2with the acquisition time of ~2 s or less. Here we report the details of this method, and, inmore » particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO 3in [001] projection for 200 keV electrons.« less

THE DYNAMICS OF HYDROGEN ATOM ABSTRACTION FROM POLYATOMIC MOLECULES.

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

LIU,X.; SUITS,A.G.

2002-11-21

The hydrogen atom abstraction reaction is an important fundamental process that is extensively involved in atmospheric and combustion chemistry. The practical significance of this type of reaction with polyatomic hydrocarbons is manifest, which has led to many kinetics studies. The detailed understanding of these reactions requires corresponding dynamics studies. However, in comparison to the A + HX {radical} AH + X reactions, the study of the dynamics of A + HR {yields} AH + R reactions is much more difficult, both experimentally and theoretically (here and in the following, A stands for an atom, X stands for a halogen atom,more » and R stands for a polyatomic hydrocarbon radical). The complication stems from the structured R, in contrast to the structureless X. First of all, there are many internal degrees of freedom in R that can participate in the reaction. In addition, there are different carbon sites from which an H atom can be abstracted, and the dynamics are correspondingly different; there are also multiple identical carbon sites in HR and in the picture of a local reaction, there exist competitions between neighboring H atoms, and so on. Despite this complexity, there have been continuing efforts to obtain insight into the dynamics of these reactions. In this chapter, some examples are presented, including the reactions of ground state H, Cl, and O atoms, with particular focus on our recent work using imaging to obtain the differential cross sections for these reactions.« less

Fast Atomic-Scale Elemental Mapping of Crystalline Materials by STEM Energy-Dispersive X-Ray Spectroscopy Achieved with Thin Specimens [Fast Atomic-Scale Chemical Imaging of Crystalline Materials by STEM Energy-Dispersive X-ray Spectroscopy Achieved with Thin Specimens].

DOE PAGES

Lu, Ping; Yuan, Renliang; Zuo, Jian Min

2017-02-23

Abstract Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm 2with the acquisition time of ~2 s or less. Here we report the details of this method, and, inmore » particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO 3in [001] projection for 200 keV electrons.« less

Carbon Isotope Chemistry in Molecular Clouds

NASA Technical Reports Server (NTRS)

Robertson, Amy N.; Willacy, Karen

2012-01-01

Few details of carbon isotope chemistry are known, especially the chemical processes that occur in astronomical environments like molecular clouds. Observational evidence shows that the C-12/C-13 abundance ratios vary due to the location of the C-13 atom within the molecular structure. The different abundances are a result of the diverse formation pathways that can occur. Modeling can be used to explore the production pathways of carbon molecules in an effort to understand and explain the chemical evolution of molecular clouds.

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

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

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Predicting RNA folding thermodynamics with a reduced chain representation model

PubMed Central

CAO, SONG; CHEN, SHI-JIE

2005-01-01

Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of Tetrahymena group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule. PMID:16251382

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy.

PubMed

Guo, Jing; You, Sifan; Wang, Zhichang; Peng, Jinbo; Ma, Runze; Jiang, Ying

2018-05-27

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal structure and probing the hydrogen-bond (H-bond) dynamics of the water molecules adsorbed on solid surfaces are fundamental issues of water science, which remains a great challenge owing to the light mass and small size of hydrogen. Scanning tunneling microscopy (STM) is a promising tool for attacking these problems, thanks to its capabilities of sub-Ångström spatial resolution, single-bond vibrational sensitivity, and atomic/molecular manipulation. The designed experimental system consists of a Cl-terminated tip and a sample fabricated by dosing water molecules in situ onto the Au(111)-supported NaCl(001) surfaces. The insulating NaCl films electronically decouple the water from the metal substrates, so the intrinsic frontier orbitals of water molecules are preserved. The Cl-tip facilitates the manipulation of the single water molecules, as well as gating the orbitals of water to the proximity of Fermi level (EF) via tip-water coupling. This paper outlines the detailed methods of submolecular resolution imaging, molecular/atomic manipulation, and single-bond vibrational spectroscopy of interfacial water. These studies open up a new route for investigating the H-bonded systems at the atomic scale.

Modelling of ‘sub-atomic’ contrast resulting from back-bonding on Si(111)-7×7

PubMed Central

Jarvis, Samuel P; Rashid, Mohammad A

2016-01-01

Summary It has recently been shown that ‘sub-atomic’ contrast can be observed during NC-AFM imaging of the Si(111)-7×7 substrate with a passivated tip, resulting in triangular shaped atoms [Sweetman et al. Nano Lett. 2014, 14, 2265]. The symmetry of the features, and the well-established nature of the dangling bond structure of the silicon adatom means that in this instance the contrast cannot arise from the orbital structure of the atoms, and it was suggested by simple symmetry arguments that the contrast could only arise from the backbonding symmetry of the surface adatoms. However, no modelling of the system has been performed in order to understand the precise origin of the contrast. In this paper we provide a detailed explanation for ‘sub-atomic’ contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking similarity to experimental results, and demonstrate how ‘sub-atomic’ contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms. PMID:27547610

How to Run FAST Simulations.

PubMed

Zimmerman, M I; Bowman, G R

2016-01-01

Molecular dynamics (MD) simulations are a powerful tool for understanding enzymes' structures and functions with full atomistic detail. These physics-based simulations model the dynamics of a protein in solution and store snapshots of its atomic coordinates at discrete time intervals. Analysis of the snapshots from these trajectories provides thermodynamic and kinetic properties such as conformational free energies, binding free energies, and transition times. Unfortunately, simulating biologically relevant timescales with brute force MD simulations requires enormous computing resources. In this chapter we detail a goal-oriented sampling algorithm, called fluctuation amplification of specific traits, that quickly generates pertinent thermodynamic and kinetic information by using an iterative series of short MD simulations to explore the vast depths of conformational space. © 2016 Elsevier Inc. All rights reserved.

Superposition of two tRNA{sup Ser} acceptor stem crystal structures: Comparison of structure, ligands and hydration

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

Eichert, Andre; Fuerste, Jens P.; Ulrich, Alexander

2010-05-07

We solved the X-ray structures of two Escherichia coli tRNA{sup Ser} acceptor stem microhelices. As both tRNAs are aminoacylated by the same seryl-tRNA-synthetase, we performed a comparative structure analysis of both duplexes to investigate the helical conformation, the hydration patterns and magnesium binding sites. It is well accepted, that the hydration of RNA plays an important role in RNA-protein interactions and that the extensive solvent content of the minor groove has a special function in RNA. The detailed comparison of both tRNA{sup Ser} microhelices provides insights into the structural arrangement of the isoacceptor tRNA aminoacyl stems with respect to themore » surrounding water molecules and may eventually help us to understand their biological function at atomic resolution.« less

Multi-scale characterization by FIB-SEM/TEM/3DAP.

PubMed

Ohkubo, T; Sepehri-Amin, H; Sasaki, T T; Hono, K

2014-11-01

In order to improve properties of functional materials, it is important to understand the relation between the structure and the properties since the structure has large effect to the properties. This can be done by using multi-scale microstructure analysis from macro-scale to nano and atomic scale. Scanning electron microscope (SEM) equipped with focused ion beam (FIB), transmission electron microscope (TEM) and 3D atom probe (3DAP) are complementary analysis tools making it possible to know the structure and the chemistry from micron to atomic resolution. SEM gives us overall microstructural and chemical information by various kinds of detectors such as secondary electron, backscattered electron, EDS and EBSD detectors. Also, it is possible to analyze 3D structure and chemistry via FIB serial sectioning. In addition, using TEM we can focus on desired region to get more complementary information from HRTEM/STEM/Lorentz images, SAED/NBD patterns and EDS/EELS to see the detail micro or nano-structure and chemistry. Especially, combination of probe Cs corrector and split EDS detectors with large detector size enable us to analyze the atomic scale elemental distribution. Furthermore, if the specimen has a complicated 3D nanostructure, or we need to analyze light elements such as hydrogen, lithium or boron, 3DAP can be used as the only technique which can visualize and analyze distribution of all constituent atoms of our materials within a few hundreds nm area. Hence, site-specific sample preparation using FIB/SEM is necessary to get desired information from region of interest. Therefore, this complementary analysis combination works very well to understand the detail of materials.In this presentation, we will show the analysis results obtained from some of functional materials by Carl Zeiss CrossBeam 1540EsB FIB/SEM, FEI Tecnai G(2) F30, Titan G2 80-200 TEMs and locally build laser assisted 3DAP. As the one of the example, result of multi-scale characterization for ultra-fine grain Nd-Fe-B permanent magnet will be shown [1]. In order to improve the magnetic properties, especially to increase the coercivity (resistance against magnetization reversal) of the magnet, decreasing the grain size and isolating each grain by non-ferromagnetic grain boundary phase are quite important since the nucleation of magnetic reversal from grain boundary phase can be suppressed and pinning force of magnetic domain wall at the grain boundary phase can be strengthened. Therefore, micro and nano structure and chemistry analysis can shed a light do grain boundary engineering.Figure 1(a,b) shows SEM BSE images of ultrafine grain Nd-Fe-B sintered magnet and the reconstructed 3D tomography of Nd-rich phases obtained by FIB/SEM serial sectioning. This data can provide us information about the distribution of Nd-rich phase and its volume fraction. Moreover, the HRTEM image from the grain boundary phase, the 3DAP maps and the concentration depth profiles are shown in Fig. 1(c,d,e). This magnet shows high coercivity (1517kA/m), and by comparing these results with the microstructures of low coercivity specimen, importance of grain boundary formation was confirmed and it gives us hint to improve the coercivity further. We will show the detail and results from other materials.jmicro;63/suppl_1/i6/DFU046F1F1DFU046F1Fig. 1.(a) SEM BSE images of ultrafine grain Nd-Fe-B sintered magnet. (b) 3D FIB/SEM tomography of Nd-rich phases. (c) HRTEM image from the grain boundary phase. (d) 3DAP maps of Nd, Cu and Al. (e) Concentration depth profiles for Fe, Nd+Pr, B, Co, Cu and Al, determined from the selected box in (d)[1]. © 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.

Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction.

PubMed

Müller, Knut; Krause, Florian F; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

2014-12-15

By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms.

Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction

NASA Astrophysics Data System (ADS)

Müller, Knut; Krause, Florian F.; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

2014-12-01

By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms.

Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction

PubMed Central

Müller, Knut; Krause, Florian F.; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

2014-01-01

By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms. PMID:25501385

Method for large-scale fabrication of atomic-scale structures on material surfaces using surface vacancies

DOEpatents

Lim, Chong Wee; Ohmori, Kenji; Petrov, Ivan Georgiev; Greene, Joseph E.

2004-07-13

A method for forming atomic-scale structures on a surface of a substrate on a large-scale includes creating a predetermined amount of surface vacancies on the surface of the substrate by removing an amount of atoms on the surface of the material corresponding to the predetermined amount of the surface vacancies. Once the surface vacancies have been created, atoms of a desired structure material are deposited on the surface of the substrate to enable the surface vacancies and the atoms of the structure material to interact. The interaction causes the atoms of the structure material to form the atomic-scale structures.

Analyzing non-LTE Kr plasmas produced in high energy density experiments: from the Z machine to the National Ignition Facility

NASA Astrophysics Data System (ADS)

Dasgupta, Arati

2015-11-01

Designing high fluence photon sources above 10 keV are a challenge for High Energy Density plasmas. This has motivated radiation source development investigations of Kr with K-shell energies around 13 keV. Recent pulsed power driven gas-puff experiments on the refurbished Z machine at Sandia have produced intense X-rays in the multi-keV photon energy range. K-shell radiative yields and efficiencies are very high for Ar, but rapidly decrease for higher atomic number (ZA) elements such as Kr. It has been suggested that an optimum exists corresponding to a trade-off between the increase of photon energy for higher ZA elements and the corresponding fall off in radiative power. However the conversion efficiency on NIF, where the drive, energy deposition process, and target dynamics are different, does not fall off with higher ZA as rapidly as on Z. We have developed detailed atomic structure and collisional data for the full K-, L- and partial M-shell of Kr using the Flexible Atomic Code (FAC). Our non-LTE atomic model includes all collisional and recombination processes, including state-specific dielectronic recombination (DR), that significantly affect ionization balance and spectra of Kr plasmas at the temperatures and densities of concern. The model couples ionization physics, radiation production and transport, and magnetohydrodynamics. In this talk, I will give a detailed description of the model and discuss 1D Kr simulations employing a multifrequency radiation transport scheme. Synthetic K- and L-shell spectra will be compared with available experimental data. This talk will analyze experimental data indicative of the differences between Z and NIF experimental data and discuss how they affect the K-shell radiative output of Kr plasma. Work supported by DOE/NNSA.

Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

PubMed

Wu, Guosheng; Robertson, Daniel H; Brooks, Charles L; Vieth, Michal

2003-10-01

The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated-annealing-based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid-based approximations to explicit all-atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all-atom representation of the protein (full force field) is used, while a lower accuracy of 66-76% is observed for grid-based methods. All docking experiments considered a 41-member protein-ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid-based docking is achieved if the explicit all-atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower-accuracy grid-based energy representations can be effectively used when followed with full force field minimization. The results of these grid-based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures. Copyright 2003 Wiley Periodicals, Inc.

CO adsorption on small Au{sub n} (n = 1–4) structures supported on hematite. I. Adsorption on iron terminated α-Fe{sub 2}O{sub 3} (0001) surface

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

Pabisiak, Tomasz; Kiejna, Adam, E-mail: kiejna@ifd.uni.wroc.pl; Winiarski, Maciej J.

2016-01-28

This is the first of two papers dealing with the adsorption of Au and formation of Au{sub n} nanostructures (n = 1–4) on hematite (0001) surface and adsorption of CO thereon. The stoichiometric Fe-terminated (0001) surface of hematite was investigated using density functional theory in the generalized gradient approximation of Perdew-Burke-Ernzerhof (PBE) form with Hubbard correction U, accounting for strong electron correlations (PBE+U). The structural, energetic, and electronic properties of the systems studied were examined for vertical and flattened configurations of Au{sub n} nanostructures adsorbed on the hematite surfaces. The flattened ones, which can be viewed as bilayer-like structures, weremore » found energetically more favored than vertical ones. For both classes of structures the adsorption binding energy increases with the number of Au atoms in a structure. The adsorption of Au{sub n} induces charge rearrangement at the Au{sub n}/oxide contact which is reflected in work function changes. In most considered cases Au{sub n} adsorption increases the work function. A detailed analysis of the bonding electron charge is presented and the corresponding electron charge rearrangements at the contacts were quantified by a Bader charge analyses. The interaction of a CO molecule with the Au{sub n} nanostructures supported on α-Fe{sub 2}O{sub 3} (0001) and the oxide support was studied. It is found that the CO adsorption binding to the hematite supported Au{sub n} structures is more than twice as strong as to the bare hematite surface. Analysis of the Bader charges on the atoms showed that in each case CO binds to the most positively charged (cationic) atom of the Au{sub n} structure. Changes in the electronic structure of the Au{sub n} species and of the oxide support, and their consequences for the interactions with CO, are discussed.« less

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

NASA Astrophysics Data System (ADS)

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-10-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.

Thermal nanostructure: An order parameter multiscale ensemble approach

NASA Astrophysics Data System (ADS)

Cheluvaraja, S.; Ortoleva, P.

2010-02-01

Deductive all-atom multiscale techniques imply that many nanosystems can be understood in terms of the slow dynamics of order parameters that coevolve with the quasiequilibrium probability density for rapidly fluctuating atomic configurations. The result of this multiscale analysis is a set of stochastic equations for the order parameters whose dynamics is driven by thermal-average forces. We present an efficient algorithm for sampling atomistic configurations in viruses and other supramillion atom nanosystems. This algorithm allows for sampling of a wide range of configurations without creating an excess of high-energy, improbable ones. It is implemented and used to calculate thermal-average forces. These forces are then used to search the free-energy landscape of a nanosystem for deep minima. The methodology is applied to thermal structures of Cowpea chlorotic mottle virus capsid. The method has wide applicability to other nanosystems whose properties are described by the CHARMM or other interatomic force field. Our implementation, denoted SIMNANOWORLD™, achieves calibration-free nanosystem modeling. Essential atomic-scale detail is preserved via a quasiequilibrium probability density while overall character is provided via predicted values of order parameters. Applications from virology to the computer-aided design of nanocapsules for delivery of therapeutic agents and of vaccines for nonenveloped viruses are envisioned.

Geometric, electronic, and bonding properties of AuNM (N = 1-7, M = Ni, Pd, Pt) clusters.

PubMed

Yuan, D W; Wang, Yang; Zeng, Zhi

2005-03-15

Employing first-principles methods, based on density functional theory, we report the ground state geometric and electronic structures of gold clusters doped with platinum group atoms, Au(N)M (N = 1-7, M = Ni, Pd, Pt). The stability and electronic properties of Ni-doped gold clusters are similar to that of pure gold clusters with an enhancement of bond strength. Due to the strong d-d or s-d interplay between impurities and gold atoms originating in the relativistic effects and unique properties of dopant delocalized s-electrons in Pd- and Pt-doped gold clusters, the dopant atoms markedly change the geometric and electronic properties of gold clusters, and stronger bond energies are found in Pt-doped clusters. The Mulliken populations analysis of impurities and detailed decompositions of bond energies as well as a variety of density of states of the most stable dopant gold clusters are given to understand the different effects of individual dopant atom on bonding and electronic properties of dopant gold clusters. From the electronic properties of dopant gold clusters, the different chemical reactivity toward O(2), CO, or NO molecule is predicted in transition metal-doped gold clusters compared to pure gold clusters.

Elucidating nitric oxide synthase domain interactions by molecular dynamics.

PubMed

Hollingsworth, Scott A; Holden, Jeffrey K; Li, Huiying; Poulos, Thomas L

2016-02-01

Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis. © 2015 The Protein Society.

Resolving the Structure of a Well-Ordered Hydroxyl Overlayer on In 2O 3 (111): Nanomanipulation and Theory

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

Wagner, Margareta; Lackner, Peter; Seiler, Steffen

Changes in chemical and physical properties resulting from water adsorption play an important role in the characterization and performance of device-relevant materials. Studies of model oxides with well-characterized surfaces can provide detailed information that is vital for a general understanding of water–oxide interactions. In this work, we study single crystals of indium oxide, the prototypical transparent contact material that is heavily used in a wide range of applications and most prominently in optoelectronic technologies. Water adsorbs dissociatively already at temperatures as low as 100 K, as confirmed by scanning tunneling microscopy (STM), photoelectron spectroscopy, and density functional theory. This dissociationmore » takes place on lattice sites of the defect-free surface. While the In 2O 3(111)-(1 × 1) surface offers four types of surface oxygen atoms (12 atoms per unit cell in total), water dissociation happens exclusively at one of them together with a neighboring pair of 5-fold coordinated In atoms. These O–In groups are symmetrically arranged around the 6-fold coordinated In atoms at the surface. At room temperature, the In 2O 3(111) surface thus saturates at three dissociated water molecules per unit cell, leading to a well-ordered hydroxylated surface with (1 × 1) symmetry, where the three water OWH groups plus the surface OSH groups are imaged together as one bright triangle in STM. Manipulations with the STM tip by means of voltage pulses preferentially remove the H atom of one surface OSH group per triangle. The change in contrast due to strong local band bending provides insights into the internal structure of these bright triangles. The experimental results are further confirmed by quantitative simulations of the STM image corrugation.« less

Resolving the Structure of a Well-Ordered Hydroxyl Overlayer on In 2O 3 (111): Nanomanipulation and Theory

DOE PAGES

Wagner, Margareta; Lackner, Peter; Seiler, Steffen; ...

2017-11-01

Changes in chemical and physical properties resulting from water adsorption play an important role in the characterization and performance of device-relevant materials. Studies of model oxides with well-characterized surfaces can provide detailed information that is vital for a general understanding of water–oxide interactions. In this work, we study single crystals of indium oxide, the prototypical transparent contact material that is heavily used in a wide range of applications and most prominently in optoelectronic technologies. Water adsorbs dissociatively already at temperatures as low as 100 K, as confirmed by scanning tunneling microscopy (STM), photoelectron spectroscopy, and density functional theory. This dissociationmore » takes place on lattice sites of the defect-free surface. While the In 2O 3(111)-(1 × 1) surface offers four types of surface oxygen atoms (12 atoms per unit cell in total), water dissociation happens exclusively at one of them together with a neighboring pair of 5-fold coordinated In atoms. These O–In groups are symmetrically arranged around the 6-fold coordinated In atoms at the surface. At room temperature, the In 2O 3(111) surface thus saturates at three dissociated water molecules per unit cell, leading to a well-ordered hydroxylated surface with (1 × 1) symmetry, where the three water OWH groups plus the surface OSH groups are imaged together as one bright triangle in STM. Manipulations with the STM tip by means of voltage pulses preferentially remove the H atom of one surface OSH group per triangle. The change in contrast due to strong local band bending provides insights into the internal structure of these bright triangles. The experimental results are further confirmed by quantitative simulations of the STM image corrugation.« less

3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.

PubMed

Kawabata, Takeshi; Nakamura, Haruki

2014-07-28

A protein-bound conformation of a target molecule can be predicted by aligning the target molecule on the reference molecule obtained from the 3D structure of the compound-protein complex. This strategy is called "similarity-based docking". For this purpose, we develop the flexible alignment program fkcombu, which aligns the target molecule based on atomic correspondences with the reference molecule. The correspondences are obtained by the maximum common substructure (MCS) of 2D chemical structures, using our program kcombu. The prediction performance was evaluated using many target-reference pairs of superimposed ligand 3D structures on the same protein in the PDB, with different ranges of chemical similarity. The details of atomic correspondence largely affected the prediction success. We found that topologically constrained disconnected MCS (TD-MCS) with the simple element-based atomic classification provides the best prediction. The crashing potential energy with the receptor protein improved the performance. We also found that the RMSD between the predicted and correct target conformations significantly correlates with the chemical similarities between target-reference molecules. Generally speaking, if the reference and target compounds have more than 70% chemical similarity, then the average RMSD of 3D conformations is <2.0 Å. We compared the performance with a rigid-body molecular alignment program based on volume-overlap scores (ShaEP). Our MCS-based flexible alignment program performed better than the rigid-body alignment program, especially when the target and reference molecules were sufficiently similar.

Interface structure in nanoscale multilayers near continuous-to-discontinuous regime

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

Pradhan, P. C.; Majhi, A.; Nayak, M., E-mail: mnayak@rrcat.gov.in

2016-07-28

Interfacial atomic diffusion, reaction, and formation of microstructure in nanoscale level are investigated in W/B{sub 4}C multilayer (ML) system as functions of thickness in ultrathin limit. Hard x-ray reflectivity (XRR) and x-ray diffuse scattering in conjunction with x-ray absorption near edge spectroscopy (XANES) in soft x-ray and hard x-ray regimes and depth profiling x-ray photoelectron spectroscopy (XPS) have been used to precisely evaluate detailed interfacial structure by systematically varying the individual layer thickness from continuous-to-discontinuous regime. It is observed that the interfacial morphology undergoes an unexpected significant modification as the layer thickness varies from continuous-to-discontinuous regime. The interfacial atomic diffusionmore » increases, the physical density of W layer decreases and that of B{sub 4}C layer increases, and further more interestingly the in-plane correlation length decreases substantially as the layer thickness varies from continuous-to-discontinuous regime. This is corroborated using combined XRR and x-ray diffused scattering analysis. XANES and XPS results show formation of more and more tungsten compounds at the interfaces as the layer thickness decreases below the percolation threshold due to increase in the contact area between the elements. The formation of compound enhances to minimize certain degree of disorder at the interfaces in the discontinuous region that enables to maintain the periodic structure in ML. The degree of interfacial atomic diffusion, interlayer interaction, and microstructure is correlated as a function of layer thickness during early stage of film growth.« less

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Multi-scale simulations of apatite-collagen composites: from molecules to materials

NASA Astrophysics Data System (ADS)

Zahn, Dirk

2017-03-01

We review scale-bridging simulation studies for the exploration of atomicto-meso scale processes that account for the unique structure and mechanic properties of apatite-protein composites. As the atomic structure and composition of such complex biocomposites only partially is known, the first part (i) of our modelling studies is dedicated to realistic crystal nucleation scenarios of inorganic-organic composites. Starting from the association of single ions, recent insights range from the mechanisms of motif formation, ripening reactions and the self-organization of nanocrystals, including their interplay with growth-controlling molecular moieties. On this basis, (ii) reliable building rules for unprejudiced scale-up models can be derived to model bulk materials. This is exemplified for (enamel-like) apatite-protein composites, encompassing up to 106 atom models to provide a realistic account of the 10 nm length scale, whilst model coarsening is used to reach μm length scales. On this basis, a series of deformation and fracture simulation studies were performed and helped to rationalize biocomposite hardness, plasticity, toughness, self-healing and fracture mechanisms. Complementing experimental work, these modelling studies provide particularly detailed insights into the relation of hierarchical composite structure and favorable mechanical properties.

A national facility for biological cryo-electron microscopy

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

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

2015-01-01

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

The molecular, electronic structures and vibrational spectra of metal-free, N,N'-dideuterio and magnesium tetra-2,3-pyridino-porphyrazines: Density functional calculations.

PubMed

Liu, Zhongqiang; Zhang, Xianxi; Zhang, Yuexing; Li, Renjie; Jiang, Jianzhuang

2006-10-01

A theoretical investigation of the fully optimized geometries and electronic structures of the metal-free (TPdPzH(2)), N,N'-dideuterio (TPdPzD(2)), and magnesium (TPdPzMg) tetra-2,3-pyridino-porphyrazine has been conducted based on density functional theory. The optimized geometries at density functional theory level for these compounds are reported here for the first time. A comparison between the different molecules for the geometry, molecular orbital, and atomic charge is made. The substituent effect of the N atoms on the molecular structures of these compounds is discussed. The IR and Raman spectra for these three compounds have also been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH, NM, and pyridine ring vibrational bands in the IR and Raman spectra have been made based on assistance of animated pictures. The simulated IR spectra of TPdPzH(2) are compared with the experimental absorption spectra, and very good consistency has been found. The isotope effect on the IR and Raman spectra is also discussed.

Ab Initio Study of Electronic Excitation Effects on SrTiO 3

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

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

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

Graphene-based two-dimensional Janus materials

NASA Astrophysics Data System (ADS)

Ng, Sze-Wing; Noor, Nuruzzaman; Zheng, Zijian

2018-04-01

Two-dimensional (2D) Janus materials with opposing components and properties on two sides have recently attracted fevered attention from various research fields for use as, for example, oil/water separating membranes, interfacial layers for mass transfer, 2D sensors and actuators. The Janus structure allows for a unidirectional transportation system and programmed response to certain stimuli to be achieved. Graphene, the 2D honeycomb network formed from one atomic layer of carbon atoms, has also received substantial research interest because of its intriguing structure and fascinating properties. The high mechanical strength, flexibility and optical transparency make graphene a unique candidate as a building block of 2D Janus materials through asymmetric modification with different functional groups on the graphene surfaces. This article reviews graphene-based 2D Janus materials, starting with a theoretical understanding of the behavior of Janus graphene. Then, different strategies for fabricating Janus graphene and its derivatives are reviewed in detail according to the chemical strategies of the modification methods. The applications of graphene-based Janus materials are discussed with a specific focus on the Janus structures that lead to bandgap engineering, as well as the construction of a responsive system on graphene.

Ab Initio Study of Electronic Excitation Effects on SrTiO 3

DOE PAGES

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

2017-11-14

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

High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape.

PubMed

Fossat, Martin J; Dao, Thuy P; Jenkins, Kelly; Dellarole, Mariano; Yang, Yinshan; McCallum, Scott A; Garcia, Angel E; Barrick, Doug; Roumestand, Christian; Royer, Catherine A

2016-12-06

A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the conformational ensemble along the entire folding reaction coordinate. Simulations can provide this level of insight for small proteins. In contrast, with the exception of hydrogen exchange, which does not monitor folding directly, experimental studies of protein folding have not yielded such structural and energetic detail. NMR can provide residue specific atomic level structural information, but its implementation in protein folding studies using chemical or temperature perturbation is problematic. Here we present a highly detailed structural and energetic map of the entire folding landscape of the leucine-rich repeat protein, pp32 (Anp32), obtained by combining pressure-dependent site-specific 1 H- 15 N HSQC data with coarse-grained molecular dynamics simulations. The results obtained using this equilibrium approach demonstrate that the main barrier to folding of pp32 is quite broad and lies near the unfolded state, with structure apparent only in the C-terminal region. Significant deviation from two-state unfolding under pressure reveals an intermediate on the folded side of the main barrier in which the N-terminal region is disordered. A nonlinear temperature dependence of the population of this intermediate suggests a large heat capacity change associated with its formation. The combination of pressure, which favors the population of folding intermediates relative to chemical denaturants; NMR, which allows their observation; and constrained structure-based simulations yield unparalleled insight into protein folding mechanisms. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Microstructure of β-Sitosterol:γ-Oryzanol Edible Organogels.

PubMed

Matheson, Andrew B; Koutsos, Vasileios; Dalkas, Georgios; Euston, Stephen; Clegg, Paul

2017-05-09

Rheology and atomic force microscopy (AFM) were employed to examine the microstructure of β-sitosterol:γ-oryzanol organogels in sunflower oil. Using time-resolved rheology, we followed gel formation, paying specific attention to the fibril aggregation process, which had not been studied in detail previously for this system. Using AFM, we observed gel structures directly and obtained detailed information on the gel structure, far exceeding previous studies. Our analysis suggests that though gels are formed by the self-assembly and aggregation of one-dimensional fibrils, the manner in which these fibrils aggregate into ribbons results in complex structures of higher dimensionality. We emphasize that it is a surprise to find ribbons and not twisted strands. Comparing AFM images of 10% w/w and 20% w/w gelator systems, we observed differences in the degree of branching which are consistent with the rheology. We also observed the individual self-assembled fibrils which make up these gels with much greater clarity than in previous microscopy studies, and the fibril diameters of ∼9.8 nm we measured agree excellently with those obtained from existing small-angle neutron scattering data. These results provide new insight into the structure and formation kinetics of this important organogel system.

Optimum Particle Size for Gold-Catalyzed CO Oxidation

PubMed Central

2018-01-01

The structure sensitivity of gold-catalyzed CO oxidation is presented by analyzing in detail the dependence of CO oxidation rate on particle size. Clusters with less than 14 gold atoms adopt a planar structure, whereas larger ones adopt a three-dimensional structure. The CO and O2 adsorption properties depend strongly on particle structure and size. All of the reaction barriers relevant to CO oxidation display linear scaling relationships with CO and O2 binding strengths as main reactivity descriptors. Planar and three-dimensional gold clusters exhibit different linear scaling relationship due to different surface topologies and different coordination numbers of the surface atoms. On the basis of these linear scaling relationships, first-principles microkinetics simulations were conducted to determine CO oxidation rates and possible rate-determining step of Au particles. Planar Au9 and three-dimensional Au79 clusters present the highest CO oxidation rates for planar and three-dimensional clusters, respectively. The planar Au9 cluster is much more active than the optimum Au79 cluster. A common feature of optimum CO oxidation performance is the intermediate binding strengths of CO and O2, resulting in intermediate coverages of CO, O2, and O. Both these optimum particles present lower performance than maximum Sabatier performance, indicating that there is sufficient room for improvement of gold catalysts for CO oxidation. PMID:29707098

A complex study of 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate: A new low-molecular-weight immune response modifier

NASA Astrophysics Data System (ADS)

Ryng, Stanisław; Zimecki, Michał; Jezierska-Mazzarello, Aneta; Panek, Jarosław J.; Mączyński, Marcin; Głowiak, Tadeusz; Sawka-Dobrowolska, Wanda; Koll, Aleksander

2011-07-01

A new potential lead structure with immunological activity, 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate, was synthesized. A detailed description of synthesis is presented together with X-ray structural analysis. In vitro assays showed that the compound had a potent immunosuppressive activity. Next, Density Functional Theory (DFT) was employed to shed a light on molecular properties of the investigated isoxazole derivative. The molecular modeling part included geometric as well as electronic structure descriptions: (i) the conformational analysis was performed to localize the most appropriate conformation; (ii) the coordination energy and Basis Set Superposition Error (BSSE) were estimated for the complex of the isoxazole derivative interacting with water molecule; (iii) the potential energy distribution was used to assign molecular vibrations, and NBO population analysis served to describe the electronic structure; (iv) the electrostatic potential map was generated to provide the graphical presentation of regions exposed for intermolecular interactions. The contacts between the water molecule and the nitrogen atom of the isoxazole ring edge were present in the solid phase. On the other hand, the theoretical DFT prediction was that the oxygen atom of the edge should form a more stable complex with the water molecule.

Structure, electronic properties, and aggregation behavior of hydroxylated carbon nanotubes

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

López-Oyama, A. B.; Silva-Molina, R. A.; Ruíz-García, J.

2014-11-07

We present a combined experimental and theoretical study to analyze the structure, electronic properties, and aggregation behavior of hydroxylated multiwalled carbon nanotubes (OH–MWCNT). Our MWCNTs have average diameters of ∼2 nm, lengths of approximately 100–300 nm, and a hydroxyl surface coverage θ∼0.1. When deposited on the air/water interface the OH–MWCNTs are partially soluble and the floating units interact and link with each other forming extended foam-like carbon networks. Surface pressure-area isotherms of the nanotube films are performed using the Langmuir balance method at different equilibration times. The films are transferred into a mica substrate and atomic force microscopy images showmore » that the foam like structure is preserved and reveals fine details of their microstructure. Density functional theory calculations performed on model hydroxylated carbon nanotubes show that low energy atomic configurations are found when the OH groups form molecular islands on the nanotube's surface. This patchy behavior for the OH species is expected to produce nanotubes having reduced wettabilities, in line with experimental observations. OH doping yields nanotubes having small HOMO–LUMO energy gaps and generates a nanotube → OH direction for the charge transfer leading to the existence of more hole carriers in the structures. Our synthesized OH–MWCNTs might have promising applications.« less

Structure, electronic properties, and aggregation behavior of hydroxylated carbon nanotubes.

PubMed

López-Oyama, A B; Silva-Molina, R A; Ruíz-García, J; Gámez-Corrales, R; Guirado-López, R A

2014-11-07

We present a combined experimental and theoretical study to analyze the structure, electronic properties, and aggregation behavior of hydroxylated multiwalled carbon nanotubes (OH-MWCNT). Our MWCNTs have average diameters of ~2 nm, lengths of approximately 100-300 nm, and a hydroxyl surface coverage θ~0.1. When deposited on the air/water interface the OH-MWCNTs are partially soluble and the floating units interact and link with each other forming extended foam-like carbon networks. Surface pressure-area isotherms of the nanotube films are performed using the Langmuir balance method at different equilibration times. The films are transferred into a mica substrate and atomic force microscopy images show that the foam like structure is preserved and reveals fine details of their microstructure. Density functional theory calculations performed on model hydroxylated carbon nanotubes show that low energy atomic configurations are found when the OH groups form molecular islands on the nanotube's surface. This patchy behavior for the OH species is expected to produce nanotubes having reduced wettabilities, in line with experimental observations. OH doping yields nanotubes having small HOMO-LUMO energy gaps and generates a nanotube → OH direction for the charge transfer leading to the existence of more hole carriers in the structures. Our synthesized OH-MWCNTs might have promising applications.

Representing and comparing protein structures as paths in three-dimensional space

PubMed Central

Zhi, Degui; Krishna, S Sri; Cao, Haibo; Pevzner, Pavel; Godzik, Adam

2006-01-01

Background Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction. Results We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure. Conclusion Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver. PMID:17052359

Correlations between interacting Rydberg atoms

NASA Astrophysics Data System (ADS)

Paris-Mandoki, Asaf; Braun, Christoph; Hofferberth, Sebastian

2018-04-01

This paper is a short introduction to Rydberg physics and quantum nonlinear optics using Rydberg atoms. It has been prepared as a compliment to a series of lectures delivered during the Latin American School of Physics "Marcos Moshinsky" 2017. We provide a short introduction to the properties of individual Rydberg atoms and discuss in detail how the interaction potential between Rydberg atom pairs is calculated. We then discuss how this interaction gives rise to the Rydberg blockade mechanism. With the aid of hallmark experiments in the field applications of the blockade for creating correlated quantum systems are discussed. Our aim is to give an overview of this exciting and rapidly evolving field. The interested reader is referred to original work and more comprehensive reviews and tutorials for further details on these subjects.

Extreme red shifted SERS nanotags† †Electronic supplementary information (ESI) available: General experimental details for the synthesis and characterization of dyes 1–14, intermediates 15–17, and HGNs; general description of the chemometrics used for principal component analysis; figures of SERS spectra of dye/HGN nanotags with 1280 nm excitation; extinction spectrum for HGNs; SERS spectra of Au and Ag nanoparticles and dye 13 aggregated with KCl; SERS spectra of dyes 13 and 14 on HGN not aggregated with KCl; details of mean plane angle calculations, tables of crystallographic data, atomic coordinates and equivalent isotropic displacement parameters, anisotropic placement parameters, bond lengths, bond angles, and hydrogen atom coordinates and isotropic displacement parameters for dye 14. CCDC 1040064. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03917c Click here for additional data file. Click here for additional data file.

PubMed Central

Bedics, Matthew A.; Kearns, Hayleigh; Cox, Jordan M.; Mabbott, Sam; Ali, Fatima; Shand, Neil C.; Faulds, Karen; Benedict, Jason B.

2015-01-01

Surfaced enhanced Raman scattering (SERS) nanotags operating with 1280 nm excitation were constructed from reporter molecules selected from a library of 14 chalcogenopyrylium dyes containing phenyl, 2-thienyl, and 2-selenophenyl substituents and a surface of hollow gold nanoshells (HGNs). These 1280 SERS nanotags are unique as they have multiple chalcogen atoms available which allow them to adsorb strongly onto the gold surface of the HGN thus producing exceptional SERS signals at this long excitation wavelength. Picomolar limits of detection (LOD) were observed and individual reporters of the library were identified by principal component analysis and classified according to their unique structure and SERS spectra. PMID:29308144

Multiscale multiphysics and multidomain models—Flexibility and rigidity

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

Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei, E-mail: wei@math.msu.edu

The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomicmore » charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of O(N{sup 2}) at most, where N is the number of atoms or residues, in contrast to O(N{sup 3}) for Hamiltonian based methods. We demonstrate that the proposed FRI gives rise to accurate prediction of protein B-Factor for a set of 263 proteins. We show that a parameter free FRI is able to achieve about 95% accuracy of the parameter optimized FRI. An interpolation algorithm is developed to construct continuous atomic flexibility functions for visualization and use with CEWAR.« less

Internal kinematic and physical properties in a BCD galaxy: Haro 15 in detail

NASA Astrophysics Data System (ADS)

Firpo, V.; Bosch, G.; Hägele, G. F.; Díaz, A. I.; Morrell, N.

2011-11-01

We present a detailed study of the kinematic and physical properties of the ionized gas in multiple knots of the blue compact dwarf galaxy Haro 15. Using echelle and long slit spectroscopy data, obtained with different instruments at Las Campanas Observatory, we study the internal kinematic and physical conditions (electron density and temperature), ionic and total chemical abundances of several atoms, reddening and ionization structure. Applying direct and empirical methods for abundance determination, we perform a comparative analysis between these regions and in their different components. On the other hand, our echelle spectra show complex kinematics in several conspicuous knots within the galaxy. To perform an in-depth 2D spectroscopic study we complete this work with high spatial and spectral resolution spectroscopy using the Integral Field Unit mode on the Gemini Multi-Object Spectrograph instrument at the Gemini South telescope. With these data we are able to resolve the complex kinematical structure within star forming knots in Haro 15 galaxy.

Synthesis, photophysical properties and structures of organotin-Schiff bases utilizing aromatic amino acid from the chiral pool and evaluation of the biological perspective of a triphenyltin compound.

PubMed

Basu Baul, Tushar S; Kehie, Pelesakuo; Duthie, Andrew; Guchhait, Nikhil; Raviprakash, Nune; Mokhamatam, Raveendra B; Manna, Sunil K; Armata, Nerina; Scopelliti, Michelangelo; Wang, Ruimin; Englert, Ulli

2017-03-01

Five new organotin(IV) complexes of compositions [Me 2 SnL 1 ] (1), [Me 2 SnL 2 ] n (2), [Me 2 SnL 3 ] (3), [Ph 3 SnL 1 H] n (4) and [Ph 3 SnL 3 H] (5) (where L 1 =(2S)-2-((E)-((Z)-4-hydroxypent-3-en-2-ylidene)amino)-3-(1H-indol-3-yl)propanoate, L 2 =(2S)-(E)-2-((2-hydroxybenzylidene)amino)-3-(1H-indol-3-yl)propanoate and L 3 =(2S)-(E)-2-((1-(2-hydroxyphenyl)ethylidene)amino)-3-(1H-indol-3-yl)propanoate were synthesized and spectroscopically characterized. The crystal structures of 1-4 were determined. For the dimethyltin derivative 2, a polymeric chain structure was observed as a result of a long Sn∙∙∙O contact involving the exocyclic carbonyl oxygen-atom from the tridentate ligand of a neighboring Sn-complex unit. The tin atom in this complex has a distorted octahedral coordination geometry, in which the long Sn-O bond is almost trans to the tridentate ligand nitrogen-atom. In contrast, the dimethyltin(IV) complexes 1 and 3 displayed discrete monomeric structures where the tin atom has distorted trigonal-bipyramidal geometry with the two coordinating L oxygen atoms defining the axial positions. On the other hand, 4 is a chain polymer in the solid state. The ligand-bridged Sn atoms adopt a trans-Ph 3 SnO 2 trigonal-bipyramidal configuration with equatorial phenyl groups. A carboxylato oxygen atom from one and the hydroxyl oxygen of the successive ligand in the chain occupy the axial positions. The solution structures were predicted by the use of 119 Sn NMR chemical shifts. The photophysical properties of the complexes were investigated in the solid and in solution. The triphenyltin(IV) compound 4 was tested in detail ex vivo against A375 (human melanoma) cell line, exhibiting an IC 50 value of 261nM to induce cell death as assessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay without significant alteration of cytolysis as determined by lactate dehydrogenase (LDH) assay. Compound 4-mediated potent cell death was also determined by Live and Dead assay and caspase-mediated cleavage of poly-ADP ribose polymerase (PARP). Potent cell death activity was not observed in primary cells, like blood-derived peripheral mononuclear cells (PBMC). Compound 4 inhibited the diphenyl hexatriene (DPH) binding to cells and decreased the micro viscosity in a dose-dependent manner. Additionally, the ability of 4 and cyclodextrin (CD) to interact was determined by molecular modelling. Copyright © 2016 Elsevier Inc. All rights reserved.

First principles modeling of the metal-electrolyte interface: A novel approach to the study of the electrochemical interface

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

Fernandez-Serra, Maria Victoria

2016-09-12

The research objective of this proposal is the computational modeling of the metal-electrolyte interface purely from first principles. The accurate calculation of the electrostatic potential at electrically biased metal-electrolyte interfaces is a current challenge for periodic “ab-initio” simulations. It is also an essential requisite for predicting the correspondence between the macroscopic voltage and the microscopic interfacial charge distribution in electrochemical fuel cells. This interfacial charge distribution is the result of the chemical bonding between solute and metal atoms, and therefore cannot be accurately calculated with the use of semi-empirical classical force fields. The project aims to study in detail themore » structure and dynamics of aqueous electrolytes at metallic interfaces taking into account the effect of the electrode potential. Another side of the project is to produce an accurate method to simulate the water/metal interface. While both experimental and theoretical surface scientists have made a lot of progress on the understanding and characterization of both atomistic structures and reactions at the solid/vacuum interface, the theoretical description of electrochemical interfaces is still lacking behind. A reason for this is that a complete and accurate first principles description of both the liquid and the metal interfaces is still computationally too expensive and complex, since their characteristics are governed by the explicit atomic and electronic structure built at the interface as a response to environmental conditions. This project will characterize in detail how different theoretical levels of modeling describer the metal/water interface. In particular the role of van der Waals interactions will be carefully analyzed and prescriptions to perform accurate simulations will be produced.« less

Structural insights, protein-ligand interactions and spectroscopic characterization of isoformononetin

NASA Astrophysics Data System (ADS)

Srivastava, Anubha; Singh, Harshita; Mishra, Rashmi; Dev, Kapil; Tandon, Poonam; Maurya, Rakesh

2017-04-01

Isoformononetin, a methoxylated isoflavone present in medicinal plants, has non-estrogenic bone forming effect via differential mitogen-activated protein kinase (MAPK) signaling. Spectroscopic (FT-Raman, FT-IR, UV-vis and NMR spectra) and quantum chemical calculations using density functional theory (DFT) and 6-311++G(d,p) as a large basis set have been employed to study the structural and electronic properties of isoformononetin. A detailed conformational analysis is performed to determine the stability among conformers and the various possibilities of intramolecular hydrogen bonding formation. Molecular docking studies with different protein kinases were performed on isoformononetin and previously studied isoflavonoid, formononetin in order to understand their inhibitory nature and the effect of functional groups on osteogenic or osteoporosis associated proteins. It is found that the oxygen atoms of methoxy, hydroxyl groups attached to phenyl rings R1, R3 and carbonyl group attached to pyran ring R2, play a major role in binding with the protein kinases that is responsible for the osteoporosis; however, no hydrophobic interactions are observed between rings of ligand and protein. The electronic properties such as HOMO and LUMO energies were determined by time-dependent TD-DFT which predict that conformer II is a little bit more stable and chemically low reactive than conformer I of isoformononetin. To estimate the structure-activity relationship, the molecular electrostatic potential (MEP) surface map, and reactivity descriptors are calculated from the optimized geometry of the molecule. From these results, it is also found that isoformononetin is kinetically more stable, less toxic, weak electrophile and chemically less reactive than formononetin. The atoms in molecules and natural bond orbital analysis are applied for the detailed analysis of intra and intermolecular hydrogen bonding interactions.

Two-dimensional functional molecular nanoarchitectures - Complementary investigations with scanning tunneling microscopy and X-ray spectroscopy

NASA Astrophysics Data System (ADS)

Klappenberger, Florian

2014-02-01

Functional molecular nanoarchitectures (FMNs) are highly relevant for the development of future nanotechnology devices. Profound knowledge about the atomically controlled construction of such nanoscale assemblies is an indispensable requirement to render the implementation of such components into a real product successful. For exploiting their full potential the architectures’ functionalities have to be characterized in detail including the ways to tailor them. In recent years a plethora of sophisticated constructs were fabricated touching a wide range of research topics. The present review summarizes important achievements of bottom-up fabricated, molecular nanostructures created on single crystal metal surfaces under ultra-high vacuum conditions. This selection focuses on examples where self-assembly mechanisms played a central role for their construction. Such systems, though typically quite complex, can be comprehensively understood by the STM+XS approach combining scanning tunneling microscopy (STM) with X-ray spectroscopy (XS) and being aided in the atomic interpretation by the appropriate theoretic analysis, often from density functional theory. The symbiosis of the techniques is especially fruitful because of the complementary character of the information accessed by the local microscopy and the space-averaging spectroscopy tools. STM delivers sub-molecular spatial-resolution, but suffers from limited sensitivity for the chemical and conformational states of the building-blocks. XS compensates these weaknesses with element- and moiety-specific data, which in turn would be hard to interpret with respect to structure formation without the topographic details revealed by STM. The united merit of this methodology allows detailed geometric information to be obtained and addresses both the electronic and chemical state of the complex organic species constituting such architectures. Thus, possible changes induced by the various processes such as surface interaction, thermal annealing, or molecular recognition can be followed with unprecedented level of detail. The well-understood nanoarchitecture construction protocols often rely on the ‘classic’ supramolecular interactions, namely hydrogen bonding and metal-organic coordination. Further examples include rarely encountered special cases where substrate-mediated processes or repulsive forces drive the emergence of order. The demonstrated functionalities include tuning of the electronic structure by confining surface state electrons and atomically defined arrays of magnetic complexes. Moreover, the high-quality templates can be utilized for imposing novel thin film growth modes or act as basic constituents of nanoswitches. Finally, the aptitude of the STM+XS approach for the emerging field of creating nanoarchitectures by on-surface covalent coupling is addressed.

Nanostructure and molecular mechanics of spider dragline silk protein assemblies

PubMed Central

Keten, Sinan; Buehler, Markus J.

2010-01-01

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

Nanostructure and molecular mechanics of spider dragline silk protein assemblies.

PubMed

Keten, Sinan; Buehler, Markus J

2010-12-06

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3₁-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.

Effect of surface Fe-S hybrid structure on the activity of the perfect and reduced α-Fe2O3(001) for chemical looping combustion

NASA Astrophysics Data System (ADS)

Xiao, Xianbin; Qin, Wu; Wang, Jianye; Li, Junhao; Dong, Changqing

2018-05-01

Sulfurization of the gradually reduced Fe2O3 surfaces is inevitable while Fe2O3 is used as an oxygen carrier (OC) for coal chemical looping combustion (CLC), which will result in formation of Fe-S hybrid structure on the surfaces. The Fe-S hybrid structure will directly alter the reactivity of the surfaces. Therefore, detailed properties of Fe-S hybrid structure over the perfect and reduced Fe2O3(001) surfaces, and its effect on the interfacial interactions, including CO oxidization and decomposition on the surfaces, were investigated by using density functional theory (DFT) calculations. The S atom prefers to chemically bind to Fe site with electron transfer from the surfaces to the S atom, and a deeper reduction of Fe2O3(001) leads to an increasing interaction between S and Fe. The formation of Fe-S hybrid structure alters the electronic properties of the gradually reduced Fe2O3(001) surfaces, promoting CO oxidation on the surfaces ranging from Fe2O3 to FeO, but depressing carbon deposition on the surfaces ranging from FeO to Fe. The sulfurized FeO acts as a watershed to realize relatively high CO oxidation rate and low carbon deposition. Results provided a fundamental understanding for controlling and optimizing the CLC processes.

Theoretical investigations of two adamantane derivatives: A combined X-ray, DFT, QTAIM analysis and molecular docking

NASA Astrophysics Data System (ADS)

Al-Wahaibi, Lamya H.; Sujay, Subramaniam; Muthu, Gangadharan Ganesh; El-Emam, Ali A.; Venkataramanan, Natarajan S.; Al-Omary, Fatmah A. M.; Ghabbour, Hazem A.; Percino, Judith; Thamotharan, Subbiah

2018-05-01

A detailed structural analysis of two adamantane derivatives namely, ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(phenyl)isothioureido]acetate I and ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(4-fluorophenyl)isothioureido]acetate II is carried out to understand the effect of fluorine substitution. The introduction of fluorine atom alters the crystal packing and is completely different from its parent compound. The fluorine substitution drastically reduced the intermolecular H⋯H contacts and this reduction is compensated by intermolecular F⋯H and F⋯F contacts. The relative contributions of various intermolecular contacts present in these structures were quantified using Hirshfeld surface analysis. Energetically significant molecular pairs were identified from the crystal structures of these compounds using PIXEL method. The structures of I and II are optimized in gas and solvent phases using the B3LYP-D3/6-311++G(d,p) level of theory. The quantum theory of atoms-in-molecules (QTAIM) analysis was carried out to estimate the strengths of various intermolecular contacts present in these molecular dimers. The results suggest that the Hsbnd H bonding take part in the stabilization of crystal structures. The experimental and theoretical UV-Vis results show the variations in HOMO and LUMO energy levels. In silico docking analysis indicates that both compounds I and II may exhibit inhibitory activity against 11-β-hydroxysteroid dehydrogenase 1 (11-β-HSD1).

Cellular Electron Cryotomography: Toward Structural Biology In Situ.

PubMed

Oikonomou, Catherine M; Jensen, Grant J

2017-06-20

Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.