Willden, Jeff
2001-01-01
"Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…
Modelling the Energetics of Encapsulation of Atoms and Atomic ...
Indian Academy of Sciences (India)
user
2015-07-04
Jul 4, 2015 ... Modelling the Energetics of Encapsulation of. Atoms and Atomic Clusters into Carbon. Nanotubes: Insights from Analytical Approaches. R. S. Swathi. School of Chemistry. Indian Institute of Science Education and Research. Thiruvananthapuram, Kerala, India ...
Stochastic models for atomic clocks
Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.
1983-01-01
For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.
"Electronium": A Quantum Atomic Teaching Model.
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Outlines an alternative atomic model to the probability model, the descriptive quantum atomic model Electronium. Discusses the way in which it is intended to support students in learning quantum-mechanical concepts. (Author/MM)
Can atom-surface potential measurements test atomic structure models?
Lonij, Vincent P A; Klauss, Catherine E; Holmgren, William F; Cronin, Alexander D
2011-06-30
van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C₃(K)/C₃(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C₃ ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C₃ ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C₃ values that depends more strongly on the permittivity of the surface.
Constructing many atomic models in $\\aleph_1$
Baldwin, John T.; Laskowski, Michael C.; Shelah, Saharon
2015-01-01
We introduce the notion of pseudo-algebraicity to study atomic models of first order theories (equivalently models of a complete sentence of $L_{\\omega_1,\\omega}$. Theorem: Let $T$ be any complete first-order theory in a countable language with an atomic model. If the pseudo-minimal types are not dense, then there are $2^{\\aleph_1}$ pairwise non-isomorphic atomic models of $T$, each of size $\\aleph_1$.
Empirical atom model of Vegard's law
Zhang, Lei; Li, Shichun
2014-02-01
Vegard's law seldom holds true for most binary continuous solid solutions. When two components form a solid solution, the atom radii of component elements will change to satisfy the continuity requirement of electron density at the interface between component atom A and atom B so that the atom with larger electron density will expand and the atom with the smaller one will contract. If the expansion and contraction of the atomic radii of A and B respectively are equal in magnitude, Vegard's law will hold true. However, the expansion and contraction of two component atoms are not equal in most situations. The magnitude of the variation will depend on the cohesive energy of corresponding element crystals. An empirical atom model of Vegard's law has been proposed to account for signs of deviations according to the electron density at Wigner-Seitz cell from Thomas-Fermi-Dirac-Cheng model.
Modeling Atom Probe Tomography: A review
Energy Technology Data Exchange (ETDEWEB)
Vurpillot, F., E-mail: francois.vurpillot@univ-rouen.fr [Groupe de Physique des Matériaux, UMR CNRS 6634, Université de Rouen, Saint Etienne du Rouvray 76801 (France); Oberdorfer, C. [Institut für Materialwissenschaft, Lehrstuhl für Materialphysik, Universität Stuttgart, Heisenbergstr. 3, 70569 Stuttgart (Germany)
2015-12-15
Improving both the precision and the accuracy of Atom Probe Tomography reconstruction requires a correct understanding of the imaging process. In this aim, numerical modeling approaches have been developed for 15 years. The injected ingredients of these modeling tools are related to the basic physic of the field evaporation mechanism. The interplay between the sample nature and structure of the analyzed sample and the reconstructed image artefacts have pushed to gradually improve and make the model more and more sophisticated. This paper reviews the evolution of the modeling approach in Atom Probe Tomography and presents some future potential directions in order to improve the method. - Highlights: • The basics of field evaporation. • The main aspects of Atom Probe Tomography modeling. • The intrinsic limitations of the current method and future potential directions to improve the understanding of tip to image ion projection.
Students' Mental Models of Atomic Spectra
Körhasan, Nilüfer Didis; Wang, Lu
2016-01-01
Mental modeling, which is a theory about knowledge organization, has been recently studied by science educators to examine students' understanding of scientific concepts. This qualitative study investigates undergraduate students' mental models of atomic spectra. Nine second-year physics students, who have already taken the basic chemistry and…
Numerical Models for Viscoelastic Liquid Atomization Spray
Directory of Open Access Journals (Sweden)
Lijuan Qian
2016-12-01
Full Text Available Atomization spray of non-Newtonian liquid plays a pivotal role in various engineering applications, especially for the energy utilization. To operate spray systems efficiently and well understand the effects of liquid rheological properties on the whole spray process, a comprehensive model using Euler-Lagrangian approaches was established to simulate the evolution of the atomization spray for viscoelastic liquid. Based on the Oldroyd model, the viscoelastic linear dispersion relation was introduced into the primary atomization; an extended viscoelastic version of Taylor analogy breakup (TAB model was proposed; and the coalescence criteria was modified by rheological parameters, such as the relaxation time, the retardation time and the zero shear viscosity. The predicted results are validated with experimental data varying air-liquid mass flow ratio (ALR. Then, numerical calculations are conducted to investigate the characteristics of viscoelastic liquid atomization process. Results showed that the evolutionary trend of droplet mean diameter, Weber number and Ohnesorge number of viscoelastic liquids along with axial direction were qualitatively similar to that of Newtonian liquid. However, the mean size of polymer solution increased more gently than that of water at the downstream of the spray, which was beneficial to stable control of the desirable size in the applications. As concerned the effects of liquid physical properties, the surface tension played an important role in the primary atomization, which indicated the benefit of selecting the solvents with lower surface tension for finer atomization effects, while, for the evolution of atomization spray, larger relaxation time and zero shear viscosity increased droplet Sauter mean diameter (SMD significantly. The zero shear viscosity was effective throughout the jet region, while the effect of relaxation time became weaken at the downstream of the spray field.
Contemporary models of the atomic nucleus
Nemirovskii, P E
2013-01-01
Contemporary Models of the Atomic Nucleus discusses nuclear structure and properties, expounding contemporary theoretical concepts of the low-energy nuclear processes underlying in nuclear models. This book focuses on subjects such as the optical nuclear model, unified or collective model, and deuteron stripping reaction. Other topics discussed include the basic nuclear properties; shell model; theoretical analysis of the shell model; and radiative transitions and alpha-decay. The deuteron theory and the liquid drop nuclear model with its application to fission theory are also mentioned, but o
Atomic size effects in continuum modeling
Ratsch, C.; Kang, M.; Caflisch, R. E.
2001-08-01
Continuum modeling of many physical systems typically assumes that the spatial extent of an atom is small compared to the quantities of interest and can therefore be neglected. We show that this is valid only asymptotically. For many applications of practical interest, the spatial extent of a discrete atom cannot be neglected. We have developed a model for the description of epitaxial growth based on the levelset method, and find that we can accurately predict quantities such as the island densities, if we implement boundary conditions in a region with atomic width, rather than just on a line without any spatial extent. Only in the limit of very large islands and island spacings can this be neglected.
Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.
1992-01-01
The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.
Model Hamiltonians for atomic and molecular systems
Carlson, J.; Moskowitz, Jules W.; Schmidt, K. E.
1989-01-01
A model Hamiltonian, designed to allow larger systems to be treated with the Green's function Monte Carlo method, is introduced for atomic and molecular systems. The model reduces the statistical variance associated with Green's function Monte Carlo calculations by reducing potential energy fluctuations in the core regions. By performing calculations of Li, LiH, and Li2 we show that this method can be used to obtain energy differences with much less computer time than required for the complete interaction. Increases in efficiency for larger systems will be even greater.
Cipolla, Laura; Ferrari, Lia A.
2016-01-01
A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).
Computer Model Of Fragmentation Of Atomic Nuclei
Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.
1995-01-01
High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.
Atomic Models for Motional Stark Effects Diagnostics
Energy Technology Data Exchange (ETDEWEB)
Gu, M F; Holcomb, C; Jayakuma, J; Allen, S; Pablant, N A; Burrell, K
2007-07-26
We present detailed atomic physics models for motional Stark effects (MSE) diagnostic on magnetic fusion devices. Excitation and ionization cross sections of the hydrogen or deuterium beam traveling in a magnetic field in collisions with electrons, ions, and neutral gas are calculated in the first Born approximation. The density matrices and polarization states of individual Stark-Zeeman components of the Balmer {alpha} line are obtained for both beam into plasma and beam into gas models. A detailed comparison of the model calculations and the MSE polarimetry and spectral intensity measurements obtained at the DIII-D tokamak is carried out. Although our beam into gas models provide a qualitative explanation for the larger {pi}/{sigma} intensity ratios and represent significant improvements over the statistical population models, empirical adjustment factors ranging from 1.0-2.0 must still be applied to individual line intensities to bring the calculations into full agreement with the observations. Nevertheless, we demonstrate that beam into gas measurements can be used successfully as calibration procedures for measuring the magnetic pitch angle through {pi}/{sigma} intensity ratios. The analyses of the filter-scan polarization spectra from the DIII-D MSE polarimetry system indicate unknown channel and time dependent light contaminations in the beam into gas measurements. Such contaminations may be the main reason for the failure of beam into gas calibration on MSE polarimetry systems.
Project Physics Text 5, Models of the Atom.
Harvard Univ., Cambridge, MA. Harvard Project Physics.
Basic atomic theories are presented in this fifth unit of the Project Physics text for use by senior high students. Chemical basis of atomic models in the early years of the 18th Century is discussed n connection with Dalton's theory, atomic properties, and periodic tables. The discovery of electrons is described by using cathode rays, Millikan's…
Operation of the computer model for microenvironment atomic oxygen exposure
Bourassa, R. J.; Gillis, J. R.; Gruenbaum, P. E.
1995-01-01
A computer model for microenvironment atomic oxygen exposure has been developed to extend atomic oxygen modeling capability to include shadowing and reflections. The model uses average exposure conditions established by the direct exposure model and extends the application of these conditions to treat surfaces of arbitrary shape and orientation.
An atomic model for neutral and singly ionized uranium
Maceda, E. L.; Miley, G. H.
1979-01-01
A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.
Geometry-dependent atomic multipole models for the water molecule.
Loboda, O; Millot, C
2017-10-28
Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.
Proposed reference models for atomic oxygen in the terrestrial atmosphere
Llewellyn, E. J.; Mcdade, I. C.; Lockerbie, M. D.
1989-01-01
A provisional Atomic Oxygen Reference model was derived from average monthly ozone profiles and the MSIS-86 reference model atmosphere. The concentrations are presented in tabular form for the altitude range 40 to 130 km.
The Quantum Atomic Model "Electronium": A Successful Teaching Tool.
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Focuses on the quantum atomic model Electronium. Outlines the Bremen teaching approach in which this model is used, and analyzes the learning of two students as they progress through the teaching unit. (Author/MM)
Developing Models: What is the Atom Really Like?
Records, Roger M.
1982-01-01
Five atomic theory activities feasible for high school students to perform are described based on the following models: (1) Dalton's Uniform Sphere Model; (2) Thomson's Raisin Pudding Model; (3) Rutherford's Nuclear Model; (4) Bohr's Energy Level Model, and (5) Orbital Model from quantum mechanics. (SK)
Modeling Solar Atmospheric Phenomena with AtomDB and PyAtomDB
Dupont, Marcus; Foster, Adam
2018-01-01
Taking advantage of the modeling tools made available by PyAtomDB (Foster 2015), we evaluated the impact of changing atomic data on solar phenomena, in particular their effects on models of coronal mass ejections (CME). Intitially, we perform modifications to the canonical SunNEI code (Murphy et al. 2011) in order to include non-equilibrium ionization (NEI) processes that occur in the CME modeled in SunNEI. The methods used involve the consideration of radiaitive cooling as well as ion balance calculations. These calculations were subsequently implemented within the SunNEI simulation. The insertion of aforementioned processes and parameter customizaton produced quite similar results of the original except for the case of iron. These differences were traced to inconsistencies in the recombination rates for Argon-like iron ions between the CHIANTI and AtomDB databases, even though they in theory use the same data. The key finding was that theoretical models are greatly impacted by the relative atomic database update cycles.Following the SunNEI comparison, we then use the AtomDB database to model the time depedencies of intensity flux spikes produced by a coronal shock wave (Ma et al. 2011). We produced a theretical representation for an ionizing plasma that interpolated over the intensity in four Astronomical Imaging Assembly (AIA) filters. Specifically, the 171 A (Fe IX) ,193 A (Fe XII, FeXXIV),211 A (Fe XIV),and 335 A (Fe XVI) wavelengths in order to assess the comparative spectral emissions between AtomDB and the observed data. The results of the theoretical model, in principle, shine light on both the equilibrium conditions before the shock and the non-equilibrium response to the shock front, as well as discrepancies introduced by changing the atomic data.
Project Physics Tests 5, Models of the Atom.
Harvard Univ., Cambridge, MA. Harvard Project Physics.
Test items relating to Project Physics Unit 5 are presented in this booklet. Included are 70 multiple-choice and 23 problem-and-essay questions. Concepts of atomic model are examined on aspects of relativistic corrections, electron emission, photoelectric effects, Compton effect, quantum theories, electrolysis experiments, atomic number and mass,…
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.
2004-01-01
framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....
The Number of Atomic Models of Uncountable Theories
Ulrich, Douglas
2016-01-01
We show there exists a complete theory in a language of size continuum possessing a unique atomic model which is not constructible. We also show it is consistent with $ZFC + \\aleph_1 < 2^{\\aleph_0}$ that there is a complete theory in a language of size $\\aleph_1$ possessing a unique atomic model which is not constructible. Finally we show it is consistent with $ZFC + \\aleph_1 < 2^{\\aleph_0}$ that for every complete theory $T$ in a language of size $\\aleph_1$, if $T$ has uncountable atomic mod...
Monte Carlo Computational Modeling of Atomic Oxygen Interactions
Banks, Bruce A.; Stueber, Thomas J.; Miller, Sharon K.; De Groh, Kim K.
2017-01-01
Computational modeling of the erosion of polymers caused by atomic oxygen in low Earth orbit (LEO) is useful for determining areas of concern for spacecraft environment durability. Successful modeling requires that the characteristics of the environment such as atomic oxygen energy distribution, flux, and angular distribution be properly represented in the model. Thus whether the atomic oxygen is arriving normal to or inclined to a surface and whether it arrives in a consistent direction or is sweeping across the surface such as in the case of polymeric solar array blankets is important to determine durability. When atomic oxygen impacts a polymer surface it can react removing a certain volume per incident atom (called the erosion yield), recombine, or be ejected as an active oxygen atom to potentially either react with other polymer atoms or exit into space. Scattered atoms can also have a lower energy as a result of partial or total thermal accommodation. Many solutions to polymer durability in LEO involve protective thin films of metal oxides such as SiO2 to prevent atomic oxygen erosion. Such protective films also have their own interaction characteristics. A Monte Carlo computational model has been developed which takes into account the various types of atomic oxygen arrival and how it reacts with a representative polymer (polyimide Kapton H) and how it reacts at defect sites in an oxide protective coating, such as SiO2 on that polymer. Although this model was initially intended to determine atomic oxygen erosion behavior at defect sites for the International Space Station solar arrays, it has been used to predict atomic oxygen erosion or oxidation behavior on many other spacecraft components including erosion of polymeric joints, durability of solar array blanket box covers, and scattering of atomic oxygen into telescopes and microwave cavities where oxidation of critical component surfaces can take place. The computational model is a two dimensional model
Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules.
Bereau, Tristan; Andrienko, Denis; von Lilienfeld, O Anatole
2015-07-14
Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular interactions. Here we introduce a machine learning model for multipole coefficients of atom types H, C, O, N, S, F, and Cl in any molecular conformation. The model is trained on quantum-chemical results for atoms in varying chemical environments drawn from thousands of organic molecules. Multipoles in systems with neutral, cationic, and anionic molecular charge states are treated with individual models. The models' predictive accuracy and applicability are illustrated by evaluating intermolecular interaction energies of nearly 1,000 dimers and the cohesive energy of the benzene crystal.
Quantum entanglement in two-electron atomic models
Energy Technology Data Exchange (ETDEWEB)
Manzano, D; Plastino, A R; Dehesa, J S [Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, Granada E-18071 (Spain); Koga, T, E-mail: arplastino@ugr.e [Applied Chemistry Research Unit, Graduate School of Engineering, Muroran Institute of Technology, Muroran, Hokkaido 050-8585 (Japan)
2010-07-09
We explore the main entanglement properties exhibited by the eigenfunctions of two exactly soluble two-electron models, the Crandall atom and the Hooke atom, and compare them with the entanglement features of helium-like systems. We compute the amount of entanglement associated with the wavefunctions corresponding to the fundamental and first few excited states of these models. We investigate the dependence of the entanglement on the parameters of the models and on the quantum numbers of the eigenstates. It is found that the amount of entanglement of the system tends to increase with energy in both models. In addition, we study the entanglement of a few states of helium-like systems, which we compute using high-quality Kinoshita-like eigenfunctions. The dependence of the entanglement of helium-like atoms on the nuclear charge and on energy is found to be consistent with the trends observed in the previous two model systems.
Eulerian Multiphase Population Balance Model of Atomizing, Swirling Flows
Directory of Open Access Journals (Sweden)
Narayana P. Rayapati
2011-06-01
Full Text Available An Eulerian/Eulerian multiphase flow model coupled with a population balance model is used as the basis for numerical simulation of atomization in swirling flows. The objective of this exercise is to develop a methodology capable of predicting the local point-wise drop size distribution in a spray, such as would be measured by the Phase Doppler Particle Analyzer (PDA. Model predictions are compared to experimental measurements of particle size distributions in an air-blast atomizer spray to demonstrate good qualitative and quantitative agreement. It is observed that the dependence of velocity on drop size inherent in a multiphase description of the drop cloud appears necessary to capture some features of the experimental data. Using this model, we demonstrate the relative contributions of secondary atomization and transport to the variation observed in the downstream spray drop size distribution.
Spontaneous emission of light from atoms: the model
Energy Technology Data Exchange (ETDEWEB)
Marecki, P. [Wyzsza Szkola Informatyki i Zarzadzania, ul. Legionow 81, 43-300 Bielsko-Biala (Poland); Szpak, N. [Institute for Theoretical Physics, J. W. Goethe University, Max-von-Laue-Str. 1, 60438 Frankfurt/Main (Germany)
2005-07-08
We investigate (non-relativistic) atomic systems interacting with quantum electromagnetic field (QEF). The resulting model describes spontaneous emission of light from a two-level atom surrounded by various initial states of the QEF. We assume that the quantum field interacts with the atom via the standard, minimal-coupling Hamiltonian, with the A{sup 2} term neglected. We also assume that there will appear at most single excitations (photons). By conducting the analysis on a general level we allow for an arbitrary initial state of the QEF (which can be for instance: the vacuum, the ground state in a cavity, or the squeezed state). We derive a Volterra-type equation which governs the time evolution of the amplitude of the excited state. The two-point function of the initial state of the QEF, integrated with a combination of atomic wavefunctions, forms the kernel of this equation. (Abstract Copyright [2005], Wiley Periodicals, Inc.)
Surface Adsorption in Nonpolarizable Atomic Models
Energy Technology Data Exchange (ETDEWEB)
Whitmer, Jonathan K.; Joshi, Abhijeet A.; Carlton, Rebecca J.; Abbott, Nicholas L.; de Pablo, Juan J.
2014-12-09
Many ionic solutions exhibit species dependent properties, including surface tension and the salting out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to develop atomistic models capable of capturing Hofmeister effects rigorously. Importantly, we aim to capture this dependence in computationally cheap “hard” ionic models, which do not exhibit dynamic polarization. To do this, we have performed an investigation detailing the effects of the water model on these properties. Though incredibly important, the role of water models in simulation of ionic solutions and biological systems is essentially unexplored. We quantify this via the ion-dependent surface attraction of the halide series (Cl, Br, I) and, in so doing, determine the relative importance of various hypothesized contributions to ionic surface free energies. Importantly, we demonstrate surface adsorption can result in hard ionic models combined with a thermodynamically accurate reprsenation of the water molecule (TIP4Q). The effect observed in simulations of iodide is commensurate with previous calculations of the surface potential of mean force in rigid molecular dynamics and polarizable density- functional models. Our calculations are direct simulation evidence of the subtle but sensitive role of water thermodynamics in atomistic simulations.
Surface Adsorption in Nonpolarizable Atomic Models.
Whitmer, Jonathan K; Joshi, Abhijeet A; Carlton, Rebecca J; Abbott, Nicholas L; de Pablo, Juan J
2014-12-09
Many ionic solutions exhibit species-dependent properties, including surface tension and the salting-out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to develop atomistic models capable of capturing Hofmeister effects rigorously. Importantly, we aim to capture this dependence in computationally cheap "hard" ionic models, which do not exhibit dynamic polarization. To do this, we have performed an investigation detailing the effects of the water model on these properties. Though incredibly important, the role of water models in simulation of ionic solutions and biological systems is essentially unexplored. We quantify this via the ion-dependent surface attraction of the halide series (Cl, Br, I) and, in so doing, determine the relative importance of various hypothesized contributions to ionic surface free energies. Importantly, we demonstrate surface adsorption can result in hard ionic models combined with a thermodynamically accurate representation of the water molecule (TIP4Q). The effect observed in simulations of iodide is commensurate with previous calculations of the surface potential of mean force in rigid molecular dynamics and polarizable density-functional models. Our calculations are direct simulation evidence of the subtle but sensitive role of water thermodynamics in atomistic simulations.
Hirshfeld atom refinement for modelling strong hydrogen bonds.
Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon
2014-09-01
High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.
Atomic Action Refinement in Model Based Testing
van der Bijl, H.M.; Rensink, Arend; Tretmans, G.J.
2007-01-01
In model based testing (MBT) test cases are derived from a specification of the system that we want to test. In general the specification is more abstract than the implementation. This may result in 1) test cases that are not executable, because their actions are too abstract (the implementation
Quan, Wei; Lv, Lin; Liu, Baiqi
2014-11-01
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
Energy Technology Data Exchange (ETDEWEB)
Quan, Wei; Lv, Lin, E-mail: lvlinlch1990@163.com; Liu, Baiqi [School of Instrument Science and Opto-Electronics Engineering, Beihang University, Beijing 100191 (China)
2014-11-15
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Learning atomic human actions using variable-length Markov models.
Liang, Yu-Ming; Shih, Sheng-Wen; Shih, Arthur Chun-Chieh; Liao, Hong-Yuan Mark; Lin, Cheng-Chung
2009-02-01
Visual analysis of human behavior has generated considerable interest in the field of computer vision because of its wide spectrum of potential applications. Human behavior can be segmented into atomic actions, each of which indicates a basic and complete movement. Learning and recognizing atomic human actions are essential to human behavior analysis. In this paper, we propose a framework for handling this task using variable-length Markov models (VLMMs). The framework is comprised of the following two modules: a posture labeling module and a VLMM atomic action learning and recognition module. First, a posture template selection algorithm, based on a modified shape context matching technique, is developed. The selected posture templates form a codebook that is used to convert input posture sequences into discrete symbol sequences for subsequent processing. Then, the VLMM technique is applied to learn the training symbol sequences of atomic actions. Finally, the constructed VLMMs are transformed into hidden Markov models (HMMs) for recognizing input atomic actions. This approach combines the advantages of the excellent learning function of a VLMM and the fault-tolerant recognition ability of an HMM. Experiments on realistic data demonstrate the efficacy of the proposed system.
Data for non equilibrium modeling with AtomDB
Foster, Adam R.; Smith, Randall K.; Brickhouse, Nancy S.
2017-03-01
AtomDB version 3.0 is available as a beta release. The main additions to this release are additions for analyzing non-equilibrium collisional plasmas, in particular ionizing plasmas. This includes revisions to the emission code APEC, and new data generation and collection. Here we briefly outline the new model, and describe in detail the new data formats.
Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.
Soteras, Ignacio; Curutchet, Carles; Bidon-Chanal, Axel; Dehez, François; Ángyán, János G; Orozco, Modesto; Chipot, Christophe; Luque, F Javier
2007-11-01
The main thrust of this investigation is the development of models of distributed atomic polarizabilities for the treatment of induction effects in molecular mechanics simulations. The models are obtained within the framework of the induced dipole theory by fitting the induction energies computed via a fast but accurate MP2/Sadlej-adjusted perturbational approach in a grid of points surrounding the molecule. Particular care is paid in the examination of the atomic quantities obtained from models of implicitly and explicitly interacting polarizabilities. Appropriateness and accuracy of the distributed models are assessed by comparing the molecular polarizabilities recovered from the models and those obtained experimentally and from MP2/Sadlej calculations. The behavior of the models is further explored by computing the polarization energy for aromatic compounds in the context of cation-π interactions and for selected neutral compounds in a TIP3P aqueous environment. The present results suggest that the computational strategy described here constitutes a very effective tool for the development of distributed models of atomic polarizabilities and can be used in the generation of new polarizable force fields.
Modeling Protein Structure at Near Atomic Resolutions With Gorgon
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
2011-01-01
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. PMID:21296162
Exactly solvable models for atom-molecule Hamiltonians.
Dukelsky, J; Dussel, G G; Esebbag, C; Pittel, S
2004-07-30
We present a family of exactly solvable generalizations of the Jaynes-Cummings model involving the interaction of an ensemble of SU(2) or SU(1,1) quasispins with a single boson field. They are obtained from the trigonometric Richardson-Gaudin models by replacing one of the SU(2) or SU(1,1) degrees of freedom by an ideal boson. The application to a system of bosonic atoms and molecules is reported.
Low Resolution Refinement of Atomic Models Against Crystallographic Data.
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, Pro
A constructive model potential method for atomic interactions
Bottcher, C.; Dalgarno, A.
1974-01-01
A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.
Modeling Non-Equilibrium Collisional Plasmas with AtomDB
Foster, Adam; Yamaguchi, H.; Smith, R. K.; Brickhouse, N. S.; Ji, L.; Kallman, T.; Wilms, J.
2013-04-01
Collisionally ionized plasmas that are in non-equilibrium ionization (NEI) show distinctly different emission from those in equilibrium. Recombining, or overionized, plasmas show significant recombination-driven continuum features, while ionizing plasmas show strong inner-shell emission lines, such as the Iron Kα line at 6.4-6.7keV. Existing models in analysis tools such as XSPEC treat only the equilibrium case and part of the ionizing plasma case due to a significant lack of atomic data. We present major updates to the AtomDB database, and new models for use XSPEC, which allow all types of these non-equilibrium plasmas to be modeled in a simple yet accurate fashion. This model has been created using a large amount of data obtained from published sources, supplemented by data we have calculated using the Flexible Atomic Code where required. We identify the spectral features that have been seen and can now be modeled using this data for existing missions as well as Astro-H. We also revisit archival data where recombining plasma emission has previously been identified.
Liguori, Lucia
2014-01-01
Atomic orbital theory is a difficult subject for many high school and beginning undergraduate students, as it includes mathematical concepts not yet covered in the school curriculum. Moreover, it requires certain ability for abstraction and imagination. A new atomic orbital model "the chocolate shop" created "by" students…
Empirical model of atomic nitrogen in the upper thermosphere
Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.
1977-01-01
Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.
Extended Hubbard models for ultracold atoms in optical lattices
Energy Technology Data Exchange (ETDEWEB)
Juergensen, Ole
2015-06-05
In this thesis, the phase diagrams and dynamics of various extended Hubbard models for ultracold atoms in optical lattices are studied. Hubbard models are the primary description for many interacting particles in periodic potentials with the paramount example of the electrons in solids. The very same models describe the behavior of ultracold quantum gases trapped in the periodic potentials generated by interfering beams of laser light. These optical lattices provide an unprecedented access to the fundamentals of the many-particle physics that govern the properties of solid-state materials. They can be used to simulate solid-state systems and validate the approximations and simplifications made in theoretical models. This thesis revisits the numerous approximations underlying the standard Hubbard models with special regard to optical lattice experiments. The incorporation of the interaction between particles on adjacent lattice sites leads to extended Hubbard models. Offsite interactions have a strong influence on the phase boundaries and can give rise to novel correlated quantum phases. The extended models are studied with the numerical methods of exact diagonalization and time evolution, a cluster Gutzwiller approximation, as well as with the strong-coupling expansion approach. In total, this thesis demonstrates the high relevance of beyond-Hubbard processes for ultracold atoms in optical lattices. Extended Hubbard models can be employed to tackle unexplained problems of solid-state physics as well as enter previously inaccessible regimes.
A Comprehensive X-Ray Absorption Model for Atomic Oxygen
Gorczyca, T. W.; Bautista, M. A.; Hasoglu, M. F.; Garcia, J.; Gatuzz, E.; Kaastra, J. S.; Kallman, T. R.; Manson, S. T.; Mendoza, C.; Raassen, A. J. J.;
2013-01-01
An analytical formula is developed to accurately represent the photoabsorption cross section of atomic Oxygen for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects, that accurately predict the absorption oscillator strengths below threshold and merge consistently and continuously to the above-threshold cross section. Further, minor adjustments are made to the threshold energies in order to reliably align the atomic Rydberg resonances after consideration of both experimental and observed line positions. At energies far below or above the K-edge region, the formulation is based on both outer- and inner-shell direct photoionization, including significant shake-up and shake-off processes that result in photoionization-excitation and double-photoionization contributions to the total cross section. The ultimate purpose for developing a definitive model for oxygen absorption is to resolve standing discrepancies between the astronomically observed and laboratory-measured line positions, and between the inferred atomic and molecular oxygen abundances in the interstellar medium from XSTAR and SPEX spectral models.
Four-component united-atom model of bitumen
DEFF Research Database (Denmark)
Hansen, Jesper Schmidt; Lemarchand, Claire; Nielsen, Erik
2013-01-01
We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based...... software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation...... the stress autocorrelation function, the shear viscosity and shear modulus are evaluated, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin...
Atomic Modeling in the Early 20th Century: 1904 - 1913
Baily, Charles
2011-01-01
The scope of this paper is to discuss the major works that appeared in the period of 1904 to 1913: atomic models proposed by Thomson and Hantaro Nagaoka (1904), Rutherford (1911), and Bohr (1913), and the experimental work that motivated them. It will be seen that, although all of the models discussed here were later shown to be incorrect or incomplete, each one represented an essential step towards an understanding of the nature of matter, a view of the physical world often taken for granted...
First-Order Quantum Phase Transition for Dicke Model Induced by Atom-Atom Interaction
Zhao, Xiu-Qin; Liu, Ni; Liang, Jiu-Qing
2017-05-01
In this article, we use the spin coherent state transformation and the ground state variational method to theoretically calculate the ground function. In order to consider the influence of the atom-atom interaction on the extended Dicke model’s ground state properties, the mean photon number, the scaled atomic population and the average ground energy are displayed. Using the self-consistent field theory to solve the atom-atom interaction, we discover the system undergoes a first-order quantum phase transition from the normal phase to the superradiant phase, but a famous Dicke-type second-order quantum phase transition without the atom-atom interaction. Meanwhile, the atom-atom interaction makes the phase transition point shift to the lower atom-photon collective coupling strength. Supported by the National Natural Science Foundation of China under Grant Nos. 11275118, 11404198, 91430109, 61505100, 51502189, and the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi Province (STIP) under Grant No. 2014102, and the Launch of the Scientific Research of Shanxi University under Grant No. 011151801004, and the National Fundamental Fund of Personnel Training under Grant No. J1103210. The Natural Science Foundation of Shanxi Province under Grant No. 2015011008
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.
Quantum Rabi model in the Brillouin zone with ultracold atoms
Felicetti, Simone; Rico, Enrique; Sabin, Carlos; Ockenfels, Till; Koch, Johannes; Leder, Martin; Grossert, Christopher; Weitz, Martin; Solano, Enrique
2017-01-01
The quantum Rabi model describes the interaction between a two-level quantum system and a single bosonic mode. We propose a method to perform a quantum simulation of the quantum Rabi model, introducing an implementation of the two-level system provided by the occupation of Bloch bands in the first Brillouin zone by ultracold atoms in tailored optical lattices. The effective qubit interacts with a quantum harmonic oscillator implemented in an optical dipole trap. Our realistic proposal allows one to experimentally investigate the quantum Rabi model for extreme parameter regimes, which are not achievable with natural light-matter interactions. When the simulated wave function exceeds the validity region of the simulation, we identify a generalized version of the quantum Rabi model in a periodic phase space.
Bounds on collapse models from cold-atom experiments
Bilardello, Marco; Donadi, Sandro; Vinante, Andrea; Bassi, Angelo
2016-11-01
The spontaneous localization mechanism of collapse models induces a Brownian motion in all physical systems. This effect is very weak, but experimental progress in creating ultracold atomic systems can be used to detect it. In this paper, we considered a recent experiment (Kovachy et al., 2015), where an atomic ensemble was cooled down to picokelvins. Any Brownian motion induces an extra increase of the position variance of the gas. We study this effect by solving the dynamical equations for the Continuous Spontaneous Localizations (CSL) model, as well as for its non-Markovian and dissipative extensions. The resulting bounds, with a 95 % of confidence level, are beaten only by measurements of spontaneous X-ray emission and by experiments with cantilever (in the latter case, only for rC ≥ 10-7 m, where rC is one of the two collapse parameters of the CSL model). We show that, contrary to the bounds given by X-ray measurements, non-Markovian effects do not change the bounds, for any reasonable choice of a frequency cutoff in the spectrum of the collapse noise. Therefore the bounds here considered are more robust. We also show that dissipative effects are unimportant for a large spectrum of temperatures of the noise, while for low temperatures the excluded region in the parameter space is the more reduced, the lower the temperature.
Reduction of collisional-radiative models for transient, atomic plasmas
Abrantes, Richard June; Karagozian, Ann; Bilyeu, David; Le, Hai
2017-10-01
Interactions between plasmas and any radiation field, whether by lasers or plasma emissions, introduce many computational challenges. One of these computational challenges involves resolving the atomic physics, which can influence other physical phenomena in the radiated system. In this work, a collisional-radiative (CR) model with reduction capabilities is developed to capture the atomic physics at a reduced computational cost. Although the model is made with any element in mind, the model is currently supplemented by LANL's argon database, which includes the relevant collisional and radiative processes for all of the ionic stages. Using the detailed data set as the true solution, reduction mechanisms in the form of Boltzmann grouping, uniform grouping, and quasi-steady-state (QSS), are implemented to compare against the true solution. Effects on the transient plasma stemming from the grouping methods are compared. Distribution A: Approved for public release; unlimited distribution, PA (Public Affairs) Clearance Number 17449. This work was supported by the Air Force Office of Scientific Research (AFOSR), Grant Number 17RQCOR463 (Dr. Jason Marshall).
Fully variational average atom model with ion-ion correlations.
Starrett, C E; Saumon, D
2012-02-01
An average atom model for dense ionized fluids that includes ion correlations is presented. The model assumes spherical symmetry and is based on density functional theory, the integral equations for uniform fluids, and a variational principle applied to the grand potential. Starting from density functional theory for a mixture of classical ions and quantum mechanical electrons, an approximate grand potential is developed, with an external field being created by a central nucleus fixed at the origin. Minimization of this grand potential with respect to electron and ion densities is carried out, resulting in equations for effective interaction potentials. A third condition resulting from minimizing the grand potential with respect to the average ion charge determines the noninteracting electron chemical potential. This system is coupled to a system of point ions and electrons with an ion fixed at the origin, and a closed set of equations is obtained. Solution of these equations results in a self-consistent electronic and ionic structure for the plasma as well as the average ionization, which is continuous as a function of temperature and density. Other average atom models are recovered by application of simplifying assumptions.
Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K
2013-04-01
When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.
Atomic structure of graphene supported heterogeneous model catalysts
Energy Technology Data Exchange (ETDEWEB)
Franz, Dirk
2017-04-15
Graphene on Ir(111) forms a moire structure with well defined nucleation centres. Therefore it can be utilized to create hexagonal metal cluster lattices with outstanding structural quality. At diffraction experiments these 2D surface lattices cause a coherent superposition of the moire cell structure factor, so that the measured signal intensity scales with the square of coherently scattering unit cells. This artificial signal enhancement enables the opportunity for X-ray diffraction to determine the atomic structure of small nano-objects, which are hardly accessible with any experimental technique. The uniform environment of every metal cluster makes the described metal cluster lattices on graphene/Ir(111) an attractive model system for the investigation of catalytic, magnetic and quantum size properties of ultra-small nano-objects. In this context the use of x-rays provides a maximum of flexibility concerning the possible sample environments (vacuum, selected gases, liquids, sample temperature) and allows in-situ/operando measurements. In the framework of the present thesis the structure of different metal clusters grown by physical vapor deposition in an UHV environment and after gas exposure have been investigated. On the one hand the obtained results will explore many aspects of the atomic structure of these small metal clusters and on the other hand the presented results will proof the capabilities of the described technique (SXRD on cluster lattices). For iridium, platinum, iridium/palladium and platinum/rhodium the growth on graphene/Ir(111) of epitaxial, crystalline clusters with an ordered hexagonal lattice arrangement has been confirmed using SXRD. The clusters nucleate at the hcp sites of the moire cell and bind via rehybridization of the carbon atoms (sp{sup 2} → sp{sup 3}) to the Ir(111) substrate. This causes small displacements of the substrate atoms, which is revealed by the diffraction experiments. All metal clusters exhibit a fcc structure
Pengembangan Alat Peraga Taktual Model Atom untuk Siswa Tunanetra Kelas VIII
Directory of Open Access Journals (Sweden)
Wahyu Triningsih
2014-12-01
This research produced an atomic model tactual props and material guidance for blind student on eight grade. Based on the appraisal of media expert, material expert, teacher, atomic and students this prop has a very good quality.
Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity
DEFF Research Database (Denmark)
Gammelmark, S.; Molmer, K.; Alt, W.
2014-01-01
We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic state...... manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory...
Niels Bohr and the quantum atom the Bohr model of atomic structure 1913-1925
Kragh, Helge
2012-01-01
Niels Bohr and the Quantum Atom is the first book that focuses in detail on the birth and development of Bohr's atomic theory and gives a comprehensive picture of it. At the same time it offers new insight into Bohr's peculiar way of thinking, what Einstein once called his 'unique instinct and tact'. Contrary to most other accounts of the Bohr atom, the book presents it in a broader perspective which includes the reception among other scientists and the criticism launched against it by scientists of a more conservative inclination. Moreover, it discusses the theory as Bohr originally conceived it, namely, as an ambitious theory covering the structure of atoms as well as molecules. By discussing the theory in its entirety it becomes possible to understand why it developed as it did and thereby to use it as an example of the dynamics of scientific theories.
Model of spacecraft atomic oxygen and solar exposure microenvironments
Bourassa, R. J.; Pippin, H. G.
1993-01-01
Computer models of environmental conditions in Earth orbit are needed for the following reasons: (1) derivation of material performance parameters from orbital test data, (2) evaluation of spacecraft hardware designs, (3) prediction of material service life, and (4) scheduling spacecraft maintenance. To meet these needs, Boeing has developed programs for modeling atomic oxygen (AO) and solar radiation exposures. The model allows determination of AO and solar ultraviolet (UV) radiation exposures for spacecraft surfaces (1) in arbitrary orientations with respect to the direction of spacecraft motion, (2) overall ranges of solar conditions, and (3) for any mission duration. The models have been successfully applied to prediction of experiment environments on the Long Duration Exposure Facility (LDEF) and for analysis of selected hardware designs for deployment on other spacecraft. The work on these models has been reported at previous LDEF conferences. Since publication of these reports, a revision has been made to the AO calculation for LDEF, and further work has been done on the microenvironments model for solar exposure.
Improving ranking of models for protein complexes with side chain modeling and atomic potentials.
Viswanath, Shruthi; Ravikant, D V S; Elber, Ron
2013-04-01
An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re-ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re-ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. Copyright © 2012 Wiley Periodicals, Inc.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Directory of Open Access Journals (Sweden)
Peter C Lai
2012-05-01
Full Text Available Olfactory receptors (ORs are a type of GTP-binding protein-coupled receptor (GPCR. These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can validate experimental functional studies as well as generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level. Here we have shown the specific advantages of simulating the dynamic environment that is associated with OR-odorant interactions. We present a rigorous methodology that ranges from the creation of a computationally-derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.
Independent-particle models for light negative atomic ions
Ganas, P. S.; Talman, J. D.; Green, A. E. S.
1980-01-01
For the purposes of astrophysical, aeronomical, and laboratory application, a precise independent-particle model for electrons in negative atomic ions of the second and third period is discussed. The optimum-potential model (OPM) of Talman et al. (1979) is first used to generate numerical potentials for eight of these ions. Results for total energies and electron affinities are found to be very close to Hartree-Fock solutions. However, the OPM and HF electron affinities both depart significantly from experimental affinities. For this reason, two analytic potentials are developed whose inner energy levels are very close to the OPM and HF levels but whose last electron eigenvalues are adjusted precisely with the magnitudes of experimental affinities. These models are: (1) a four-parameter analytic characterization of the OPM potential and (2) a two-parameter potential model of the Green, Sellin, Zachor type. The system O(-) or e-O, which is important in upper atmospheric physics is examined in some detail.
Energy Technology Data Exchange (ETDEWEB)
Khater, Antoine; Szczesniak, Dominik [Laboratoire de Physique de l' Etat Condense UMR 6087, Universite du Maine, 72085 Le Mans (France)
2011-04-01
An analytical model is presented for the electronic conductance in a one dimensional atomic chain across an isolated defect. The model system consists of two semi infinite lead atomic chains with the defect atom making the junction between the two leads. The calculation is based on a linear combination of atomic orbitals in the tight-binding approximation, with a single atomic one s-like orbital chosen in the present case. The matching method is used to derive analytical expressions for the scattering cross sections for the reflection and transmission processes across the defect, in the Landauer-Buttiker representation. These analytical results verify the known limits for an infinite atomic chain with no defects. The model can be applied numerically for one dimensional atomic systems supported by appropriate templates. It is also of interest since it would help establish efficient procedures for ensemble averages over a field of impurity configurations in real physical systems.
Löbling, L.
2017-03-01
Aluminum (Al) nucleosynthesis takes place during the asymptotic-giant-branch (AGB) phase of stellar evolution. Al abundance determinations in hot white dwarf stars provide constraints to understand this process. Precise abundance measurements require advanced non-local thermodynamic stellar-atmosphere models and reliable atomic data. In the framework of the German Astrophysical Virtual Observatory (GAVO), the Tübingen Model-Atom Database (TMAD) contains ready-to- use model atoms for elements from hydrogen to barium. A revised, elaborated Al model atom has recently been added. We present preliminary stellar-atmosphere models and emergent Al line spectra for the hot white dwarfs G191-B2B and RE 0503-289.
One-dimensional extended Hubbard model in the atomic limit.
Mancini, F; Mancini, F P
2008-06-01
We present the exact solution of the one-dimensional extended Hubbard model in the atomic limit within the Green's function and equations of motion formalism. We provide a comprehensive and systematic analysis of the model by considering all the relevant response and correlation functions as well as thermodynamic quantities in the whole parameters space. At zero temperature we identify four phases in the plane (U,n) ( U is the on-site potential and n is the filling) and relative phase transitions as well as different types of charge ordering. These features are endorsed by investigating at T=0 the chemical potential and pertinent local correlators, the particle and double occupancy correlation functions, the entropy, and by studying the behavior in the limit T-->0 of the charge and spin susceptibilities. A detailed study of the thermodynamic quantities is also presented at finite temperature. This study evidences that a finite-range order persists for a wide range of the temperature, as shown by the behavior of the correlation functions and by the two-peak structure exhibited by the charge susceptibility and by the entropy. Moreover, the equations of motion formalism, together with the use of composite operators, allows us to exactly determine the set of elementary excitations. As a result, the density of states can be determined and a detailed analysis of the specific heat allows for identifying the excitations and for ascribing its two-peak structure to a redistribution of the charge density.
Global atmospheric model for mercury including oxidation by bromine atoms
Directory of Open Access Journals (Sweden)
C. D. Holmes
2010-12-01
Full Text Available Global models of atmospheric mercury generally assume that gas-phase OH and ozone are the main oxidants converting Hg^{0} to Hg^{II} and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg^{0} oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming gas-phase Br to be the sole Hg^{0} oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O_{3} model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O_{3} models, we add an aqueous photochemical reduction of Hg^{II} in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O_{3} models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of Hg^{II} deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux to the Arctic of 60 Mg a^{−1}. Summertime events of depleted Hg^{0} at Antarctic sites due to subsidence are much better simulated by
Development of a phenomenological model for coal slurry atomization
Energy Technology Data Exchange (ETDEWEB)
Dooher, J.P. [Adelphi Univ., Garden City, NY (United States)
1995-11-01
Highly concentrated suspensions of coal particles in water or alternate fluids appear to have a wide range of applications for energy production. For enhanced implementation of coal slurry fuel technology, an understanding of coal slurry atomization as a function coal and slurry properties for specific mechanical configurations of nozzle atomizers should be developed.
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.
1993-01-01
The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.
Kinetic model of the bichromatic dark trap for atoms
Krasnov, I. V.
2017-08-01
A kinetic model of atom confinement in a bichromatic dark trap (BDT) is developed with the goal of describing its dissipative properties. The operating principle of the deep BDT is based on using the combination of multiple bichromatic cosine-Gaussian optical beams (CGBs) for creating high-potential barriers, which is described in our previous work (Krasnov 2016 Laser Phys. 26 105501). In the indicated work, particle motion in the BDT is described in terms of classical trajectories. In the present study, particle motion is analyzed by means of the Wigner function (phase-space distribution function (DF)), which allows one to properly take into account the quantum fluctuations of optical forces. Besides, we consider an improved scheme of the BDT, where CGBs create, apart from plane potential barriers, a narrow cooling layer. We find an asymptotic solution of the Fokker-Planck equation for the DF and show that the DF of particles deeply trapped in a BDT with a cooling layer is the Tsallis distribution with the effective temperature, which can be considerably lower than in a BDT without a cooling layer. Moreover, it can be adjusted by slightly changing the CGBs’ radii. We also study the effect of particle escape from the trap due to the scattering of resonant photons and show that the particle lifetime in a BDT can exceed several tens of hours when it is limited by photon scattering.
Classical-field model of the hydrogen atom
Rashkovskiy, Sergey A.
2017-06-01
It is shown that all of the basic properties of the hydrogen atom can be consistently described in terms of classical electrodynamics if instead of considering the electron to be a particle, we consider an electrically charged classical wave field—an "electron wave"—which is held by the electrostatic field of the proton. It is shown that quantum mechanics must be considered not as a theory of particles but as a classical field theory in the spirit of classical electrodynamics. In this case, we are not faced with difficulties in interpreting the results of the theory. In the framework of classical electrodynamics, all of the well-known regularities of the spontaneous emission of the hydrogen atom are obtained, which is usually derived in the framework of quantum electrodynamics. It is shown that there are no discrete states and discrete energy levels of the atom: the energy of the atom and its states change continuously. An explanation of the conventional corpuscular-statistical interpretation of atomic phenomena is given. It is shown that this explanation is only a misinterpretation of continuous deterministic processes. In the framework of classical electrodynamics, the nonlinear Schrödinger equation is obtained, which accounts for the inverse action of self-electromagnetic radiation of the electron wave and completely describes the spontaneous emissions of an atom.
Modeling and understanding of effects of randomness in arrays of resonant meta-atoms
DEFF Research Database (Denmark)
Tretyakov, Sergei A.; Albooyeh, Mohammad; Alitalo, Pekka
2013-01-01
In this review presentation we will discuss approaches to modeling and understanding electromagnetic properties of 2D and 3D lattices of small resonant particles (meta-atoms) in transition from regular (periodic) to random (amorphous) states. Nanostructured metasurfaces (2D) and metamaterials (3D......) are arrangements of optically small but resonant particles (meta-atoms). We will present our results on analytical modeling of metasurfaces with periodical and random arrangements of electrically and magnetically resonant meta-atoms with identical or random sizes, both for the normal and oblique-angle excitations......) of the arrangements of meta-atoms....
Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I.
Bautista, M. A.; Fivet, V.; Quinet, P.; Dunn, J.; Gull, T. R.; Kallman, T. R.; Mendoza, C.
2013-01-01
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data.We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of Oiii and Fe ii and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe ii]. Key words: atomic data - atomic processes - line: formation - methods: data analysis - molecular data - molecular processes - techniques: spectroscopic
Crystal structures and atomic model of NADPH oxidase
Magnani, Francesca; Nenci, Simone; Fananas, Elisa Millana; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W.; Mattevi, Andrea
2017-01-01
NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic
Atomic force microscopy on domains in biological model membranes
Rinia, H.A.
2001-01-01
This thesis describes the preparation and imaging of supported lipid bilayers, which can be regarded as biological modelmembranes, in the light of the formation of domains. The bilayers were prepared with either the Langmuir-Blodgett method, or with vesicle fusion. They were imaged with Atomic Force
Baron, R; de Vries, AH; Hunenberger, PH; van Gunsteren, WF
2006-01-01
Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model
Analytical model for relativistic corrections to the nuclear magnetic shielding constant in atoms
Energy Technology Data Exchange (ETDEWEB)
Romero, Rodolfo H. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)]. E-mail: rhromero@exa.unne.edu.ar; Gomez, Sergio S. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)
2006-04-24
We present a simple analytical model for calculating and rationalizing the main relativistic corrections to the nuclear magnetic shielding constant in atoms. It provides good estimates for those corrections and their trends, in reasonable agreement with accurate four-component calculations and perturbation methods. The origin of the effects in deep core atomic orbitals is manifestly shown.
Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness
Park, Eun Jung; Light, Gregory
2009-01-01
Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…
Seldam, C.A. ten; Groot, S.R. de
1952-01-01
From Jensen's and Gombás' modification of the statistical Thomas-Fermi atom model, a theory for compressed atoms is developed by changing the boundary conditions. Internal kinetic energy and polarizability of argon are calculated as functions of pressure. At 1000 atm. an internal kinetic energy of
Mg I as a probe of the solar chromosphere - The atomic model
Mauas, Pablo J.; Avrett, Eugene H.; Loeser, Rudolf
1988-01-01
This paper presents a complete atomic model for Mg I line synthesis, where all the atomic parameters are based on recent experimental and theoretical data. It is shown how the computed profiles at 4571 A and 5173 A are influenced by the choice of these parameters and the number of levels included in the model atom. In addition, observed profiles of the 5173 A b2 line and theoretical profiles for comparison (based on a recent atmospheric model for the average quiet sun) are presented.
Atomic forces for geometry-dependent point multipole and gaussian multipole models.
Elking, Dennis M; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G
2010-11-30
In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In this study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives partial derivative D(m'm)(l)/partial derivative Omega. The force equations can be applied to electrostatic models based on atomic point multipoles or gaussian multipole charge density. Hydrogen-bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. 2010 Wiley Periodicals, Inc.
Quantum Spin-Ice and Dimer Models with Rydberg Atoms
Directory of Open Access Journals (Sweden)
A. W. Glaetzle
2014-11-01
Full Text Available Quantum spin-ice represents a paradigmatic example of how the physics of frustrated magnets is related to gauge theories. In the present work, we address the problem of approximately realizing quantum spin ice in two dimensions with cold atoms in optical lattices. The relevant interactions are obtained by weakly laser-admixing Rydberg states to the atomic ground-states, exploiting the strong angular dependence of van der Waals interactions between Rydberg p states together with the possibility of designing steplike potentials. This allows us to implement Abelian gauge theories in a series of geometries, which could be demonstrated within state-of-the-art atomic Rydberg experiments. We numerically analyze the family of resulting microscopic Hamiltonians and find that they exhibit both classical and quantum order by disorder, the latter yielding a quantum plaquette valence bond solid. We also present strategies to implement Abelian gauge theories using both s- and p-Rydberg states in exotic geometries, e.g., on a 4–8 lattice.
Quantum Spin-Ice and Dimer Models with Rydberg Atoms
Glaetzle, A. W.; Dalmonte, M.; Nath, R.; Rousochatzakis, I.; Moessner, R.; Zoller, P.
2014-10-01
Quantum spin-ice represents a paradigmatic example of how the physics of frustrated magnets is related to gauge theories. In the present work, we address the problem of approximately realizing quantum spin ice in two dimensions with cold atoms in optical lattices. The relevant interactions are obtained by weakly laser-admixing Rydberg states to the atomic ground-states, exploiting the strong angular dependence of van der Waals interactions between Rydberg p states together with the possibility of designing steplike potentials. This allows us to implement Abelian gauge theories in a series of geometries, which could be demonstrated within state-of-the-art atomic Rydberg experiments. We numerically analyze the family of resulting microscopic Hamiltonians and find that they exhibit both classical and quantum order by disorder, the latter yielding a quantum plaquette valence bond solid. We also present strategies to implement Abelian gauge theories using both s - and p -Rydberg states in exotic geometries, e.g., on a 4-8 lattice.
An Analytical Model for Adsorption and Diffusion of Atoms/Ions on Graphene Surface
Directory of Open Access Journals (Sweden)
Yan-Zi Yu
2015-01-01
Full Text Available Theoretical investigations are made on adsorption and diffusion of atoms/ions on graphene surface based on an analytical continuous model. An atom/ion interacts with every carbon atom of graphene through a pairwise potential which can be approximated by the Lennard-Jones (L-J potential. Using the Fourier expansion of the interaction potential, the total interaction energy between the adsorption atom/ion and a monolayer graphene is derived. The energy-distance relationships in the normal and lateral directions for varied atoms/ions, including gold atom (Au, platinum atom (Pt, manganese ion (Mn2+, sodium ion (Na1+, and lithium-ion (Li1+, on monolayer graphene surface are analyzed. The equilibrium position and binding energy of the atoms/ions at three particular adsorption sites (hollow, bridge, and top are calculated, and the adsorption stability is discussed. The results show that H-site is the most stable adsorption site, which is in agreement with the results of other literatures. What is more, the periodic interaction energy and interaction forces of lithium-ion diffusing along specific paths on graphene surface are also obtained and analyzed. The minimum energy barrier for diffusion is calculated. The possible applications of present study include drug delivery system (DDS, atomic scale friction, rechargeable lithium-ion graphene battery, and energy storage in carbon materials.
Early twentieth century atomic models: from classical physics to the introduction of quantum theory
Lopes, Cesar Valmor Machado; PUC/SP
2010-01-01
The present research examines the history of atomic models in the early twentieth century approaching the contributions of Joseph John Thomson, Hantaro Nagaoka, Ernest Rutherford, John William Nicholson and Niels Bohr and his contemporaries.
Modeling hydrogen storage in boron-substituted graphene decorated with potassium metal atoms
CSIR Research Space (South Africa)
Tokarev, A
2015-03-01
Full Text Available Boron-substituted graphene decorated with potassium metal atoms was considered as a novel material for hydrogen storage. Density functional theory calculations were used to model key properties of the material, such as geometry, hydrogen packing...
Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling
Energy Technology Data Exchange (ETDEWEB)
Tawara, H. [ed.
1997-01-01
This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)
Fano-Hopfield model and photonic band gaps for an arbitrary atomic lattice
Antezza, Mauro; Castin, Yvan
2009-01-01
15 pages; 6 figures; International audience; We study the light dispersion relation in a periodic ensemble of atoms at fixed positions in the Fano-Hopfield model (the atomic dipole being modeled with harmonic oscillators). Compared to earlier works, we do not restrict to cubic lattices, and we do not regularize the theory by hand but we renormalize it in a systematic way using a Gaussian cut-off in momentum space. Whereas no omnidirectional spectral gap is known for light in a Bravais atomic ...
Jung, Hyunseung; In, Chihun; Choi, Hyunyong; Lee, Hojin
2014-06-09
Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems.
Urzhumtsev, Alexandre; Afonine, Pavel V; Van Benschoten, Andrew H; Fraser, James S; Adams, Paul D
2016-09-01
Researcher feedback has indicated that in Urzhumtsev et al. [(2015) Acta Cryst. D71, 1668-1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. These issues are addressed in this article.
Classical trajectory perspective of atomic ionization in strong laser fields semiclassical modeling
Liu, Jie
2014-01-01
The ionization of atoms and molecules in strong laser fields is an active field in modern physics and has versatile applications in such as attosecond physics, X-ray generation, inertial confined fusion (ICF), medical science and so on. Classical Trajectory Perspective of Atomic Ionization in Strong Laser Fields covers the basic concepts in this field and discusses many interesting topics using the semiclassical model of classical trajectory ensemble simulation, which is one of the most successful ionization models and has the advantages of a clear picture, feasible computing and accounting for many exquisite experiments quantitatively. The book also presents many applications of the model in such topics as the single ionization, double ionization, neutral atom acceleration and other timely issues in strong field physics, and delivers useful messages to readers with presenting the classical trajectory perspective on the strong field atomic ionization. The book is intended for graduate students and researchers...
Using a matter wave model to study the structure of the electron inside an atom
Chang, Donald
In Bohr's atomic model, the atom was conceptually modeled as a miniature solar system. With the development of the Schrödinger equation, the wave function of the electron inside an atom becomes much better known. But the electron is still regarded as a pointed object; according to the Copenhagen Interpretation, the wave function is thought to describe only the probability of finding the electron. Such an interpretation, however, has raised some conceptual questions. For example, how can a point-like electron form a chemical bond between neighboring atoms? In an attempt to overcome this difficulty, we use a matter wave theory to model the structure of an electron inside the atom. This model is inspired by noticing the similarity between a free electron and a photon; both particles behave like a corpuscular object as well as a physical wave. Thus, we hypothesize that, like the photon, an electron is an excitation wave of a real physical field. Based on this hypothesis, we have derived a basic wave equation for the free electron. We show that, in the presence of an electrical potential, this basic wave equation can lead to the Schrödinger equation. This work implies that the solution of the Schrödinger equation actually represents the physical waves of the electron. Thus, the electron inside the atom should behave more like a topologically distributive wave than a pointed object. In this presentation, we will discuss the advantages and limitations of this model.
YUP.SCX: coaxing atomic models into medium resolution electron density maps.
Tan, Robert K-Z; Devkota, Batsal; Harvey, Stephen C
2008-08-01
The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33A, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.
DFT Modeling of Cross-Linked Polyethylene: Role of Gold Atoms and Dispersion Interactions.
Blaško, Martin; Mach, Pavel; Antušek, Andrej; Urban, Miroslav
2018-02-08
Using DFT modeling, we analyze the concerted action of gold atoms and dispersion interactions in cross-linked polyethylene. Our model consists of two oligomer chains (PEn) with 7, 11, 15, 19, or 23 carbon atoms in each oligomer cross-linked with one to three Au atoms through C-Au-C bonds. In structures with a single gold atom the C-Au-C bond is located in the central position of the oligomer. Binding energies (BEs) with respect to two oligomer radical fragments and Au are as high as 362-489 kJ/mol depending on the length of the oligomer chain. When the dispersion contribution in PEn-Au-PEn oligomers is omitted, BE is almost independent of the number of carbon atoms, lying between 293 and 296 kJ/mol. The dispersion energy contributions to BEs in PEn-Au-PEn rise nearly linearly with the number of carbon atoms in the PEn chain. The carbon-carbon distance in the C-Au-C moiety is around 4.1 Å, similar to the bond distance between saturated closed shell chains in the polyethylene crystal. BEs of pure saturated closed shell PEn-PEn oligomers are 51-187 kJ/mol. Both Au atoms and dispersion interactions contribute considerably to the creation of nearly parallel chains of oligomers with reasonably high binding energies.
Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.
Orben, Claudia M; Dittrich, Birger
2014-06-01
For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å(-1). The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å(-1), but requires good low-order data.
Engineering the Dynamics of Effective Spin-Chain Models for Strongly Interacting Atomic Gases
DEFF Research Database (Denmark)
Volosniev, A. G.; Petrosyan, D.; Valiente, M.
2015-01-01
We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We...... find that bosonic atoms offer more flexibility for tuning independently the parameters of the spin Hamiltonian through interatomic (intra-species) interaction which is absent for fermions due to the Pauli exclusion principle. Our formalism can have important implications for control and manipulation...
Studying the Consistency between and within the Student Mental Models for Atomic Structure
Zarkadis, Nikolaos; Papageorgiou, George; Stamovlasis, Dimitrios
2017-01-01
Science education research has revealed a number of student mental models for atomic structure, among which, the one based on Bohr's model seems to be the most dominant. The aim of the current study is to investigate the coherence of these models when students apply them for the explanation of a variety of situations. For this purpose, a set of…
UNCERTAINTIES IN ATOMIC DATA AND THEIR PROPAGATION THROUGH SPECTRAL MODELS. I
Energy Technology Data Exchange (ETDEWEB)
Bautista, M. A.; Fivet, V. [Department of Physics, Western Michigan University, Kalamazoo, MI 49008 (United States); Quinet, P. [Astrophysique et Spectroscopie, Universite de Mons-UMONS, B-7000 Mons (Belgium); Dunn, J. [Physical Science Department, Georgia Perimeter College, Dunwoody, GA 30338 (United States); Gull, T. R. [Code 667, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Kallman, T. R. [Code 662, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Mendoza, C., E-mail: manuel.bautista@wmich.edu [Centro de Fisica, Instituto Venezolano de Investigaciones Cientificas (IVIC), P.O. Box 20632, Caracas 1020A (Venezuela, Bolivarian Republic of)
2013-06-10
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data. We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of O III and Fe II and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe II].
Atomic scale simulations for improved CRUD and fuel performance modeling
Energy Technology Data Exchange (ETDEWEB)
Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cooper, Michael William Donald [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2017-01-06
A more mechanistic description of fuel performance codes can be achieved by deriving models and parameters from atomistic scale simulations rather than fitting models empirically to experimental data. The same argument applies to modeling deposition of corrosion products on fuel rods (CRUD). Here are some results from publications in 2016 carried out using the CASL allocation at LANL.
Model Development for Atomic Force Microscope Stage Mechanisms
National Research Council Canada - National Science Library
Smith, Ralph C; Hatch, Andrew G; De, Tathagata; Salapaka, Murti V; Raye, Julie K; del Rosario, Ricardo C
2005-01-01
In this paper, we develop nonlinear constitutive equations and resulting system models quantifying the nonlinear and hysteretic field-displacement relations inherent to lead zirconate titanate (PZT...
JANNUS: experimental validation at the scale of atomic modelling
Serruys, Yves; Ruault, Marie-Odile; Trocellier, Patrick; Miro, Sandrine; Barbu, Alain; Boulanger, Loïc; Kaïtasov, Odile; Henry, Sylvain; Leseigneur, Olivier; Trouslard, Philippe; Pellegrino, Stéphanie; Vaubaillon, Sylvain
2008-04-01
Ion irradiation is well suited to simulate neutron irradiation because primary knock-on atoms (PKA) produced by neutron collisions are self ions of the target. As the main difference, the energy spectrum of ion-produced PKAs is somewhat broader than in the case of fast neutrons. Studies of the combined effects of target damaging, ion implantation effects, helium and hydrogen production, and the occurrence of nuclear reactions should be performed by co-irradiation experiments (dual or triple beam irradiation). The JANNUS project (Joint Accelerators for Nanosciences and NUclear Simulation) was started in 2002 in the frame of a collaboration between CEA (Commissariat à l'Énergie Atomique) and CNRS-IN2P3 (Centre National de la Recherche Scientifique-Institut National de Physique Nucléaire et de Physique des Particules). Two experimental sites are involved. At Saclay, three electrostatic accelerators are being coupled: a new 3 MV Pelletron™ machine equipped with an ECR multi-charged ion source, a 2.5 MV single ended Van de Graaff and a 2.25 MV General Ionex tandem. At Orsay, the 2 MV tandem ARAMIS and the 190 kV ion implanter IRMA are being coupled with a 200 kV TECNAI™ transmission electron microscope to allow simultaneous co-irradiation and observation. This paper will first discuss both advantages and limitations of the use of ion beam irradiation to simulate neutron irradiation. A technical description of both set-ups is then presented, and some details will be given concerning multi-irradiation facilities running worldwide. The main application fields of JANNUS will be further detailed. To cite this article: Y. Serruys et al., C. R. Physique 9 (2008).
A theoretical-electron-density databank using a model of real and virtual spherical atoms.
Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian
2017-08-01
A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.
Mapping the Two-Component Atomic Fermi Gas to the Nuclear Shell-Model
DEFF Research Database (Denmark)
Özen, C.; Zinner, Nikolaj Thomas
2014-01-01
of the external potential becomes important. A system of two-species fermionic cold atoms with an attractive zero-range interaction is analogous to a simple model of nucleus in which neutrons and protons interact only through a residual pairing interaction. In this article, we discuss how the problem of a two......-component atomic fermi gas in a tight external trap can be mapped to the nuclear shell model so that readily available many-body techniques in nuclear physics, such as the Shell Model Monte Carlo (SMMC) method, can be directly applied to the study of these systems. We demonstrate an application of the SMMC method...
Reasoning with Atomic-Scale Molecular Dynamic Models
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen
Banks, Bruce A.; Miller, Sharon K.
2004-01-01
Atomic oxygen is one of the predominant constituents of Earth's upper atmosphere. It is created by the photodissociation of molecular oxygen (O2) into single O atoms by ultraviolet radiation. It is chemically very reactive because a single O atom readily combines with another O atom or with other atoms or molecules that can form a stable oxide. The effects of atomic oxygen on the external surfaces of spacecraft in low Earth orbit can have dire consequences for spacecraft life, and this is a well-known and much studied problem. Much less information is known about the effects of atomic oxygen on the internal surfaces of spacecraft. This degradation can occur when openings in components of the spacecraft exterior exist that allow the entry of atomic oxygen into regions that may not have direct atomic oxygen attack but rather scattered attack. Openings can exist because of spacecraft venting, microwave cavities, and apertures for Earth viewing, Sun sensors, or star trackers. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft were simulated at the NASA Glenn Research Center by using Monte Carlo computational techniques. A two-dimensional model was used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of the distance into a parallel-walled cavity. The model allows the atomic oxygen arrival direction, the Maxwell Boltzman temperature, and the ram energy to be varied along with the interaction parameters of the degree of recombination upon impact with polymer or nonreactive surfaces, the initial reaction probability, the reaction probability dependence upon energy and angle of attack, degree of specularity of scattering of reactive and nonreactive surfaces, and the degree of thermal accommodation upon impact with reactive and non-reactive surfaces to be varied to allow the model to produce atomic oxygen erosion geometries that replicate actual experimental results from space. The degree of
López-Guerra, Enrique A; Solares, Santiago D
2014-01-01
We examine different approaches to model viscoelasticity within atomic force microscopy (AFM) simulation. Our study ranges from very simple linear spring-dashpot models to more sophisticated nonlinear systems that are able to reproduce fundamental properties of viscoelastic surfaces, including creep, stress relaxation and the presence of multiple relaxation times. Some of the models examined have been previously used in AFM simulation, but their applicability to different situations has not yet been examined in detail. The behavior of each model is analyzed here in terms of force-distance curves, dissipated energy and any inherent unphysical artifacts. We focus in this paper on single-eigenmode tip-sample impacts, but the models and results can also be useful in the context of multifrequency AFM, in which the tip trajectories are very complex and there is a wider range of sample deformation frequencies (descriptions of tip-sample model behaviors in the context of multifrequency AFM require detailed studies and are beyond the scope of this work).
Nano Goes to School: A Teaching Model of the Atomic Force Microscope
Planinsic, Gorazd; Kovac, Janez
2008-01-01
The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…
Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E
2017-04-07
The inclusion of atomic polarizations for describing molecular electronic structure changes on vibration is shown to be necessary for coherent infrared intensity modeling. Atomic charges from the ChelpG partition scheme and atomic charges and dipoles from Quantum Theory of Atoms in Molecules (QTAIM) were employed within two different models to describe the stretching and bending vibrational intensities of the C-H, C-F, and C=O groups. The model employing the QTAIM parameters was the Charge-Charge Transfer and Dipolar Polarization model (QTAIM/CCTDP), and the model employing the ChelpG charges was the Equilibrium Charge-Charge Flux (ChelpG/ECCF). The QTAIM/CCTDP models result in characteristic proportions of the charge-charge transfer-dipolar polarization contributions even though their sums giving the total intensities do not discriminate between these vibrations. According to the QTAIM/CCTDP model, the carbon monoxide intensity has electronic structure changes similar to those of the carbonyl stretches whereas they resemble those of the CH stretches for the ChelpG/ECCF model.
Sunyono; Yuanita, L.; Ibrahim, M.
2015-01-01
The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…
A Comprehensive X-Ray Absorption Model for Atomic Oxygen
Gorzyca, T.W.; Bautista, M.A.; Hasoglu, M.F.; García, J.; Gatuzz, E.; Kaastra, J.S.; Kallman, T.R.; Manson, S.T.; Mendoza, C.; Raassen, A.J.J.; de Vries, C.P.; Zatsarinny, O.
2013-01-01
An analytical formula is developed to accurately represent the photoabsorption cross section of O I for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects,
The contribution of atom accessibility to site of metabolism models for cytochromes P450
DEFF Research Database (Denmark)
Rydberg, Patrik; Rostkowski, M.; Gloriam, D.E.
2013-01-01
Three different types of atom accessibility descriptors are investigated in relation to site of metabolism predictions. To enable the integration of local accessibility we have constructed 2DSASA, a method for the calculation of the atomic solvent accessible surface area that is independent of 3D...... coordinates. The method was implemented in the SMARTCyp site of metabolism prediction models and improved the results by up to 4 percentage points for nine cytochrome P450 isoforms. The final models are made available at http://www.farma.ku.dk/smartcyp....
Popa, Alexandru
2013-01-01
Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamic Systems is intended for scientists and graduate students interested in the foundations of quantum mechanics and applied scientists interested in accurate atomic and molecular models. This is a reference to those working in the new field of relativistic optics, in topics related to relativistic interactions between very intense laser beams and particles, and is based on 30 years of research. The novelty of this work consists of accurate connections between the properties of quantum equations and correspon
Galilean invariance in the exponential model of atomic collisions
Energy Technology Data Exchange (ETDEWEB)
del Pozo, A.; Riera, A.; Yaez, M.
1986-11-01
Using the X/sup n//sup +/(1s/sup 2/)+He/sup 2+/ colliding systems as specific examples, we study the origin dependence of results in the application of the two-state exponential model, and we show the relevance of polarization effects in that study. Our analysis shows that polarization effects of the He/sup +/(1s) orbital due to interaction with X/sup (//sup n//sup +1)+/ ion in the exit channel yield a very small contribution to the energy difference and render the dynamical coupling so strongly origin dependent that it invalidates the basic premises of the model. Further study, incorporating translation factors in the formalism, is needed.
An atomic model of brome mosaic virus using direct electron detection and real-space optimization
Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah
2014-01-01
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. PMID:25185801
An atomic model of brome mosaic virus using direct electron detection and real-space optimization
Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah
2014-09-01
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.
Building a pseudo-atomic model of the anaphase-promoting complex
Energy Technology Data Exchange (ETDEWEB)
Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; Fonseca, Paula C. A. da; Barford, David, E-mail: david.barford@icr.ac.uk [Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB (United Kingdom)
2013-11-01
This article describes an example of molecular replacement in which atomic models are used to interpret electron-density maps determined using single-particle electron-microscopy data. The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14–15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.
Partial Atomic Charges and Screened Charge Models of the Electrostatic Potential.
Wang, Bo; Truhlar, Donald G
2012-06-12
We propose a new screened charge method for calculating partial atomic charges in molecules by electrostatic potential (ESP) fitting. The model, called full density screening (FDS), is used to approximate the screening effect of full charge densities of atoms in molecules. The results are compared to the conventional ESP fitting method based on point charges and to our previously proposed outer density screening (ODS) method, in which the parameters are reoptimized for the present purpose. In ODS, the charge density of an atom is represented by the sum of a point charge and a smeared negative charge distributed in a Slater-type orbital (STO). In FDS, the charge density of an atom is taken to be the sum of the charge density of the neutral atom and a partial atomic charge (of either sign) distributed in an STO. The ζ values of the STOs used in these two models are optimized in the present study to best reproduce the electrostatic potentials. The quality of the fit to the electrostatics is improved in the screened charge methods, especially for the regions that are within one van der Waals radius of the centers of atoms. It is also found that the charges derived by fitting electrostatic potentials with screened charges are less sensitive to the positions of the fitting points than are those derived with conventional electrostatic fitting. Moreover, we found that the electrostatic-potential-fitted (ESP) charges from the screened charge methods are similar to those from the point-charge method except for molecules containing the methyl group, where we have explored the use of restraints on nonpolar H atoms. We recommend the FDS model if the only goal is ESP fitting to obtain partial atomic charges or a fit to the ESP field. However, the ODS model is more accurate for electronic embedding in combined quantum mechanical and molecular mechanical (QM/MM) modeling and is more accurate than point-charge models for ESP fitting, and it is recommended for applications
Mixed Rabi Jaynes-Cummings model of a three-level atom interacting with two quantized fields
Torosov, Boyan T.; Longhi, Stefano; Della Valle, Giuseppe
2015-07-01
The quantum Rabi model describes the ultrastrong interaction of a two-level atom coupled to a single quantized bosonic mode. As compared to the Jaynes-Cummings model, in the Rabi model the absorption and emission processes do not need to satisfy energy conservation and the usual rotating wave approximation (RWA) breaks down. As a result, the atom-field dynamics in the Hilbert space splits into two independent parity chains, exhibiting a collapse-revival pattern and exact periodic dynamics in the limit of degenerate atomic levels. Here we introduce a mixed Rabi Jaynes-Cummings model by considering a three-level atom interacting with two quantized bosonic fields, in which the RWA is made for one transition (with a weak atom-field coupling) but not for the other one (with an ultrastrong atom-field coupling). As a result, we show that the field in the weak coupled atomic transition can be used as a tool to control the atom-field dynamics of the other (strong coupled) transition, thus realizing an effective two-level quantum Rabi model with a controllable field. In particular, a periodic temporal dynamics of the atom-field state can be realized by appropriate tuning of the weak control field, even for non-degenerate atomic levels. A photonic simulator of the mixed Rabi Jaynes-Cummings model, based on light transport in evanescently coupled optical waveguide lattices, is also briefly discussed.
Explicit all-atom modeling of realistically sized ligand-capped nanocrystals
Kaushik, Ananth P.
2012-01-01
We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.
De Backer, A; Martinez, G T; Rosenauer, A; Van Aert, S
2013-11-01
In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration. © 2013 Elsevier B.V. All rights reserved.
Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep
2015-02-02
Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Predicting Transcription Factor Specificity with All-Atom Models
Rahi, Sahand Jamal; Mirny, Leonid A; Kardar, Mehran
2008-01-01
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rather start with the structure of a protein-DNA complex. We study the PurR E. coli TF, and explore to which extent atomistic models of protein-DNA complexes can be used to distinguish between cognate and non-cognate DNA sites. Particular emphasis is placed on systematic evaluation of this approach by comparing its performance with bioinformatic methods, by testing it against random decoys and sites of homologous TFs. We also examine a set of experimental mutations in both DNA and the protein. Using our explicit estimates of energy, we show that the specificity for PurR is dominated by direct protein-DNA interactions, and w...
Atomicrex—a general purpose tool for the construction of atomic interaction models
Stukowski, Alexander; Fransson, Erik; Mock, Markus; Erhart, Paul
2017-07-01
We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms.
Lattice location of dopant atoms: An N-body model calculation
Indian Academy of Sciences (India)
Abstract. The channelling and scattering yields of 1 MeV α-particles in the (100),. (110) and (111) directions of silicon implanted with bismuth and ytterbium have been simulated using N-body model. The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and ...
A simple model for atomic layer doped field-effect transistor (ALD-FET) electronic states
Energy Technology Data Exchange (ETDEWEB)
Mora R, M.E. [Centro de Investigaciones en Optica, Unidad Aguascalientes. Juan de Montoro 207, Zona Centro, 20000 Aguascalientes (Mexico); Gaggero S, L.M. [Escuela de Fisica, Universidad Autonoma de Zacatecas, Av. Preparatoria 301, 98060 Zacatecas (Mexico)
1998-12-31
We propose a simple potential model based on the Thomas-Fermi approximation to reproduce the main properties of the electronic structure of an atomic layer doped field effect transistor. Preliminary numerical results for a Si-based ALD-FET justify why bound electronic states are not observed in the experiment. (Author)
Lattice location of dopant atoms: An N-body model calculation
Indian Academy of Sciences (India)
2015-11-27
Nov 27, 2015 ... The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and Fontenille method. All previous works reported in literature so far have been done with computer programmes using a statistical analytical expression or by a binary collision model or a ...
Plasma-statistical models of the atom in the theory of some collisional and radiative processes
Astapenko, VA
2002-01-01
A plasma-statistical model was used to describe collisional and radiative processes involving target ionization, namely, collisional ionization of atoms and incoherent polarization bremsstrahlung. The cross sections of these processes were expressed through the Compton profile of X-ray scattering,
Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides.
Verstraelen, Toon; Pauwels, Ewald; De Proft, Frank; Van Speybroeck, Veronique; Geerlings, Paul; Waroquier, Michel
2012-02-14
The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q(0), that is suitable to describe biological systems bearing many locally charged functional groups.
Atomic Dipole Squeezing in the Correlated Two-Mode Two-Photon Jaynes-Cummings Model
Dong, Zhengchao; Zhao, Yonglin
1996-01-01
In this paper, we study the atomic dipole squeezing in the correlated two-mode two-photon JC model with the field initially in the correlated two-mode SU(1,1) coherent state. The effects of detuning, field intensity and number difference between the two field modes are investigated through numerical calculation.
UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions.
Siebert, Xavier; Navaza, Jorge
2009-07-01
Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30-10 A range and sometimes even beyond 10 A. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/.
Popa, Alexandru
2013-01-01
Applications of Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamical Systems is a reference on the new field of relativistic optics, examining topics related to relativistic interactions between very intense laser beams and particles. Based on 30 years of research, this unique book connects the properties of quantum equations to corresponding classical equations used to calculate the energetic values and the symmetry properties of atomic, molecular and electrodynamical systems. In addition, it examines applications for these methods, and for the calculation of
Kozlov, Alex; Quiney, Harry
2016-01-01
We describe a method for the calculation of photoionization cross-sections using square-integrable amplitudes obtained from the diagonalization of finite-basis set representations of the electronic Hamiltonian. Three examples are considered: a model example in which the final state is a free particle, the hydrogen atom and neutral atomic sodium. The method exploits the Whittaker-Shannon-Kotel'nikov sampling theorem, which is widely used in digital signal sampling and reconstruction. The approach reproduces known data with very good accuracy and converges to the exact solution with increase of the basis set size.
Modeling of inelastic transport in one-dimensional metallic atomic wires
DEFF Research Database (Denmark)
Frederiksen, Thomas; Brandbyge, Mads; Lorente, N
2004-01-01
Atomic-size conductors represent the ultimate limit of miniaturization, and understanding their properties is an important problem in the fields of nanoelectronics and molecular electronics. Quantum effects become important which leads to a physical behavior fundamentally different from macroscopic...... devices. A full description of the transport properties of atomic-size conductors therefore requires a quantum mechanical treatment of both the electronic and mechanical degrees of freedom. In this paper, we study a one-dimensional tight-binding model of the conducting electrons combined with a balls...
Dynamics for a two-atom two-mode intensity-dependent Raman coupled model
Energy Technology Data Exchange (ETDEWEB)
Singh, S., E-mail: vasudha-rnc1@rediffmail.com, E-mail: sudhhasingh@gmail.com; Gilhare, K. [Ranchi University, Department of Physics (India)
2016-06-15
We study the quantum dynamics of a two-atom Raman coupled model interacting with a quantized bimodal field with intensity-dependent coupling terms in a lossless cavity. The unitary transformation method used to solve the time-dependent problem also gives the eigensolutions of the interaction Hamiltonian. We study the atomic-population dynamics and dynamics of the photon statistics in the two cavity modes, and present evidence of cooperative effects in the production of antibunching and anticorrelations between the modes. We also investigate the effect of detuning on the evolution of second-order correlation functions and observe that the oscillations become more rapid for large detuning.
Modeling inelastic phonon scattering in atomic- and molecular-wire junctions
DEFF Research Database (Denmark)
Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads
2005-01-01
Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between...... the full nonequilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including nonequilibrium heating and provide...... a convenient way of parameterizing the physics. This is exemplified by fitting the expressions to the experimentally observed conductances through both an atomic gold wire and a hydrogen molecule....
Finite Bias Calculations to Model Interface Dipoles in Electrochemical Cells at the Atomic Scale
DEFF Research Database (Denmark)
Hansen, Martin Hangaard; Jin, Chengjun; Thygesen, Kristian Sommer
2016-01-01
The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure t...... to satisfy the thermodynamic constraints imposed by the environment. This is captured by the generalized computational hydrogen electrode model, which enables us to make efficient first-principles calculations of atomic scale properties of the electrochemical interface.......The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure...
Volkmann, Niels
2012-02-01
A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field. Copyright © 2011 Elsevier Ltd. All rights reserved.
Huang, Lei; Roux, Benoît
2013-08-13
Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out.
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
Energy Technology Data Exchange (ETDEWEB)
Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Jackson, Bret [Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom); Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main (Germany); Martinazzo, Rocco, E-mail: rocco.martinazzo@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Richerche, v. Golgi 19, 20133 Milano (Italy)
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.
An attempt for modeling the atmospheric transport of 3H around Kakrapar Atomic Power Station.
Patra, A K; Nankar, D P; Joshi, C P; Venkataraman, S; Sundar, D; Hegde, A G
2008-01-01
Prediction of downwind tritium air concentrations in the environment around Kakrapar Atomic Power Station (KAPS) was studied on the basis of Gaussian plume dispersion model. The tritium air concentration by field measurement [measured tritium air concentrations in the areas adjacent to KAPS] were compared with the theoretically calculated values (predicted) to validate the model. This approach will be useful in evaluating environmental radiological impacts due to pressurised heavy water reactors.
Accurate model annotation of a near-atomic resolution cryo-EM map.
Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah
2017-03-21
Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.
De Backer, A; Jones, L; Lobato, I; Altantzis, T; Goris, B; Nellist, P D; Bals, S; Van Aert, S
2017-06-29
In order to fully exploit structure-property relations of nanomaterials, three-dimensional (3D) characterization at the atomic scale is often required. In recent years, the resolution of electron tomography has reached the atomic scale. However, such tomography typically requires several projection images demanding substantial electron dose. A newly developed alternative circumvents this by counting the number of atoms across a single projection. These atom counts can be used to create an initial atomic model with which an energy minimization can be applied to obtain a relaxed 3D reconstruction of the nanoparticle. Here, we compare, at the atomic scale, this single projection reconstruction approach with tomography and find an excellent agreement. This new approach allows for the characterization of beam-sensitive materials or where the acquisition of a tilt series is impossible. As an example, the utility is illustrated by the 3D atomic scale characterization of a nanodumbbell on an in situ heating holder of limited tilt range.
Polat-Yaseen, Zeynep
2012-01-01
This study was designed for two major goals, which are to describe students' mental models about atom concept from 6th to 8th grade and to compare students' mental models with visual representations of atom in textbooks. Qualitative and quantitative data were collected with 4 open-ended questions including drawings which were quantified using the…
Protein Nano-Object Integrator (ProNOI for generating atomic style objects for molecular modeling
Directory of Open Access Journals (Sweden)
Smith Nicholas
2012-12-01
Full Text Available Abstract Background With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results Here we report the Protein Nano-Object Integrator (ProNOI which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions The Protein Nano-Object Integrator (ProNOI is a convenient tool for
Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling.
Smith, Nicholas; Campbell, Brandon; Li, Lin; Li, Chuan; Alexov, Emil
2012-12-05
With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Here we report the Protein Nano-Object Integrator (ProNOI) which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB) format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR) file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE) file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. The Protein Nano-Object Integrator (ProNOI) is a convenient tool for generating atomic-style nano shapes in conjunction with
Energy Technology Data Exchange (ETDEWEB)
Balleza D, E
2004-07-01
In the first chapter of this work we will show a detailed analysis of the one cooling Doppler phenomenon that appears when a laser induces a dipolar moment to the atoms in such a way that these may interact with him to transfer moment to the field with the subsequent decrease of kinetic energy that macroscopically it is translated in cooling of the atomic cloud. When the experiments of atomic cooling were carried out it was observed that the temperature was smaller to the one than it predicted the cooling Doppler, this originates the creation of a theory but it dies in which the over simplification is eliminated that the alone atom consists of two energy levels and levels are introduced of it structures fine that are able to explain the extra cooling. To this phenomenon it is called Sisifo effect and it is studied detailedly in the chapter two. The first two chapters talk each other about the atomic cooling, but it stops that the atomic cloud can be manipulated, before being confined, problem that we will expose in the chapter three with experimental solutions that at the moment they are implemented in the laboratories around the world. In particular we will concentrate on the traps FORT (Far Off Resonance Trap, trap very outside of resonance) that confine to the atoms in optic nets. The lasers gaussianos originate a potential sinusoidal along the propagation address and gaussiano in the perpendicular plane to this. In the I surrender four he/she intends a three-dimensional model that substitutes To the variation sinusoidal for a function crenel and he/she makes an approach To first order in the radial dependence to obtain an oscillator potential Harmonic instead of the gaussiano that you taenia. The pattern is solved in a similar way To the pattern unidimensional of bands: they are the functions of wave solution For every period and they are coupled among if so that they satisfy conditions of rhythm, When making this you arrives to a womb that couples the
Observation of antiferromagnetic correlations in the Hubbard model with ultracold atoms.
Hart, Russell A; Duarte, Pedro M; Yang, Tsung-Lin; Liu, Xinxing; Paiva, Thereza; Khatami, Ehsan; Scalettar, Richard T; Trivedi, Nandini; Huse, David A; Hulet, Randall G
2015-03-12
Ultracold atoms in optical lattices have great potential to contribute to a better understanding of some of the most important issues in many-body physics, such as high-temperature superconductivity. The Hubbard model--a simplified representation of fermions moving on a periodic lattice--is thought to describe the essential details of copper oxide superconductivity. This model describes many of the features shared by the copper oxides, including an interaction-driven Mott insulating state and an antiferromagnetic (AFM) state. Optical lattices filled with a two-spin-component Fermi gas of ultracold atoms can faithfully realize the Hubbard model with readily tunable parameters, and thus provide a platform for the systematic exploration of its phase diagram. Realization of strongly correlated phases, however, has been hindered by the need to cool the atoms to temperatures as low as the magnetic exchange energy, and also by the lack of reliable thermometry. Here we demonstrate spin-sensitive Bragg scattering of light to measure AFM spin correlations in a realization of the three-dimensional Hubbard model at temperatures down to 1.4 times that of the AFM phase transition. This temperature regime is beyond the range of validity of a simple high-temperature series expansion, which brings our experiment close to the limit of the capabilities of current numerical techniques, particularly at metallic densities. We reach these low temperatures using a compensated optical lattice technique, in which the confinement of each lattice beam is compensated by a blue-detuned laser beam. The temperature of the atoms in the lattice is deduced by comparing the light scattering to determinant quantum Monte Carlo simulations and numerical linked-cluster expansion calculations. Further refinement of the compensated lattice may produce even lower temperatures which, along with light scattering thermometry, would open avenues for producing and characterizing other novel quantum states of
Building a pseudo-atomic model of the anaphase-promoting complex.
Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; da Fonseca, Paula C A; Barford, David
2013-11-01
The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14-15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.
Spatial Distributions of Metal Atoms During Carbon SWNTs Formation: Measurements and Modelling
Cau, M.; Dorval, N.; Attal-Tretout, B.; Cochon, J. L.; Loiseau, A.; Farhat, S.; Hinkov, I.; Scott, C. D.
2004-01-01
Experiments and modelling have been undertaken to clarify the role of metal catalysts during single-wall carbon nanotube formation. For instance, we wonder whether the metal catalyst is active as an atom, a cluster, a liquid or solid nanoparticle [1]. A reactor has been developed for synthesis by continuous CO2-laser vaporisation of a carbon-nickel-cobalt target in laminar helium flow. The laser induced fluorescence technique [2] is applied for local probing of gaseous Ni, Co and CZ species throughout the hot carbon flow of the target heated up to 3500 K. A rapid depletion of C2 in contrast to the spatial extent of metal atoms is observed in the plume (Fig. 1). This asserts that C2 condenses earlier than Ni and Co atoms.[3, 4]. The depletion is even faster when catalysts are present. It may indicate that an interaction between metal atoms and carbon dimers takes place in the gas as soon as they are expelled from the target surface. Two methods of modelling are used: a spatially I-D calculation developed originally for the arc process [5], and a zero-D time dependent calculation, solving the chemical kinetics along the streamlines [6]. The latter includes Ni cluster formation. The peak of C2 density is calculated close to the target surface where the temperature is the highest. In the hot region, C; is dominant. As the carbon products move away from the target and mix with the ambient helium, they recombine into larger clusters, as demonstrated by the peak of C5 density around 1 mm. The profile of Ni-atom density compares fairly well with the measured one (Fig. 2). The early increase is due to the drop of temperature, and the final decrease beyond 6 mm results from Ni cluster formation at the eutectic temperature (approx.1600 K).
Xu, Dong; Zhang, Yang
2011-11-16
Most protein structural prediction algorithms assemble structures as reduced models that represent amino acids by a reduced number of atoms to speed up the conformational search. Building accurate full-atom models from these reduced models is a necessary step toward a detailed function analysis. However, it is difficult to ensure that the atomic models retain the desired global topology while maintaining a sound local atomic geometry because the reduced models often have unphysical local distortions. To address this issue, we developed a new program, called ModRefiner, to construct and refine protein structures from Cα traces based on a two-step, atomic-level energy minimization. The main-chain structures are first constructed from initial Cα traces and the side-chain rotamers are then refined together with the backbone atoms with the use of a composite physics- and knowledge-based force field. We tested the method by performing an atomic structure refinement of 261 proteins with the initial models constructed from both ab initio and template-based structure assemblies. Compared with other state-of-art programs, ModRefiner shows improvements in both global and local structures, which have more accurate side-chain positions, better hydrogen-bonding networks, and fewer atomic overlaps. ModRefiner is freely available at http://zhanglab.ccmb.med.umich.edu/ModRefiner. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Why has the bohr-sommerfeld model of the atom been ignoredby general chemistry textbooks?
Niaz, Mansoor; Cardellini, Liberato
2011-12-01
Bohr's model of the atom is considered to be important by general chemistry textbooks. A major shortcoming of this model was that it could not explain the spectra of atoms containing more than one electron. In order to increase the explanatory power of the model, Sommerfeld hypothesized the existence of elliptical orbits. This study has the following objectives: 1) Formulation of criteria based on a history and philosophy of science framework; and 2) Evaluation of university-level general chemistry textbooks based on the criteria, published in Italy and U.S.A. Presentation of a textbook was considered to be "satisfactory" if it included a description of the Bohr-Sommerfeld model along with diagrams of the elliptical orbits. Of the 28 textbooks published in Italy that were analyzed, only five were classified as "satisfactory". Of the 46 textbooks published in U.S.A., only three were classified as "satisfactory". This study has the following educational implications: a) Sommerfeld's innovation (auxiliary hypothesis) by introducing elliptical orbits, helped to restore the viability of Bohr's model; b) Bohr-Sommerfeld's model went no further than the alkali metals, which led scientists to look for other models; c) This clearly shows that scientific models are tentative in nature; d) Textbook authors and chemistry teachers do not consider the tentative nature of scientific knowledge to be important; e) Inclusion of the Bohr-Sommerfeld model in textbooks can help our students to understand how science progresses.
Atomization modeling in a multiphase flow environment and comparison with experiments
Liang, P. Y.; Schuman, M. D.
1990-01-01
An atomization model based on Reitz's instability wave analysis has been implemented into the ARICC3D multiphase CFD combustion code. Preliminary test runs with cold non-evaporating liquid jet and coaxial gas-liquid atomization cases appeared to have verified basic performance of the model, generating realistic-looking sprays. Furthermore, the extended liquid jet is explicitly resolved, and predicted jet lengths agree well with classical correlations. Fair agreement with test data is obtained for predicted spray tip penetrations and liquid mass flux radial distributions, with obvious room for improvement. Some numerical problems also appear to have resulted with the current implementation when low gas Mach number and high liquid velocities are involved.
Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy
Yonekura, Koji; Maki-Yonekura, Saori; Namba, Keiichi
2003-08-01
The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in two distinct conformations, L- and R-type, for supercoiling. The X-ray crystal structure of a flagellin fragment lacking about 100 terminal residues revealed the protofilament structure, but the full filament structure is still essential for understanding the mechanism of supercoiling and polymerization. Here we report a complete atomic model of the R-type filament by electron cryomicroscopy. A density map obtained from image data up to 4Å resolution shows the feature of α-helical backbone and some large side chains. The atomic model built on the map reveals intricate molecular packing and an α-helical coiled coil formed by the terminal chains in the inner core of the filament, with its intersubunit hydrophobic interactions having an important role in stabilizing the filament.
Yonekura, Koji; Maki-Yonekura, Saori; Namba, Keiichi
2005-03-01
The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a well-ordered helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments, each in either of the two distinct conformations, L- and R-type, for supercoiling. We have been studying the three-dimensional structures of the flagellar filaments by electron cryomicroscopy and recently obtained a density map of the R-type filament up to 4 angstroms resolution from an image data set containing only about 41,000 molecular images. The density map showed the features of the alpha-helical backbone and some large side chains, which allowed us to build the complete atomic model as one of the first atomic models of macromolecules obtained solely by electron microscopy image analysis (Yonekura et al., 2003a). We briefly review the structure and the structure analysis, and point out essential techniques that have made this analysis possible.
Directory of Open Access Journals (Sweden)
J. Jünemann
2017-09-01
Full Text Available Understanding the robustness of topological phases of matter in the presence of strong interactions and synthesizing novel strongly correlated topological materials lie among the most important and difficult challenges of modern theoretical and experimental physics. In this work, we present a complete theoretical analysis of the synthetic Creutz-Hubbard ladder, which is a paradigmatic model that provides a neat playground to address these challenges. We give special attention to the competition of correlated topological phases and orbital quantum magnetism in the regime of strong interactions. These results are, furthermore, confirmed and extended by extensive numerical simulations. Moreover, we propose how to experimentally realize this model in a synthetic ladder made of two internal states of ultracold fermionic atoms in a one-dimensional optical lattice. Our work paves the way towards quantum simulators of interacting topological insulators with cold atoms.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Directory of Open Access Journals (Sweden)
Andrzej Koliński
2013-05-01
Full Text Available 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.
Directory of Open Access Journals (Sweden)
Tcheou Michel P
2007-01-01
Full Text Available The number of waveforms monitored in power systems is increasing rapidly. This creates a demand for computational tools that aid in the analysis of the phenomena and also that allow efficient transmission and storage of the information acquired. In this context, signal processing techniques play a fundamental role. This work is a tutorial reviewing the principles and applications of atomic signal modeling of electric disturbance signals. The disturbance signal is modeled using a linear combination of damped sinusoidal components which are closely related to the phenomena typically observed in power systems. The signal model obtained is then employed for disturbance signal denoising, filtering of "DC components," and compression.
Error sources in atomic force microscopy for dimensional measurements: Taxonomy and modeling
DEFF Research Database (Denmark)
Marinello, F.; Voltan, A.; Savio, E.
2010-01-01
This paper aimed at identifying the error sources that occur in dimensional measurements performed using atomic force microscopy. In particular, a set of characterization techniques for errors quantification is presented. The discussion on error sources is organized in four main categories......: scanning system, tip-surface interaction, environment, and data processing. The discussed errors include scaling effects, squareness errors, hysteresis, creep, tip convolution, and thermal drift. A mathematical model of the measurement system is eventually described, as a reference basis for errors...
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
Jonikas, Magdalena A; Radmer, Randall J; Altman, Russ B
2009-12-15
The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87-3.31 A RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 A RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure. Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a. russ.altman@stanford.edu
On the emergence of molecular structure from atomic shape in the 1/r2 harmonium model.
Müller-Herold, Ulrich
2006-01-07
The formal similarity of the three-body Hamiltonians for helium and the hydrogen molecule ion is used to demonstrate the unfolding of a rotating dumbbell-like proton distribution from a (1s)2-type electron distribution by smooth variation of the particles' masses in the 1/r2 harmonium model. The 1/r2 harmonium is an exactly solvable modification of the harmonium model (also known as Hooke's law atom) where the attraction between different particles is harmonic and the repulsion between the two equal particles is given by a 1/r2 potential. The dumbbell-like molecular structure appears as an expression of increasing spatial correlation due to increasing mass. It gradually appears in the one-density distribution of the two equal particles if their mass exceeds a critical value depending on the mass of the third particle. For large mass of the equal particles, their one-density distribution approaches an asymptotic form derived from the Born-Oppenheimer treatment of H2+ in the 1/r2 harmonium model. Below the critical value, the one density is a spherical, Gaussian-type atomic density distribution with a maximum at the center of mass. The topological transition at the critical value separates molecular structure and atomic shape as two qualitatively different manifestations of spatial structure.
COUPLED ATOMIZATION AND SPRAY MODELLING IN THE SPRAY FORMING PROCESS USING OPENFOAM
DEFF Research Database (Denmark)
Gjesing, Rasmus; Hattel, Jesper Henri; Fritsching, Udo
2009-01-01
The paper presents a numerical model capable of simulating the atomization, break-up and in-flight spray phenomena in the spray forming process. The model is developed and implemented in the freeware code openFOAM. The focus is on studying the coupling effect of the melt break-up phenomena...... with the local gas and droplets flow fields. The work is based on an Eulerian-Lagrangian description, which is implemented in a full 3D representation. The gas is described by the incompressible RANS equations, whereas the movement of the droplets is modeled by a tracking approach, together with a full thermal...... model for droplet cooling and solidification. The model is tested and validated against results from literature and experiments. Subsequently, the model is used to simulate the complex flow fields in the spray forming process and the results are discussed. The presented model of the spray forming...
A quasi-stationary numerical model of atomized metal droplets, II: Prediction and assessment
DEFF Research Database (Denmark)
Pryds, Nini H.; Hattel, Jesper Henri; Thorborg, Jesper
1999-01-01
A new model which extends previous studies and includes the interaction between enveloping gas and an array of droplets has been developed and presented in a previous paper. The model incorporates the probability density function of atomized metallic droplets into the heat transfer equations....... The main thrust of the model is that the gas temperature was not predetermined and calculated empirically but calculated numerically based on heat balance consideration. In this paper, the accuracy of the numerical model and the applicability of the model as a predictive tool have been investigated...... been illustrated.A comparison between the numerical model and the experimental results shows an excellent agreement and demonstrates the validity of the present model, e.g. the calculated gas temperature which has an important influence on the droplet solidification behaviour as well as the calculated...
Directory of Open Access Journals (Sweden)
Hyuntae Na
2015-10-01
Full Text Available Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.
Netzell, Elisabeth
2016-01-01
This report presents the results from a survey study on Swedish upper secondary school physics andchemistry teachers’ use of models and representations in teaching the atom. The study builds upon an earlier systematic international literature review on the role of models and representations in the teaching, learning and understanding of the atom. The overall aim of the study is to explore what models and representations are used by Swedish upper secondary school physics and chemistry teachers...
An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water
Energy Technology Data Exchange (ETDEWEB)
Stauffer, D.; Dragneva, N.; Floriano, W. B.; Rubel, O. [Thunder Bay Regional Research Institute, 290 Munro St, Thunder Bay, Ontario P7B 6V4 (Canada); Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7A 7T1 (Canada); Mawhinney, R. C. [Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7A 7T1 (Canada); Fanchini, G. [Physics and Astronomy, University of Western Ontario, 1151 Richmond St, London, Ontario N6A 3K7 (Canada); French, S. [University of Calgary, South Health Campus, 4448 Front St. SE, Calgary, Alberta T3M 1M4 (Canada)
2014-07-28
Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.
Atomic Weights Confirm Bipolar Model of Oscillations in a Chain System
Directory of Open Access Journals (Sweden)
Ries A.
2013-10-01
Full Text Available We apply the bipolar model of oscillations in a chain system to the data set of standard atomic weights. 90% of these masses could be reproduced by this model and were expressed in continued fraction form, where all numerators are Euler’s number and the sum of the free link and all partial denominators yields zero. All outliers were either radioactive or polynuclidic elements whose isotopic compositions as found in samples on Earth might not be fully representative for the mean values when considering samples from all parts of the universe.
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
Yang, Yantao; Cui, Junzhi; Han, Tiansi
2016-08-01
Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.
Atomic-Scale Modeling of Particle Size Effects for the Oxygen Reduction Reaction of Pt
DEFF Research Database (Denmark)
Tritsaris, Georgios; Greeley, Jeffrey Philip; Rossmeisl, Jan
2011-01-01
We estimate the activity of the oxygen reduction reaction on platinum nanoparticles of sizes of practical importance. The proposed model explicitly accounts for surface irregularities and their effect on the activity of neighboring sites. The model reproduces the experimentally observed trends...... in both the specific and mass activities for particle sizes in the range between 2 and 30 nm. The mass activity is calculated to be maximized for particles of a diameter between 2 and 4 nm. Our study demonstrates how an atomic-scale description of the surface microstructure is a key component...
A Si I atomic model for NLTE spectropolarimetric diagnostics of the 10 827 Å line
Shchukina, N. G.; Sukhorukov, A. V.; Trujillo Bueno, J.
2017-07-01
Aims: The Si I 10 827 Å line is commonly used for spectropolarimetric diagnostics of the solar atmosphere. First, we aim at quantifying the sensitivity of the Stokes profiles of this line to non-local thermodynamic equilibrium (NLTE) effects. Second, we aim at facilitating NLTE diagnostics of the Si I 10 827 Å line. To this end, we propose the use of a relatively simple silicon model atom, which allows a fast and accurate computation of Stokes profiles. The NLTE Stokes profiles calculated using this simple model atom are very similar to those obtained via the use of a very comprehensive silicon model atom. Methods: We investigate the impact of the NLTE effects on the Si I 10 827 Å line by means of multilevel radiative transfer calculations in a three-dimensional (3D) model atmosphere taken from a state-of-the-art magneto-convection simulation with small-scale dynamo action. We calculate the emergent Stokes profiles for this line at the solar disk center and for every vertical column of the 3D snapshot model, neglecting the effects of horizontal radiative transfer. Results: We find significant departures from LTE in the Si I 10 827 Å line, not only in the intensity but also in the linearly and circularly polarized profiles. At wavelengths around 0.1 Å, where most of the Stokes Q, U, and V peaks of the Si I 10 827 Å line occur, the differences between the NLTE and LTE profiles are comparable with the Stokes amplitudes themselves. The deviations from LTE increase with increasing Stokes Q, U, and V signals. Concerning the Stokes V profiles, the NLTE effects correlate with the magnetic field strength in the layers where such circular polarization signals are formed. Conclusions: The NLTE effects should be taken into account when diagnosing the emergent Stokes I profiles as well as the Stokes Q, U, and V profiles of the Si I 10 827 Å line. The sixteen-level silicon model atom proposed here, with six radiative bound-bound transitions, is suitable to account for the
DEFF Research Database (Denmark)
Valentin, Jan B.; Andreetta, Christian; Boomsma, Wouter
2014-01-01
We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length...... scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy...... terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive...
Joseph, Agnel Praveen; Malhotra, Sony; Burnley, Tom; Wood, Chris; Clare, Daniel K; Winn, Martyn; Topf, Maya
2016-05-01
As the resolutions of Three Dimensional Electron Microscopic reconstructions of biological macromolecules are being improved, there is a need for better fitting and refinement methods at high resolutions and robust approaches for model assessment. Flex-EM/MODELLER has been used for flexible fitting of atomic models in intermediate-to-low resolution density maps of different biological systems. Here, we demonstrate the suitability of the method to successfully refine structures at higher resolutions (2.5-4.5Å) using both simulated and experimental data, including a newly processed map of Apo-GroEL. A hierarchical refinement protocol was adopted where the rigid body definitions are relaxed and atom displacement steps are reduced progressively at successive stages of refinement. For the assessment of local fit, we used the SMOC (segment-based Manders' overlap coefficient) score, while the model quality was checked using the Qmean score. Comparison of SMOC profiles at different stages of refinement helped in detecting regions that are poorly fitted. We also show how initial model errors can have significant impact on the goodness-of-fit. Finally, we discuss the implementation of Flex-EM in the CCP-EM software suite. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Kandel, Yudhishthir; Chandonait, Jonathan; Melvin, Lawrence S.; Marokkey, Sajan; Yan, Qiliang; Grzeskowiak, Steven; Painter, Benjamin; Denbeaux, Gregory
2017-03-01
Extreme ultraviolet (EUV) lithography at 13.5 nm stands at the crossroads of next generation patterning technology for high volume manufacturing of integrated circuits. Photo resist models that form the part of overall pattern transform model for lithography play a vital role in supporting this effort. The physics and chemistry of these resists must be understood to enable the construction of accurate models for EUV Optical Proximity Correction (OPC). In this study, we explore the possibility of improving EUV photo-resist models by directly correlating the parameters obtained from experimentally measured atomic scale physical properties; namely, the effect of interaction of EUV photons with photo acid generators in standard chemically amplified EUV photoresist, and associated electron energy loss events. Atomic scale physical properties will be inferred from the measurements carried out in Electron Resist Interaction Chamber (ERIC). This study will use measured physical parameters to establish a relationship with lithographically important properties, such as line edge roughness and CD variation. The data gathered from these measurements is used to construct OPC models of the resist.
Quantum simulation of the Hubbard model with dopant atoms in silicon.
Salfi, J; Mol, J A; Rahman, R; Klimeck, G; Simmons, M Y; Hollenberg, L C L; Rogge, S
2016-04-20
In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose-Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model.
Baldus, Sabrina; Schröder, Daniel; Bibinov, Nikita; Schulz-von der Gathen, Volker; Awakowicz, Peter
2015-06-01
Cold atmospheric pressure plasmas are a promising alternative therapy for treatment of chronic wounds, as they have already shown in clinical trials. In this study an air dielectric barrier discharge (DBD) developed for therapeutic use in dermatology is characterized with respect to the plasma produced reactive oxygen species, namely atomic oxygen and ozone, which are known to be of great importance to wound healing. To understand the plasma chemistry of the applied DBD, xenon-calibrated two-photon laser-induced fluorescence spectroscopy and optical absorption spectroscopy are applied. The measured spatial distributions are shown and compared to each other. A model of the afterglow chemistry based on optical emission spectroscopy is developed to cross-check the measurement results and obtain insight into the dynamics of the considered reactive oxygen species. The atomic oxygen density is found to be located mostly between the electrodes with a maximum density of {{n}\\text{O}}=6× {{10}16} cm-3 . Time resolved measurements reveal a constant atomic oxygen density between two high voltage pulses. The ozone is measured up to 3 mm outside the active plasma volume, reaching a maximum value of {{n}{{\\text{O}3}}}=3× {{10}16} cm-3 between the electrodes.
Coqblin-Schrieffer model for an ultracold gas of ytterbium atoms with metastable state
Kuzmenko, Igor; Kuzmenko, Tetyana; Avishai, Yshai; Jo, Gyu-Boong
2016-03-01
Motivated by the impressive recent advance in manipulating cold ytterbium atoms, we explore and substantiate the feasibility of realizing the Coqblin-Schrieffer model in a gas of cold fermionic 173Yb atoms. Making use of different AC polarizabillity of the electronic ground state (electronic configuration S10) and the long lived metastable state (electronic configuration P30), it is substantiated that the latter can be localized and serve as a magnetic impurity while the former remains itinerant. The exchange mechanism between the itinerant S10 and the localized P30 atoms is analyzed and shown to be antiferromagnetic. The ensuing SU(6) symmetric Coqblin-Schrieffer Hamiltonian is constructed, and, using the calculated exchange constant J , perturbative renormalization group (RG) analysis yields the Kondo temperature TK that is experimentally accessible. A number of thermodynamic measurable observables are calculated in the weak-coupling regime T >TK (using perturbative RG analysis) and in the strong-coupling regime T
Embedded-atom method potential for modeling hydrogen and hydrogen-defect interaction in tungsten
Wang, Li-Fang; Shu, Xiaolin; Lu, Guang-Hong; Gao, Fei
2017-11-01
An embedded-atom method potential has been developed for modeling hydrogen in body-centered-cubic (bcc) tungsten by fitting to an extensive database of density functional theory (DFT) calculations. Comprehensive evaluations of the new potential are conducted by comparing various hydrogen properties with DFT calculations and available experimental data, as well as all the other tungsten–hydrogen potentials. The new potential accurately reproduces the point defect properties of hydrogen, the interaction among hydrogen atoms, the interplay between hydrogen and a monovacancy, and the thermal diffusion of hydrogen in tungsten. The successful validation of the new potential confirms its good reliability and transferability, which enables large-scale atomistic simulations of tungsten–hydrogen system. The new potential is afterward employed to investigate the interplay between hydrogen and other defects, including [1 1 1] self-interstitial atoms (SIAs) and vacancy clusters in tungsten. It is found that both the [1 1 1] SIAs and the vacancy clusters exhibit considerable attraction for hydrogen. Hydrogen solution and diffusion in strained tungsten are also studied using the present potential, which demonstrates that tensile (compressive) stress facilitates (impedes) hydrogen solution, and isotropic tensile (compressive) stress impedes (facilitates) hydrogen diffusion while anisotropic tensile (compressive) stress facilitates (impedes) hydrogen diffusion.
SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases
Goldenstein, Christopher S.; Miller, Victor A.; Mitchell Spearrin, R.; Strand, Christopher L.
2017-10-01
SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: (1) atomic and molecular absorption spectra, (2) atomic and molecular emission spectra, (3) transition linestrengths, and (4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermodynamic conditions to be visualized in an interactive plot window. The primary objective of this paper is to describe the architecture and spectroscopic models employed by SpectraPlot in order to provide its users with the knowledge required to understand the capabilities and limitations of simulations performed using SpectraPlot. Further, this manuscript discusses the accuracy of several underlying approximations used to decrease computational time, in particular, the use of far-wing cutoff criteria.
Partial ionization in dense plasmas: comparisons among average-atom density functional models.
Murillo, Michael S; Weisheit, Jon; Hansen, Stephanie B; Dharma-wardana, M W C
2013-06-01
Nuclei interacting with electrons in dense plasmas acquire electronic bound states, modify continuum states, generate resonances and hopping electron states, and generate short-range ionic order. The mean ionization state (MIS), i.e, the mean charge Z of an average ion in such plasmas, is a valuable concept: Pseudopotentials, pair-distribution functions, equations of state, transport properties, energy-relaxation rates, opacity, radiative processes, etc., can all be formulated using the MIS of the plasma more concisely than with an all-electron description. However, the MIS does not have a unique definition and is used and defined differently in different statistical models of plasmas. Here, using the MIS formulations of several average-atom models based on density functional theory, we compare numerical results for Be, Al, and Cu plasmas for conditions inclusive of incomplete atomic ionization and partial electron degeneracy. By contrasting modern orbital-based models with orbital-free Thomas-Fermi models, we quantify the effects of shell structure, continuum resonances, the role of exchange and correlation, and the effects of different choices of the fundamental cell and boundary conditions. Finally, the role of the MIS in plasma applications is illustrated in the context of x-ray Thomson scattering in warm dense matter.
From deep TLS validation to ensembles of atomic models built from elemental motions
Energy Technology Data Exchange (ETDEWEB)
Urzhumtsev, Alexandre, E-mail: sacha@igbmc.fr [Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Université de Lorraine, BP 239, 54506 Vandoeuvre-les-Nancy (France); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); Van Benschoten, Andrew H.; Fraser, James S. [University of California, San Francisco, San Francisco, CA 94158 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); University of California Berkeley, Berkeley, CA 94720 (United States); Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France)
2015-07-28
Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
From deep TLS validation to ensembles of atomic models built from elemental motions.
Urzhumtsev, Alexandre; Afonine, Pavel V; Van Benschoten, Andrew H; Fraser, James S; Adams, Paul D
2015-08-01
The translation-libration-screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
Energy Technology Data Exchange (ETDEWEB)
Deng, Zhang; He, Wenjie; Duan, Chenlong [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Chen, Rong, E-mail: rongchen@mail.hust.edu.cn [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Shan, Bin [State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)
2016-01-15
Spatial atomic layer deposition (SALD) is a promising technology with the aim of combining the advantages of excellent uniformity and conformity of temporal atomic layer deposition (ALD), and an industrial scalable and continuous process. In this manuscript, an experimental and numerical combined model of atmospheric SALD system is presented. To establish the connection between the process parameters and the growth efficiency, a quantitative model on reactant isolation, throughput, and precursor utilization is performed based on the separation gas flow rate, carrier gas flow rate, and precursor mass fraction. The simulation results based on this model show an inverse relation between the precursor usage and the carrier gas flow rate. With the constant carrier gas flow, the relationship of precursor usage and precursor mass fraction follows monotonic function. The precursor concentration, regardless of gas velocity, is the determinant factor of the minimal residual time. The narrow gap between precursor injecting heads and the substrate surface in general SALD system leads to a low Péclet number. In this situation, the gas diffusion act as a leading role in the precursor transport in the small gap rather than the convection. Fluid kinetics from the numerical model is independent of the specific structure, which is instructive for the SALD geometry design as well as its process optimization.
National Research Council Canada - National Science Library
Hatch, Andrew; Smith, Ralph G; De, Tathagata
2004-01-01
This paper addresses the development and experimental validation of a model-based, open loop control design for mitigating the frequency-dependent effects of hysteresis in an atomic force microscope (AFM...
Benosman, H; T. Benouaz; A CHIKHAOUI
2012-01-01
Optical properties of a dielectric medium consisting of an atomic vapor are investigated theoretically using the model of elastically bound electrons. This model describes the interaction of an electromagnetic field with the bound electrons to the vapor atoms [7]. In this paper, we propose a formalism which takes into accurate the effect of the number of electrons on the vapor index. We use the approximation of free electrons (no interaction between free electrons)...
Silva, Arnaldo F; Richter, Wagner E; Meneses, Helen G C; Bruns, Roy E
2014-11-14
Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.
A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution.
Shelley, Mee Y; Selvan, Myvizhi Esai; Zhao, Jun; Babin, Volodymyr; Liao, Chenyi; Li, Jianing; Shelley, John C
2017-08-08
We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG), for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented, while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions. These characteristics fit well with the requirements for studying peptide association and aggregation, where the system sizes and time scales require considerable computational resources with all-atom models. In particular, AACG is well suited for biologics since changes in peptide shape and long-range electrostatics may play an important role. The application of AACG to melittin, a 26-residue peptide with a well-known propensity to aggregate in solution, serves as an initial demonstration of this technology for studying peptide aggregation. We observed the formation of melittin aggregates during our simulations and characterized the time-evolution of aggregate size distribution, buried surface areas, and residue contacts. Key interactions including π-cation and π-stacking involving TRP19 were also examined. Our AACG simulations demonstrated a clear salt effect and a moderate temperature effect on aggregation and support the molten globule model of melittin aggregates. As a showcase, this work illustrates the useful role for AACG in investigations of peptide aggregation and its potential to guide formulation and design of biologics.
Wang, Junmei; Cieplak, Piotr; Li, Jie; Hou, Tingjun; Luo, Ray; Duan, Yong
2011-03-31
In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, that is, whether the interactions of two atoms that form the bond, bond angle, and dihedral angle are turned off or scaled down. When 1-2 (bonded) and 1-3 (separated by two bonds) interactions are turned off, 1-4 (separated by three bonds) interactions are scaled down, or both, all models including the Applequist model achieved similar performance: the average percentage error (APE) ranges from 1.15 to 1.23%, and the average unsigned error (AUE) ranges from 0.143 to 0.158 Å(3). When the short-range 1-2, 1-3, and full 1-4 terms are taken into account (set D models), the APE ranges from 1.30 to 1.58% for the three Thole models, whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å(3) for the three Thole models, compared with 0.446 Å(3) for the Applequist model. Further assessment using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact have smaller errors than the models developed using this particular data set (set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy.
State-to-state modeling of non equilibrium low-temperature atomic plasmas
Bultel, Arnaud; Morel, Vincent; Annaloro, Julien; Druguet, Marie-Claude
2017-03-01
The most relevant approach leading to a thorough understanding of the behavior of non equilibrium atomic plasmas is to elaborate state-to-state models in which the mass conservation equation is applied directly to atoms or ions on their excited states. The present communication reports the elaboration of such models and the results obtained. Two situations close to each other are considered. First, the plasmas produced behind shock fronts obtained in ground test facilities (shock tubes) or during planetary atmospheric entries of spacecrafts are discussed. We focused our attention on the nitrogen case for which a complete implementation of the CoRaM-N2 collisional-radiative model has been performed in a steady one-dimensional computation code based on the Rankine-Hugoniot assumptions. Second, the plasmas produced by the interaction between an ultra short laser pulse and a tungsten sample are discussed in the framework of the elaboration of the Laser-Induced Breakdown Spectroscopy (LIBS) technique. In the present case, tungsten has been chosen in the purpose of validating an in situ experimental method able to provide the elemental composition of the divertor wall of a tokamak like WEST or ITER undergoing high energetic deuterium and tritium nuclei fluxes.
High-performance Atomic Clock Modeling and Its Application in Precise Point Positioning
Directory of Open Access Journals (Sweden)
ZHANG Xiaohong
2015-04-01
Full Text Available Presently, many IGS tracking stations have been equipped with high performance atomic clocks. In this paper, the modified Allan variance method is used to analyze the time-domain characterization of random noise of receiver clocks from different IGS tracking stations. Then, we not only evaluate the short-term stability of different types of receiver clock and the feasibility of clock modeling, but also take advantage of the observational data of Active Hydrogen Maser from IGS station in order to constrain random variation of receiver clock offset by implementing short-term clock modeling in precise point positioning(PPP algorithm and improve positioning performance of PPP. The experiment results show that the method of clock modeling reduces the correlation between the height component, the zenith path delay and receiver clock offset parameter, the accuracy of height component can be improved by 50%. The proposed method can improve the PPP performance in crustal deformation monitoring, LEO satellite orbit determination, GNSS methodology and many other high precise GNSS geoscience fields when a high-performance atomic clock is deployed.
Application of atomic force microscopy to the study of natural and model soil particles.
Cheng, S; Bryant, R; Doerr, S H; Rhodri Williams, P; Wright, C J
2008-09-01
The structure and surface chemistry of soil particles has extensive impact on many bulk scale properties and processes of soil systems and consequently the environments that they support. There are a number of physiochemical mechanisms that operate at the nanoscale which affect the soil's capability to maintain native vegetation and crops; this includes soil hydrophobicity and the soil's capacity to hold water and nutrients. The present study used atomic force microscopy in a novel approach to provide unique insight into the nanoscale properties of natural soil particles that control the physiochemical interaction of material within the soil column. There have been few atomic force microscopy studies of soil, perhaps a reflection of the heterogeneous nature of the system. The present study adopted an imaging and force measurement research strategy that accounted for the heterogeneity and used model systems to aid interpretation. The surface roughness of natural soil particles increased with depth in the soil column a consequence of the attachment of organic material within the crevices of the soil particles. The roughness root mean square calculated from ten 25 microm(2) images for five different soil particles from a Netherlands soil was 53.0 nm, 68.0 nm, 92.2 nm and 106.4 nm for the respective soil depths of 0-10 cm, 10-20 cm, 20-30 cm and 30-40 cm. A novel analysis method of atomic force microscopy phase images based on phase angle distribution across a surface was used to interpret the nanoscale distribution of organic material attached to natural and model soil particles. Phase angle distributions obtained from phase images of model surfaces were found to be bimodal, indicating multiple layers of material, which changed with the concentration of adsorbed humic acid. Phase angle distributions obtained from phase images of natural soil particles indicated a trend of decreasing surface coverage with increasing depth in the soil column. This was consistent with
Lu, Shih-I.
2018-01-01
We use the discrete solvent reaction field model to evaluate the linear and second-order nonlinear optical susceptibilities of 3-methyl-4-nitropyridine-1-oxyde crystal. In this approach, crystal environment is created by supercell architecture. A self-consistent procedure is used to obtain charges and polarizabilities for environmental atoms. Impact of atomic polarizabilities on the properties of interest is highlighted. This approach is shown to give the second-order nonlinear optical susceptibilities within error bar of experiment as well as the linear optical susceptibilities in the same order as experiment. Similar quality of calculations are also applied to both 4-N,N-dimethylamino-3-acetamidonitrobenzene and 2-methyl-4-nitroaniline crystals.
Valentin, Jan B; Andreetta, Christian; Boomsma, Wouter; Bottaro, Sandro; Ferkinghoff-Borg, Jesper; Frellsen, Jes; Mardia, Kanti V; Tian, Pengfei; Hamelryck, Thomas
2014-02-01
We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications. Copyright © 2013 Wiley Periodicals, Inc.
Energy Technology Data Exchange (ETDEWEB)
Ren, Jiaqi; Liu, Pinkuan, E-mail: pkliu@sjtu.edu.cn; Zhu, Xiaobo; Zhang, Fan; Chen, Guozhen [State Key Laboratory of Mechanical System and Vibration, School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China)
2014-08-21
Nanochannels are essential features of many microelectronic and biomedical devices. To date, the most commonly employed method to fabricate these nanochannels is atomic force microscopy (AFM). However, there is presently a very poor understanding on the fundamental principles underlying this process, which limits its reliability and controllability. In this study, we present a comprehensive multiscale model by incorporating strain gradient plasticity and strain gradient elasticity theories, which can predict nanochannel depths during AFM-based nanofabrication. The modeling results are directly verified with experiments performed on Cu and Pt substrates. As this model can also be extended to include many additional conditions, it has broad applicability in a wide range of AFM-based nanofabrication applications.
Topological phases of the kicked Harper-Kitaev model with ultracold atoms
Chen, M. N.; Mei, Feng; Su, W.; Wang, Huai-Qiang; Zhu, Shi-Liang; Sheng, L.; Xing, D. Y.
2017-01-01
We propose using ultracold atoms trapped in a one-dimensional periodically driven optical lattice to realize the Harper-Kitaev model, where the on-site energies are periodically kicked. Such a system provides a natural platform to study both Chern insulators and Majorana fermions. Based on calculating the quasienergy spectra, we find that both Floquet Majorana modes and Hall chiral edge modes could appear at the sample boundary in the gaps between the quasienergy bands. We also study the competition of topological superconductor and Chern insulator states in the model. We calculate the {{{Z}}2}× {{{Z}}2} index and Floquet Chern number to characterize the above two different topological states, including the topological phase transitions in the kicked Harper-Kitaev model with the increase in the strength of the kick.
Directory of Open Access Journals (Sweden)
Marco A. M. Rodrigues
2007-01-01
Full Text Available The number of waveforms monitored in power systems is increasing rapidly. This creates a demand for computational tools that aid in the analysis of the phenomena and also that allow efficient transmission and storage of the information acquired. In this context, signal processing techniques play a fundamental role. This work is a tutorial reviewing the principles and applications of atomic signal modeling of electric disturbance signals. The disturbance signal is modeled using a linear combination of damped sinusoidal components which are closely related to the phenomena typically observed in power systems. The signal model obtained is then employed for disturbance signal denoising, filtering of “DC components,” and compression.
Hu, Jie; Chen, Tao; Wang, Moye; Chan, Hue Sun; Zhang, Zhuqing
2017-05-31
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations. The conformations in the unfolded state in common Gō models are more extended, and are thus more in line with experiment, than those from all-atom MD simulations. Nevertheless, the structural features of transition states obtained by the two types of models are largely similar. In contrast, the folding transition paths are significantly more sensitive to modeling details. In particular, when common Gō-like models are augmented with nonnative interactions, the predicted dimensions of the unfolded conformations become similar to those computed using all-atom MD. With this connection, the large deviations of all-atom MD from simple diffusion theory are likely caused in part by the presence of significant nonnative effects in folding processes modelled by current atomic force fields. The ramifications of our findings to the application of coarse-grained modeling to more complex biomolecular systems are discussed.
Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model
Kuno, Yoshihito; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2016-01-01
In this paper, we study atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice. We start from an extended 3D Bose-Hubbard model with nearest-neighbor repulsions and show that it can simulate a U(1) gauge-Higgs model with next nearest-neighbor Higgs couplings. Here the phase of the boson variable on each site of the optical lattice describes the vector potential on each link of the gauge-model lattice. To determine the phase diagram of the gauge-Higgs model at a zero temperature, we perform Monte-Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the three phases, i.e., the confinement, Coulomb and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time-evolution of an electric flux initially put on a straight line connecting two external point charges. We also calculate the potential energy between this pair ...
A coarse-grained computational model of DNA from all-atom molecular dynamics simulations.
Papoian, Garegin; Savelyev, Alexey
2007-03-01
DNA folds into a highly compact chromatin structure in the eukariotic cells. Counterions and the aqueous solvent provide a stabilizing medium for the maintanence of the highly compact and organized DNA structures. Thus, detailed understanding of counterion condensation around DNA is required to build a coarse-grained computational model of a chromatin fiber. We carried out large-scale all-atom Molecular Dynamics simulations of a 16-mer DNA in explicit water with Na+ and K+ counterions to gain insight into generic aspects of monovalent counterion condensation around the whole DNA molecule, focusing on the discrete nature of water and ions. We found that the Na+ ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K+ ions. We have provided a microscopic explanation for the larger Na+ affinity towards DNA, that is based on a combination of steric, electrostatic, and hydration effects. Our simulations are consistent with the prior DNA compaction and electrophoretic mobility experiments. We developed a coarse-grained DNA model based on the results of these all-atom simulations.
Energy Technology Data Exchange (ETDEWEB)
Bertolus, Marjorie, E-mail: marjorie.bertolus@cea.fr [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Freyss, Michel; Dorado, Boris; Martin, Guillaume; Hoang, Kiet; Maillard, Serge; Skorek, Richard; Garcia, Philippe; Valot, Carole [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Chartier, Alain; Van Brutzel, Laurent; Fossati, Paul [CEA, DEN, DPC/SCCME, 91191 Gif-sur-Yvette (France); Grimes, Robin W.; Parfitt, David C.; Bishop, Clare L.; Murphy, Samuel T.; Rushton, Michael J.D. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Staicu, Dragos; Yakub, Eugen; Nichenko, Sergii [European Commission, Joint Research Centre, Institute for Transuranium Elements, 76125 Karlsruhe (Germany); and others
2015-07-15
This article presents a synthesis of the investigations at the atomic scale of the transport properties of defects and fission gases in uranium dioxide, as well as of the transfer of results from the atomic scale to models at the mesoscopic scale, performed during the F-BRIDGE European project (2008–2012). We first present the mesoscale models used to investigate uranium oxide fuel under irradiation, and in particular the cluster dynamics and kinetic Monte Carlo methods employed to model the behaviour of defects and fission gases in UO{sub 2}, as well as the parameters of these models. Second, we describe briefly the atomic scale methods employed, i.e. electronic structure calculations and empirical potential methods. Then, we show the results of the calculation of the data necessary for the mesoscale models using these atomic scale methods. Finally, we summarise the links built between the atomic and mesoscopic scale by listing the data calculated at the atomic scale which are to be used as input in mesoscale modelling. Despite specific difficulties in the description of fuel materials, the results obtained in F-BRIDGE show that atomic scale modelling methods are now mature enough to obtain precise data to feed higher scale models and help interpret experiments on nuclear fuels. These methods bring valuable insight, in particular the formation, binding and migration energies of point and extended defects, fission product localization, incorporation energies and migration pathways, elementary mechanisms of irradiation induced processes. These studies open the way for the investigation of other significant phenomena involved in fuel behaviour, in particular the thermochemical and thermomechanical properties and their evolution in-pile, complex microstructures, as well as of more complex fuels.
Winters, C.; Eckert, Z.; Yin, Z.; Frederickson, K.; Adamovich, I. V.
2018-01-01
This work presents the results of number density measurements of metastable Ar atoms and ground state H atoms in diluted mixtures of H2 and O2 with Ar, as well as ground state O atoms in diluted H2–O2–Ar, CH4–O2–Ar, C3H8–O2–Ar, and C2H4–O2–Ar mixtures excited by a repetitive nanosecond pulse discharge. The measurements have been made in a nanosecond pulse, double dielectric barrier discharge plasma sustained in a flow reactor between two plane electrodes encapsulated within dielectric material, at an initial temperature of 500 K and pressures ranging from 300 Torr to 700 Torr. Metastable Ar atom number density distribution in the afterglow is measured by tunable diode laser absorption spectroscopy, and used to characterize plasma uniformity. Temperature rise in the reacting flow is measured by Rayleigh scattering. H atom and O atom number densities are measured by two-photon absorption laser induced fluorescence. The results are compared with kinetic model predictions, showing good agreement, with the exception of extremely lean mixtures. O atoms and H atoms in the plasma are produced mainly during quenching of electronically excited Ar atoms generated by electron impact. In H2–Ar and O2–Ar mixtures, the atoms decay by three-body recombination. In H2–O2–Ar, CH4–O2–Ar, and C3H8–O2–Ar mixtures, O atoms decay in a reaction with OH, generated during H atom reaction with HO2, with the latter produced by three-body H atom recombination with O2. The net process of O atom decay is O + H → OH, such that the decay rate is controlled by the amount of H atoms produced in the discharge. In extra lean mixtures of propane and ethylene with O2–Ar the model underpredicts the O atom decay rate. At these conditions, when fuel is completely oxidized by the end of the discharge burst, the net process of O atom decay, O + O → O2, becomes nearly independent of H atom number density. Lack of agreement with the
Harrison, Allan G.; Treagust, David F.
2000-01-01
Reports in detail on a year-long case study of multiple-model use at grade 11. Suggests that students who socially negotiated the shared and unshared attributes of common analogical models for atoms, molecules, and chemical bonds used these models more consistently in their explanations. (Author/CCM)
Comparison of all-atom and coarse-grained normal mode analysis in the elastic network model
Energy Technology Data Exchange (ETDEWEB)
Hu, Ming Wen; O' Riordan, Brian; Kim, Byung [University of Massachusetts Amherst, Amherst (United States); Kim, Moon Ki [Sungkyunkwan University, Suwon (Korea, Republic of)
2013-11-15
Elastic network-based normal mode analyses (EN-NMA) of four pairs of open-closed proteins (Lactoferrin, Maltodextrin-binding protein, LAO-binding protein, and Adenylate kinase) were conducted using both all-atom and coarse-grained models. The results indicated that the performance of the all-atom model was similar to that of the coarse-grained model in terms of predicting the conformational changes of backbones. Moreover, dynamic behavior was examined by studying relative atomic displacements and shapes of the dominant mode. For instance, for Maltodextrin-binding protein, the results from the all-atom model differed from those of the coarse-grained model, especially for residues that are biologically relevant. The coarse-grained model has better computational efficiency than the allatom model. However, the former may misrepresent the key dynamics of a protein related to biological functions as a consequence of excessive coarse approximation. Considering that the current power even in a high-end personal computer is sufficient to handle most of protein structures with up to 1,000 residues in a reasonable manner, which can only be used with supercomputers a few decades ago, an all-atom-based EN-NMA may deserve more attention as a reliable and powerful computational tool for protein dynamics study over the conventional coarse-graining approach.
Directory of Open Access Journals (Sweden)
Nuri Yazdani
2014-03-01
Full Text Available Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD. Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.
Energy Technology Data Exchange (ETDEWEB)
Johns, H. M., E-mail: hjohns@lanl.gov; Lanier, N. E.; Kline, J. L.; Fontes, C. J.; Perry, T. S.; Fryer, C. L.; Sherrill, M. E. [Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87544 (United States); Brown, C. R. D.; Morton, J. W. [AWE Aldermaston, Berkshire, Reading RG7 4PR (United Kingdom); Hager, J. D. [Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87544 (United States); Lockheed-Martin, 497 Electronics Parkway, Syracuse, New York 13221 (United States)
2016-11-15
We present synthetic transmission spectra generated with PrismSPECT utilizing both the ATBASE model and the Los Alamos opacity library (OPLIB) to evaluate whether an alternative choice in atomic data will impact modeling of experimental data from radiation transport experiments using Sc-doped aerogel foams (ScSi{sub 6}O{sub 12} at 75 mg/cm{sup 3} density). We have determined that in the 50-200 eV T{sub e} range there is a significant difference in the 1s-3p spectra, especially below 100 eV, and for T{sub e} = 200 eV above 5000 eV in photon energy. Examining synthetic spectra generated using OPLIB with 300 resolving power reveals spectral sensitivity to T{sub e} changes of ∼3 eV.
Malinska, Maura; Dauter, Zbigniew
2016-06-01
In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.
The Pre-Service Science Teachers' Mental Models for Concept of Atoms and Learning Difficulties
Kiray, Seyit Ahmet
2016-01-01
The purpose of this study is to reveal the pre-service science teachers' difficulties about the concept of atoms. The data was collected from two different sources: The Draw an Atom Test (DAAT) and face-to-face interviews. Draw an atom test (DAAT) were administered to the 142 science teacher candidates. To elaborate the results, the researcher…
Applications of a versatile modelling approach to 3D atom probe simulations.
Oberdorfer, Christian; Eich, Sebastian Manuel; Lütkemeyer, Martin; Schmitz, Guido
2015-12-01
The article addresses application examples of a flexible simulation approach, which is based on an irregular mesh of Voronoi cells. The detailed atomic structure of APT field emitters is represented by Wigner-Seitz cells. In this way, arbitrary crystal structures can be modelled. The electric field results from the solution of the Poisson equation. The evaporation sequence of atoms from the emitter surface is enabled by calculation of the field-induced force, which acts on the surface cells. Presented examples show simulated field desorption maps of a cubic fcc structure in comparison to the close-packed hcp structure. Additionally, the desorption maps of the cubic sc, bcc, and fcc lattices in orientation are presented. The effect of inhomogeneous evaporation conditions on the emitter apex curvature is demonstrated. Reconstructions derived from the simulation of Σ5 GBs differently inclined with respect to the emitter axis are analyzed. Finally, the stress exerted on an embedded nano-particle during the simulated evaporation with inhomogeneous evaporation thresholds is estimated. Copyright © 2015 Elsevier B.V. All rights reserved.
Non-local correlation and quantum discord in two atoms in the non-degenerate model
Energy Technology Data Exchange (ETDEWEB)
Mohamed, A.-B.A., E-mail: Abdelbastm@yahoo.com
2012-12-15
By using geometric quantum discord (GQD) and measurement-induced nonlocality (MIN), quantum correlation is investigated for two atoms in the non-degenerate two-photon Tavis-Cummings model. It is shown that there is no asymptotic decay for MIN while asymptotic decay exists for GQD. Quantum correlations can be strengthened by introducing the dipole-dipole interaction. The evolvement period of quantum correlation gets shorter with the increase in the dipole-dipole parameter. It is found that there exists not only quantum nonlocality without entanglement but also quantum nonlocality without quantum discord. Also, the MIN and GQD are raised rather than entanglement, and also with weak initial entanglement, there are MIN and entanglement in a interval of death quantum discord. - Highlights: Black-Right-Pointing-Pointer Geometric quantum discord (GQD) and measurement induced nonlocality (MIN) are used to investigate the correlations of two two-level atoms. Black-Right-Pointing-Pointer There is no asymptotic decay for MIN while asymptotic decay exists for GQD. Black-Right-Pointing-Pointer Quantum correlations can be strengthened by introducing the dipole-dipole interaction. Black-Right-Pointing-Pointer There exists not only quantum nonlocality without entanglement but also without discord. Black-Right-Pointing-Pointer Weak initial entanglement leads to MIN and entanglement in intervals of death discord.
How Sommerfeld extended Bohr's model of the atom (1913-1916)
Eckert, Michael
2014-04-01
Sommerfeld's extension of Bohr's atomic model was motivated by the quest for a theory of the Zeeman and Stark effects. The crucial idea was that a spectral line is made up of coinciding frequencies which are decomposed in an applied field. In October 1914 Johannes Stark had published the results of his experimental investigation on the splitting of spectral lines in hydrogen (Balmer lines) in electric fields, which showed that the frequency of each Balmer line becomes decomposed into a multiplet of frequencies. The number of lines in such a decomposition grows with the index of the line in the Balmer series. Sommerfeld concluded from this observation that the quantization in Bohr's model had to be altered in order to allow for such decompositions. He outlined this idea in a lecture in winter 1914/15, but did not publish it. The First World War further delayed its elaboration. When Bohr published new results in autumn 1915, Sommerfeld finally developed his theory in a provisional form in two memoirs which he presented in December 1915 and January 1916 to the Bavarian Academy of Science. In July 1916 he published the refined version in the Annalen der Physik. The focus here is on the preliminary Academy memoirs whose rudimentary form is better suited for a historical approach to Sommerfeld's atomic theory than the finished Annalen-paper. This introductory essay reconstructs the historical context (mainly based on Sommerfeld's correspondence). It will become clear that the extension of Bohr's model did not emerge in a singular stroke of genius but resulted from an evolving process.
Wandtke, Claudia M; Weil, Matthias; Simpson, Jim; Dittrich, Birger
2017-10-01
Modelling coordination compounds has been shown to be feasible using the invariom method; for the best fit to a given set of diffraction data, additional steps other than using lookup tables of scattering factors need to be carried out. Here such procedures are applied to a number of `duplicate structures', where structures of two or more supposedly different coordination complexes with identical ligand environments, but with different 3d metal ions, were published. However, only one metal atom can be plausibly correct in these structures, and other spectroscopic data are unavailable. Using aspherical scattering factors, a structure can be identified as correct from the deposited Bragg intensities alone and modelling only the ligand environment often suffices to make this distinction. This is not possible in classical refinements using the independent atom model. Quantum-chemical computations of the better model obtained after aspherical-atom refinement further confirm the assignment of the element in the respective figures of merit.
DiMaio, F; Chiu, W
2016-01-01
Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.
Akaygun, Sevil
2016-01-01
Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…
Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2016-01-01
In this paper, we study atomic quantum simulations of $(1+1)$-dimensional($(1+1)$D) U(1) gauge-Higgs models (GHMs) defined on a lattice. We explain how U(1) lattice GHMs appear from an extended Bose-Hubbard model (EBHM) describing ultra-cold atoms with a nearest neighbor repulsion in a 1D optical lattice. We first study a phase diagram of the 1D EBHM at low fillings by means of a quantum Monte-Carlo(MC) simulation. Next, we study the EBHM at large fillings and also GHMs by the MC simulations in the path-integral formalism and show that there are four phases, i.e., the Higgs phase(superfluid), the confinement phase (Mott insulator), and phases corresponding to the density wave and the supersolid. With the obtained phase diagrams, we investigate the relationship between the two models. Finally, we study real-time dynamic of an electric flux in the GHMs by the Gross-Pitaevskii equations and the truncated Wigner approximation.
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F
2007-02-19
Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.
Dislocation core structure and dynamics in two atomic models of {alpha}-zirconium
Energy Technology Data Exchange (ETDEWEB)
Khater, H.A., E-mail: hassan.khater@upc.edu [Department of Engineering, University of Liverpool, Brownlow Hill, Liverpool L69 3GH (United Kingdom); Bacon, D.J. [Department of Engineering, University of Liverpool, Brownlow Hill, Liverpool L69 3GH (United Kingdom)
2010-05-15
Properties of basal and first order prism plane dislocations with Burgers vector 1/3 <112-bar 0> in {alpha}-Zr have been investigated by computer simulation. Results for a recent interatomic potential (MA07) are assessed and compared with an older one (AWB95). The elastic constants have been calculated with the inner relaxations allowed for and the energy and vector of metastable stacking faults have been determined and compared with published ab initio estimates. The core of the screw dislocation spreads principally in the prism plane in the MA07 model, in contrast to basal plane dissociation in the AWB95 model, and the prism-to-basal ratio of the Peierls stress for the screw is 0.28 with the MA07 model, compared with 3.31 with the AWB95 model. Simulation of the dynamics of dislocation motion under applied stress reveal how the drag coefficient varies with slip system and temperature. The results for the MA07 model are consistent with the known slip geometry of Zr, suggesting that it offers significant advantages for large-scale atomic simulation of dislocation behaviour.
Atomic-scale modelling of primary damage and properties of radiation defects in metals
Osetsky, Y N
2003-01-01
Considerable success has been achieved in recent years in the understanding of radiation damage production in high-energy displacement cascades, the properties of the defects and evolution of radiation damage in metals. Two main reasons form the basis of this success. First, the significant increase in computing power has allowed simulation of realistic cascade energies with good statistics and relatively long-time evolution of defects to be carried out. Second, new experimental findings and corresponding theoretical calculations have allowed interpretation of a number of mechanisms and phenomena crucial for understanding and prediction of practically important radiation effects, such as void swelling, radiation growth, matrix hardening and plastic flow localisation. In this paper we review the most significant results in atomic-scale computer modelling related to these issues, mainly focusing on new achievements such as the formation of extended defect clusters, the dynamic properties of defect clusters, int...
Atomic model for the dimeric FO region of mitochondrial ATP synthase.
Guo, Hui; Bueler, Stephanie A; Rubinstein, John L
2017-10-26
Mitochondrial ATP synthase produces the majority of ATP in eukaryotic cells and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded FO region turns the rotor that drives ATP synthesis in the soluble F1 region. While crystal structures of the F1 region have illustrated how rotation leads to ATP synthesis, the lack of an experimental atomic model for the FO region has prevented understanding how proton translocation produces rotation. We determined the structure of the dimeric FO complex from Saccharomyces cerevisiae at 3.6 Å resolution by electron cryomicroscopy. The structure reveals the proton path through the complex, how the complex dimerizes, and suggests how it bends the membrane to produce cristae. Copyright © 2017, American Association for the Advancement of Science.
Atomic Force Microscopy Based Nanorobotics Modelling, Simulation, Setup Building and Experiments
Xie, Hui; Régnier, Stéphane; Sitti, Metin
2012-01-01
The atomic force microscope (AFM) has been successfully used to perform nanorobotic manipulation operations on nanoscale entities such as particles, nanotubes, nanowires, nanocrystals, and DNA since 1990s. There have been many progress on modeling, imaging, teleoperated or automated control, human-machine interfacing, instrumentation, and applications of AFM based nanorobotic manipulation systems in literature. This book aims to include all of such state-of-the-art progress in an organized, structured, and detailed manner as a reference book and also potentially a textbook in nanorobotics and any other nanoscale dynamics, systems and controls related research and education. Clearly written and well-organized, this text introduces designs and prototypes of the nanorobotic systems in detail with innovative principles of three-dimensional manipulation force microscopy and parallel imaging/manipulation force microscopy.
Suzuki, C.; Murakami, I.; Koike, F.; Tamura, N.; Sakaue, H. A.; Morita, S.; Goto, M.; Kato, D.; Ohashi, H.; Higashiguchi, T.; Sudo, S.; O'Sullivan, G.
2017-01-01
We report recent results of extreme ultraviolet (EUV) spectroscopy of highly charged heavy ions in plasmas produced in the Large Helical Device (LHD). The LHD is an ideal source of experimental databases of EUV spectra because of high brightness and low opacity, combined with the availability of pellet injection systems and reliable diagnostic tools. The measured heavy elements include tungsten, tin, lanthanides and bismuth, which are motivated by ITER as well as a variety of plasma applications such as EUV lithography and biological microscopy. The observed spectral features drastically change between quasicontinuum and discrete depending on the plasma temperature, which leads to some new experimental identifications of spectral lines. We have developed collisional-radiative models for some of these ions based on the measurements. The atomic number dependence of the spectral feature is also discussed.
Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.
Dou, Hang; Burrows, Derek W; Baker, Matthew L; Ju, Tao
2017-06-20
Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step. Compared with current methods on both simulated and experimental density maps, our method not only achieves greater accuracy for proteins with large deformations but also runs as fast or faster than many of the other flexible fitting routines. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
A model for energy transfer in collisions of atoms with highly excited molecules.
Houston, Paul L; Conte, Riccardo; Bowman, Joel M
2015-05-21
A model for energy transfer in the collision between an atom and a highly excited target molecule has been developed on the basis of classical mechanics and turning point analysis. The predictions of the model have been tested against the results of trajectory calculations for collisions of five different target molecules with argon or helium under a variety of temperatures, collision energies, and initial rotational levels. The model predicts selected moments of the joint probability distribution, P(Jf,ΔE) with an R(2) ≈ 0.90. The calculation is efficient, in most cases taking less than one CPU-hour. The model provides several insights into the energy transfer process. The joint probability distribution is strongly dependent on rotational energy transfer and conservation laws and less dependent on vibrational energy transfer. There are two mechanisms for rotational excitation, one due to motion normal to the intermolecular potential and one due to motion tangential to it and perpendicular to the line of centers. Energy transfer is found to depend strongly on the intermolecular potential and only weakly on the intramolecular potential. Highly efficient collisions are a natural consequence of the energy transfer and arise due to collisions at "sweet spots" in the space of impact parameter and molecular orientation.
A quasi-stationary numerical model of atomized metal droplets, I: Model formulation
DEFF Research Database (Denmark)
Hattel, Jesper Henri; Pryds, Nini H; Thorborg, Jesper
1999-01-01
A mathematical model for accelerating powder particles by a gas and for their thermal behavior during flight has been developed. Usually, dealing with the solidification of metal droplets, the interaction between an array of droplets and the surrounding gas is not integrated into the modeling...... of such a process, e.g. in the literature the gas temperature is often modeled by an empirical expression. In the present model, however, the interaction between the enveloping gas and an array of droplets has been coupled and calculated numerically. The applicability of the empirical relation of the gas...... temperature proposed in the literature has been discussed in relation to the present model. One of the major advantages of the present modeling is that it provides a tool to predict the thermal behavior of droplets during flight without the need of experimental parameters, i.e. gas temperature. Furthermore...
Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems.
Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; Kestell, John D; Boscoboinik, Alejandro M; Kim, Taejin; Stacchiola, Dario J; Lu, Deyu; Boscoboinik, J Anibal
2017-07-17
The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. In this work, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, the permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. These findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.
Van der Waals interactions and the limits of isolated atom models at interfaces
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
Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems
Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; Kestell, John D.; Boscoboinik, Alejandro M.; Kim, Taejin; Stacchiola, Dario J.; Lu, Deyu; Boscoboinik, J. Anibal
2017-07-01
The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. In this work, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, the permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. These findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.
Spatially resolved modeling and measurements of metastable argon atoms in argon-helium microplasmas
Hoskinson, Alan R.; Gregório, José; Hopwood, Jeffrey; Galbally-Kinney, Kristin L.; Davis, Steven J.; Rawlins, Wilson T.
2017-04-01
Microwave-driven plasmas operating near atmospheric pressure have been shown to be a promising technique for producing the high density of argon metastable atoms required for optically pumped rare gas laser systems. Stable microwave-driven plasmas can be generated at high pressures using microstrip-based resonator circuits. We present results from computational modeling and laser absorption measurements of argon metastable densities in such plasmas operating in argon-helium gas mixtures at pressures up to 300 Torr. The model and measurements resolve the plasma characteristics both perpendicular to the substrate surface and along the resonator length. The measurements qualitatively and in many aspects quantitatively confirm the accuracy of the model. The plasmas exhibit distinct behaviors depending on whether the operating gas is mostly argon or mostly helium. In high-argon plasmas, the metastable density has a large peak value but is confined very closely to the electrode surfaces as well as being reduced near the discharge gap itself. In contrast, metastable densities in high helium-fraction mixtures extend through most of the plasma. In all systems, increasing the power extends the region of metastable along the resonator length, while the extent away from the substrate surface remains approximately constant.
De Backer, A.; van den Bos, K. H. W.; Van den Broek, W.; Sijbers, J.; Van Aert, S.
2017-09-01
An efficient model-based estimation algorithm is introduced in order to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for the overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, is investigated. The highest attainable precision is reached even for low dose images. Furthermore, advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.
Cantrell, John H., Jr.; Cantrell, Sean A.
2008-01-01
A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.
Microfabricated Waveguide Atom Traps.
Energy Technology Data Exchange (ETDEWEB)
Jau, Yuan-Yu [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-09-01
A nanoscale , microfabricated waveguide structure can in - principle be used to trap atoms in well - defined locations and enable strong photon-atom interactions . A neutral - atom platform based on this microfabrication technology will be prealigned , which is especially important for quantum - control applications. At present, there is still no reported demonstration of evanescent - field atom trapping using a microfabricated waveguide structure. We described the capabilities established by our team for future development of the waveguide atom - trapping technology at SNL and report our studies to overcome the technical challenges of loading cold atoms into the waveguide atom traps, efficient and broadband optical coupling to a waveguide, and the waveguide material for high - power optical transmission. From the atomic - physics and the waveguide modeling, w e have shown that a square nano-waveguide can be utilized t o achieve better atomic spin squeezing than using a nanofiber for first time.
Adsorption of metal atoms at a buckled graphene grain boundary using model potentials
Directory of Open Access Journals (Sweden)
Edit E. Helgee
2016-01-01
Full Text Available Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable.
Xia, Ke; Shen, Guang-Bin; Zhu, Xiao-Qing
2015-06-14
32 F420 coenzyme models with alkylation of the three different N atoms (N1, N3 and N10) in the core structure (XFH(-)) were designed and synthesized and the thermodynamic driving forces (defined in terms of the molar enthalpy changes or the standard redox potentials in this work) of the 32 XFH(-) releasing hydride ions, hydrogen atoms and electrons, the thermodynamic driving forces of the 32 XFH˙ releasing protons and hydrogen atoms and the thermodynamic driving forces of XF(-)˙ releasing electrons in acetonitrile were determined using titration calorimetry and electrochemical methods. The effects of the methyl group at N1, N3 and N10 and a negative charge on N1 and N10 atoms on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were examined; the results show that seating arrangements of the methyl group and the negative charge have remarkably different effects on the thermodynamic properties of the F420 coenzyme models and their related reaction intermediates. The effects of the substituents at C7 and C8 on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were also examined; the results show that the substituents at C7 and C8 have good Hammett linear free energy relationships with the six thermodynamic parameters. Meanwhile, a reasonable determination of possible reactions between members of the F420 family and NADH family in vivo was given according to a thermodynamic analysis platform constructed using the elementary step thermodynamic parameter of F420 coenzyme model 2FH(-) and NADH model MNAH releasing hydride ions in acetonitrile. The information disclosed in this work can not only fill a gap in the chemical thermodynamics of F420 coenzyme models as a class of very important organic sources of electrons, hydride ions, hydrogen atoms and protons, but also strongly promote the fast development of the chemistry and applications of F420 coenzyme.
Atomic spin-chain realization of a model for quantum criticality
Toskovic, R.; van den Berg, R.; Spinelli, A.; Eliens, I.S.; van den Toorn, B.; Bryant, B.; Caux, J.-S.; Otte, A.F.
The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum computing and spintronic devices; on the other hand, they can be
Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling.
Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki
2016-01-07
Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene.
Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom
Clark, Ted M.; Chamberlain, Julia M.
2014-01-01
An activity supporting the PhET interactive simulation, Models of the Hydrogen Atom, has been designed and used in the laboratory portion of a general chemistry course. This article describes the framework used to successfully accomplish implementation on a large scale. The activity guides students through a comparison and analysis of the six…
Prayekti
2017-01-01
This research was aimed at developing printed teaching materials of Atomic Physics PEFI4421 Course using Research and Development (R & D) model; which consisted of three major set of activities. The first set consisted of seven stages, the second set consisted of one stage, and the third set consisted of seven stages. This research study was…
Ortega, A; Amorós, D; García de la Torre, J
2011-08-17
Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom, the latter contains one bead per amino acid (or nucleotide) residue, thus allowing calculations when atomic resolution is not available or coarse-grained models are preferred. We parameterized the effective hydrodynamic radius of the elements in the atomic- and residue-level models using a very large set of experimental data for translational and rotational coefficients (intrinsic viscosity and radius of gyration) for >50 proteins. We also extended the calculations to very large proteins and macromolecular complexes, such as the whole 70S ribosome. We show that with proper parameterization, the two levels of resolution yield similar and rather good agreement with experimental data. The new version of HYDROPRO, in addition to considering various computational and modeling schemes, is far more efficient computationally and can be handled with the use of a graphical interface. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Aguiar, Joana G.; Correia, Paulo R. M.
2016-01-01
In this paper, we explore the use of concept maps (Cmaps) as instructional materials prepared by teachers, to foster the understanding of chemistry. We choose fireworks as a macroscopic event to teach basic chemical principles related to the Bohr atomic model and matter-energy interaction. During teachers' Cmap navigation, students can experience…
Savall-Alemany, Francisco; Domènech-Blanco, Josep Lluís; Guisasola, Jenaro; Martínez-Torregrosa, Joaquín
2016-01-01
Our study sets out to identify the difficulties that high school students, teachers, and university students encounter when trying to explain atomic spectra. To do so, we identify the key concepts that any quantum model for the emission and absorption of electromagnetic radiation must include to account for the gas spectra and we then design two…
Energy Technology Data Exchange (ETDEWEB)
A.V.G. Chizmeshya; M.J. McKelvy; G.H. Wolf; R.W. Carpenter; D.A. Gormley; J.R. Diefenbacher; R. Marzke
2006-03-01
have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO2 mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH)2. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO2 mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach has provided a deeper understanding of the key reaction mechanisms than either individual approach can alone. We used ab initio techniques to significantly advance our understanding of atomic-level processes at the solid
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
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Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl; Kolinski, Andrzej [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw (Poland); Co, Nguyen Truong [Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City (Viet Nam); Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City (Viet Nam); Nguyen, Phuong H. [Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan, E-mail: masli@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)
2015-04-14
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in
AxBAxB… pulsed atomic layer deposition: Numerical growth model and experiments
Muneshwar, Triratna; Cadien, Ken
2016-02-01
Atomic layer deposition (ALD) is widely used for the fabrication of advanced semiconductor devices and related nanoscale structures. During ALD, large precursor doses (>1000 L per pulse) are often required to achieve surface saturation, of which only a small fraction is utilized in film growth while the rest is pumped from the system. Since the metal precursor constitutes a significant cost of ALD, strategies to enhance precursor utilization are essential for the scaling of ALD processes. In the precursor reaction step, precursor physisorption is restricted by steric hindrance (mA1) from ligands on the precursor molecules. On reaction, some of these ligands are removed as by-products resulting in chemisorbed species with reduced steric hindrance (mA1 → mA2, where mA2 mA1) and some of the initially hindered surface reaction sites becoming accessible for further precursor physisorption. To utilize these additional reaction sites, we propose a generalized AxBAxB… pulsed deposition where the total precursor dose (ΦA) is introduced as multiple x (x > 1, x ∈ I) short-pulses rather than a single pulse. A numerical first-order surface reaction kinetics growth model is presented and applied to study the effect of AxBAxB… pulsed ALD on the growth per cycle (GPC). The model calculations predict higher GPC for AxBAxB… pulsing than with ABAB… deposition. In agreement with the model predictions, with AxBAxB… pulsed deposition, the GPC was found to increase by ˜46% for ZrN plasma enhanced ALD (PEALD), ˜49% for HfO2 PEALD, and ˜8% for thermal Al2O3 ALD with respect to conventional ABAB… pulsed growth.
Modeling of an atomizer for two fluids; Modelacion de un atomizador de dos fluidos
Energy Technology Data Exchange (ETDEWEB)
Tapia Ramirez, Zoili [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)
1998-09-01
The work reported in this article presents the results of the effort to improve the basic understanding of the flow structure that is formed in a two fluid sprayer before and after the interaction between the sprayed fluid and the spraying fluid. The images in the interior of the mixing chamber of the atomizer are shown, which were taken with a high velocity video camera. Also the results of the numerical simulation of the internal flow obtained by means of a package of commercial modeling are shown. [Espanol] El trabajo reportado en este articulo presenta los resultados del esfuerzo por mejorar el entendimiento basico de la estructura del flujo que se forma en un atomizador de dos fluidos antes y despues de la interaccion entre el fluido atomizado y el fluido atomizante. Se muestran imagenes del flujo en el interior de la camara de mezclado del atomizador, las cuales fueron tomadas con una camara de video de alta velocidad. Tambien se incluyen los resultados de la simulacion numerica del flujo interno obtenidas por medio de un paquete de modelacion comercial.
Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.
2016-01-01
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229
Matsumoto, Atsushi; Miyazaki, Naoyuki; Takagi, Junichi; Iwasaki, Kenji
2017-03-23
In this study, we develop an approach termed "2D hybrid analysis" for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.
Directory of Open Access Journals (Sweden)
Sri Mursiti
2010-06-01
Full Text Available The research of Computer Asissted Instruction with animation and simulation was used to misconception remediation of atomic orbital, molecular orbital, and hibridiziation concepts. The applicated instruction model was focused on concept approach with macromedia flash player and power point programme. The subject of this research were the 2nd semestre students of Chemistry Department. The data were collected by using of true-false pre-test and post- test followed by the reason of its. The analysis reveals that the Computer Asissted Instruction with animation and simulation model increased the understanding of atomic orbital, molecular orbital, and hibridiziation concepts or remediation of concepts missconception, shown by the significant score gained between before and after the implementation of Computer Asissted Instruction with animation and simulation model. The instruction model developed the students's generic skills too. Keywords: animation simulation,misconception remediation, orbital, hibridization
Energy Technology Data Exchange (ETDEWEB)
Pittel, S. [Bartol Research Institute, University of Delaware, Newark, Delaware 19716 (United States); Dukelsky, J. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, Serrano 123, 28006 Madrid (Spain); Dussel, G.G. [Departamento de Fisica Juan Jose Giambiagi, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina)
2004-12-01
We present a family of exactly-solvable models involving the interaction of an ensemble of coupled SU(2) or SU(1,1) systems with a single bosonic field. They arise from the trigonometric Richardson-Gaudin models by replacing one SU(2) or SU(1,1) degree of freedom by an ideal boson. A first application to a system of bosonic atoms and a molecule dimer is reported. (Author) 14 refs., 3 figs.
Directory of Open Access Journals (Sweden)
Qing-Sheng Yang
2014-01-01
Full Text Available This investigation focuses on the design of functionalization configuration at the atomic level to determine the influence of atomic structure on the mechanical properties of functionalized carbon nanotubes (F-CNTs and their composites. Tension and compressive buckling behaviors of different configurations of CNTs functionalized by H atoms are studied by a molecular dynamics (MD method. It is shown that H-atom functionalization reduces Young’s modulus of CNTs, but Young’s modulus is not sensitive to the functionalization configuration. The configuration does, however, affect the tensile strength and critical buckling stress of CNTs. Further, the stress-strain relations of composites reinforced by nonfunctionalized and various functionalized CNTs are analyzed.
Zhou, Chong-Wen; Simmie, John M; Somers, Kieran P; Goldsmith, C Franklin; Curran, Henry J
2017-03-09
Hydrogen atom abstraction from allylic C-H bonds by molecular oxygen plays a very important role in determining the reactivity of fuel molecules having allylic hydrogen atoms. Rate constants for hydrogen atom abstraction by molecular oxygen from molecules with allylic sites have been calculated. A series of molecules with primary, secondary, tertiary, and super secondary allylic hydrogen atoms of alkene, furan, and alkylbenzene families are taken into consideration. Those molecules include propene, 2-butene, isobutene, 2-methylfuran, and toluene containing the primary allylic hydrogen atom; 1-butene, 1-pentene, 2-ethylfuran, ethylbenzene, and n-propylbenzene containing the secondary allylic hydrogen atom; 3-methyl-1-butene, 2-isopropylfuran, and isopropylbenzene containing tertiary allylic hydrogen atom; and 1-4-pentadiene containing super allylic secondary hydrogen atoms. The M06-2X/6-311++G(d,p) level of theory was used to optimize the geometries of all of the reactants, transition states, products and also the hinder rotation treatments for lower frequency modes. The G4 level of theory was used to calculate the electronic single point energies for those species to determine the 0 K barriers to reaction. Conventional transition state theory with Eckart tunnelling corrections was used to calculate the rate constants. The comparison between our calculated rate constants with the available experimental results from the literature shows good agreement for the reactions of propene and isobutene with molecular oxygen. The rate constant for toluene with O 2 is about an order magnitude slower than that experimentally derived from a comprehensive model proposed by Oehlschlaeger and coauthors. The results clearly indicate the need for a more detailed investigation of the combustion kinetics of toluene oxidation and its key pyrolysis and oxidation intermediates. Despite this, our computed barriers and rate constants retain an important internal consistency. Rate constants
Gleadall, Andrew; Pan, Jingzhe; Ding, Lifeng; Kruft, Marc-Anton; Curcó, David
2015-11-01
Molecular dynamics (MD) simulations are widely used to analyse materials at the atomic scale. However, MD has high computational demands, which may inhibit its use for simulations of structures involving large numbers of atoms such as amorphous polymer structures. An atomic-scale finite element method (AFEM) is presented in this study with significantly lower computational demands than MD. Due to the reduced computational demands, AFEM is suitable for the analysis of Young's modulus of amorphous polymer structures. This is of particular interest when studying the degradation of bioresorbable polymers, which is the topic of an accompanying paper. AFEM is derived from the inter-atomic potential energy functions of an MD force field. The nonlinear MD functions were adapted to enable static linear analysis. Finite element formulations were derived to represent interatomic potential energy functions between two, three and four atoms. Validation of the AFEM was conducted through its application to atomic structures for crystalline and amorphous poly(lactide). Copyright © 2015 Elsevier Ltd. All rights reserved.
Model of a realistic InP surface quantum dot extrapolated from atomic force microscopy results.
Barettin, Daniele; De Angelis, Roberta; Prosposito, Paolo; Auf der Maur, Matthias; Casalboni, Mauro; Pecchia, Alessandro
2014-05-16
We report on numerical simulations of a zincblende InP surface quantum dot (QD) on In₀.₄₈Ga₀.₅₂ buffer. Our model is strictly based on experimental structures, since we extrapolated a three-dimensional dot directly by atomic force microscopy results. Continuum electromechanical, [Formula: see text] bandstructure and optical calculations are presented for this realistic structure, together with benchmark calculations for a lens-shape QD with the same radius and height of the extrapolated dot. Interesting similarities and differences are shown by comparing the results obtained with the two different structures, leading to the conclusion that the use of a more realistic structure can provide significant improvements in the modeling of QDs fact, the remarkable splitting for the electron p-like levels of the extrapolated dot seems to prove that a realistic experimental structure can reproduce the right symmetry and a correct splitting usually given by atomistic calculations even within the multiband [Formula: see text] approach. Moreover, the energy levels and the symmetry of the holes are strongly dependent on the shape of the dot. In particular, as far as we know, their wave function symmetries do not seem to resemble to any results previously obtained with simulations of zincblende ideal structures, such as lenses or truncated pyramids. The magnitude of the oscillator strengths is also strongly dependent on the shape of the dot, showing a lower intensity for the extrapolated dot, especially for the transition between the electrons and holes ground state, as a result of a relevant reduction of the wave functions overlap. We also compare an experimental photoluminescence spectrum measured on an homogeneous sample containing about 60 dots with a numerical ensemble average derived from single dot calculations. The broader energy range of the numerical spectrum motivated us to perform further verifications, which have clarified some aspects of the experimental
Energy Technology Data Exchange (ETDEWEB)
von Lilienfeld, O. Anatole [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel, Basel Switzerland; Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass Avenue Lemont Illinois 60439; Ramakrishnan, Raghunathan [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel, Basel Switzerland; Rupp, Matthias [Department of Chemistry, Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, University of Basel, Basel Switzerland; Knoll, Aaron [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne Illinois 60439; Texas Advanced Computing Center, University of Texas, Austin Texas
2015-04-20
We introduce a fingerprint representation of molecules based on a Fourier series of atomic radial distribution functions. This fingerprint is unique (except for chirality), continuous, and differentiable with respect to atomic coordinates and nuclear charges. It is invariant with respect to translation, rotation, and nuclear permutation, and requires no preconceived knowledge about chemical bonding, topology, or electronic orbitals. As such, it meets many important criteria for a good molecular representation, suggesting its usefulness for machine learning models of molecular properties trained across chemical compound space. To assess the performance of this new descriptor, we have trained machine learning models of molecular enthalpies of atomization for training sets with up to 10 k organic molecules, drawn at random from a published set of 134 k organic molecules with an average atomization enthalpy of over 1770 kcal/mol. We validate the descriptor on all remaining molecules of the 134 k set. For a training set of 10 k molecules, the fingerprint descriptor achieves a mean absolute error of 8.0 kcal/mol. This is slightly worse than the performance attained using the Coulomb matrix, another popular alternative, reaching 6.2 kcal/mol for the same training and test sets. (c) 2015 Wiley Periodicals, Inc.
DiMaio, Frank; Song, Yifan; Li, Xueming; Brunner, Matthias J; Xu, Chunfu; Conticello, Vincent; Egelman, Edward; Marlovits, Thomas; Cheng, Yifan; Baker, David
2015-04-01
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.
Energy Technology Data Exchange (ETDEWEB)
De Backer, A.; Bos, K.H.W. van den [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Van den Broek, W. [AG Strukturforschung/Elektronenmikroskopie, Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Sijbers, J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)
2016-12-15
An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. - Highlights: • An efficient model-based method for quantitative electron microscopy is introduced. • Images are modelled as a superposition of 2D Gaussian peaks. • Overlap between neighbouring columns is taken into account. • Structure parameters can be obtained with the highest precision and accuracy. • StatSTEM, auser friendly program (GNU public license) is developed.
Floquet Engineering of Correlated Tunneling in the Bose-Hubbard Model with Ultracold Atoms.
Meinert, F; Mark, M J; Lauber, K; Daley, A J; Nägerl, H-C
2016-05-20
We report on the experimental implementation of tunable occupation-dependent tunneling in a Bose-Hubbard system of ultracold atoms via time-periodic modulation of the on-site interaction energy. The tunneling rate is inferred from a time-resolved measurement of the lattice site occupation after a quantum quench. We demonstrate coherent control of the tunneling dynamics in the correlated many-body system, including full suppression of tunneling as predicted within the framework of Floquet theory. We find that the tunneling rate explicitly depends on the atom number difference in neighboring lattice sites. Our results may open up ways to realize artificial gauge fields that feature density dependence with ultracold atoms.
Atomic-scale Modelling of Electro-catalytic Surfaces and Dynamic Electrochemical Interfaces
DEFF Research Database (Denmark)
Hansen, Martin Hangaard
This dissertation addresses numerical calculations on the atomic scale to study catalytic surfaces for electrochemistry. The first half of the thesis deals with calculations on the properties of catalytic surfaces, using well known methodology, whereas the second half of the thesis deals with the......This dissertation addresses numerical calculations on the atomic scale to study catalytic surfaces for electrochemistry. The first half of the thesis deals with calculations on the properties of catalytic surfaces, using well known methodology, whereas the second half of the thesis deals...... with the development of new methodology to explicitly include the electrolyte in the atomic scale calculations. Chapter 3 presents calculations on contracted and reconstructed platinum surfaces, which are relevant for development of catalysts for proton exchange membrane fuel cells. Correlation of the results...
Luan, P.; Knoll, A. J.; Wang, H.; Kondeti, V. S. S. K.; Bruggeman, P. J.; Oehrlein, G. S.
2017-01-01
The surface interaction of a well-characterized time modulated radio frequency (RF) plasma jet with polystyrene, poly(methyl methacrylate) and poly(vinyl alcohol) as model polymers is investigated. The RF plasma jet shows fast polymer etching but mild chemical modification with a characteristic carbonate ester and NO formation on the etched surface. By varying the plasma treatment conditions including feed gas composition, environment gaseous composition, and treatment distance, we find that short lived species, especially atomic O for Ar/1% O2 and 1% air plasma and OH for Ar/1% H2O plasma, play an essential role for polymer etching. For O2 containing plasma, we find that atomic O initiates polymer etching and the etching depth mirrors the measured decay of O atoms in the gas phase as the nozzle-surface distance increases. The etching reaction probability of an O atom ranging from 10-4 to 10-3 is consistent with low pressure plasma research. We also find that adding O2 and H2O simultaneously into Ar feed gas quenches polymer etching compared to adding them separately which suggests the reduction of O and OH density in Ar/O2/H2O plasma.
Atomic model of anti-phase boundaries in a face-centred icosahedral Zn-Mg-Dy quasicrystal
Wang Jian Bo; Wang Ren Hui
2003-01-01
An atomic model in the physical space for an anti-phase boundary (APB) in the ordered face-centred icosahedral Zn-Mg-Dy quasicrystal phase is presented, based on a six-dimensional model suggested by Ishimasa and Shimizu (2000 Mater. Sci. Eng. A 294-296 232, Ishimasa 2001 private communication). The physical space atomic positions of the defected structure were used for the calculation of the corresponding exit-plane wavefunction and high-resolution transmission electron microscopy images. The analysis of the defect by inverse Fourier transformation reveals that when superstructure reflection spots are used for back-transformation, then at the APB, bright lattice fringes are found to turn into dark ones, and vice versa. When fundamental reflections are used, the APB is not visible. This phenomenon is the same as the corresponding experimental study recently published by Heggen et al(2001a Phys. Rev. B 64 014202). Based on this atomic model it is found that the APB perpendicular to a fivefold axis A5 (APB-A5) i...
A Computer-Controlled Classroom Model of an Atomic Force Microscope
Engstrom, Tyler A.; Johnson, Matthew M.; Eklund, Peter C.; Russin, Timothy J.
2015-01-01
The concept of "seeing by feeling" as a way to circumvent limitations on sight is universal on the macroscopic scale--reading Braille, feeling one's way around a dark room, etc. The development of the atomic force microscope (AFM) in 1986 extended this concept to imaging in the nanoscale. While there are classroom demonstrations that use…
Characterization and modeling of atomic layer deposited high-density trench capacitors in silicon
Matters-Kammerer, M.K.; Jinesh, K.B.; Rijks, T.G.S.M.; Roozeboom, F.; Klootwijk, J.H.
2012-01-01
A detailed electrical analysis of multiple layer trench capacitors fabricated in silicon with atomic-layer-deposited Al 2O 3 and TiN is presented. It is shown that in situ ozone annealing of the Al 2O 3 layers prior to the TiN electrode deposition significantly improves the electric properties of
Klahr, Benjamin M.
An increasing global demand for energy, combined with an awareness of anthropogenic climate change, has recently fueled the search for abundant, carbon neutral energy sources. The sun offers an enormous amount of energy that is practically inexhaustible and well distributed across Earth. Thus, it is an ideal source for meeting our future energy needs in a carbon neutral fashion. This work focuses on using hematite and sunlight to oxidize water, which is the rate limiting step of splitting water into the energy dense fuel, hydrogen, and the byproduct, oxygen. Hematite is abundant, absorbs a large fraction of the solar spectrum and has an appropriately placed valence band for water oxidation. However, the often cited poor bulk properties, and slow charge transfer kinetics require large applied potentials to oxidize water. Atomic layer deposition (ALD) was utilized to deposit uniform thin films of hematite on transparent conductive substrates as model electrodes to better understand the nature of the limitations in the bulk and at the surface. Comparison of the oxidation of water to the oxidation of fast redox shuttles allowed for the separation of bulk and surface processes. A combination of electrochemical impedance spectroscopy, photoelectrochemical and electrochemical measurements were employed to determine the cause of the large required applied potential. It was found that photogenerated holes initially oxidize the electrode surface under water oxidation conditions, which is attributed to the first step in water oxidation. A critical number of these surface intermediates need to be generated in order for subsequent hole-transfer steps to proceed. At low applied potentials, these intermediates are subject to recombination from the large concentration of electrons in the conduction band due to low band bending. At higher applied potentials, high band bending eliminates surface recombination and the charge collection efficiency of the electrolyte reaches unity. A
Energy Technology Data Exchange (ETDEWEB)
Khuseynov, Dmitry; Blackstone, Christopher C.; Culberson, Lori M.; Sanov, Andrei, E-mail: sanov@u.arizona.edu [Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 (United States)
2014-09-28
We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO{sup −} photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions.
Pollak, Eli
2016-07-21
This year we celebrate the 80th anniversary of the Landau-Teller model for energy exchange in a collinear collision of an atom with a harmonic diatomic molecule. Even after 80 years though, the analytic theory to date has not included in it the back-influence of the oscillator's motion on the energy transfer between the approaching particle and the molecule. This is the topic of the present paper. The back-influence can be obtained by employing classical second-order perturbation theory. The second-order theory is used in both a classical and semiclassical context. Classically, analytic expressions are derived for the final phase and action of the diatom, after the collision. The energy loss of the atom is shown to decrease linearly with the increasing energy of the oscillator. The magnitude of this decrease is a direct consequence of the back-reaction of the oscillator on the translational motion. The qualitative result is universal, in the sense that it is not dependent on the details of the interaction of the atom with the oscillator. A numerical application to a model collision of an Ar atom with a Br2 diatom demonstrates the importance and accuracy of the second-order perturbation theory. The same results are then used to derive a second-order perturbation theory semiclassical expression for the quantum transition probability from initial vibrational state ni to final vibrational state nf of the oscillator. A comparison of the theory with exact quantum data is presented for a model collision of Br2 with a hydrogen molecule, where the hydrogen molecule is considered as a single approaching particle.
Sun, Shoutian; Ramu Ramachandran, Bala; Wick, Collin D.
2018-02-01
New interatomic potentials for pure Ti and Al, and binary TiAl were developed utilizing the second nearest neighbour modified embedded-atom method (MEAM) formalism. The potentials were parameterized to reproduce multiple properties spanning bulk solids, solid surfaces, solid/liquid phase changes, and liquid interfacial properties. This was carried out using a newly developed optimization procedure that combined the simple minimization of a fitness function with a genetic algorithm to efficiently span the parameter space. The resulting MEAM potentials gave good agreement with experimental and DFT solid and liquid properties, and reproduced the melting points for Ti, Al, and TiAl. However, the surface tensions from the model consistently underestimated experimental values. Liquid TiAl’s surface was found to be mostly covered with Al atoms, showing that Al has a significant propensity for the liquid/air interface.
Universal bosonic tetramers of dimer-atom-atom structure
Deltuva, A.
2012-01-01
Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.
Johnson, T H; Yuan, Y; Bao, W; Clark, S R; Foot, C; Jaksch, D
2016-06-17
We investigate cold bosonic impurity atoms trapped in a vortex lattice formed by condensed bosons of another species. We describe the dynamics of the impurities by a bosonic Hubbard model containing occupation-dependent parameters to capture the effects of strong impurity-impurity interactions. These include both a repulsive direct interaction and an attractive effective interaction mediated by the Bose-Einstein condensate. The occupation dependence of these two competing interactions drastically affects the Hubbard model phase diagram, including causing the disappearance of some Mott lobes.
Kashefiolasl, Sepide; Foerch, Christian; Pfeilschifter, Waltraud
2013-02-15
Intracerebral hemorrhage (ICH) accounts for 10% of all strokes and has a significantly higher mortality than cerebral ischemia. For decades, ICH has been neglected by experimental stroke researchers. Recently, however, clinical trials on acute blood pressure lowering or hyperacute supplementation of coagulation factors in ICH have spurred an interest to also design and improve translational animal models of spontaneous and anticoagulant-associated ICH. Hematoma volume is a substantial outcome parameter of most experimental ICH studies. We present graphite furnace atomic absorption spectrophotometric analysis (AAS) as a suitable method to precisely quantify hematoma volumes in rodent models of ICH. Copyright © 2012 Elsevier B.V. All rights reserved.
Fast and accurate conversion of atomic models into electron density maps
Directory of Open Access Journals (Sweden)
Carlos O.S. Sorzano
2015-03-01
Full Text Available New image processing methodologies and algorithms have greatly contributed to the signi cant progress in three-dimensional electron microscopy (3DEM of biological complexes we have seen over the last decades. Naturally, the availability of accurate procedures for the objective testing of new algorithms is a crucial requirement for the further advancement of the eld. A good and accepted testing work ow involves the generation of realistic 3DEM-like maps of biological macromolecules from which some measure of ground truth can be derived, ideally because their 3D atomic structure is already known. In this work we propose a very accurate generation of maps using atomic form factors for electron scattering. We thoroughly review current approaches in the eld, quantitatively demonstrating the bene ts of the new methodology. Additionally, we study a concrete example of the use of this approach for hypothesis testing in 3D Electron Microscopy.
A simple nonbinary scattering model applicable to atomic collisions is crystals at 1ow energies
DEFF Research Database (Denmark)
Andersen, Hans Henrik; Sigmund, Peter
1966-01-01
the projectile and each ring atom is described by a Born-Mayer potential, and the scattering is assumed to be elastic and governed by the classical equations of motion. Because of symmetry, the problem can be reduced to plane motion of a particle in a potential of elliptic symmetry. The elliptic force field...... the elliptic to the spherical potential are investigated. Special attention is paid to proper definitions of collision time and collision length which are important in collisions in crystals. Limitations to classical scattering arising from the uncertainty principle prove to be more serious than assumed...... previously. Inelastic contributions to the energy loss can easily be included. The oscillator forces binding lattice atoms turn out to influence the scattering process only at very small energies. The validity of the so-called momentum approximation and a related perturbation method are also investigated....
Li, Yunqi; Zhang, Yang
2009-08-15
Protein structure prediction approaches usually perform modeling simulations based on reduced representation of protein structures. For biological utilizations, it is an important step to construct full atomic models from the reduced structure decoys. Most of the current full atomic model reconstruction procedures have defects which either could not completely remove the steric clashes among backbone atoms or generate final atomic models with worse topology similarity relative to the native structures than the reduced models. In this work, we develop a new protocol, called REMO, to generate full atomic protein models by optimizing the hydrogen-bonding network with basic fragments matched from a newly constructed backbone isomer library of solved protein structures. The algorithm is benchmarked on 230 nonhomologous proteins with reduced structure decoys generated by I-TASSER simulations. The results show that REMO has a significant ability to remove steric clashes, and meanwhile retains good topology of the reduced model. The hydrogen-bonding network of the final models is dramatically improved during the procedure. The REMO algorithm has been exploited in the recent CASP8 experiment which demonstrated significant improvements of the I-TASSER models in both atomic-level structural refinement and hydrogen-bonding network construction. 2009 Wiley-Liss, Inc.
Farrow, Christopher L.; Billinge, Simon J. L.
2008-01-01
Here we show explicitly the relationship between the functions used in the atomic pair distribution function (PDF) method and those commonly used in small angle scattering (SAS) analyses. The origin of the sloping baseline, $-4\\pi r\\rho_0$, in PDFs of bulk materials is identified as originating from the SAS intensity that is neglected in PDF measurements. The non-linear baseline in nanoparticles has the same origin, and contains information about the shape and size of the nanoparticles.
Dynamic response of chlorine atoms on a RuO(2)(110) model catalyst surface.
Hofmann, Jan Philipp; Zweidinger, Stefan; Seitsonen, Ari Paavo; Farkas, Attila; Knapp, Marcus; Balmes, Olivier; Lundgren, Edvin; Andersen, Jesper N; Over, Herbert
2010-12-21
The dynamic behavior of surface accommodated chlorine atoms on RuO(2)(110) was studied by a variety of experimental methods including high resolution core level shift, thermal desorption-, and in situ infrared spectroscopy as well as in situ surface X-ray diffraction in combination with state-of-the-art density functional theory calculations. On the chlorinated RuO(2)(110) surface the undercoordinated oxygen atoms have been selectively replaced by chlorine. These strongly bound surface chlorine atoms shift from bridging to on-top sites when the sample is annealed in oxygen, while the reverse shift of Cl from on-top into bridge positions is observed during CO exposure; the vacant bridge position is then occupied by either chlorine or CO. For the CO oxidation reaction over chlorinated RuO(2)(110), the reactant induced site switching of chlorine causes a site-blocking of the catalytically active one-fold coordinatively unsaturated (1f-cus) Ru sites. This site blocking reduces the number of active sites and, even more important, on-top Cl blocks the free migration of the adsorbed reactants along the one-dimensional 1f-cus Ru rows, thus leading to a loss of catalytic activity.
Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca
2017-06-01
ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural and chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.
Energy Technology Data Exchange (ETDEWEB)
Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca
2017-03-20
ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural and chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.
Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang
2015-04-01
The phase behavior of multicomponent metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamical aspects of a model ternary metallic liquid Cu40Zr51Al9 using molecular dynamics simulations with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (self diffusion coefficient, self relaxation time, and shear viscosity) bordered at Tx˜1300 K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs well above the melting point of the system (Tm˜900 K) in the equilibrium liquid state; and the crossover temperature Tx is roughly twice of the glass-transition temperature of the system (Tg). Below Tx, we found the elemental dynamics decoupled and the Stokes-Einstein relation broke down, indicating the onset of heterogeneous spatially correlated dynamics in the system mediated by dynamic communications among local configurational excitations. To directly characterize and visualize the correlated dynamics, we employed a nonparametric, unsupervised machine learning technique and identified dynamical clusters of atoms with similar atomic mobility. The revealed average dynamical cluster size shows an accelerated increase below Tx and mimics the trend observed in other ensemble averaged quantities that are commonly used to quantify the spatially heterogeneous dynamics such as the non-Gaussian parameter α2 and the four-point correlation function χ4.
Energy Technology Data Exchange (ETDEWEB)
Safronova, M. S. [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Mitroy, J. [School of Engineering, Charles Darwin University, Darwin NT 0909 (Australia); Clark, Charles W. [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, Gaithersburg, Maryland 20899-8410 (United States); Kozlov, M. G. [Petersburg Nuclear Physics Institute, Gatchina 188300 (Russian Federation)
2015-01-22
The atomic dipole polarizability governs the first-order response of an atom to an applied electric field. Atomic polarization phenomena impinge upon a number of areas and processes in physics and have been the subject of considerable interest and heightened importance in recent years. In this paper, we will summarize some of the recent applications of atomic polarizability studies. A summary of results for polarizabilities of noble gases, monovalent, and divalent atoms is given. The development of the CI+all-order method that combines configuration interaction and linearized coupled-cluster approaches is discussed.
Foot, Christopher J
2007-01-01
This text will thoroughly update the existing literature on atomic physics. Intended to accompany an advanced undergraduate course in atomic physics, the book will lead the students up to the latest advances and the applications to Bose-Einstein Condensation of atoms, matter-wave inter-ferometry and quantum computing with trapped ions. The elementary atomic physics covered in the early chapters should be accessible to undergraduates when they are first introduced to the subject. To complement. the usual quantum mechanical treatment of atomic structure the book strongly emphasizes the experimen
National Research Council Canada - National Science Library
Nguyen, Tam L; Schoehn, Guy; Weissenhorn, Winfried; Hermone, Ann R; Burnett, James C; Panchal, Rekha G; McGrath, Connor; Zaharevitz, Dan W; Aman, M. J; Gussio, Rick; Bavari, Sina
2005-01-01
...) to a resolution of approximately 30A. In this paper, we present the refinement of the EM reconstruction of truncated hexameric VP40 to approximately 20A and the construction of an all-atom model (residues 44-212...
Leite, Fabio L.; Bueno, Carolina C.; Da Róz, Alessandra L.; Ziemath, Ervino C.; Oliveira, Osvaldo N.
2012-01-01
The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of AFS, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution. PMID:23202925
Leite, Fabio L; Bueno, Carolina C; Da Róz, Alessandra L; Ziemath, Ervino C; Oliveira, Osvaldo N
2012-10-08
The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of afs, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution.
DEFF Research Database (Denmark)
Krüger, Peter; Hofferberth, S.; Haller, E.
2005-01-01
Miniaturized potentials near the surface of atom chips can be used as flexible and versatile tools for the manipulation of ultracold atoms on a microscale. The full scope of possibilities is only accessible if atom-surface distances can be reduced to microns. We discuss experiments in this regime...
Directory of Open Access Journals (Sweden)
Zhichao Wu
2017-01-01
Full Text Available A new electromechanical coupling model was built to quantitatively analyze the tuning fork probes, especially the complex ones. A special feature of a novel, soft tuning fork probe, that the second eigenfrequency of the probe was insensitive to the effective force gradient, was found and used in a homemade bimodal atomic force microscopy to measure power dissipation quantitatively. By transforming the mechanical parameters to the electrical parameters, a monotonous and concise method without using phase to calculate the power dissipation was proposed.
Energy Technology Data Exchange (ETDEWEB)
Mauche, C W; Liedahl, D A; Akiyama, S; Plewa, T
2008-02-08
We describe the results of an effort, funded by the Lawrence Livermore National Laboratory Directed Research and Development Program, to model, using FLASH time-dependent adaptive-mesh hydrodynamic simulations, XSTAR photoionization calculations, HULLAC atomic data, and Monte Carlo radiation transport, the radiatively-driven photoionized wind and accretion flow of high-mass X-ray binaries (HMXBs). In this final report, we describe the purpose, approach, and technical accomplishments of this effort, including maps of the density, temperature, velocity, ionization parameter, and emissivity distributions of the X-ray emission lines of the well-studied HMXB Vela X-1.
Modelling three-dimensional-quench cooling for alkaline-earth atoms
Mehlstaeubler, T E; Douillet, A; Rehbein, N; Rasel, E M; Ertmer, W
2003-01-01
Quench cooling is a promising technique to reach ultra-cold temperatures in alkaline-earth atoms by Doppler cooling on ultra-narrow transitions. The principles of quench cooling are derived from an effective two-level system with a linewidth adjustable by the quenching laser. A tunable linewidth reconciles the contradictory requirements of a fast cooling rate and a high velocity selectivity at high and low temperatures, respectively. In this paper, we investigate the efficiency of quench cooling in alkaline-earth systems. We present a one-dimensional analytical description of the quenching process. Cooling and trapping in three dimensions is studied with semi-classical Monte Carlo simulations. Our results for magnesium indicate a loading efficiency of up to 40% of pre-cooled atoms at 2 mK into a QuenchMOT. Final temperatures of 9 mu K and an increase in phase-space density by almost five orders of magnitude are observed in the simulations.
Michaud, Georges; Richer, Jacques
2015-01-01
This book gives an overview of atomic diffusion, a fundamental physical process, as applied to all types of stars, from the main sequence to neutron stars. The superficial abundances of stars as well as their evolution can be significantly affected. The authors show where atomic diffusion plays an essential role and how it can be implemented in modelling. In Part I, the authors describe the tools that are required to include atomic diffusion in models of stellar interiors and atmospheres. An important role is played by the gradient of partial radiative pressure, or radiative acceleration, which is usually neglected in stellar evolution. In Part II, the authors systematically review the contribution of atomic diffusion to each evolutionary step. The dominant effects of atomic diffusion are accompanied by more subtle effects on a large number of structural properties throughout evolution. One of the goals of this book is to provide the means for the astrophysicist or graduate student to evaluate the importanc...
Solares, Santiago D
2015-01-01
This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.
Shen, Lin; Yang, Weitao
2016-04-12
We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.
Pan, Lurong; Aller, Stephen G
2015-01-20
P-glycoprotein (Pgp) is an ATP-binding cassette (ABC) transporter that alternates between inward- and outward-facing conformations to capture and force substrates out of cells like a peristaltic pump. The high degree of similarity in outward-facing structures across evolution of ABC transporters allowed construction of a high-confidence outward-facing Pgp atomic model based on crystal structures of outward-facing Sav1866 and inward-facing Pgp. The model adhered to previous experimentally determined secondary- and tertiary- configurations during all-atom molecular dynamics simulations in the presence or absence of MgATP. Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access. The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket. Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms.
Scientific models red atoms, white lies and black boxes in a yellow book
Gerlee, Philip
2016-01-01
A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches a...
Energy Technology Data Exchange (ETDEWEB)
Song, Yuan [State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Lu, Qipeng, E-mail: Luqipeng51@126.com [State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033 (China); Gong, Xuepeng [State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033 (China)
2016-08-01
The use of atomic hydrogen to clean carbon contaminants on multilayers in extreme ultraviolet lithography systems has been extensively investigated. Additional knowledge of the cleaning rate would not only provide a better understanding of the reaction mechanism but would also inform the industry's cleaning process. In this paper, which focuses on the atomic-hydrogen-based carbon contamination cleaning process, a possible mechanism for the associated reactions is studied and a cleaning model is established. The calculated results are in good agreement with the existing experimental data in the literature. The influences of the main factors – such as activation energy and types of contamination – on the cleaning rate are addressed by the model. The model shows that the cleaning rate depends on the type of carbon contamination. The rate for a polymer-like carbon layer is higher than the rate for graphitic and diamond-like carbon layers. At 340 K, the rate for a polymer-like carbon layer is 10 times higher than for graphitic carbon layers. This model could be used effectively to predict and evaluate the cleaning rates for various carbon contamination types. - Highlights: • Mechanism of H{sup 0} cleaning with C contamination on EUV multilayers is given. • Reflectivity of multilayers rely on various types of C contamination is analyzed. • A model of H{sup 0} cleaning various types of C contamination layers is built. • Accurate predicting and evaluating the rate of H{sup 0} cleaning by the mode is proved. • It would be beneficial for improving H{sup 0} cleaning process of carbon layers.
Rakesh, Ramachandran; Srinivasan, Narayanaswamy
2016-01-01
Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpretation at atomic level. Hence they are combined with high resolution structures along with information from other experimental or bioinformatics techniques to obtain pseudo-atomic models. Here, we describe the use of evolutionary conservation of residues as obtained from protein structures and alignments of homologous proteins to detect errors in the fitting of atomic structures as well as improve accuracy of the protein-protein interfacial regions in the cryo-EM density maps.
Huang, Jen-Ching; Weng, Yung-Jin
2014-01-01
This study focused on the nanomachining property and cutting model of single-crystal sapphire during nanomachining. The coated diamond probe is used to as a tool, and the atomic force microscopy (AFM) is as an experimental platform for nanomachining. To understand the effect of normal force on single-crystal sapphire machining, this study tested nano-line machining and nano-rectangular pattern machining at different normal force. In nano-line machining test, the experimental results showed that the normal force increased, the groove depth from nano-line machining also increased. And the trend is logarithmic type. In nano-rectangular pattern machining test, it is found when the normal force increases, the groove depth also increased, but rather the accumulation of small chips. This paper combined the blew by air blower, the cleaning by ultrasonic cleaning machine and using contact mode probe to scan the surface topology after nanomaching, and proposed the "criterion of nanomachining cutting model," in order to determine the cutting model of single-crystal sapphire in the nanomachining is ductile regime cutting model or brittle regime cutting model. After analysis, the single-crystal sapphire substrate is processed in small normal force during nano-linear machining; its cutting modes are ductile regime cutting model. In the nano-rectangular pattern machining, due to the impact of machined zones overlap, the cutting mode is converted into a brittle regime cutting model. © 2014 Wiley Periodicals, Inc.
Energy Technology Data Exchange (ETDEWEB)
Zhang, Yihang; Zhou, Xueqi; Cao, Kun [State Key Laboratory of Digital of Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Chen, Xiuguo; Deng, Zhang [State Key Laboratory of Digital of Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Liu, Shiyuan, E-mail: shyliu@hust.edu.cn [State Key Laboratory of Digital of Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Shan, Bin [State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Chen, Rong, E-mail: rongchen@mail.hust.edu.cn [State Key Laboratory of Digital of Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074 (China)
2015-10-30
Maxwell–Garnett effective medium approximation (MG-EMA) model is chosen to study Pd ultrathin film grown on Si substrate, as well as its growth on self-assembled monolayers (SAMs) modified substrate respectively. The general oscillator (GO) model with one Drude and two Lorentz oscillators is firstly applied to fix the optical constants of Pd. Compared with Pd bulk model, MG-EMA model with GO is more reliable to predict the film thickness verified by X-ray reflection test. The stable growth rate on Si substrate reveals our methods are feasible and the quartz crystal microbalance measurement confirms the stability of the ALD chamber. For Pd coverage, MG-EMA fitting result is similar to the statistical computation from scanning electron microscope when Pd ALD cycles are over 400, while large bias exists for cycles under 400, might be due to that air is not the proper filling medium between nanoparticles. Then we change the filling medium into SAMs as a comparison, better fitting performance is obtained. It is demonstrated that the filling medium between nanoparticles is important for the application of MG-EMA model. - Highlights: • Ultrathin Pd thin films were grown by atomic layer deposition. • The measurement of thin film was important to understand initial growth behavior. • Maxwell–Garnett effective medium approximation model was applied. • Pd nanoparticle size and coverage were studied. • The filling medium between nanoparticles was important for model application.
Energy Technology Data Exchange (ETDEWEB)
Mehring, C.E.
1979-01-01
The problem of this study was to find or develop an appropriate model for a world order which would maintain a balance between it and the various national governments. Underpinning the problem were the assumptions that the world has, historically, moved in the direction of ever larger units of government and of international cooperation, that nationalism and patriotism have always represented major obstacles to this movement, and that world order is necessary to solve the world's major problems. The International Atomic Energy Agency (IAEA) experience, its formal Statute, and its staff were considered as the basis for projecting a model of world order. An autonomous body related to the United Nations, the successes which the IAEA has enjoyed were considered the result of the sound processes and principles on which it is based.
Kulikov, D. A.; Potapov, A. A.; Rassadin, A. E.; Stepanov, A. V.
2017-10-01
In the paper, methods of verification of models for growth of solid state surface by means of atomic force microscopy are suggested. Simulation of growth of fractals with cylindrical generatrix on the solid state surface is presented. Our mathematical model of this process is based on generalization of the Kardar-Parisi-Zhang equation. Corner stones of this generalization are both conjecture of anisotropy of growth of the surface and approximation of small angles. The method of characteristics has been applied to solve the Kardar-Parisi-Zhang equation. Its solution should be considered up to the gradient catastrophe. The difficulty of nondifferentiability of fractal initial generatrix has been overcome by transition from a mathematical fractal to a physical one.
Energy Technology Data Exchange (ETDEWEB)
Grau, A.; Arcos, J. M. los
1986-07-01
The present paper develops a three L-subshell a and K, M-a hells atomic model in order to obtain the counting efficiency in liquid scintillation counting. Mathematical expressions are given to calculate the probabilities of 264 different atomic rearrangement way so as the corresponding effective energies. This new model will permit to test the influence of the different atomic and nuclear parameters upon the counting efficiency nuclides of low and medium atomic number decaying by electron capture. (Author) 8 refs.
Born, Max
1969-01-01
The Nobel Laureate's brilliant exposition of the kinetic theory of gases, elementary particles, the nuclear atom, wave-corpuscles, atomic structure and spectral lines, electron spin and Pauli's principle, quantum statistics, molecular structure and nuclear physics. Over 40 appendices, a bibliography, numerous figures and graphs.
Indian Academy of Sciences (India)
http://www.ias.ac.in/article/fulltext/reso/015/10/0905-0925. Keywords. Atomic theory; Avogadro's hypothesis; atomic weights; periodic table; valence; molecular weights; molecular formula; isomerism. Author Affiliations. S Ramasesha1. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, ...
Genheden, Samuel
2017-10-01
We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.
Atomistic modeling of metallic thin films by modified embedded atom method
Hao, Huali; Lau, Denvid
2017-11-01
Molecular dynamics simulation is applied to investigate the deposition process of metallic thin films. Eight metals, titanium, vanadium, iron, cobalt, nickel, copper, tungsten, and gold, are chosen to be deposited on the aluminum substrate. The second nearest-neighbor modified embedded atom method potential is adopted to predict their thermal and mechanical properties. When quantifying the screening parameters of the potential, the error for Young's modulus and coefficient of thermal expansion between the simulated results and the experimental measurements is less than 15%, demonstrating the reliability of the potential to predict metallic behaviors related to thermal and mechanical properties. A set of potential parameters which governs the interactions between aluminum and other metals in a binary system is also generated from ab initio calculation. The details of interfacial structures between the chosen films and substrate are successfully simulated with the help of these parameters. Our results indicate that the preferred orientation of film growth depends on the film crystal structure, and the inter-diffusion at the interface is correlated the cohesive energy parameter of potential for the binary system. Such finding provides an important basis to further understand the interfacial science, which contributes to the improvement of the mechanical properties, reliability and durability of films.
Physics-based all-atom modeling of RNA energetics and structure.
Smith, Louis G; Zhao, Jianbo; Mathews, David H; Turner, Douglas H
2017-09-01
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422. © 2017 Wiley Periodicals, Inc.
Single atom electrochemical and atomic analytics
Vasudevan, Rama
In the past decade, advances in electron and scanning-probe based microscopies have led to a wealth of imaging and spectroscopic data with atomic resolution, yielding substantial insight into local physics and chemistry in a diverse range of systems such as oxide catalysts, multiferroics, manganites, and 2D materials. However, typical analysis of atomically resolved images is limited, despite the fact that image intensities and distortions of the atoms from their idealized positions contain unique information on the physical and chemical properties inherent to the system. Here, we present approaches to data mine atomically resolved images in oxides, specifically in the hole-doped manganite La5/8Ca3/8MnO3, on epitaxial films studied by in-situ scanning tunnelling microscopy (STM). Through application of bias to the STM tip, atomic-scale electrochemistry is demonstrated on the manganite surface. STM images are then further analyzed through a suite of algorithms including 2D autocorrelations, sliding window Fourier transforms, and others, and can be combined with basic thermodynamic modelling to reveal relevant physical and chemical descriptors including segregation energies, existence and strength of atomic-scale diffusion barriers, surface energies and sub-surface chemical species identification. These approaches promise to provide tremendous insights from atomically resolved functional imaging, can provide relevant thermodynamic parameters, and auger well for use with first-principles calculations to yield quantitative atomic-level chemical identification and structure-property relations. This research was sponsored by the Division of Materials Sciences and Engineering, BES, DOE. Research was conducted at the Center for Nanophase Materials Sciences, which also provided support and is a DOE Office of Science User Facility.
Xiao, Ke; Malvankar, Nikhil S; Shu, Chuanjun; Martz, Eric; Lovley, Derek R; Sun, Xiao
2016-03-22
The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.
Chan, Chi Keung
The aim of this study was to examine the contribution of students' meta-conceptual awareness and modelling skills to their conceptual change when learning atomic-molecular theory. Instructional materials used in the intervention covered three sub-topics: atomic structure, chemical bonding, and structures and properties. Glynn's (1991) Teaching with Analogy model and Chambliss's (2002) guidelines for constructing scientific texts were used as the frameworks for designing and implementing instructional materials for the intervention. Forty-five Secondary 4 chemistry students from two classes at a secondary school in Hong Kong participated in the study. The two classes were taught by the same teacher. The study consisted of two phases. During Phase I, which lasted for 6 weeks, Class A (n = 13) used the above-mentioned instructional materials to learn the three sub-topics, whereas Class B (n = 32) learned the same sub-topics using traditional textbook materials. To further examine the effects of the intervention, a 2-week switching-replication treatment was implemented in Phase II. Class A used traditional textbook materials for revision whereas Class B used the tailor-made instructional materials. A mixed-methods design was used to assess the effectiveness of the intervention. Based on the student misconceptions documented in the literature, a written test of the three sub-topics was developed. The test comprised 33 two-tier multiple-choice items. The test was administered three times: before Phase I (T1), just after Phase I and before Phase II (T2), and 2 weeks after Phase II (T3). Qualitative data were gathered from semi-structured interviews with five students. Three students from Class A and two students from Class B were interviewed individually after Phase I and Phase II, respectively, to assess students' understanding of the essential theoretical concepts and to assess students' modelling skills. The results of paired-samples t-test showed that there was a
Visualization and modeling of impurity atom migration for superdiffusion in semiconductors
Energy Technology Data Exchange (ETDEWEB)
Wada, T. [Nagoya Sangyo University, Aichi (Japan); Kojiguchi, K. [Nagoya Sangyo University, Aichi (Japan); Nagao, H. [Graduate School of information Science, Nagoya University (Japan); Fujimoto, H. [Daido institute of Technology, Nagoya (Japan)]. E-mail: fujimoto@daido-it.ac.jp
2006-04-01
Radiation-enhanced superdiffusion in two-layered structures, comprised of an impurity overlayer and a semiconductor substrate, subjected to electron beam irradiation is modeled and visualized using computer graphics animation. The important and experimentally observed large sticking probabilities of impurities at the wafer surface were modeled in the algorithm, and the animation was found to behave as expected under irradiation. Programming of the animation algorithm was performed using an object modeling technique. The animation generated a continuous display of radiation-enhanced superdiffusion that was qualitatively consistent with experimental observations, thereby facilitating understanding of the superdiffusion process.
Farina, William J.; Bodzin, Alec M.
2017-12-01
Web-based learning is a growing field in education, yet empirical research into the design of high quality Web-based university science instruction is scarce. A one-week asynchronous online module on the Bohr Model of the atom was developed and implemented guided by the knowledge integration framework. The unit design aligned with three identified metaprinciples of science learning: making science accessible, making thinking visible, and promoting autonomy. Students in an introductory chemistry course at a large east coast university completed either an online module or traditional classroom instruction. Data from 99 students were analyzed and results showed significant knowledge growth in both online and traditional formats. For the online learning group, findings revealed positive student perceptions of their learning experiences, highly positive feedback for online science learning, and an interest amongst students to learn chemistry within an online environment.
Quantum-kinetic modeling of electron release in low-energy surface collisions of atoms and molecules
Energy Technology Data Exchange (ETDEWEB)
Marbach, Johannes
2012-09-20
In this work we present a theoretical description of electron release in the collision of atomic and molecular projectiles with metallic and especially dielectric surfaces. The associated electron yield, the secondary electron emission coefficient, is an important input parameter for numerical simulations of dielectric barrier discharges and other bounded low-temperature gas discharges. The available reference data for emission coefficients is, however, very sparse and often uncertain, especially for molecular projectiles. With the present work we aim to contribute to the filling of these gaps by providing a flexible and easy-to-use model that allows for a convenient calculation of the emission coefficient and related quantities for a wide range of projectile-surface systems and the most dominant reaction channels.
Surzhykov, Andrey; Koval, Peter; Fritzsche, Stephan
2005-01-01
Today, the 'hydrogen atom model' is known to play its role not only in teaching the basic elements of quantum mechanics but also for building up effective theories in atomic and molecular physics, quantum optics, plasma physics, or even in the design of semiconductor devices. Therefore, the analytical as well as numerical solutions of the hydrogen-like ions are frequently required both, for analyzing experimental data and for carrying out quite advanced theoretical studies. In order to support a fast and consistent access to these (Coulomb-field) solutions, here we present the DIRAC program which has been developed originally for studying the properties and dynamical behavior of the (hydrogen-like) ions. In the present version, a set of MAPLE procedures is provided for the Coulomb wave and Green's functions by applying the (wave) equations from both, the nonrelativistic and relativistic theory. Apart from the interactive access to these functions, moreover, a number of radial integrals are also implemented in the DIRAC program which may help the user to construct transition amplitudes and cross sections as they occur frequently in the theory of ion-atom and ion-photon collisions. Program summaryTitle of program:DIRAC Catalogue number: ADUQ Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUQ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Computer for which the program is designed and has been tested: All computers with a license of the computer algebra package MAPLE [1] Program language used: Maple 8 and 9 No. of lines in distributed program, including test data, etc.:2186 No. of bytes in distributed program, including test data, etc.: 162 591 Distribution format: tar gzip file CPC Program Library subprograms required: None Nature of the physical problem: Analytical solutions of the hydrogen atom are widely used in very different fields of physics [2,3]. Despite of the rather simple structure
Derman, Aysegül; Kayacan, Kadriye
2017-01-01
A non-experimental descriptive and correlational design was used to examine the "notion of the nature of scientific model, atom achievement and correlation between the two" held by a total sample of 76 prospective science teachers. "Students' Understanding of Models in Science" scale was utilized to evaluate the views of the…
Application of cluster-plus-glue-atom model to barrierless Cu–Ni–Ti and Cu–Ni–Ta films
Energy Technology Data Exchange (ETDEWEB)
Li, Xiaona, E-mail: lixiaona@dlut.edu.cn; Ding, Jianxin; Wang, Miao; Dong, Chuang [Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024 (China); Chu, Jinn P. [Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China)
2014-11-01
To improve the thermal stability of copper and avoid its diffusion into surrounding dielectrics or interfacial reactions with them, the authors applied the cluster-plus-glue-atom model to investigate barrierless Cu–Ni–M (M = Ti or Ta) seed layers. The dissolution of the third element (Ti or Ta) in the Cu lattice with the aid of Ni significantly improved the thermal stability of the Cu seed layer. The appropriate M/Ni (M = Ti or Ta) ratio was selected to obtain a low resistivity: the resistivity was as low as 2.5 μΩ cm for the (Ti{sub 1.5/13.5}Ni{sub 12/13.5}){sub 0.3}Cu{sub 99.7} film and 2.8 μΩ cm for the (Ta{sub 1.1/13.1}Ni{sub 12/13.1}){sub 0.4}Cu{sub 99.6} film after annealing at 500 °C for 1 h. After annealing at 500 °C for 40 h, the two films remained stable without forming a Cu{sub 3}Si compound. The authors confirmed that the range of applications of the cluster-plus-glue-atom model could be extended. Therefore, a third element M with negative enthalpies of mixing with both Cu and Ni could be selected, under the premise that the mixing enthalpy of M–Ni is more negative than that of M–Cu.
Producing high-accuracy lattice models from protein atomic coordinates including side chains.
Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M
2012-01-01
Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.
Energy Technology Data Exchange (ETDEWEB)
Tetchou Nganso, Hugues [Universite Catholique de Louvain (Belgium); University of Douala (Cameroon); Popov, Yuri [Moscow State University (Russian Federation); Piraux, Bernard [Universite Catholique de Louvain (Belgium); Madronero, Javier [Technische Universitaet Muenchen (Germany); Kwato Njock, Moise Godfroy [University of Douala (Cameroon)
2011-07-01
We consider the ionization of atomic hydrogen by a strong infrared field. By starting from the corresponding time-dependent Schroedinger equation in momentum space, we develop a model in which the kernel of the non-local Coulomb potential is replaced by a finite sum of separable potentials. Each separable potential supports one bound state of atomic hydrogen. Here, we consider only the 1s, 2s and 2p states. In this way, the full 3-dimensional Schroedinger equation reduces to a system of a few coupled 1-dimensional linear Volterra integral equations. This model is a theoretical tool to understand the actual role of the atomic potential in the intensity regime where tunnel ionization is supposed to take place and where the experimental data for the first ATI peaks are in contradiction with the theoretical predictions based on the strong field approximation model.
Impact of state-specific flowfield modeling on atomic nitrogen radiation
Johnston, Christopher O.; Panesi, Marco
2018-01-01
A hypersonic flowfield model that treats electronic levels of the dominant afterbody radiator N as individual species is presented. This model allows electron-ion recombination rate and two-temperature modeling improvements, the latter which are shown to decrease afterbody radiative heating by up to 30%. This decrease is primarily due to the addition of the electron-impact excitation energy-exchange term to the energy equation governing the vibrational-electronic electron temperature. This model also allows the validity of the often applied quasi-steady-state (QSS) approximation to be assessed. The QSS approximation is shown to fail throughout most of the afterbody region for lower electronic states, although this impacts the radiative intensity reaching the surface by less than 15%. By computing the electronic-state populations of N within the flowfield solver, instead of through the QSS approximation in the radiation solver, the coupling of nonlocal radiative transition rates to the species continuity equations becomes feasible. Implementation of this higher-fidelity level of coupling between the flowfield and radiation solvers is shown to increase the afterbody radiation by up to 50% relative to the conventional model.
Energy Technology Data Exchange (ETDEWEB)
Pogorelov, Nikolai [Univ. of Alabama, Huntsville, AL (United States); Zhang, Ming [Florida Inst. of Technology, Melbourne, FL (United States)
2016-07-31
Interactions of flows of partially ionized, magnetized plasma are frequently accompanied by the presence of both thermal and non-thermal (pickup) ion components. Such interactions cannot be modeled using traditional MHD equations and require more advanced approaches to treat them. If a nonthermal component of ions is formed due to charge exchange and collisions between the thermal (core) ions and neutrals, it experiences the action of magnetic field, its distribution function is isotropized, and it soon acquires the velocity of the ambient plasma without being thermodynamically equilibrated. This situation, e. g., takes place in the outer heliosphere –- the part of interstellar space beyond the solar system whose properties are determined by the solar wind interaction with the local interstellar medium. This is also possible in laboratory, at million degrees and above, when plasma is conducting electricity far too well, which makes Ohmic heating ineffective. To attain the target temperatures one needs additional heating eventually playing a dominant role. Among such sources is a so-called neutral particle beam heating. This is a wide-spread technique (Joint European Torus and International Thermonuclear Experimental Reactor experiments) based on the injection of powerful beams of neutral atoms into ohmically preheated plasma. In this project we have investigated the energy and density separation between the thermal and nonthermal components in the solar wind and interstellar plasmas. A new model has been developed in which we solve the ideal MHD equations for mixture of all ions and the kinetic Boltzmann equation to describe the transport of neutral atoms. As a separate capability, we can treat the flow of neutral atoms in a multi-component fashion, where neutral atoms born in each thermodynamically distinct region are governed by the Euler gas dynamic equations. We also describe the behavior of pickup ions either kinetically, using the Fokker--Planck equation
Energy Technology Data Exchange (ETDEWEB)
Pogorelov, Nikolai [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and; Zhang, Ming [Florida Inst. of Technology, Melbourne, FL (United States). Physics and Space Sciences Dept.; Borovikov, Sergey [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and Aeronomic Research; Heerikhuisen, Jacob [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and Aeronomic Research; Zank, Gary [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and Aeronomic Research; Gamayunov, Konstantin [Florida Inst. of Technology, Melbourne, FL (United States). Physics and Space Sciences Dept.; Colella, Phillip [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
2016-07-31
Interactions of flows of partially ionized, magnetized plasma are frequently accompanied by the presence of both thermal and non-thermal (pickup) ion components. Such interactions cannot be modeled using traditional MHD equations and require more advanced approaches to treat them. If a nonthermal component of ions is formed due to charge exchange and collisions between the thermal (core) ions and neutrals, it experiences the action of magnetic field, its distribution function is isotropized, and it soon acquires the velocity of the ambient plasma without being thermodynamically equilibrated. This situation, e. g., takes place in the outer heliosphere - the part of interstellar space beyond the solar system whose properties are determined by the solar wind interaction with the local interstellar medium. This is also possible in laboratory, at million degrees and above, when plasma is conducting electricity far too well, which makes Ohmic heating ineffective. To attain the target temperatures one needs additional heating eventually playing a dominant role. Among such sources is a so-called neutral particle beam heating. This is a wide-spread technique (Joint European Torus and International Thermonuclear Experimental Reactor experiments) based on the injection of powerful beams of neutral atoms into ohmically preheated plasma. In this project we have investigated the energy and density separation between the thermal and nonthermal components in the solar wind and interstellar plasmas. A new model has been developed in which we solve the ideal MHD equations for mixture of all ions and the kinetic Boltzmann equation to describe the transport of neutral atoms. As a separate capability, we can treat the flow of neutral atoms in a multi-component fashion, where neutral atoms born in each thermodynamically distinct regions are governed by the Euler gas dynamic equations. We also describe the behavior of pickup ions either kinetically, using the Fokker–Planck equation, or
Prasai, Binay; Wilson, A R; Wiley, B J; Ren, Y; Petkov, Valeri
2015-11-14
The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au(100-x)Pd(x) (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when "tuned up" against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design.
Directory of Open Access Journals (Sweden)
Graves N.
2013-01-01
Full Text Available A model is proposed for the hydrogen atom in which the electron is an objectively real particle orbiting at very near to light speed. The model is based on the postulate that certain velocity terms associated with orbiting bodies can be considered as being af- fected by relativity. This leads to a model for the atom in which the stable electron orbits are associated with orbital velocities where Gamma is n /α , leading to the idea that it is Gamma that is quantized and not angular momentum as in the Bohr and other models. The model provides a mechanism which leads to quantization of energy levels within the atom and also provides a simple mechanical explanation for the Fine Struc- ture Constant. The mechanism is closely associated with the Sampling theorem and the related phenomenon of aliasing developed in the mid-20th century by engineers at Bell labs.
Bagot, P. A. J.; Kreuzer, H. J.; Cerezo, A.; Smith, G. D. W.
2011-08-01
Using a purpose-built 3D atom probe, we have previously shown that exposure to oxidising gases (NO, N2O, O2) induces Rh surface segregation in Pt-Rh alloys, the extent of which is strongly dependent on treatment temperature, crystallographic plane and the presence of ternary alloy additions. In this paper, the segregation trends identified on three different crystallographic surfaces of Pt-Rh are analysed using thermodynamic and kinetic arguments. The segregation model we present is generic for diffusion on alloy surfaces in the presence of active gases. From it we obtain activation energies and diffusion coefficients for the processes of metal-oxide species diffusion both perpendicular to and laterally across the surface. Using these we propose a simple model for the interaction of chemically active gases with the surfaces of such alloys. Applying this understanding to sequential oxidation/reduction treatments would in principle allow improved control of the surface composition of alloy catalysts. Related applications of this model include optimisation of core-shell catalyst nanoparticles.
Cheng, Shuying; Bryant, Robert; Doerr, Stefan H; Wright, Christopher I; Williams, P Rhodri
2009-09-01
Surface images and force measurements obtained using atomic force microscopy (AFM) were used to assess the hydrophobicity of particles from soils and model soil material (smooth glass and acid-washed sand (AWS) exposed to soil-derived humic acid (HA) or lecithin (LE)). Height and phase images, and phase distributions (from soil particles) show complex morphology and heterogeneously distributed organic matter. Forces at model surfaces indicate that, in air, reduction in adhesion corresponded with increased hydrophobicity, but in water, corresponded with a decrease (and serve to guide interpretation of data from natural particles). Adhesion forces on hydrophobic soil particles in water were larger than those for hydrophilic ones, but surface roughness and complexity may obscure any opposite trend for measurements in air. Combination of force measurements, applied forthe first time to soil particles, together with those on model surfaces, and independent assessments of hydrophobicity of corresponding single particle layers, indicate good, but not consistent qualitative agreement between hydophobicity at bulk and nanoscales. AFM is likely to facilitate detailed evaluation of soil particle surface hydrophobicity, which contributes to bulk wetting behavior of soils and other porous systems, including assessments of the potential for contributons to supehydrophobicity from surfaces at the micro- and nanoscales.
Energy Technology Data Exchange (ETDEWEB)
Magnotti, G.M.; Genzale, C.L. (GIT)
2017-12-01
The physical mechanisms characterizing the breakup of a diesel spray into droplets are still unknown. This gap in knowledge has largely been due to the challenges of directly imaging this process or quantitatively measuring the outcomes of spray breakup, such as droplet size. Recent x-ray measurements by Argonne National Laboratory, utilized in this work, provide needed information about the spatial evolution of droplet sizes in selected regions of the spray under a range of injection pressures (50–150 MPa) and ambient densities (7.6–22.8 kg/m3) relevant for diesel operating conditions. Ultra-small angle x-ray scattering (USAXS) measurements performed at the Advanced Photon Source are presented, which quantify Sauter mean diameters (SMD) within optically thick regions of the spray that are inaccessible by conventional droplet sizing measurement techniques, namely in the near-nozzle region, along the spray centerline, and within the core of the spray. To quantify droplet sizes along the periphery of the spray, a complementary technique is proposed and introduced, which leverages the ratio of path-integrated x-ray and visible laser extinction (SAMR) measurements to quantify SMD. The SAMR and USAXS measurements are then utilized to evaluate current spray models used for engine computational fluid dynamic (CFD) simulations. We explore the ability of a carefully calibrated spray model, premised on aerodynamic wave growth theory, to capture the experimentally observed trends of SMD throughout the spray. The spray structure is best predicted with an aerodynamic primary and secondary breakup process that is represented with a slower time constant and larger formed droplet size than conventionally recommended for diesel spray models. Additionally, spray model predictions suggest that droplet collisions may not influence the resultant droplet size distribution along the spray centerline in downstream regions of the spray.
Atomic data for a five-configuration model of Fe XIV
Bhatia, A. K.; Kastner, S. O.
1993-01-01
Collision strengths calculated in the distorted wave approximation are presented for electron excitation of Fe XIV at incident energies of 10, 20 and 30 Rydbergs. Configurations 3s(2)3p, 3s3p(2), 3s(2)3d, 3p(3), and 3s3p3d are included, comprising 40 levels, and wave function mixing coefficients are tabulated. Radiative transition rates are given for the same model using the Superstructure program.
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
Directory of Open Access Journals (Sweden)
Xiaojun Xu
2015-01-01
Full Text Available While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM and small angle X-ray scattering (SAXS have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair.
Atomic masses above /sup 146/Gd derived from a shell model analysis of high spin states
Blomqvist, J; Daly, P J; Kleinheinz, P
1981-01-01
Using extensive spectroscopic data on high spin states involving aligned valence nucleons in very neutron deficient nuclei above /sup 146/Gd the authors have derived the ground state masses of /sup 146 /Gd, /sup 147,148/Tb, /sup 148,149,150/Dy, /sup 149,150,151/Ho, and /sup 150,151,152/Er from a shell model analysis. The mass values show a pronounced irregularity in the two-proton separation energies at /sup 146/Gd. The results also link nine alpha -decay chains to the known masses. (0 refs).
DEFF Research Database (Denmark)
Hukkerikar, Amol; Sarup, Bent; Sin, Gürkan
concentration. The application of the developed methodology is highlighted through a set of molecules not used in the parameter estimation step. The developed methodology can be used to assist uncertainty and sensitivity analysis of product/process design to obtain rationally the risk/ safety factors...... and atomic connectivity index method) has been employed to create the missing groups and predict their contributions through the regressed contributions of connectivity indices. The objective of this work is to develop a systematic methodology to carry out uncertainty analysis of group contribution based...... and atom connectivity index based property prediction models. This includes: (i) parameter estimation using available MG based property prediction models and large training sets to determine improved group and atom contributions; and (ii) uncertainty analysis to establish statistical information...
Hybrid-PIC Modeling of the Transport of Atomic Boron in a Hall Thruster
Smith, Brandon D.; Boyd, Iaian D.; Kamhawi, Hani
2015-01-01
Computational analysis of the transport of boron eroded from the walls of a Hall thruster is performed by implementing sputter yields of hexagonal boron nitride and velocity distribution functions of boron within the hybrid-PIC model HPHall. The model is applied to simulate NASA's HiVHAc Hall thruster at a discharge voltage of 500V and discharge powers of 1-3 kW. The number densities of ground- and 4P-state boron are computed. The density of ground-state boron is shown to be a factor of about 30 less than the plasma density. The density of the excited state is shown to be about three orders of magnitude less than that of the ground state, indicating that electron impact excitation does not significantly affect the density of ground-state boron in the discharge channel or near-field plume of a Hall thruster. Comparing the rates of excitation and ionization suggests that ionization has a greater influence on the density of ground-state boron, but is still negligible. The ground-state boron density is then integrated and compared to cavity ring-down spectroscopy (CRDS) measurements for each operating point. The simulation results show good agreement with the measurements for all operating points and provide evidence in support of CRDS as a tool for measuring Hall thruster erosion in situ.
Sacchi, Mattia; Balleza, Daniel; Vena, Giulia; Puia, Giulia; Facci, Paolo; Alessandrini, Andrea
2015-05-01
Amphiphilic molecules which have a biological effect on specific membrane proteins, could also affect lipid bilayer properties possibly resulting in a modulation of the overall membrane behavior. In light of this consideration, it is important to study the possible effects of amphiphilic molecule of pharmacological interest on model systems which recapitulate some of the main properties of the biological plasma membranes. In this work we studied the effect of a neurosteroid, Allopregnanolone (3α,5α-tetrahydroprogesterone or Allo), on a model bilayer composed by the ternary lipid mixture DOPC/bSM/chol. We chose ternary mixtures which present, at room temperature, a phase coexistence of liquid ordered (Lo) and liquid disordered (Ld) domains and which reside near to a critical point. We found that Allo, which is able to strongly partition in the lipid bilayer, induces a marked increase in the bilayer area and modifies the relative proportion of the two phases favoring the Ld phase. We also found that the neurosteroid shifts the miscibility temperature to higher values in a way similarly to what happens when the cholesterol concentration is decreased. Interestingly, an isoform of Allo, isoAllopregnanolone (3β,5α-tetrahydroprogesterone or isoAllo), known to inhibit the effects of Allo on GABAA receptors, has an opposite effect on the bilayer properties. Copyright © 2015 Elsevier B.V. All rights reserved.
Jain, Vaibhav; Maiti, Prabal K; Bharatam, Prasad V
2016-09-28
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH 2 ) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH 2 ) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH 2 ) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an
Wallace, Rodrick
2015-08-01
The stabilization of human cognition via feedback from embedding social and cultural contexts is a dynamic process deeply intertwined with it, constituting, in a sense, the riverbanks directing the flow of a stream of generalized consciousness at different scales: Cultural norms and social interaction are synergistic with individual and group cognition and their disorders. A canonical failure mode in atomistic cultures is found to be a 'ground state' collapse well represented by atomistic models of economic interaction that are increasingly characterized as divorced from reality by heterodox economists. That is, high rates of psychopathic and antisocial personality disorder and obsessive compulsive disorder emerge as culture-bound syndromes particular to Western or Westernizing societies, or to those undergoing social disintegration.
Size effects and strain localization in atomic-scale cleavage modeling
Elsner, B. A. M.; Müller, S.
2015-09-01
In this work, we study the adhesion and decohesion of Cu(1 0 0) surfaces using density functional theory (DFT) calculations. An upper stress to surface decohesion is obtained via the universal binding energy relation (UBER), but the model is limited to rigid separation of bulk-terminated surfaces. When structural relaxations are included, an unphysical size effect arises if decohesion is considered to occur as soon as the strain energy equals the energy of the newly formed surfaces. We employ the nudged elastic band (NEB) method to show that this size effect is opposed by a size-dependency of the energy barriers involved in the transition. Further, we find that the transition occurs via a localization of bond strain in the vicinity of the cleavage plane, which resembles the strain localization at the tip of a sharp crack that is predicted by linear elastic fracture mechanics.
Directory of Open Access Journals (Sweden)
Berta Gumí-Audenis
2016-12-01
Full Text Available Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs. Atomic force microscope (AFM is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information.
Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua
2013-04-01
The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments. Copyright © 2012 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Li Yuqin
2014-01-01
Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.
Cail, Tracy L.; Hochella, Michael F.
2005-06-01
Atomic force microscopy (AFM) and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory in combination with the interaction force boundary layer (IFBL) model have been used to empirically and theoretically calculate sticking efficiencies (α) of Enterococcus faecalis cells against a silica glass surface. Sticking efficiencies were calculated in solutions of varying pH and ionic strength and related to maximum distances of transport through a hypothetical soil block using colloid filtration theory. AFM measurements show that the repulsive and attractive forces between E. faecalis cells and a glass surface are a function of ionic strength but are less sensitive to changes in solution pH. Zeta (ζ)-potential measurements of the cells and glass surfaces correlate with these trends. Calculated DLVO energy profiles predict much greater sensitivity to changing solution chemistry. Sticking efficiencies derived from AFM measurements range from 9.6 × 10 -17 to 1 in solutions of low ionic strength (IS) and from 2.6 × 10 -33 to 1 at higher IS. Corresponding α values determined from DLVO theory are essentially zero in all tested solutions. Sticking efficiencies calculated in this study are smaller than values determined from column and field studies in similar systems; however, α derived from AFM data and the IFBL model more closely represent field data than do values calculated from DLVO energy values. A comparison with different methods of calculating α suggests that reversible adhesion may be significant in column-scale transport studies.
Nguyen, Hung T.; Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois; Case, David A.
2014-12-01
A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb+ and Sr2+) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein-Zernike equations, with results from the Kovalenko-Hirata closure being closest to experiment for the cases studied here.
Nguyen, Hung T; Pabit, Suzette A; Meisburger, Steve P; Pollack, Lois; Case, David A
2014-12-14
A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb(+) and Sr(2+)) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein-Zernike equations, with results from the Kovalenko-Hirata closure being closest to experiment for the cases studied here.
Loring, FH
2014-01-01
Summarising the most novel facts and theories which were coming into prominence at the time, particularly those which had not yet been incorporated into standard textbooks, this important work was first published in 1921. The subjects treated cover a wide range of research that was being conducted into the atom, and include Quantum Theory, the Bohr Theory, the Sommerfield extension of Bohr's work, the Octet Theory and Isotopes, as well as Ionisation Potentials and Solar Phenomena. Because much of the material of Atomic Theories lies on the boundary between experimentally verified fact and spec
African Journals Online (AJOL)
Atomic Power. By Denis Taylor: Dr. Taylor was formerly Chief UNESCO Advisor at the University. College, Nairobi, Kenya and is now Professor of Electrical Engineering in the Uni- versity of ... method of producing radioactive isotopes, which are materials .... the sealing and the pressure balancing, all can be carried out ...
Horsten, N.; Samaey, G.; Baelmans, M.
2017-11-01
Neutral particles play a crucial role in the plasma edge due to their strong interaction with the plasma. To capture all physics details most often a kinetic equation is solved using a Monte Carlo (MC) approach. Unfortunately, the MC noise hampers the convergence assessment of the solution of the coupled plasma-neutral equations. Moreover, the MC calculation time increases for high-collisional detached cases. In these high-collisional cases, however, the kinetic model may be well-approximated by a fluid neutral model, which can be solved deterministically. In this paper, we assess different fluid neutral models by comparing the resulting plasma sources to the sources from an MC simulation of the kinetic equation. The fluid models take into account the microscopic cross-sections and rate coefficients from the AMJUEL-HYDHEL databases, as well as the microscopic TRIM reflection model. We accomplish the latter without the introduction of any user-defined fitting parameters. We show that a pure pressure-diffusion equation provides accurate results for the particle source, but is inaccurate for the parallel momentum and ion energy source. Adding a parallel momentum equation gives maximum errors of about 9% for the momentum and 32% for the energy source. These errors are further reduced to respectively 6% and 14% by adding a separate neutral energy equation.
Sarkadi, L
2015-01-01
The three-body dynamics of the ionization of the atomic hydrogen by 30 keV antiproton impact has been investigated by calculation of fully differential cross sections (FDCS) using the classical trajectory Monte Carlo (CTMC) method. The results of the calculations are compared with the predictions of quantum mechanical descriptions: The semi-classical time-dependent close-coupling theory, the fully quantal, time-independent close-coupling theory, and the continuum-distorted-wave-eikonal-initial-state model. In the analysis particular emphasis was put on the role of the nucleus-nucleus (NN) interaction played in the ionization process. For low-energy electron ejection CTMC predicts a large NN interaction effect on FDCS, in agreement with the quantum mechanical descriptions. By examining individual particle trajectories it was found that the relative motion between the electron and the nuclei is coupled very weakly with that between the nuclei, consequently the two motions can be treated independently. A simple ...
Gomes, Carla P; Lopes, Cátia D F; Leitner, Michael; Ebner, Andreas; Hinterdorfer, Peter; Pêgo, Ana P
2017-11-01
The ability to design nanoparticle delivery systems capable of selectively target their payloads to specific cell populations is still a major caveat in nanomedicine. One of the main hurdles is the fact that each nanoparticle formulation needs to be precisely tuned to match the specificities of the target cell and route of administration. In this work, molecular recognition force spectroscopy (MRFS) is presented as a tool to evaluate the specificity of neuron-targeted trimethyl chitosan nanoparticles to neuronal cell populations in biological samples of different complexity. The use of atomic force microscopy tips functionalized with targeted or non-targeted nanoparticles made it possible to assess the specific interaction of each formulation with determined cell surface receptors in a precise fashion. More importantly, the combination of MRFS with fluorescent microscopy allowed to probe the nanoparticles vectoring capacity in models of high complexity, such as primary mixed cultures, as well as specific subcellular regions in histological tissues. Overall, this work contributes for the establishment of MRFS as a powerful alternative technique to animal testing in vector design and opens new avenues for the development of advanced targeted nanomedicines. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Energy Technology Data Exchange (ETDEWEB)
Grau Malonda, A.; Fernandez Martinez, A.
1985-07-01
The present paper develops a four-shells atomic model in order to obtain the efficiency of detection in liquid scintillation courting, Mathematical expressions are given to calculate the probabilities of the 229 different atomic rearrangements so as the corresponding effective energies. This new model will permit the study of the influence of the different parameters upon the counting efficiency for nuclides of high atomic number. (Author) 7 refs.
Novoseletsky, Valery; Malak, Olfat A; Loussouarn, Gildas; Sokolova, Olga S
2018-01-01
Voltage-gated potassium channels play pivotal roles in excitable and non-excitable cells. For many decades, structural properties and molecular mechanisms of these channels were inferred from functional observations. At the turn of the twenty-first century, structural biology revealed major aspects in the structural basis of ion channel organization, permeation, and gating. Among the available tools, homology modeling associated with low resolution microscopy helps in delineating the different structural elements of voltage-gated channels. Here, we describe in detail the methodology of homology modeling, using the 3D structure of the Kv2.1ΔCTA ion channel as a reference.
Ko, Jae-Hyeon; Yoo, Dongsuk; Kim, Yong-Hyun
2016-12-22
We formulated atomic models of cation-rich surfaces passivated with anionic ligands for IV-VI, II-VI, and III-V colloidal quantum dots, employing electron counting models and quantum mechanical calculations. We found that the fractional dangling bonds of cation-rich (100) and (111) surfaces could be greatly stabilized by dimerization-anion passivation and amine-anion co-passivation.
Energy Technology Data Exchange (ETDEWEB)
Manos Mavrikakis; James Dumesic; Rahul Nabar; Calvin Bartholonew; Hu Zou; Uchenna Paul
2008-09-29
measurements. The results provide a platform for further development of microkinetic models of FTS on Fe and a basis for more precise modeling of FTS activity of Fe catalysts. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on various realistic models of industrial, Fe-based FTS catalysts. Close-packed, most stable Fe(110) facet was analyzed and subsequently carbide formation was found to be facile leading to the choice of the FeC(110) model representing a Fe facet with a sub-surface C atom. The Pt adatom (Fe{sup Pt}(110)) was found to be the most stable model for our studies into Pt promotion and finally the role of steps was elucidated by recourse to the defected Fe(211) facet. Binding Energies(BEs), preferred adsorption sites and geometries for all FTS relevant stable species and intermediates were evaluated on each model catalyst facet. A mechanistic model (comprising of 32 elementary steps involving 19 species) was constructed and each elementary step therein was fully characterized with respect to its thermochemistry and kinetics. Kinetic calculations involved evaluation of the Minimum Energy Pathways (MEPs) and activation energies (barriers) for each step. Vibrational frequencies were evaluated for the preferred adsorption configuration of each species with the aim of evaluating entropy-changes, pre exponential factors and serving as a useful connection with experimental surface science techniques. Comparative analysis among these four facets revealed important trends in their relative behavior and roles in FTS catalysis. Overall the First Principles Calculations afforded us a new insight into FTS catalysis on Fe and modified-Fe catalysts.
Yuqin, Li; Guirong, You; Zhen, Yang; Caihong, Liu; Baoxiu, Jia; Jiao, Chen; Yurong, Guo
2014-01-01
The interaction of patulin with human serum albumin (HSA) was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis), circular dichroism (CD), atomic force microscopy (AFM), and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K) were 2.60 × 10(4), 4.59 × 10(4), and 7.01 × 10(4) M(-1) at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG (0), ΔH (0), and ΔS (0) values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.
Crease, Robert P.
2009-01-01
The American composer John Adams uses opera to dramatize controversial current events. His 1987 work Nixon in China was about the landmark meeting in 1972 between US President Richard Nixon and Chairman Mao Zedong of China; The Death of Klinghoffer (1991) was a musical re-enactment of an incident in 1985 when Palestinian terrorists kidnapped and murdered a wheelchair-bound Jewish tourist on a cruise ship. Adams's latest opera, Doctor Atomic, is also tied to a controversial event: the first atomic-bomb test in Alamogordo, New Mexico, on 16 June 1945. The opera premièred in San Francisco in 2005, had a highly publicized debut at the Metropolitan Opera in New York in 2008, and will have another debut on 25 February - with essentially the same cast - at the English National Opera in London.
Energy Technology Data Exchange (ETDEWEB)
Goldschmidt, B.
1990-01-01
This book is a memoir of rivalries among the Allies over the bomb, by a participant and observer. Nuclear proliferation began in the uneasy wartime collaboration of the United States, England, Canada, and Free France to produce the atom bomb. Through the changes of history, a young French chemist had a role in almost every act of this international drama. This memoir is based on Goldschmidt's own recollections, interviews with other leading figures, and 3,000 pages of newly declassified documents in Allied archives. From his own start as Marie Curie's lab assistant, Goldschmidt's career was closely intertwined with Frances complicated rise to membership in the nuclear club. As a refugee from the Nazis, he became part of the wartime nuclear energy project in Canada and found himself the only French scientist to work (although briefly) on the American atom bomb project.
Alania, M; Lobato, I; Van Aert, S
2018-01-01
In this paper, both the frozen lattice (FL) and the absorptive potential (AP) approximation models are compared in terms of the integrated intensity and the precision with which atomic columns can be located from an image acquired using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM). The comparison is made for atoms of Cu, Ag, and Au. The integrated intensity is computed for both an isolated atomic column and an atomic column inside an FCC structure. The precision has been computed using the so-called Cramér-Rao Lower Bound (CRLB), which provides a theoretical lower bound on the variance with which parameters can be estimated. It is shown that the AP model results into accurate measurements for the integrated intensity only for small detector ranges under relatively low angles and for small thicknesses. In terms of the attainable precision, both methods show similar results indicating picometer range precision under realistic experimental conditions. Copyright © 2017 Elsevier B.V. All rights reserved.
Gu, Ming Feng
2018-02-01
FAC calculates various atomic radiative and collisional processes, including radiative transition rates, collisional excitation and ionization by electron impact, energy levels, photoionization, and autoionization, and their inverse processes radiative recombination and dielectronic capture. The package also includes a collisional radiative model to construct synthetic spectra for plasmas under different physical conditions.
Zhang, Juling; Gu, Huaimin; Zhang, Xiaohui
2014-01-30
The interaction of 4-thiothymidine (S(4)TdR) with human serum albumin (HSA) was studied by equilibrium dialysis under normal physiological conditions. In this work, the mechanism of the interaction between S(4)TdR and human serum albumin (HSA) was exploited by fluorescence, UV, CD circular, and SERS spectroscopic. Fluorescence and UV spectroscopy suggest that HSA intensities are significantly decreased when adding S(4)TdR to HAS, and the quenching mechanism of the fluorescence is static. Also, the ΔG, ΔH, and ΔS values across temperature indicated that hydrophobic interaction was the predominant binding force. The CD circular results show that there is little change in the secondary structure of HSA except the environment of amino acid changes when adding S(4)TdR to HSA. The surface-enhanced Raman scattering (SERS) shows that the interaction between S(4)TdR and HSA can be achieved through different binding sites which are probably located in the II A and III A hydrophobic pockets of HSA which correspond to Sudlow's I and II binding sites. In addition, the molecular modeling displays that S(4)TdR-HSA complex is stabilized by hydrophobic forces, which result from amino acid residues. The atomic force microscopy results revealed that the single HSA molecular dimensions were larger after interaction of 4-thiothymidine. This work would be useful to understand the state of the transportation, distribution, and metabolism of the anticancer drugs in the human body, and it could provide a useful biochemistry parameter for the development of new anti-cancer drugs and research of pharmacology mechanisms. Copyright © 2013 Elsevier Ltd. All rights reserved.
Guo, Fei; Liu, Zheng; Fang, Ping-An; Zhang, Qinfen; Wright, Elena T; Wu, Weimin; Zhang, Ci; Vago, Frank; Ren, Yue; Jakana, Joanita; Chiu, Wah; Serwer, Philip; Jiang, Wen
2014-10-28
Many dsDNA viruses first assemble a DNA-free procapsid, using a scaffolding protein-dependent process. The procapsid, then, undergoes dramatic conformational maturation while packaging DNA. For bacteriophage T7 we report the following four single-particle cryo-EM 3D reconstructions and the derived atomic models: procapsid (4.6-Å resolution), an early-stage DNA packaging intermediate (3.5 Å), a later-stage packaging intermediate (6.6 Å), and the final infectious phage (3.6 Å). In the procapsid, the N terminus of the major capsid protein, gp10, has a six-turn helix at the inner surface of the shell, where each skewed hexamer of gp10 interacts with two scaffolding proteins. With the exit of scaffolding proteins during maturation the gp10 N-terminal helix unfolds and swings through the capsid shell to the outer surface. The refolded N-terminal region has a hairpin that forms a novel noncovalent, joint-like, intercapsomeric interaction with a pocket formed during shell expansion. These large conformational changes also result in a new noncovalent, intracapsomeric topological linking. Both interactions further stabilize the capsids by interlocking all pentameric and hexameric capsomeres in both DNA packaging intermediate and phage. Although the final phage shell has nearly identical structure to the shell of the DNA-free intermediate, surprisingly we found that the icosahedral faces of the phage are slightly (∼4 Å) contracted relative to the faces of the intermediate, despite the internal pressure from the densely packaged DNA genome. These structures provide a basis for understanding the capsid maturation process during DNA packaging that is essential for large numbers of dsDNA viruses.
Happer, William; Walker, Thad
2010-01-01
Covering the most important knowledge on optical pumping of atoms, this ready reference is backed by numerous examples of modelling computation for optical pumped systems. The authors show for the first time that modern scientific computing software makes it practical to analyze the full, multilevel system of optically pumped atoms. To make the discussion less abstract, the authors have illustrated key points with sections of MATLAB codes. To make most effective use of contemporary mathematical software, it is especially useful to analyze optical pumping situations in the Liouville spa
Reddy, Karnati Konda; Singh, Sanjeev Kumar; Dessalew, Nigus; Tripathi, Sunil Kumar; Selvaraj, Chandrabose
2012-06-01
Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to N-methyl pyrimidones as HIV-1 integrase inhibitors. Based on the ligand-based pharmacophore model, we got 5-point pharmacophore model AADDR, with two hydrogen bond acceptors (A), two hydrogen bond donors (D) and one aromatic ring (R). The generated pharmacophore-based alignment was used to derive a predictive atom-based 3D-QSAR model for the training set (r(2) = 0.92, SD = 0.16, F = 84.8, N = 40) and for test set (Q(2) = 0.71, RMSE = 0.06, Pearson R = 0.90, N = 10). From these results, AADDR pharmacophore feature was selected as best common pharmacophore hypothesis, and atom-based 3D-QSAR results also support the outcome by means of favourable and unfavourable regions of hydrophobic and electron-withdrawing groups for the most potent compound 30. These results can be useful for further design of new and potent HIV-1 IN inhibitors.
Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy; He, Jing
2017-01-01
Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.
Jordan, Thomas M.; And Others
1992-01-01
Presents a model of a generic atom that is used to represent the movement of electrons from lower to higher levels and vice-versa due to excitation and de-excitation of the atom. As the process of de-excitation takes place, photons represented by colored ping-pong balls are emitted, indicating the emission of light. (MDH)
Bouchikhi, A.
2017-09-01
The physical properties of Ne-Xe DC glow discharges at low pressure are reported for a gap length of 1 cm for the first time in the literature. The model deals specifically with the first three moments of Boltzmann’s equation and includes the radiation processes and metastable atom densities. The spatio-temporal distributions of the electron and neon and xenon ion densities, the neon and xenon metastable atom densities, the electric potential and the electric field as well as the mean electron energy are presented at 1.5 Torr and 250 V. The current-voltage characteristic is shown at 3 Torr, and it is compared with previous work for pure neon gas. The model is validated theoretically and experimentally in the case of pure gas.
Atom Skimmers and Atom Lasers Utilizing Them
Hulet, Randall; Tollett, Jeff; Franke, Kurt; Moss, Steve; Sackett, Charles; Gerton, Jordan; Ghaffari, Bita; McAlexander, W.; Strecker, K.; Homan, D.
2005-01-01
Atom skimmers are devices that act as low-pass velocity filters for atoms in thermal atomic beams. An atom skimmer operating in conjunction with a suitable thermal atomic-beam source (e.g., an oven in which cesium is heated) can serve as a source of slow atoms for a magneto-optical trap or other apparatus in an atomic-physics experiment. Phenomena that are studied in such apparatuses include Bose-Einstein condensation of atomic gases, spectra of trapped atoms, and collisions of slowly moving atoms. An atom skimmer includes a curved, low-thermal-conduction tube that leads from the outlet of a thermal atomic-beam source to the inlet of a magneto-optical trap or other device in which the selected low-velocity atoms are to be used. Permanent rare-earth magnets are placed around the tube in a yoke of high-magnetic-permeability material to establish a quadrupole or octupole magnetic field leading from the source to the trap. The atoms are attracted to the locus of minimum magnetic-field intensity in the middle of the tube, and the gradient of the magnetic field provides centripetal force that guides the atoms around the curve along the axis of the tube. The threshold velocity for guiding is dictated by the gradient of the magnetic field and the radius of curvature of the tube. Atoms moving at lesser velocities are successfully guided; faster atoms strike the tube wall and are lost from the beam.
Caffau, E.; Ludwig, H.-G.; Bonifacio, P.; Faraggiana, R.; Steffen, M.; Freytag, B.; Kamp, I.; Ayres, T. R.
Context. The analysis of the solar spectra using hydrodynamical simulations, with a specific selection of lines, atomic data, and method for computing deviations from local thermodynamical equilibrium, has led to a downward revision of the solar metallicity, Z. We are using the latest simulations
Piras, D.; Sadeghian Marnani, H.
2017-01-01
Ultrasound atomic force microscopy (US-AFM) has been used for subsurface imaging of nanostructures. The contact stiffness variations have been suggested as the origin of the image contrast. Therefore, to analyze the image contrast, the local changes in the contact stiffness due to the presence of
High Atom Number in Microsized Atom Traps
2015-12-14
Final Performance Report on ONR Grant N00014-12-1-0608 High atom number in microsized atom traps for the period 15 May 2012 through 14 September...TYPE Final Technical Report 3. DATES COVERED (From - To) 05/15/2012-09/14/2012 4. TITLE AND SUBTITLE High atom number in microsized atom traps...forces for implementing a small-footprint, large-number atom -chip instrument. Bichromatic forces rely on absorption and stimulated emission to produce
Zhou, Chong-Wen; Simmie, John M; Pitz, William J; Curran, Henry J
2016-09-15
Theoretical aspects of the development of a chemical kinetic model for the pyrolysis and combustion of a cyclic ketone, cyclopentanone, are considered. Calculated thermodynamic and kinetic data are presented for the first time for the principal species including 2- and 3-oxo-cyclopentyl radicals, which are in reasonable agreement with the literature. These radicals can be formed via H atom abstraction reactions by Ḣ and Ö atoms and ȮH, HȮ2, and ĊH3 radicals, the rate constants of which have been calculated. Abstraction from the β-hydrogen atom is the dominant process when ȮH is involved, but the reverse holds true for HȮ2 radicals. The subsequent β-scission of the radicals formed is also determined, and it is shown that recent tunable VUV photoionization mass spectrometry experiments can be interpreted in this light. The bulk of the calculations used the composite model chemistry G4, which was benchmarked in the simplest case with a coupled cluster treatment, CCSD(T), in the complete basis set limit.
Hill, Katalin; Pénzes, Csanád Botond; Schnöller, Donát; Horváti, Kata; Bosze, Szilvia; Hudecz, Ferenc; Keszthelyi, Tamás; Kiss, Eva
2010-10-07
Tensiometry, sum-frequency vibrational spectroscopy, and atomic force microscopy were employed to assess the cell penetration ability of a peptide conjugate of the antituberculotic agent isoniazide. Isoniazide was conjugated to peptide (91)SEFAYGSFVRTVSLPV(106), a functional T-cell epitope of the immunodominant 16 kDa protein of Mycobacterium tuberculosis. As a simple but versatile model of the cell membrane a phospholipid Langmuir monolayer at the liquid/air interface was used. Changes induced in the structure of the phospholipid monolayer by injection of the peptide conjugate into the subphase were followed by tensiometry and sum-frequency vibrational spectroscopy. The drug penetrated lipid films were transferred to a solid support by the Langmuir-Blodgett technique, and their structures were characterized by atomic force microscopy. Peptide conjugation was found to strongly enhance the cell penetration ability of isoniazide.
Atomic layer deposition for semiconductors
Hwang, Cheol Seong
2014-01-01
This edited volume discusses atomic layer deposition (ALD) for all modern semiconductor devices, moving from the basic chemistry of ALD and modeling of ALD processes to sections on ALD for memories, logic devices, and machines.
Tests of stratospheric models - The reactions of atomic chlorine with O3 and CH4 at low temperature
Demore, W. B.
1991-01-01
The rate-constant ratio of the photochemical reactions of atomic chlorine with O3 and CH4 was determined using data from laboratory experiments on competitive chlorination of O3/CH4 mixtures at stratospheric temperatures (197-217 K). Two experimental approaches were used: (1) measuring the k1/k2 ratio for the reactions of atomic chlorine with ozone and methane and (2) testing for some of the ClO/CH3O2 chemistry. The chlorine and ozone concentrations were monitored by UV-Vis spectroscopy, and the CH3Cl concentration was measured by FTIR. The results on the k1/k2 ratio are in excellent agreement with the current NASA recommendation (DeMore et al., 1990), being only 12 percent higher. On the other hand, results on the ClO + CH3O2 reaction do not support the rate constant suggested by Simon et al. (1989).
Farrow, Christopher L; Billinge, Simon J L
2009-05-01
The relationship between the equations used in the atomic pair distribution function (PDF) method and those commonly used in small-angle-scattering (SAS) analyses is explicitly shown. The origin of the sloping baseline, -4pirrho0, in PDFs of bulk materials is identified as originating from the SAS intensity that is neglected in PDF measurements. The nonlinear baseline in nanoparticles has the same origin, and contains information about the shape and size of the nanoparticles.
Atoms – How Small, and How Large!
Indian Academy of Sciences (India)
IAS Admin
Introduction. −Richard Feynman. Famous physicist Feynman's quote highlighting the atomic concept as an important achievement of mankind, has come nearly ... philosophy to science. How small are atoms actually? Niels Bohr in his atomic model (1913) answered this question by assigning a radius a0 (= 0.529Å) to the.
Surface modelling on heavy atom crystalline compounds: HfO{sub 2} and UO{sub 2} fluorite structures
Energy Technology Data Exchange (ETDEWEB)
Evarestov, Robert [Department of Quantum Chemistry, St. Petersburg State University, 26 Universitetsky Prospect, Peterhof, St. Petersburg 198504 (Russian Federation)], E-mail: re1973@re1973.spb.edu; Bandura, Andrei; Blokhin, Eugeny [Department of Quantum Chemistry, St. Petersburg State University, 26 Universitetsky Prospect, Peterhof, St. Petersburg 198504 (Russian Federation)
2009-01-15
The study of the bulk and surface properties of cubic (fluorite structure) HfO{sub 2} and UO{sub 2} was performed using the hybrid Hartree-Fock density functional theory linear combination of atomic orbitals simulations via the CRYSTAL06 computer code. The Stuttgart small-core pseudopotentials and corresponding basis sets were used for the core-valence interactions. The influence of relativistic effects on the structure and properties of the systems was studied. It was found that surface properties of Mott-Hubbard dielectric UO{sub 2} differ from those found for other metal oxides with the closed-shell configuration of d-electrons.
Knowledge Extraction from Atomically Resolved Images.
Vlcek, Lukas; Maksov, Artem; Pan, Minghu; Vasudevan, Rama K; Kalinin, Sergei V
2017-10-24
Tremendous strides in experimental capabilities of scanning transmission electron microscopy and scanning tunneling microscopy (STM) over the past 30 years made atomically resolved imaging routine. However, consistent integration and use of atomically resolved data with generative models is unavailable, so information on local thermodynamics and other microscopic driving forces encoded in the observed atomic configurations remains hidden. Here, we present a framework based on statistical distance minimization to consistently utilize the information available from atomic configurations obtained from an atomically resolved image and extract meaningful physical interaction parameters. We illustrate the applicability of the framework on an STM image of a FeSe x Te 1-x superconductor, with the segregation of the chalcogen atoms investigated using a nonideal interacting solid solution model. This universal method makes full use of the microscopic degrees of freedom sampled in an atomically resolved image and can be extended via Bayesian inference toward unbiased model selection with uncertainty quantification.
Banks, Bruce A.; Auer, Bruce M.; Rutledge, Sharon K.; Degroh, Kim K.; Gebauer, Linda
1992-01-01
The results of ground laboratory and in-space exposure of polymeric materials to atomic oxygen has enabled the development of a Monte Carlo computational model which simulates the oxidation processes of both environments. The cost effective projection of long-term low-Earth-orbital durability of protected polymeric materials such as SiO(x)-coated polyimide Kapton photovoltaic array blankets will require ground-based testing to assure power system reliability. Although silicon dioxide thin film protective coatings can greatly extend the useful life of polymeric materials in ground-based testing, the projection of in-space durability based on these results can be made more reliable through the use of modeling which simulates the mechanistic properties of atomic oxygen interaction, and replicates test results in both environments. Techniques to project long-term performance of protected materials, such as the Space Station Freedom solar array blankets, are developed based on ground laboratory experiments, in-space experiments, and computational modeling.
Kochukhov, O.; Ryabchikova, T. A.
2018-02-01
A series of recent theoretical atomic diffusion studies has address the challenging problem of predicting inhomogeneous vertical and horizontal chemical element distributions in the atmospheres of magnetic ApBp stars. Here we critically assess the most sophisticated of such diffusion models - based on a time-dependent treatment of the atomic diffusion in a magnetized stellar atmosphere - by direct comparison with observations as well by testing the widely used surface mapping tools with the spectral line profiles predicted by this theory. We show that the mean abundances of Fe and Cr are grossly underestimated by the time-dependent theoretical diffusion model, with discrepancies reaching a factor of 1000 for Cr. We also demonstrate that Doppler imaging inversion codes, based either on modelling of individual metal lines or line-averaged profiles simulated according to theoretical three-dimensional abundance distribution, are able to reconstruct correct horizontal chemical spot maps despite ignoring the vertical abundance variation. These numerical experiments justify a direct comparison of the empirical two-dimensional Doppler maps with theoretical diffusion calculations. This comparison is generally unfavourable for the current diffusion theory, as very few chemical elements are observed to form overabundance rings in the horizontal field regions as predicted by the theory and there are numerous examples of element accumulations in the vicinity of radial field zones, which cannot be explained by diffusion calculations.
Peng, Junhui; Zhang, Zhiyong
2016-07-05
Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.
Energy Technology Data Exchange (ETDEWEB)
Lim, Suh Yeon
2006-08-15
This book is written to teach atom structure in very easy way. It is divided into nine chapters, which indicates what is the components of matter? when we divide matter continuously, it becomes atom, what did atom look like? particles comprised of matter is not only atom, discover of particles comprised of atom, symbol of element, various radiation, form alchemy to nuclear transmutation, shape of atom is evolving. It also has various pictures in each chapters to explain easily.
Saedi, Amirmehdi; van Houselt, Arie; van Gastel, Raoul; Poelsema, Bene; Zandvliet, Harold J W
2009-05-01
We demonstrate the feasibility of controlling an atomic scale mechanical device by an external electrical signal. On a germanium substrate, a switching motion of pairs of atoms is induced by electrons that are directly injected into the atoms with a scanning tunneling microscope tip. By precisely controlling the tip current and distance we make two atom pairs behave like the flippers of an atomic-sized pinball machine. This atomic scale mechanical device exhibits six different configurations.
AtomPy: an open atomic-data curation environment
Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka
2014-06-01
We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.
Nasser, Jamil A.; Chassagne, Luc; Topçu, Suat; Linares, Jorge; Alayli, Yasser
2014-03-01
In spin-conversion (SC) compounds containing molecules organized around an iron (II) ion the fundamental level of the ion is low spin (LS), S = 0, and its first excited one is high spin (HS), S = 2. This energy diagram is due to the ligands field interaction on 3d electrons and to the spin pairing energy. Heating the compound increases the magnetic susceptibility which corresponds to a change of populations of both levels and consequently a change of spin value of the molecules. This mechanism, called spin conversion (SC), can be accompagnied by thermal hysteresis observed by studying magnetic susceptibility or high spin fraction. In that case one considers that the (SC) takes place through a first-order phase transition due to intermolecular interactions. In the atom-phonon coupling model the molecules are considered as two-level systems, or two-level atoms, and it is assumed that the elastic force constant value of the spring which links two atoms first neighbours is depending on the electronic states of both atoms. In this study we calculate the partition function of a linear chain of N atoms (N ≤ 16) and we describe the role of phonons and that of the parameter Δ which corresponds to the distance in energy between both levels. The chain free-energy function is Fatph. We introduce for the chain a free-energy function defined by the set (FHS, FLS, Fbarr) and we show that Fatph tends towards the previous set when N → ∞. The previous set allows to describe a first order phase transition between a (LS) phase and a (HS) one. At the crossing point between the function FLS and FHS, and around this point, there is an intermediate free-energy barrier which prevents the chain to change phase which can lead to thermal hysteresis. The energy gap between the free-energy function Fatph and that defined by the set (FHS, FLS, Fbarr) is small. So we can expect that a nanoparticule takes for free-energy function that defined by the set and then displays a thermal
Frappier, Vincent; Najmanovich, Rafael J
2014-04-01
Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.
Directory of Open Access Journals (Sweden)
Vincent Frappier
2014-04-01
Full Text Available Normal mode analysis (NMA methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.
Directory of Open Access Journals (Sweden)
M. E. Foglio
2012-09-01
Full Text Available We consider the cumulant expansion of the periodic Anderson model (PAM in the case of a finite electronic correlation U, employing the hybridization as perturbation, and obtain a formal expression of the exact one-electron Green's function (GF. This expression contains effective cumulants that are as difficult to calculate as the original GF, and the atomic approach consists in substituting the effective cumulants by the ones that correspond to the atomic case, namely by taking a conduction band of zeroth width and local hybridization. In a previous work (T. Lobo, M. S. Figueira, and M. E. Foglio, Nanotechnology 21, 274007 (201010.1088/0957-4484/21/27/274007 we developed the atomic approach by considering only one variational parameter that is used to adjust the correct height of the Kondo peak by imposing the satisfaction of the Friedel sum rule. To obtain the correct width of the Kondo peak in the present work, we consider an additional variational parameter that guarantees this quantity. The two constraints now imposed on the formalism are the satisfaction of the Friedel sum rule and the correct Kondo temperature. In the first part of the work, we present a general derivation of the method for the single impurity Anderson model (SIAM, and we calculate several density of states representative of the Kondo regime for finite correlation U, including the symmetrical case. In the second part, we apply the method to study the electronic transport through a quantum dot (QD embedded in a quantum wire (QW, which is realized experimentally by a single electron transistor (SET. We calculate the conductance of the SET and obtain a good agreement with available experimental and theoretical results.
Directory of Open Access Journals (Sweden)
R. Tayebee
2003-12-01
Full Text Available Stretching and bending normal vibrations of AB2(C2v, AB3(D3h, AB4(D4h, and AB5(D3h molecules are described by correlating the vibrational displacement vectors of the attached atoms with the standard representations of s, p and d atomic orbitals of the central atom in ABn(n=2-5 molecules. It is found that stretching and bending normal vibrations of simple molecules accord with probability density of hybrid orbitals of the central atom. So, stretching and bending normal vibrations can be determined based on the irreducible representations of each vibration, and symbols for the representations which are suggested by Muliken.
Energy Technology Data Exchange (ETDEWEB)
Es-sebbar, Et; C-Gazeau, M; Benilan, Y; Jolly, A [LISA, Universites Paris-Est Creteil Val de Marne (UPEC) and Paris Denis Diderot, CNRS-UMR 7583, 61, avenue du General de Gaulle, 94010 Creteil Cedex (France); Pintassilgo, C D, E-mail: essebbar@lisa.univ-paris12.f [Instituto de Plasmas e Fusao Nuclear-Laboratorio Associado, Instituto Superior Tecnico, 1049-001 Lisboa (Portugal)
2010-08-25
Following a first study on a late afterglow in flowing pure nitrogen post discharge, we report new two-photon absorption laser-induced fluorescence (TALIF) measurements of the absolute ground-state atomic nitrogen density N({sup 4}S) and investigate the influence of methane introduced downstream from the discharge by varying the CH{sub 4} mixing ratio from 0% up to 50%. The N ({sup 4}S) maximum density is about 2.2 x 10{sup 15} cm{sup -3} in pure N{sub 2} for a residence time of 22 ms and does not change significantly for methane mixing ratio up to {approx}15%, while above, a drastic decrease is observed. The influence of the residence time has been studied. A kinetic model has been developed to determine the elementary processes responsible for the evolution of the N ({sup 4}S) density in N{sub 2}/CH{sub 4} late afterglow. This model shows the same decrease as the experimental results even though absolute density values are always larger by about a factor of 3. In the late afterglow three-body recombination dominates the loss of N ({sup 4}S) atoms whatever the CH{sub 4} mixing ratio. For high CH{sub 4} mixing ratio, the destruction process through collisions with CH{sub 3}, H{sub 2}CN and NH becomes important and is responsible for the observed decrease of the N ({sup 4}S) density.
Kumar, Sivakumar Prasanth; Jha, Prakash C; Jasrai, Yogesh T; Pandya, Himanshu A
2016-01-01
The estimation of atomic partial charges of the small molecules to calculate molecular interaction fields (MIFs) is an important process in field-based quantitative structure-activity relationship (QSAR). Several studies showed the influence of partial charge schemes that drastically affects the prediction accuracy of the QSAR model and focused on the selection of appropriate charge models that provide highest cross-validated correlation coefficient ([Formula: see text] or q(2)) to explain the variation in chemical structures against biological endpoints. This study shift this focus in a direction to understand the molecular regions deemed to explain SAR in various charge models and recognize a consensus picture of activity-correlating molecular regions. We selected eleven diverse dataset and developed MIF-based QSAR models using various charge schemes including Gasteiger-Marsili, Del Re, Merck Molecular Force Field, Hückel, Gasteiger-Hückel, and Pullman. The generalized resultant QSAR models were then compared with Open3DQSAR model to interpret the MIF descriptors decisively. We suggest the regions of activity contribution or optimization can be effectively determined by studying various charge-based models to understand SAR precisely.
Directory of Open Access Journals (Sweden)
Hua Wong
Full Text Available In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.
Solares, Santiago D
2014-01-01
This paper presents computational simulations of single-mode and bimodal atomic force microscopy (AFM) with particular focus on the viscoelastic interactions occurring during tip-sample impact. The surface is modeled by using a standard linear solid model, which is the simplest system that can reproduce creep compliance and stress relaxation, which are fundamental behaviors exhibited by viscoelastic surfaces. The relaxation of the surface in combination with the complexities of bimodal tip-sample impacts gives rise to unique dynamic behaviors that have important consequences with regards to the acquisition of quantitative relationships between the sample properties and the AFM observables. The physics of the tip-sample interactions and its effect on the observables are illustrated and discussed, and a brief research outlook on viscoelasticity measurement with intermittent-contact AFM is provided.
Energy Technology Data Exchange (ETDEWEB)
Park, Jong Gwan [I and Book, Seoul (Korea, Republic of)
2003-04-15
This book has a lot of explanation of nuclear energy with articles. Their titles are the bad man likes atomic, the secret of atom, nuclear explosion, NPT?, the secret of uranium fuel rod, nuclear power plant vs nuclear bomb, I hate atomic, keep plutonium in control, atomic in peace and find out alternative energy.
Neutral atom traps of radioactives
Behr, J A
2003-01-01
Neutral atoms trapped with modern laser cooling techniques offer the promise of improving several broad classes of experiments with radioactive isotopes. In nuclear beta decay, neutrino spectroscopy from beta-recoil coincidences, along with highly polarized samples, enable experiments to search for non-Standard Model interactions, test whether parity symmetry is maximally violated, and search for new sources of time reversal violation. Ongoing efforts at TRIUMF, Los Alamos and Berkeley will be highlighted. The traps also offer bright sources for Doppler-free spectroscopy, particularly in high-Z atoms where precision measurements could measure the strength of weak neutral nucleon-nucleon and electron-nucleon interactions. Physics with francium atoms has been vigorously pursued at Stony Brook. Several facilities plan work with radioactive atom traps; concrete plans and efforts at KVI Groningen and Legnaro will be among those summarized. Contributions to the multidisciplinary field of trace analysis will be left...
Breast cancer risk in atomic bomb survivors from multi-model inference with incidence data 1958-1998
Energy Technology Data Exchange (ETDEWEB)
Kaiser, J.C.; Jacob, P.; Meckbach, R. [Institute of Radiation Protection, Helmholtz-Zentrum Muenchen, German Research Centre for Environmental Health, Neuherberg (Germany); Cullings, H.M. [Radiation Effects Research Foundation, Department of Statistics, Hiroshima (Japan)
2012-03-15
Breast cancer risk from radiation exposure has been analyzed in the cohort of Japanese a-bomb survivors using empirical models and mechanistic two-step clonal expansion (TSCE) models with incidence data from 1958 to 1998. TSCE models rely on a phenomenological representation of cell transition processes on the path to cancer. They describe the data as good as empirical models and this fact has been exploited for risk assessment. Adequate models of both types have been selected with a statistical protocol based on parsimonious parameter deployment and their risk estimates have been combined using multi-model inference techniques. TSCE models relate the radiation risk to cell processes which are controlled by age-increasing rates of initiating mutations and by changes in hormone levels due to menopause. For exposure at young age, they predict an enhanced excess relative risk (ERR) whereas the preferred empirical model shows no dependence on age at exposure. At attained age 70, the multi-model median of the ERR at 1 Gy decreases moderately from 1.2 Gy{sup -1} (90% CI 0.72; 2.1) for exposure at age 25 to a 30% lower value for exposure at age 55. For cohort strata with few cases, where model predictions diverge, uncertainty intervals from multi-model inference are enhanced by up to a factor of 1.6 compared to the preferred empirical model. Multi-model inference provides a joint risk estimate from several plausible models rather than relying on a single model of choice. It produces more reliable point estimates and improves the characterization of uncertainties. The method is recommended for risk assessment in practical radiation protection. (orig.)
Piras, Daniele; Sadeghian, Hamed
2017-06-01
Ultrasound atomic force microscopy (US-AFM) has been used for subsurface imaging of nanostructures. The contact stiffness variations have been suggested as the origin of the image contrast. Therefore, to analyze the image contrast, the local changes in the contact stiffness due to the presence of subsurface features should be calculated. So far, only static simulations have been conducted to analyze the local changes in the contact stiffness and, consequently, the contrast in US-AFM. Such a static approach does not fully represent the real US-AFM experiment, where an ultrasound wave is launched either into the sample or at the tip, which modulates the contact stiffness. This is a time-dependent nonlinear dynamic problem rather than a static and stationary one. This paper presents dynamic 3D ultrasound analysis of contact stiffness in US-AFM (in contrast to static analysis) to realistically predict the changes in contact stiffness and thus the changes in the subsurface image contrast. The modulation frequency also influences the contact stiffness variations and, thus, the image contrast. The three-dimensional time-dependent ultrasound analysis will greatly aid in the contrast optimization of subsurface nano imaging with US-AFM.
McLeod, Roger; McLeod, David
2008-04-01
We posited flatland electron loop strings from transversely vibrating neutrino strings. Loop traveling waves TWs alternately become upwardly deflecting standing waves SWs along each half-wave segment between non-vibrating node pairs. Descending SWs again revert to TWs at flatland, as far as the next two adjacent nodal pairs, where folding continues and new SWs descend, then ascend, and repetition follows. Three dimensional objects, not points, result. A broken ``linear'' electron string and its electron spring constant are compressed within stars until linear mass density is compatible with incorporation into a stable three-ring proton string. The created neutron has two down quarks and one up, but must be unstable because it lacks overpass-underpass interlocks of our proton that shared its linear charge density of two up quarks and one down quark with the electron, becoming neutral. Anu transversely aligned neutron can have one of its ``notches'' pushed into the acceptor notch of a proton, and deuterium results. Tritium may be a compatible ``catch'' of another neutron. An alpha particle follows when a second proton is forced in, creating a stable ``tic-tac-toe'' grid. Atom building proceeds routinely.
Graf, Peter; Kim, Kwiseon; Jones, Wesley; Wang, Lin-Wang
2007-03-01
The first step in simulating properties of nanostructures is generation of accurate atomic configurations. For complex objects such as the multiply branched heterostructures synthesized by Alivisatos et al.^1, this is nontrivial. We report here on our code, ``tetra,'' that accomplishes this task. Borrowing from techniques of computer graphics, we represent the complex structure as a tree, each node of which is a shape with fixed crystal structure, and use concatenation of 4 by 4 homogeneous transformation matrices to arrange these fixed building blocks into the final object. A simple text based input ``language'' describes the connectivity and dimensions of the structure. The ultimate purpose of this code is use within a package that will explore and optimize electronic properties of such structures with respect to their geometry^2. We will present examples of both structures and subsequent semi-empirical pseudopotential-based^3 electronic structure calculations. [1] A. P. Alivisatos, et al., Nature, 430, 190 (2004). [2] J. Li and L. W. Wang, NanoLetters, 3, 10, 1357-1363 (2003). [3] L. W. Wang and A. Zunger, Phys. Rev. B 51, 17398 (1995).
Sub-atom shot noise Faraday imaging of ultracold atom clouds
Kristensen, M. A.; Gajdacz, M.; Pedersen, P. L.; Klempt, C.; Sherson, J. F.; Arlt, J. J.; Hilliard, A. J.
2017-02-01
We demonstrate that a dispersive imaging technique based on the Faraday effect can measure the atom number in a large, ultracold atom cloud with a precision below the atom shot noise level. The minimally destructive character of the technique allows us to take multiple images of the same cloud, which enables sub-atom shot noise measurement precision of the atom number and allows for an in situ determination of the measurement precision. We have developed a noise model that quantitatively describes the noise contributions due to photon shot noise in the detected light and the noise associated with single atom loss. This model contains no free parameters and is calculated through an analysis of the fluctuations in the acquired images. For clouds containing N∼ 5× {10}6 atoms, we achieve a precision more than a factor of two below the atom shot noise level.
Coffee Cup Atomic Force Microscopy
Ashkenaz, David E.; Hall, W. Paige; Haynes, Christy L.; Hicks, Erin M.; McFarland, Adam D.; Sherry, Leif J.; Stuart, Douglas A.; Wheeler, Korin E.; Yonzon, Chanda R.; Zhao, Jing; Godwin, Hilary A.; Van Duyne, Richard P.
2010-01-01
In this activity, students use a model created from a coffee cup or cardstock cutout to explore the working principle of an atomic force microscope (AFM). Students manipulate a model of an AFM, using it to examine various objects to retrieve topographic data and then graph and interpret results. The students observe that movement of the AFM…
Energy Technology Data Exchange (ETDEWEB)
Spurgeon, Steven R.; Du, Yingge; Chambers, Scott A.
2017-04-05
With the development of affordable aberration correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive X-ray spectroscopy (EDS) in particular has grown in popularity, as it enables elemental mapping over a wide range of ionization energies. However, the interpretation of atomically resolved data is greatly complicated by beam–sample interactions that are often overlooked by novice users. Here we describe the practical factors—namely, sample thickness and the choice of ionization edge—that affect the quantification of a model perovskite oxide interface. Our measurements of the same sample, in regions of different thickness, indicate that interface profiles can vary by as much as 2–5 unit cells, depending on the spectral feature. This finding is supported by multislice simulations, which reveal that on-axis maps of even perfectly abrupt interfaces exhibit significant delocalization. Quantification of thicker samples is further complicated by channeling to heavier sites across the interface, as well as an increased signal background. We show that extreme care must be taken to prepare samples to minimize channeling effects and argue that it may not be possible to extract atomically resolved information from many chemical maps.
Spurgeon, Steven R; Du, Yingge; Chambers, Scott A
2017-06-01
With the development of affordable aberration correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive X-ray spectroscopy (EDS) in particular has grown in popularity, as it enables elemental mapping over a wide range of ionization energies. However, the interpretation of atomically resolved data is greatly complicated by beam-sample interactions that are often overlooked by novice users. Here we describe the practical factors-namely, sample thickness and the choice of ionization edge-that affect the quantification of a model perovskite oxide interface. Our measurements of the same sample, in regions of different thickness, indicate that interface profiles can vary by as much as 2-5 unit cells, depending on the spectral feature. This finding is supported by multislice simulations, which reveal that on-axis maps of even perfectly abrupt interfaces exhibit significant delocalization. Quantification of thicker samples is further complicated by channeling to heavier sites across the interface, as well as an increased signal background. We show that extreme care must be taken to prepare samples to minimize channeling effects and argue that it may not be possible to extract atomically resolved information from many chemical maps.
Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal
2016-11-01
Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study, pharmacophore and atom-based 3D-QSAR studies were carried out for pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC50 ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2 )= .9949), cross validation coefficient (Q(2 )= .7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R(2) value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.
Periodic systems of N-atom molecules
Hefferlin, R. A.; Zhuvikin, G. V.; Caviness, K. E.; Duerksen, P. J.
1984-10-01
The atoms have long been classified into a periodic system, which is now based on quantum mechanics and group theory. A classification of molecules containing any number (N) of atoms is proposed. It is an extension of the periodic system of the atoms. The approach in this paper is that of group theory, although the proposed system has been subjected to exhaustive comparison with experimental and ab initio computational results for diatomic molecules, and conforms to the commonly known behaviors of molecules with larger N. Orthonormal transformations are performed so that the molecules can be arranged according to their numbers of electrons and to the differences of atomic numbers of the constituent atoms. These arrangements parallel the physical reality of atomic bonding and permit partial three-dimensional models of the systems to be constructed for molecules with as many as four atoms.
Atomic and molecular manipulation
Mayne, Andrew J
2011-01-01
Work with individual atoms and molecules aims to demonstrate that miniaturized electronic, optical, magnetic, and mechanical devices can operate ultimately even at the level of a single atom or molecule. As such, atomic and molecular manipulation has played an emblematic role in the development of the field of nanoscience. New methods based on the use of the scanning tunnelling microscope (STM) have been developed to characterize and manipulate all the degrees of freedom of individual atoms and molecules with an unprecedented precision. In the meantime, new concepts have emerged to design molecules and substrates having specific optical, mechanical and electronic functions, thus opening the way to the fabrication of real nano-machines. Manipulation of individual atoms and molecules has also opened up completely new areas of research and knowledge, raising fundamental questions of "Optics at the atomic scale", "Mechanics at the atomic scale", Electronics at the atomic scale", "Quantum physics at the atomic sca...
Advances in atomic spectroscopy
Sneddon, J
2000-01-01
This fifth volume of the successful series Advances in Atomic Spectroscopy continues to discuss and investigate the area of atomic spectroscopy.It begins with a description of the use of various atomic spectroscopic methods and applications of speciation studies in atomic spectroscopy. The emphasis is on combining atomic spectroscopy with gas and liquid chromatography. In chapter two the authors describe new developments in tunable lasers and the impact they will have on atomic spectroscopy. The traditional methods of detection, such as photography and the photomultiplier, and how they are being replaced by new detectors is discussed in chapter three. The very active area of glow discharge atomic spectrometry is presented in chapter four where, after a brief introduction and historical review, the use of glow discharge lamps for atomic spectroscopy and mass spectrometry are discussed. Included in this discussion is geometry and radiofrequency power. The future of this source in atomic spectroscopy is also dis...
Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin
2017-03-01
The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.
DEFF Research Database (Denmark)
Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit
2012-01-01
resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...... in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable...... to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A...
Energy Technology Data Exchange (ETDEWEB)
Bhardwaj, Anil; Raghuram, Susarla, E-mail: bhardwaj_spl@yahoo.com, E-mail: anil_bhardwaj@vssc.gov.in, E-mail: raghuramsusarla@gmail.com [Space Physics Laboratory, Vikram Sarabhai Space Centre, Trivandrum 695022 (India)
2012-03-20
The green (5577 Angstrom-Sign ) and red-doublet (6300, 6364 Angstrom-Sign ) lines are prompt emissions of metastable oxygen atoms in the {sup 1}S and {sup 1}D states, respectively, that have been observed in several comets. The value of the intensity ratio of green to red-doublet (G/R ratio) of 0.1 has been used as a benchmark to identify the parent molecule of oxygen lines as H{sub 2}O. A coupled chemistry-emission model is developed to study the production and loss mechanisms of the O({sup 1}S) and O({sup 1}D) atoms and the generation of red and green lines in the coma of C/1996 B2 Hyakutake. The G/R ratio depends not only on photochemistry, but also on the projected area observed for cometary coma, which is a function of the dimension of the slit used and the geocentric distance of the comet. Calculations show that the contribution of photodissociation of H{sub 2}O to the green (red) line emission is 30%-70% (60%-90%), while CO{sub 2} and CO are the next potential sources contributing 25%-50% (<5%). The ratio of the photoproduction rate of O({sup 1} S) to O({sup 1} D) would be around 0.03 ({+-}0.01) if H{sub 2}O is the main source of oxygen lines, whereas it is {approx}0.6 if the parent is CO{sub 2}. Our calculations suggest that the yield of O({sup 1} S) production in the photodissociation of H{sub 2}O cannot be larger than 1%. The model-calculated radial brightness profiles of the red and green lines and G/R ratios are in good agreement with the observations made on the comet Hyakutake in 1996 March.
Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H
2015-01-01
Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many
Plattner, Nuria; Doerr, Stefan; de Fabritiis, Gianni; Noé, Frank
2017-10-01
Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.
Energy Technology Data Exchange (ETDEWEB)
Sewall, N.; Harris, W.; Beeler, R.; Wooldridge, J.; Chen, H.L.
1986-09-01
This report presents information on the Atomic Vapor Density Monitor (AVDM) system that measures the density of a vapor by measuring the absorption of light from a swept-wavelength laser that passes through an atomic vapor stream.
2011-03-01
with the above initial conditions can be converted to a nonlinear Volterra integral equation of the second kind. In Equation (23) we assume thatQ > 1...dτ and the initial conditions become x(0) = ẋ(0) = 0. Equation (39) with the above initial conditions converts to a nonlinear Volterra integral ...Experimental Model to a Dual Integral Equation
Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea
2012-05-08
Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard.
Theoretical Calculations of Atomic Data for Spectroscopy
Bautista, Manuel A.
2000-01-01
Several different approximations and techniques have been developed for the calculation of atomic structure, ionization, and excitation of atoms and ions. These techniques have been used to compute large amounts of spectroscopic data of various levels of accuracy. This paper presents a review of these theoretical methods to help non-experts in atomic physics to better understand the qualities and limitations of various data sources and assess how reliable are spectral models based on those data.
Wehbe, Nimer; Heile, Andreas; Arlinghaus, Heinrich F; Bertrand, Patrick; Delcorte, Arnaud
2008-08-15
A model alkane molecule, triacontane, is used to assess the effects of condensed gold and silver nanoparticles on the molecular ion yields upon atomic (Ga(+) and In(+)) and polyatomic (C60(+) and Bi3(+)) ion bombardment in metal-assisted secondary ion mass spectrometry (MetA-SIMS). Molecular films spin-coated on silicon were metallized using a sputter-coater system, in order to deposit controlled quantities of gold and silver on the surface (from 0 to 15 nm equivalent thickness). The effects of gold and silver islets condensed on triacontane are also compared to the situation of thin triacontane overlayers on metallic substrates (gold and silver). The results focus primarily on the measured yields of quasi-molecular ions, such as (M - H)(+) and (2M - 2H)(+), and metal-cationized molecules, such as (M + Au)(+) and (M + Ag)(+), as a function of the quantity of metal on the surface. They confirm the absence of a simple rule to explain the secondary ion yield improvement in MetA-SIMS. The behavior is strongly dependent on the specific projectile/metal couple used for the experiment. Under atomic bombardment (Ga(+), In(+)), the characteristic ion yields an increase with the gold dose up to approximately 6 nm equivalent thickness. The yield enhancement factor between gold-metallized and pristine samples can be as large as approximately 70 (for (M - H)(+) under Ga(+) bombardment; 10 nm of Au). In contrast, with cluster projectiles such as Bi3(+) and C60(+), the presence of gold and silver leads to a dramatic molecular ion yield decrease. Cluster projectiles prove to be beneficial for triacontane overlayers spin-coated on silicon or metal substrates (Au, Ag) but not in the situation of MetA-SIMS. The fundamental difference of behavior between atomic and cluster primary ions is tentatively explained by arguments involving the different energy deposition mechanisms of these projectiles. Our results also show that Au and Ag nanoparticles do not induce the same behavior in Met
Energy Technology Data Exchange (ETDEWEB)
Migunov, V., E-mail: v.migunov@fz-juelich.de; Dunin-Borkowski, R. E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C) and Peter Grünberg Institute (PGI), Forschungszentrum Jülich, D-52425 Jülich (Germany); London, A. [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Farle, M. [Fakultät für Physik and Center of Nanointegration (CeNIDE), Universität Duisburg-Essen, D-47048 Duisburg (Germany)
2015-04-07
The one-dimensional charge density distribution along an electrically biased Fe atom probe needle is measured using a model-independent approach based on off-axis electron holography in the transmission electron microscope. Both the mean inner potential and the magnetic contribution to the phase shift are subtracted by taking differences between electron-optical phase images recorded with different voltages applied to the needle. The measured one-dimensional charge density distribution along the needle is compared with a similar result obtained using model-based fitting of the phase shift surrounding the needle. On the assumption of cylindrical symmetry, it is then used to infer the three-dimensional electric field and electrostatic potential around the needle with ∼10 nm spatial resolution, without needing to consider either the influence of the perturbed reference wave or the extension of the projected potential outside the field of view of the electron hologram. The present study illustrates how a model-independent approach can be used to measure local variations in charge density in a material using electron holography in the presence of additional contributions to the phase, such as those arising from changes in mean inner potential and specimen thickness.
Cuellar, José Luis; Llarena, Irantzu; Iturri, Jagoba J; Donath, Edwin; Moya, Sergio Enrique
2013-12-07
The thickness of a poly(sulfo propyl methacrylate) (PSPM) brush is determined by Atomic Force Microscopy (AFM) imaging as a function of the loading force at different ionic strengths, ranging from Milli-Q water to 1 M NaCl. Imaging is performed both with a sharp tip and a colloidal probe. The brush thickness strongly depends both on the applied load and on the ionic strength. A brush thickness of 150 nm is measured in Millipore water when applying the minimal loading force. Imaging with an 8 μm silica particle as a colloidal probe results in a thickness of 30 nm larger than that measured with the tip. Increasing the ionic strength causes the well known reduction of the thickness of the brush. The apparent thickness of the brush decreases with increasing loading forces. An empirical model analogous to that of a compressible fluid is applied to describe the dependence of the apparent thickness of the brush with loading force. The model comprises three ionic strength dependent parameters for the brush: thickness at infinite compression, energy, and cohesive force. The meaning and significance of these parameters are discussed. A particular advantage of the model is that it allows for determination of the brush thickness at zero loading force.
SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access) This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.
Saedi, A.; van Houselt, Arie; van Gastel, Raoul; Poelsema, Bene; Zandvliet, Henricus J.W.
2009-01-01
We demonstrate the feasibility of controlling an atomic scale mechanical device by an external electrical signal. On a germanium substrate, a switching motion of pairs of atoms is induced by electrons that are directly injected into the atoms with a scanning tunneling microscope tip. By precisely
Desaphy, Jean-François; Camerino, Diana Conte; Franchini, Carlo; Lentini, Giovanni; Tortorella, Vincenzo; De Luca, Annamaria
1999-01-01
The antiarrhythmic drug mexiletine (Mex) is also used against myotonia. Searching for a more efficient drug, a new compound (Me5) was synthesized substituting the methyl group on the chiral carbon atom of Mex by an isopropyl group. Effects of Me5 on Na+ channels were compared to those of Mex in rat skeletal muscle fibres using the cell-attached patch clamp method.Me5 (10 μM) reduced the maximal sodium current (INa) by 29.7±4.4 % (n=6) at a frequency of stimulation of 0.3 Hz and 65.7±4.4 % (n=6) at 1 Hz. At same concentration (10 μM), Mex was incapable of producing any effect (n=3). Me5 also shifted the steady-state inactivation curves by −7.9±0.9 mV (n=6) at 0.3 Hz and −12.2±1.0 mV (n=6) at 1 Hz.In the presence of sea anemone toxin II (ATX; 5 μM), INa decayed more slowly and no longer to zero, providing a model of sodium channel myotonia. The effects of Me5 on peak INa were similar whatever ATX was present or not. Interestingly, Me5 did not modify the INa decay time constant nor the steady-state INa to peak INa ratio.Analysis of ATX-induced late Na+ channel activity shows that Me5 did not affect mean open times and single-channel conductance, thus excluding open channel block property.These results indicate that increasing hindrance on the chiral atom of Mex increases drug potency on wild-type and ATX-induced noninactivating INa and that Me5 might improve the prophylaxis of myotonia. PMID:10578128
Delay in atomic photoionization
Kheifets, A S
2010-01-01
We analyze the time delay between emission of photoelectrons from the outer valence $ns$ and $np$ sub-shells in noble gas atoms following absorption of an attosecond XUV pulse. By solving the time dependent Schr\\"odinger equation and carefully examining the time evolution of the photoelectron wave packet, we establish the apparent "time zero" when the photoelectron leaves the atom. Various processes such as elastic scattering of the photoelectron on the parent ion and many-electron correlation affect the quantum phase of the dipole transition matrix element, the energy dependence of which defines the emission timing. This qualitatively explains the time delay between photoemission from the $2s$ and $2p$ sub-shells of Ne as determined experimentally by attosecond streaking [{\\em Science} {\\bf 328}, 1658 (2010)]. However, with our extensive numerical modeling, we were only able to account for less than a half of the measured time delay of $21\\pm5$~as. We argue that the XUV pulse alone cannot produce such a larg...
Atomization characteristics of a prefilming airblast atomizer
Hayashi, Shigeru; Koito, Atsushi; Hishiki, Manabu
1992-01-01
The size distribution of water test sprays generated by a prefilming airblast atomizer used for aeroengines was measured in swirling and non-swirling flows with the well established laser scattering particle sizing technique. Atomizing air velocity (or pressure difference) was varied in a range wider than the conditions of actual engines. The Sauter Mean Diameter (SMD) decreased at approximately a 1.5 power of the atomizing air velocity, being a higher velocity index than the previously reported values of 1 to 1.2. It was unexpectedly found that the effect of the liquid/air flow ratio was small. Since swirling flow increased the SMD at lower air velocities yet decreased it at higher ones, it is suggested that the reverse flow near the nozzle pintle adversely affects atomization.
Three-body recombination of two-component cold atomic gases into deep dimers in an optical model
DEFF Research Database (Denmark)
Mikkelsen, Mathias; Jensen, A. S.; Fedorov, D. V.
2015-01-01
to the decay rate or recombination probability of the three-body system. The method is formulated in details and the relevant qualitative features are discussed as functions of scattering lengths and masses. We use zero-range model in analyses of recent recombination data. The dominating scattering length...... is usually related to the non-equal two-body systems. We account for temperature smearing which tends to wipe out the higher-lying Efimov peaks. The range and the strength of the imaginary potential determine positions and shapes of the Efimov peaks as well as the absolute value of the recombination rate...
Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M
2016-09-21
The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO 2 ) 57.5 -(B 2 O 3 ) 10 -(Na 2 O) 15 -(CaO) 15 -(MoO 3 ) 2.5 and (SiO 2 ) 57.3 -(B 2 O 3 ) 20 -(Na 2 O) 6.8 -(Li 2 O) 13.4 -(MoO 3 ) 2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na 2 MoO 4 and CaMoO 4 ). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.
Motruk, Johannes; Pollmann, Frank
2017-10-01
We investigate the fate of hardcore bosons in a Harper-Hofstadter model which was experimentally realized by Aidelsburger et al. [Nat. Phys. 11, 162 (2015), 10.1038/nphys3171] at half-filling of the lowest band. We discuss the stability of an emergent fractional Chern insulator (FCI) state in a finite region of the phase diagram that is separated from a superfluid state by a first-order transition when tuning the band topology following the protocol used in the experiment. Since crossing a first-order transition is unfavorable for adiabatically preparing the FCI state, we extend the model to stabilize a featureless insulating state. The transition between this phase and the topological state proves to be continuous, providing a path in parameter space along which an FCI state could be adiabatically prepared. To further corroborate this statement, we perform time-dependent DMRG calculations which demonstrate that the FCI state may indeed be reached by adiabatically tuning a simple product state.
Multilevel Atomic Coherent States and Atomic Holomorphic Representation
Cao, Chang-Qi; Haake, Fritz
1996-01-01
The notion of atomic coherent states is extended to the case of multilevel atom collective. Based on atomic coherent states, a holomorphic representation for atom collective states and operators is defined. An example is given to illustrate its application.
Extension of Mediema's Macroscopic Atom Model to the Elements of Group 16 (O, S, Se, Te ,Po)
Neuhausen, J
2003-01-01
A consistent set of Miedema-parameters has been developed for the elements of the chalcogen group (Group 16 of the periodic table of the elements: 0, S, Se, Te, Po) from ab-initio quantum-mechanical calculations as weIl as empirical correlations. Using this parameter set thermochemical properties such as enthalpies of formation of solid metal chalcogenides, partial molar enthalpies of solution of chalcogens in liquid and solid metaIs, partial molar enthalpies of evaporation of the chalcogens from liquid metal solution into the monoatomic gaseous state, partial molar enthalpies of adsorption of chalcogenides on metal surfaces at zero coverage and partial molar enthalpies of segregation of the chalcogens in trace amounts within solid metal matrices have been calculated. These properties are compared with available experimental data and discussed with an emphasis on the periodic behaviour of the elements. The model calculations show that a description of the thermochemical properties of the chalcogens using the ...
Energy Technology Data Exchange (ETDEWEB)
Manos Mavrikakis; James A. Dumesic; Rahul P. Nabar
2006-09-29
Work continued on the development of a microkinetic model of Fischer-Tropsch synthesis (FTS) on supported and unsupported Fe catalysts. The following aspects of the FT mechanism on unsupported iron catalysts were investigated on during this third year: (1) the collection of rate data in a Berty CSTR reactor based on sequential design of experiments; (2) CO adsorption and CO-TPD for obtaining the heat of adsorption of CO on polycrystalline iron; and (3) isothermal hydrogenation (IH) after Fischer Tropsch reaction to identify and quantify surface carbonaceous species. Rates of C{sub 2+} formation on unsupported iron catalysts at 220 C and 20 atm correlated well to a Langmuir-Hinshelwood type expression, derived assuming carbon hydrogenation to CH and OH recombination to water to be rate-determining steps. From desorption of molecularly adsorbed CO at different temperatures the heat of adsorption of CO on polycrystalline iron was determined to be 100 kJ/mol. Amounts and types of carbonaceous species formed after FT reaction for 5-10 minutes at 150, 175, 200 and 285 C vary significantly with temperature. Mr. Brian Critchfield completed his M.S. thesis work on a statistically designed study of the kinetics of FTS on 20% Fe/alumina. Preparation of a paper describing this work is in progress. Results of these studies were reported at the Annual Meeting of the Western States Catalysis and at the San Francisco AIChE meeting. In the coming period, studies will focus on quantitative determination of the rates of kinetically-relevant elementary steps on unsupported Fe catalysts with/without K and Pt promoters by SSITKA method. This study will help us to (1) understand effects of promoter and support on elementary kinetic parameters and (2) build a microkinetics model for FTS on iron. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on models of defected Fe surfaces, most significantly the stepped Fe(211) surface. Binding
Cooling Atomic Gases With Disorder
Paiva, Thereza; Khatami, Ehsan; Yang, Shuxiang; Rousseau, Valéry; Jarrell, Mark; Moreno, Juana; Hulet, Randall G.; Scalettar, Richard T.
2015-12-01
Cold atomic gases have proven capable of emulating a number of fundamental condensed matter phenomena including Bose-Einstein condensation, the Mott transition, Fulde-Ferrell-Larkin-Ovchinnikov pairing, and the quantum Hall effect. Cooling to a low enough temperature to explore magnetism and exotic superconductivity in lattices of fermionic atoms remains a challenge. We propose a method to produce a low temperature gas by preparing it in a disordered potential and following a constant entropy trajectory to deliver the gas into a nondisordered state which exhibits these incompletely understood phases. We show, using quantum Monte Carlo simulations, that we can approach the Néel temperature of the three-dimensional Hubbard model for experimentally achievable parameters. Recent experimental estimates suggest the randomness required lies in a regime where atom transport and equilibration are still robust.
Atomic bonding between metal and graphene
Wang, Hongtao
2013-03-07
To understand structural and chemical properties of metal-graphene composites, it is crucial to unveil the chemical bonding along the interface. We provide direct experimental evidence of atomic bonding between typical metal nano structures and graphene, agreeing well with density functional theory studies. Single Cr atoms are located in the valleys of a zigzag edge, and few-atom ensembles preferentially form atomic chains by self-assembly. Low migration barriers lead to rich dynamics of metal atoms and clusters under electron irradiation. We demonstrate no electron-instigated interaction between Cr clusters and pristine graphene, though Cr has been reported to be highly reactive to graphene. The metal-mediated etching is a dynamic effect between metal clusters and pre-existing defects. The resolved atomic configurations of typical nano metal structures on graphene offer insight into modeling and simulations on properties of metal-decorated graphene for both catalysis and future carbon-based electronics. © 2013 American Chemical Society.
Structure of the PolIIIα-τc-DNA complex suggests an atomic model of the replisome.
Liu, Bin; Lin, Jinzhong; Steitz, Thomas A
2013-04-02
The C-terminal domain (CTD) of the τ subunit of the clamp loader (τc) binds to both the DnaB helicase and the DNA polymerase III α subunit (PolIIIα), and determines their relative positions and orientations on the leading and lagging strands. Here, we present a 3.2 Å resolution structure of Thermus aquaticus PolIIIα in complex with τc and a DNA substrate. The structure reveals that the CTD of τc interacts with the CTD of PolIIIα through its C-terminal helix and the adjacent loop. Additionally, in this complex PolIIIα displays an open conformation that includes the reorientations of the oligonucleotide-binding fold and the thumb domain, which may be an indirect result of crystal packing due to the presence of the τc. Nevertheless, the position of the τc on PolIIIα allows us to suggest an approximate model for how the PolIIIα is oriented and positioned on the DnaB helicase. Copyright © 2013 Elsevier Ltd. All rights reserved.
Ab initio and all-atom modeling of detergent organization around Aquaporin-0 based on SAXS data.
Koutsioubas, Alexandros; Berthaud, Alice; Mangenot, Stéphanie; Pérez, Javier
2013-10-31
A necessary initial step for the application of small angle X-ray scattering (SAXS) as an analytical probe for structural investigations of membrane proteins in solution is the precise knowledge of the structure of spontaneously formed detergent assemblies around the protein. Following our recent article (Berthaud et al. J. Am. Chem. Soc. 2012, 134, 10080-10088) on the study of the n-dodecyl β-D-maltopyranoside (dDM) corona surrounding Aquaporin-0 tetramers in solution, we aimed at the development of more elaborate models, exploiting the information content of the scattering data. Two additional approaches are developed here for the fit of SAXS experimental data, one based on a generalized ab initio algorithm for the construction of a coarse-grained representation of the detergent assemblies, and a second based on atomistic molecular dynamics. Accordingly, we are able to fit the SAXS experimental data and obtain a better insight concerning the structure of the detergent corona around the hydrophobic part of the Aquaporin-0 surface. The present analysis scheme represents an additional step toward future conformational studies of transmembrane proteins in solution.
Extension of Mediema's Macroscopic Atom Model to the Elements of Group 16 (O, S, Se, Te ,Po)
Energy Technology Data Exchange (ETDEWEB)
Neuhausen, J.; Eichler, B
2003-09-01
A consistent set of Miedema-parameters has been developed for the elements of the chalcogen group (Group 16 of the periodic table of the elements: 0, S, Se, Te, Po) from ab-initio quantum-mechanical calculations as weIl as empirical correlations. Using this parameter set thermochemical properties such as enthalpies of formation of solid metal chalcogenides, partial molar enthalpies of solution of chalcogens in liquid and solid metaIs, partial molar enthalpies of evaporation of the chalcogens from liquid metal solution into the monoatomic gaseous state, partial molar enthalpies of adsorption of chalcogenides on metal surfaces at zero coverage and partial molar enthalpies of segregation of the chalcogens in trace amounts within solid metal matrices have been calculated. These properties are compared with available experimental data and discussed with an emphasis on the periodic behaviour of the elements. The model calculations show that a description of the thermochemical properties of the chalcogens using the semi-empirical Miedema approach is possible. The calculated properties can serve as a basis for the prediction of the chemical interactions for metal-chalcogen combinations that have not been studied experimentally so far. (author)
Wang, Chia-Yu; Barrow, Lloyd H.
2013-01-01
The purpose of the study was to explore students' conceptual frameworks of models of atomic structure and periodic variations, chemical bonding, and molecular shape and polarity, and how these conceptual frameworks influence their quality of explanations and ability to shift among chemical representations. This study employed a purposeful sampling…
Smiar, Karen; Mendez, J. D.
2016-01-01
Molecular model kits have been used in chemistry classrooms for decades but have seen very little recent innovation. Using 3D printing, three sets of physical models were created for a first semester, introductory chemistry course. Students manipulated these interactive models during class activities as a supplement to existing teaching tools for…
Cvitas, Marko T.; Soldan, Pavel; Hutson, Jeremy M.
2005-01-01
The long-range forces that act between three atoms are analysed in both atom-diatom and atom-atom-atom representations. Expressions for atom-diatom dispersion coefficients are obtained in terms of 3-body nonadditive coefficients. The anisotropy of atom-diatom C_6 dispersion coefficients arises primarily from nonadditive triple-dipole and quadruple-dipole forces, while pairwise-additive forces and nonadditive triple-dipole and dipole-dipole-quadrupole forces contribute significantly to atom-di...
Coexistence of photonic and atomic Bose-Einstein condensates in ideal atomic gases
Directory of Open Access Journals (Sweden)
N. Boichenko
2015-12-01
Full Text Available We have studied conditions of photon Bose-Einstein condensate formation that is in thermodynamic equilibrium with ideal gas of two-level Bose atoms below the degeneracy temperature. Equations describing thermodynamic equilibrium in the system were formulated; critical temperatures and densities of photonic and atomic gas subsystems were obtained analytically. Coexistence conditions of these photonic and atomic Bose-Einstein condensates were found. There was predicted the possibility of an abrupt type of photon condensation in the presence of Bose condensate of ground-state atoms: it was shown that the slightest decrease of the temperature could cause a significant gathering of photons in the condensate. This case could be treated as a simple model of the situation known as "stopped light" in cold atomic gas. We also showed how population inversion of atomic levels can be created by lowering the temperature. The latter situation looks promising for light accumulation in atomic vapor at very low temperatures.
Atom localization in 2D for five-level atomic schemes in X-configuration
Raheli, Ali; Hamedi, H. R.; Sahrai, M.
2015-09-01
A five-level X-type atomic scheme is proposed to elucidate the two-dimensional (2D) atom localization in sub-wavelength domain by using different coupling situations of the atom with standing wave fields. The scheme is a mixture of two upper V- and lower Λ -type usual three level systems which both are connected at a common intermediate level. The combination of the upper and lower systems can lead to different atom localization patterns as lattice-, chain-, crater-, wave-, and spike-like structures. We discuss how these structures may depend on different coupling conditions of the atom with the standing wave fields. Finally, an experimental implementation for such an atomic model is presented using the 87Rb atoms.
Energy Technology Data Exchange (ETDEWEB)
Favalli, Renata Cristina
2002-07-01
The aim of the present work is to numerically simulate the behaviour of the drying system for several sets of operating conditions in order to improve and optimize this process. However, the mathematical modeling adopted here can be employed to simulate other systems such as the processes that occur in liquid-fueled engines with direct spray injection and ceramic spraying for hard surfacing. Then, mathematical and physical models were established to simulate the interaction of continuous and disperse phases in drying processes of ceramic slurries. Solving the set of governing coupled partial differential equations, it is possible to study the influence of drying air on the atomized droplets of alumina slurry, and vice-versa. The materials used as continuous and disperse phase, air and alumina slurry respectively, are representative since any kind of gas and slurry can be used if its thermodynamic and transport properties are known. Several experimental tests were carried out in a spray dryer in the 'Laboratorio de Insumos', at IPEN - Instituto de Pesquisas Energeticas e Nucleares for different sets of operating conditions: initial temperature of the drying air, the gas flow rate, the slurry feed rate and atomiser configuration among others. Measurements of the wet and the dry bulb temperatures were made in some experimental tests to allow the calculations of the air humidity. The dynamic pressure were also measured in order to determine the gas flow rate. Some samples of the material used in the tile industry and of the one produced at IPEN were analysed to determine: the morphology of the atomized material and the range of granules diameter through scanning electron microscopy; the amount of pores and the bulk density through porosimetry; the residual moisture of the material through thermogravimetry; and the granulometric distribution of granules and particles through laser diffraction. Important information about the process and the final material are
Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben
2011-10-01
Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.
Stochastic analysis/synthesis using sinusoidal atoms
DEFF Research Database (Denmark)
Jensen, Kristoffer
2008-01-01
This work proposes a method for re-synthesizing music for use in perceptual experiments regarding structural changes and in music creation. Atoms are estimated from music audio, modelled in a stochastic model, and re-synthesized from the model pa- rameters. The atoms are found by splitting...... sinusoids into short segments, and modelled into amplitude and envelope shape, frequency, time and duration. A simple model for creating envelopes with percussive, sustained or crescendo shape is presented. Single variable and joint probability density functions are created from the atom parameters and used...... to re-create sounds with the same distribution of the atoms parameters. A novel method for visualization music, the musigram, permits a better understanding of the re- synthesized sounds....
Natarajan, Vasant
2015-01-01
Much of our understanding of physics in the last 30-plus years has come from research on atoms, photons, and their interactions. Collecting information previously scattered throughout the literature, Modern Atomic Physics provides students with one unified guide to contemporary developments in the field. After reviewing metrology and preliminary material, the text explains core areas of atomic physics. Important topics discussed include the spontaneous emission of radiation, stimulated transitions and the properties of gas, the physics and applications of resonance fluorescence, coherence, cooling and trapping of charged and neutral particles, and atomic beam magnetic resonance experiments. Covering standards, a different way of looking at a photon, stimulated radiation, and frequency combs, the appendices avoid jargon and use historical notes and personal anecdotes to make the topics accessible to non-atomic physics students. Written by a leader in atomic and optical physics, this text gives a state-of-the...
Zhou, Wu; Oxley, Mark P; Lupini, Andrew R; Krivanek, Ondrej L; Pennycook, Stephen J; Idrobo, Juan-Carlos
2012-12-01
We show that aberration-corrected scanning transmission electron microscopy operating at low accelerating voltages is able to analyze, simultaneously and with single atom resolution and sensitivity, the local atomic configuration, chemical identities, and optical response at point defect sites in monolayer graphene. Sequential fast-scan annular dark-field (ADF) imaging provides direct visualization of point defect diffusion within the graphene lattice, with all atoms clearly resolved and identified via quantitative image analysis. Summing multiple ADF frames of stationary defects produce images with minimized statistical noise and reduced distortions of atomic positions. Electron energy-loss spectrum imaging of single atoms allows the delocalization of inelastic scattering to be quantified, and full quantum mechanical calculations are able to describe the delocalization effect with good accuracy. These capabilities open new opportunities to probe the defect structure, defect dynamics, and local optical properties in 2D materials with single atom sensitivity.
Li, Yan Jun; Lee, Seung Hwan; Kinoshita, Yukinori; Ma, Zong Min; Wen, Huanfei; Nomura, Hikaru; Naitoh, Yoshitaka; Sugawara, Yasuhiro
2016-05-20
We present an experimental study of coexisting p(2 × 1) and c(6 × 2) phases on an oxygen-terminated Cu(110) surface by noncontact atomic force microscopy (NC-AFM) at 78 K. Ball models of the growth processes of coexisting p(2 × 1)/c(6 × 2) phases on a terrace and near a step are proposed. We found that the p(2 × 1) and c(6 × 2) phases are grown from the super Cu atoms on both sides of O-Cu-O rows of an atomic spacing. In this paper, we summarize our investigations of an oxygen-terminated Cu(110) surface by NC-AFM employing O- and Cu-terminated tips. Also, we state several problems and issues for future investigation.
Hitchcock, Andrew; Hunter, C Neil; Sener, Melih
2017-04-20
Cell doubling times of the purple bacterium Rhodobacter sphaeroides during photosynthetic growth are determined experimentally and computationally as a function of illumination. For this purpose, energy conversion processes in an intracytoplasmic membrane vesicle, the chromatophore, are described based on an atomic detail structural model. The cell doubling time and its illumination dependence are computed in terms of the return-on-investment (ROI) time of the chromatophore, determined computationally from the ATP production rate, and the mass ratio of chromatophores in the cell, determined experimentally from whole cell absorbance spectra. The ROI time is defined as the time it takes to produce enough ATP to pay for the construction of another chromatophore. The ROI time of the low light-growth chromatophore is 4.5-2.6 h for a typical illumination range of 10-100 μmol photons m -2 s -1 , respectively, with corresponding cell doubling times of 8.2-3.9 h. When energy expenditure is considered as a currency, the benefit-to-cost ratio computed for the chromatophore as an energy harvesting device is 2-8 times greater than for photovoltaic and fossil fuel-based energy solutions and the corresponding ROI times are approximately 3-4 orders of magnitude shorter for the chromatophore than for synthetic systems.
Raja, Muhammad Asif Zahoor; Zameer, Aneela; Khan, Aziz Ullah; Wazwaz, Abdul Majid
2016-01-01
In this study, a novel bio-inspired computing approach is developed to analyze the dynamics of nonlinear singular Thomas-Fermi equation (TFE) arising in potential and charge density models of an atom by exploiting the strength of finite difference scheme (FDS) for discretization and optimization through genetic algorithms (GAs) hybrid with sequential quadratic programming. The FDS procedures are used to transform the TFE differential equations into a system of nonlinear equations. A fitness function is constructed based on the residual error of constituent equations in the mean square sense and is formulated as the minimization problem. Optimization of parameters for the system is carried out with GAs, used as a tool for viable global search integrated with SQP algorithm for rapid refinement of the results. The design scheme is applied to solve TFE for five different scenarios by taking various step sizes and different input intervals. Comparison of the proposed results with the state of the art numerical and analytical solutions reveals that the worth of our scheme in terms of accuracy and convergence. The reliability and effectiveness of the proposed scheme are validated through consistently getting optimal values of statistical performance indices calculated for a sufficiently large number of independent runs to establish its significance.
Šponer, Judit E; Szabla, Rafał; Góra, Robert W; Saitta, A Marco; Pietrucci, Fabio; Saija, Franz; Di Mauro, Ernesto; Saladino, Raffaele; Ferus, Martin; Civiš, Svatopluk; Šponer, Jiří
2016-07-27
The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments. Modern computations can provide unique atomic-level insights into the structural and electronic aspects as well as the energetics of key prebiotic chemical reactions. Many of these insights are not directly obtainable from the experimental techniques and the computations are thus becoming indispensable for proper interpretation of many experiments and for qualified predictions. This review illustrates the synergy between experiment and theory in the origin of life research focusing on the prebiotic synthesis of various nucleic acid building blocks and on the self-assembly of nucleotides leading to the first functional oligonucleotides.
Solar Spectroscopy: Atomic Processes
Mason, H.; Murdin, P.
2000-11-01
A Greek philosopher called DEMOCRITUS (c. 460-370 BC) first introduced the concept of atoms (which means indivisible). His atoms do not precisely correspond to our atoms of today, which are not indivisible, but made up of a nucleus (protons with positive charge and neutrons which have no charge) and orbiting electrons (with negative charge). Indeed, in the solar atmosphere, the temperature is suc...
Advances in atomic spectroscopy
Sneddon, J
1997-01-01
This series describes selected advances in the area of atomic spectroscopy. It is primarily intended for the reader who has a background in atmoic spectroscopy; suitable to the novice and expert. Although a widely used and accepted method for metal and non-metal analysis in a variety of complex samples, Advances in Atomic Spectroscopy covers a wide range of materials. Each Chapter will completely cover an area of atomic spectroscopy where rapid development has occurred.
Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach.
Oña, Ofelia B; De Clercq, Olivier; Alcoba, Diego R; Torre, Alicia; Lain, Luis; Van Neck, Dimitri; Bultinck, Patrick
2016-09-19
The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Tsyganov, D. L.
2017-11-01
A new model for calculating the rates of reactions of excitation, ionization, and atomic exchange is proposed. Diatomic molecule AB is an unstructured particle M upon the exchange of elastic-vibrational (VT) energy, i.e., a model of a shock forceful oscillator with a change in Hamiltonian (SFOH). The SFOH model is based on the quantum theory of strong perturbations. The SFOH model allows generalization in simulating the rates of the reactions of excitation, ionization, and atomic exchange in the vibrational-vibrational (VV) energy exchange of diatomic molecules, and the exchange of VV- and VT-energy of polyatomic molecules. The rate constants of the excitation of metastables A 3Σ u +, B 3Π g , W 3Δ u , B'3Σ u -, a'3Σ u -, and the ionization of a nitrogen molecules from ground state X2Σ g + upon a collision with a heavy structureless particle (a nitrogen molecule), are found as examples.
Machine Learning Estimation of Atom Condensed Fukui Functions.
Zhang, Qingyou; Zheng, Fangfang; Zhao, Tanfeng; Qu, Xiaohui; Aires-de-Sousa, João
2016-02-01
To enable the fast estimation of atom condensed Fukui functions, machine learning algorithms were trained with databases of DFT pre-calculated values for ca. 23,000 atoms in organic molecules. The problem was approached as the ranking of atom types with the Bradley-Terry (BT) model, and as the regression of the Fukui function. Random Forests (RF) were trained to predict the condensed Fukui function, to rank atoms in a molecule, and to classify atoms as high/low Fukui function. Atomic descriptors were based on counts of atom types in spheres around the kernel atom. The BT coefficients assigned to atom types enabled the identification (93-94 % accuracy) of the atom with the highest Fukui function in pairs of atoms in the same molecule with differences ≥0.1. In whole molecules, the atom with the top Fukui function could be recognized in ca. 50 % of the cases and, on the average, about 3 of the top 4 atoms could be recognized in a shortlist of 4. Regression RF yielded predictions for test sets with R(2) =0.68-0.69, improving the ability of BT coefficients to rank atoms in a molecule. Atom classification (as high/low Fukui function) was obtained with RF with sensitivity of 55-61 % and specificity of 94-95 %. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Frederick National Laboratory's Contribution to ATOM | FNLCR
As a founding member organization of ATOM, the Frederick National Laboratory will contribute scientific expertise in precision oncology, computational chemistry and cancer biology, as well as support for open sharing of data sets and predictive model
Cafarelli, P; Benazeth, C; Nieuwjaer, N; Lorente, N
2003-01-01
We compare the azimuthal distribution of H atoms after scattering off Ag(1 1 0) obtained by molecular dynamics with different H-Ag(1 1 0) potential energy surfaces (PES) and experimental results. We use grazing incident H atoms and low energies (up to 4 keV). Density functional theory (DFT) calculations are performed for the static case of an H atom in front of an Ag(1 1 0) surface. The surface is represented by an 8-atom slab, and the H atoms form 1x1 and 2x2 supercells. The generalized gradient approximation is used. Classical trajectories are evaluated on the obtained PES, and the azimuthal distribution of the scattered atoms is calculated. Good agreement with experiment is obtained which gives us some confidence in the correct description of the system at low energies by the static DFT calculations. These results are also compared with pair-potential calculations. The accuracy of trajectories may be important for the correct evaluation of charge transfer, energy loss and straggling during ion-surface coll...
Atoms, Molecules, and Compounds
Manning, Phillip
2007-01-01
Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.
Atoms, Molecules and Radiation
Indian Academy of Sciences (India)
IAS Admin
A Refresher Course in Applications of Quantum Mechanics to 'Atoms, Molecules and Radiation' will be held at the Indian Academy of Sciences, Bangalore from December 8 to 20. 2014. The Course is primarily aimed at teachers teaching quantum mechanics and/ or atomic and molecular physics at the UG / PG level.
Talanquer, Vicente
2013-01-01
Chemistry students and teachers often explain the chemical reactivity of atoms, molecules, and chemical substances in terms of purposes or needs (e.g., atoms want or need to gain, lose, or share electrons in order to become more stable). These teleological explanations seem to have pedagogical value as they help students understand and use…
Atomicity in Electronic Commerce,
1996-01-01
Atomicity in Electronic Commerce J. D. Tygar January 1996 CMU-CS-96-112 School of Computer Science Carnegie Mellon University Pittsburgh, PA 15213...other research sponsor. Keywords: electronic commerce , atomicity, NetBill, IBIP, cryptography, transaction pro- cessing, ACID, franking, electronic ...goods over networks. Electronic commerce has inspired a large variety of work. Unfortunately, much of that work ignores traditional transaction
Friedrich, Harald
2017-01-01
This expanded and updated well-established textbook contains an advanced presentation of quantum mechanics adapted to the requirements of modern atomic physics. It includes topics of current interest such as semiclassical theory, chaos, atom optics and Bose-Einstein condensation in atomic gases. In order to facilitate the consolidation of the material covered, various problems are included, together with complete solutions. The emphasis on theory enables the reader to appreciate the fundamental assumptions underlying standard theoretical constructs and to embark on independent research projects. The fourth edition of Theoretical Atomic Physics contains an updated treatment of the sections involving scattering theory and near-threshold phenomena manifest in the behaviour of cold atoms (and molecules). Special attention is given to the quantization of weakly bound states just below the continuum threshold and to low-energy scattering and quantum reflection just above. Particular emphasis is laid on the fundamen...
Directory of Open Access Journals (Sweden)
Janusz Brzozowski
2014-05-01
Full Text Available The atoms of a regular language are non-empty intersections of complemented and uncomplemented quotients of the language. Tight upper bounds on the number of atoms of a language and on the quotient complexities of atoms are known. We introduce a new class of regular languages, called the maximally atomic languages, consisting of all languages meeting these bounds. We prove the following result: If L is a regular language of quotient complexity n and G is the subgroup of permutations in the transition semigroup T of the minimal DFA of L, then L is maximally atomic if and only if G is transitive on k-subsets of 1,...,n for 0 <= k <= n and T contains a transformation of rank n-1.
A new approach to entangling neutral atoms.
Energy Technology Data Exchange (ETDEWEB)
Lee, Jongmin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Martin, Michael J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jau, Yuan-Yu [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Deutsch, Ivan H. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Biedermann, Grant W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2016-11-01
Our team has developed a new approach to entangling neutral atoms with a Rydberg-dressed interaction. Entangling neutral atoms is an essential key of quantum technologies such as quantum computation, many-body quantum simulation, and high-precision atomic sensors . The demonstrated Rydberg-dressed protocol involves adiabatically imposing a light shift on the ground state by coupling an excited Rydberg state with a tuned laser field. Using this technique, we have demonstrated a strong and tunable dipole - dipole interaction between two individually trapped atoms with energy shifts of order 1 MHz, which has been challenging to achieve in other protocols . During this program, we experimentally demonstrated Bell-state entanglement and the isomorphism to the Jaynes - Cumming model of a Rydberg-dressed two-atom system. Our theoretical calculations of a CPHASE quantum logic gate and arbitrary Dicke state quantum control in this system encourage further work.
Vibration spectra of single atomic nanocontacts
Energy Technology Data Exchange (ETDEWEB)
Bourahla, B [Laboratoire de Physique et Chimie Quantique, Departement de Physique, Faculte des Sciences, Universite Mouloud Mammeri de Tizi-Ouzou, 15000 Tizi-Ouzou (Algeria); Khater, A [Laboratoire de Physique de l' Etat Condense UMR 6087, Universite du Maine, 72085 Le Mans (France); Rafil, O [Laboratoire de Physique de l' Etat Condense UMR 6087, Universite du Maine, 72085 Le Mans (France); Tigrine, R [Laboratoire de Physique et Chimie Quantique, Departement de Physique, Faculte des Sciences, Universite Mouloud Mammeri de Tizi-Ouzou, 15000 Tizi-Ouzou (Algeria)
2006-10-04
This paper introduces a simple model for an atomic nanocontact, where its mechanical properties are analysed by calculating numerically the local spectral properties at the contact atom and the nearby atoms. The standard methodology for calculating phonon spectral densities is extended to enable the calculation of localized contact modes and local density of states (DOS). The model system considered for the nanocontact consists of two sets of triple parallel semi-infinite atomic chains joined by a single atom in between. The matching method is used, in the harmonic approximation, to calculate the local Green's functions for the irreducible set of sites that constitute the inhomogeneous nanocontact domain. The Green's functions yield the vibration spectra and the DOS for the atomic sites. These are numerically calculated for different cases of elastic hardening and softening of the nanocontact domain. The purpose is to investigate how the local dynamics respond to local changes in the elastic environment. The analysis of the spectra and of the DOS identifies characteristic features and demonstrates the central role of a core subset of these sites for the dynamics of the nanocontact. The system models a situation which may be appropriate for contact atomic force microscopy.
The impact of atomic precision measurements in high energy physics
Casalbuoni, Roberto
2000-01-01
In this talk I discuss the relevance of atomic physics in understanding some important questions about elementary particle physics. A particular attention is devoted to atomic parity violation measurements which seem to suggest new physics beyond the Standard Model. Atomic physics might also be relevant in discovering possible violations of the CPT symmetry.
Determination of Atomic Data Pertinent to the Fusion Energy Program
Energy Technology Data Exchange (ETDEWEB)
Reader, J.
2013-06-11
We summarize progress that has been made on the determination of atomic data pertinent to the fusion energy program. Work is reported on the identification of spectral lines of impurity ions, spectroscopic data assessment and compilations, expansion and upgrade of the NIST atomic databases, collision and spectroscopy experiments with highly charged ions on EBIT, and atomic structure calculations and modeling of plasma spectra.
Resonant quantum transitions in trapped antihydrogen atoms.
Amole, C; Ashkezari, M D; Baquero-Ruiz, M; Bertsche, W; Bowe, P D; Butler, E; Capra, A; Cesar, C L; Charlton, M; Deller, A; Donnan, P H; Eriksson, S; Fajans, J; Friesen, T; Fujiwara, M C; Gill, D R; Gutierrez, A; Hangst, J S; Hardy, W N; Hayden, M E; Humphries, A J; Isaac, C A; Jonsell, S; Kurchaninov, L; Little, A; Madsen, N; McKenna, J T K; Menary, S; Napoli, S C; Nolan, P; Olchanski, K; Olin, A; Pusa, P; Rasmussen, C Ø; Robicheaux, F; Sarid, E; Shields, C R; Silveira, D M; Stracka, S; So, C; Thompson, R I; van der Werf, D P; Wurtele, J S
2012-03-07
The hydrogen atom is one of the most important and influential model systems in modern physics. Attempts to understand its spectrum are inextricably linked to the early history and development of quantum mechanics. The hydrogen atom's stature lies in its simplicity and in the accuracy with which its spectrum can be measured and compared to theory. Today its spectrum remains a valuable tool for determining the values of fundamental constants and for challenging the limits of modern physics, including the validity of quantum electrodynamics and--by comparison with measurements on its antimatter counterpart, antihydrogen--the validity of CPT (charge conjugation, parity and time reversal) symmetry. Here we report spectroscopy of a pure antimatter atom, demonstrating resonant quantum transitions in antihydrogen. We have manipulated the internal spin state of antihydrogen atoms so as to induce magnetic resonance transitions between hyperfine levels of the positronic ground state. We used resonant microwave radiation to flip the spin of the positron in antihydrogen atoms that were magnetically trapped in the ALPHA apparatus. The spin flip causes trapped anti-atoms to be ejected from the trap. We look for evidence of resonant interaction by comparing the survival rate of trapped atoms irradiated with microwaves on-resonance to that of atoms subjected to microwaves that are off-resonance. In one variant of the experiment, we detect 23 atoms that survive in 110 trapping attempts with microwaves off-resonance (0.21 per attempt), and only two atoms that survive in 103 attempts with microwaves on-resonance (0.02 per attempt). We also describe the direct detection of the annihilation of antihydrogen atoms ejected by the microwaves.
BOOK REVIEW: Computational Atomic Structure
Post, Douglass E.
1998-02-01
introduction to atomic structure. It covers single and many electron systems, how to set up a basis set of wavefunctions for a many electron system, LS coupling, single and multi-electron Hamiltonians, the elementary Hartree-Fock approximation and how variational methods are used to determine the ground state energy and wavefunctions. The computational methods used in the codes are outlined and there are exercises at the end of each chapter. For a number of candidate atomic configurations, explicit examples are given that illustrate the physics, the approximations and the computational methods involved, and which provide the reader with the opportunity to check that he is using the suite of codes correctly. Relativistic effects are covered as perturbations with Breit-Pauli Hamiltonians. Isotope and hyperfine level splitting are also covered. A summary chapter covers allowed and forbidden bound-bound transitions. It describes how to set up the matrix elements for transition operators, and the determination of selection rules and computational aspects of the methods for allowed and forbidden lines. The last chapter provides a brief introduction to continuum transitions, including how to compute the necessary wavefunctions to calculate photoionization or photodetachment and autoionization processes. Several appendices provide a summary of angular momentum theory, an introduction to the Dirac and Breit-Pauli theory for relativistic processes, and a description of the input parameters needed to run the programs. In summary, the book is an almost essential guide to anyone planning to use the Multi-Configuration Hartree-Fock suite of codes. With this guide, even someone not thoroughly familiar with the details of the subject or the codes should be able to use them to obtain energy levels, wavefunctions and transition rates for any atomic system of interest. This book serves as a model example for the general computational physics community of how to document an important suite of
Chammas, Oliver; Bonass, William A; Thomson, Neil H
2017-05-01
The influence of heparin and heparan sulphate (HepS) on the appearance and analysis of open promoter complex (RPo) formation by E. coli RNA polymerase (RNAP) holoenzyme (σ70RNAP) on linear DNA using ex situ imaging by atomic force microscopy (AFM) has been investigated. Introducing heparin or HepS into the reaction mix significantly reduces non-specific interactions of the σ70RNAP and RNAP after RPo formation allowing for better interpretation of complexes shown within AFM images, particularly on DNA templates containing more than one promoter. Previous expectation was that negatively charged polysaccharides, often used as competitive inhibitors of σRNAP binding and RPo formation, would also inhibit binding of the DNA template to the mica support surface and thereby lower the imaging yield of active RNAP-DNA complexes. We found that the reverse of this was true, and that the yield of RPo formation detected by AFM, for a simple tandem gene model containing two λPR promoters, increased. Moreover and unexpectedly, HepS was more efficient than heparin, with both of them having a dispersive effect on the sample, minimising unwanted RNAP-RNAP interactions as well as non-specific interactions between the RNAP and DNA template. The success of this method relied on the observation that E. coli RNAP has the highest affinity for the mica surface of all the molecular components. For our system, the affinity of the three constituent biopolymers to muscovite mica was RNAP>Heparin or HepS>DNA. While we observed that heparin and HepS can inhibit DNA binding to the mica, the presence of E. coli RNAP overcomes this effect allowing a greater yield of RPos for AFM analysis. This method can be extended to other DNA binding proteins and enzymes, which have an affinity to mica higher than DNA, to improve sample preparation for AFM studies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Atom trap loss, elastic collisions, and technology
Booth, James
2012-10-01
The study of collisions and scattering has been one of the most productive approaches for modern physics, illuminating the fundamental structure of crystals, surfaces, atoms, and sub-atomic particles. In the field of cold atoms, this is no less true: studies of cold atom collisions were essential to the production of quantum degenerate matter, the formation of cold molecules, and so on. Over the past few years it has been my delight to investigate elastic collisions between cold atoms trapped in either a magneto-optical trap (MOT) or a magnetic trap with hot, background gas in the vacuum environment through the measurement of the loss of atoms from the trap. Motivated by the goal of creating cold atom-based technology, we are deciphering what the trapped atoms are communicating about their environment through the observed loss rate. These measurements have the advantages of being straightforward to implement and they provide information about the underlying, fundamental inter-atomic processes. In this talk I will present some of our recent work, including the observation of the trap depth dependence on loss rate for argon-rubidium collisions. The data follow the computed loss rate curve based on the long-range Van der Waals interaction between the two species. The implications of these findings are exciting: trap depths can be determined from the trap loss measurement under controlled background density conditions; observation of trap loss rate in comparison to models for elastic, inelastic, and chemical processes can lead to improved understanding and characterization of these fundamental interactions; finally the marriage of cold atoms with collision modeling offers the promise of creating a novel pressure sensor and pressure standard for the high and ultra-high vacuum regime.
Quantitative High-Resolution Transmission Electron Microscopy of Single Atoms
Gamm, B.; Popescu, R.; Blank, H.; Schneider, R; Beyer, A.; Gölzhäuser, A.; Gerthsen, D.
2010-01-01
Single atoms can be considered as basic objects for electron microscopy to test the microscope performance and basic concepts for modeling of image contrast. In this work high-resolution transmission electron microscopy was applied to image single platinum atoms in an aberration-corrected transmission electron microscope. The atoms are deposited on a self-assembled monolayer substrate which induces only negligible contrast. Single-atom contrast simulations were performed on the basis of Weick...
Thermodynamic properties of average-atom interatomic potentials for alloys
Nöhring, Wolfram Georg; Curtin, William
2016-01-01
The atomistic mechanisms of deformation in multicomponent random alloys are challenging to model because of their extensive structural and compositional disorder. For embedded-atom-method interatomic potentials, a formal averaging procedure can generate an average-atom EAM potential and this average-atom potential has recently been shown to accurately predict many zero-temperature properties of the true random alloy. Here, the finite-temperature thermodynamic properties of the average-atom po...
Atoms, molecules and optical physics 1. Atoms and spectroscopy
Energy Technology Data Exchange (ETDEWEB)
Hertel, Ingolf V.; Schulz, Claus-Peter
2015-09-01
This is the first volume of textbooks on atomic, molecular and optical physics, aiming at a comprehensive presentation of this highly productive branch of modern physics as an indispensable basis for many areas in physics and chemistry as well as in state of the art bio- and material-sciences. It primarily addresses advanced students (including PhD students), but in a number of selected subject areas the reader is lead up to the frontiers of present research. Thus even the active scientist is addressed. This volume 1 provides the canonical knowledge in atomic physics together with basics of modern spectroscopy. Starting from the fundamentals of quantum physics, the reader is familiarized in well structured chapters step by step with the most important phenomena, models and measuring techniques. The emphasis is always on the experiment and its interpretation, while the necessary theory is introduced from this perspective in a compact and occasionally somewhat heuristic manner, easy to follow even for beginners.
Prati, Enrico
2013-01-01
Single-Atom Nanoelectronics covers the fabrication of single-atom devices and related technology, as well as the relevant electronic equipment and the intriguing new phenomena related to single-atom and single-electron effects in quantum devices. It also covers the alternative approaches related to both silicon- and carbon-based technologies, also from the point of view of large-scale industrial production. The publication provides a comprehensive picture of the state of the art at the cutting edge and constitutes a milestone in the emerging field of beyond-CMOS technology. Although there are
Wehr, Russell M; Adair, Thomas W
1984-01-01
The fourth edition of Physics of the Atom is designed to meet the modern need for a better understanding of the atomic age. It is an introduction suitable for students with a background in university physics and mathematical competence at the level of calculus. This book is designed to be an extension of the introductory university physics course into the realm of atomic physics. It should give students a proficiency in this field comparable to their proficiency in mechanics, heat, sound, light, and electricity.
Deprince, J.; Fritzsche, S.; Kallman, T. R.; Palmeri, P.; Quinet, P.
2017-01-01
The influence of plasma environment on the atomic parameters associated with the K-vacancy states has been investigated theoretically for several iron ions. To do this, a time-averaged Debye-Huckel potential for both the electron-nucleus and electron-electron interactions has been considered in the framework of relativistic multiconfiguration Dirac-Fock computations. More particularly, the plasma screening effects on ionization potentials, K-thresholds, transition energies, and radiative rates have been estimated in the astrophysical context of accretion disks around black holes. In the present paper, we describe the behavior of those atomic parameters for Ne-, Na-, Ar-, and K-like iron ions.
Effect of atomizer scale and fluid properties on atomization mechanisms and spray characteristics
Waind, Travis
instability development and growth along with the resulting spray characteristics, allowing for correlations to be made between the two data sets as the more recent mechanism-based atomization models do. Existing mechanism-based models from the literature are compared to the experimental results, as these existing models have not been evaluated significantly with changing atomizer geometry, high-viscosity fluids, and high flow regimes as was done here. Additionally, two experimental campaigns were undertaken with atomizers used to operate the University of Utah's PDU-scale (process development unit) entrained flow gasifier. The first campaign showed the effect of gas velocity, atomizer load (total flow), and gas-liquid impingement angle on the qualitative cold-flow atomizer performance. These trends are then tied to behavior of the entrained flow gasifier, showing the existence of a minimum required degree of atomization to avoid substantial losses in fuel conversion and efficiency in a gasifier. The second campaign showed the effect of gas flow, liquid flow, and fluid on the quantitative cold-flow atomizer performance. While in the literature, changing fluid properties of Newtonian fluids are shown to have a relatively linear response on atomizer performance, the behavior of non-Newtonian fluids was shown to be much more complex and difficult to predict. The correlations developed for the small-scale atomizers are applied to the micro-hole atomizers and found to be erroneous for the change in atomizer geometry. Buckingham-(Pi) theorem is then used to develop correlations to predict the spray Sauter mean diameter for the micro-hole atomizers. Slurry-fed combustion and gasification systems are but one industrial implementation of atomization. Atomization plays important roles in numerous other industries, and despite decades of study, it is not well understood. This document serves to shed some light on a few small, specific subsets of the topic.
Lattice dynamics and correlated atomic motion from the atomic pair distribution function
Jeong, I. -K.; Heffner, R. H.; Graf, M. J.; Billinge, S. J. L.
2002-01-01
The mean-square relative displacements (MSRD) of atomic pair motions in crystals are studied as a function of pair distance and temperature using the atomic pair distribution function (PDF). The effects of the lattice vibrations on the PDF peak widths are modelled using both a multi-parameter Born von-Karman (BvK) force model and a single-parameter Debye model. These results are compared to experimentally determined PDFs. We find that the near-neighbor atomic motions are strongly correlated, ...
Joseph, Agnel P; Swapna, Lakshmipuram S; Rakesh, Ramachandran; Srinivasan, Narayanaswamy
2016-09-01
Protein-protein interface residues, especially those at the core of the interface, exhibit higher conservation than residues in solvent exposed regions. Here, we explore the ability of this differential conservation to evaluate fittings of atomic models in low-resolution cryo-EM maps and select models from the ensemble of solutions that are often proposed by different model fitting techniques. As a prelude, using a non-redundant and high-resolution structural dataset involving 125 permanent and 95 transient complexes, we confirm that core interface residues are conserved significantly better than nearby non-interface residues and this result is used in the cryo-EM map analysis. From the analysis of inter-component interfaces in a set of fitted models associated with low-resolution cryo-EM maps of ribosomes, chaperones and proteasomes we note that a few poorly conserved residues occur at interfaces. Interestingly a few conserved residues are not in the interface, though they are close to the interface. These observations raise the potential requirement of refitting the models in the cryo-EM maps. We show that sampling an ensemble of models and selection of models with high residue conservation at the interface and in good agreement with the density helps in improving the accuracy of the fit. This study indicates that evolutionary information can serve as an additional input to improve and validate fitting of atomic models in cryo-EM density maps. Copyright © 2016 Elsevier Inc. All rights reserved.
Atomic & Molecular Interactions
Energy Technology Data Exchange (ETDEWEB)
None
2002-07-12
The Gordon Research Conference (GRC) on Atomic & Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.
Energy Technology Data Exchange (ETDEWEB)
Razmi, H. [Department of Physics, University of Qom, Qom 37185-359 (Iran, Islamic Republic of)], E-mail: razmi@qom.ac.ir; Abdollahi, M. [Department of Physics, University of Qom, Qom 37185-359 (Iran, Islamic Republic of)], E-mail: mah.abdollahi@gmail.com
2008-11-10
We want to introduce an atomic pendulum whose driving force (torque) is due to the quantum vacuum fluctuations. Applying the well-known Casimir-Polder effect to a special configuration (a combined structure of an atomic nanostring and a conducting plate), an atomic pendulum (Casimir atomic pendulum) is designed. Using practically acceptable data corresponding to the already known world of nanotechnology and based on reasonable/reliable numerical estimates, the period of oscillation for the pendulum is computed. This pendulum can be considered as both a new micro(nano)-electromechanical system and a new simple vacuum machine. Its design may be considered as a first step towards realizing the visualized vacuum (Casimir) clock{exclamation_point}.
Razmi, H.; Abdollahi, M.
2008-11-01
We want to introduce an atomic pendulum whose driving force (torque) is due to the quantum vacuum fluctuations. Applying the well-known Casimir-Polder effect to a special configuration (a combined structure of an atomic nanostring and a conducting plate), an atomic pendulum (Casimir atomic pendulum) is designed. Using practically acceptable data corresponding to the already known world of nanotechnology and based on reasonable/reliable numerical estimates, the period of oscillation for the pendulum is computed. This pendulum can be considered as both a new micro(nano)-electromechanical system and a new simple vacuum machine. Its design may be considered as a first step towards realizing the visualized vacuum (Casimir) clock!
Advances in atomic spectroscopy
Sneddon, J
1998-01-01
This volume continues the series'' cutting-edge reviews on developments in this field. Since its invention in the 1920s, electrostatic precipitation has been extensively used in industrial hygiene to remove dust and particulate matter from gases before entering the atmosphere. This combination of electrostatic precipitation is reported upon in the first chapter. Following this, chapter two reviews recent advances in the area of chemical modification in electrothermal atomization. Chapter three consists of a review which deal with advances and uses of electrothermal atomization atomic absorption spectrometry. Flow injection atomic spectroscopy has developed rapidly in recent years and after a general introduction, various aspects of this technique are looked at in chapter four. Finally, in chapter five the use of various spectrometric techniques for the determination of mercury are described.
National Research Council Canada - National Science Library
DOBBIN, LEONARD
1896-01-01
WITH reference to the communications from the authors and from the reviewer of the "New View of the Origin of Dalton's Atomic Theory," published in NATURE for May 14, I beg leave to offer the following remarks...
National Aeronautics and Space Administration — Vertical cavity surface emitting lasers (VCSELs) is a new technology which can be used for developing high performance laser components for atom-based sensors...
Burkhardt, Charles E
2006-01-01
The study of atomic physics propelled us into the quantum age in the early twentieth century and carried us into the twenty-first century with a wealth of new and, in some cases, unexplained phenomena. Topics in Atomic Physics provides a foundation for students to begin research in modern atomic physics. It can also serve as a reference because it contains material that is not easily located in other sources. A distinguishing feature is the thorough exposition of the quantum mechanical hydrogen atom using both the traditional formulation and an alternative treatment not usually found in textbooks. The alternative treatment exploits the preeminent nature of the pure Coulomb potential and places the Lenz vector operator on an equal footing with other operators corresponding to classically conserved quantities. A number of difficult to find proofs and derivations are included as is development of operator formalism that permits facile solution of the Stark effect in hydrogen. Discussion of the classical hydrogen...
Zeeman atomic absorption spectrometry
Energy Technology Data Exchange (ETDEWEB)
Hadeishi, T.; McLaughlin, R.
1978-08-01
The design and development of a Zeeman atomic absorption spectrometer for trace element analysis are described. An instruction manual is included which details the operation, adjustment, and maintenance. Specifications and circuit diagrams are given. (WHK)
A strong failure of aleph_0-stability for atomic classes
Laskowski, Michael C.; Shelah, Saharon
2017-01-01
We study classes of atomic models At_T of a countable, complete first-order theory T . We prove that if At_T is not pcl-small, i.e., there is an atomic model N that realizes uncountably many types over pcl(a) for some finite tuple a from N, then there are 2^aleph1 non-isomorphic atomic models of T, each of size aleph1.
Atomic Clocks Research - An Overview.
1987-08-15
magnet. Since atomic deflection in an inhomogeneous magnetic field is inversely proportional to the square of the atomic speed, the atomic velocity...purifier and controlled leak; an atomic source (i.e., the dissociator under 39 study); a dipole electromagnetic with pole pieces shaped to produce an...34Relaxation Magnetique d’Atomes de Rubidium sur des Parois Paraffines," J. Phys. (Paris) 24, 379 (1963). 21. S. Wexler, "Deposition of Atomic Beams
Bukhari, Ijaz; Nuhman-ul-Haq; Hyat, Khizar
2013-01-01
Watermarking helps in ensuring originality, ownership and copyrights of a digital image. This paper aims at embedding a Watermark in an image using Wave Atom Transform. Preference of Wave Atoms on other transformations has been due to its sparser expansion, adaptability to the direction of local pattern, and sharp frequency localization. In this scheme, we had tried to spread the watermark in an image so that the information at one place is very small and undetectable. In order to extract the...
Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan
2014-09-01
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
Graybill, George
2007-01-01
Young scientists will be thrilled to explore the invisible world of atoms, molecules and elements. Our resource provides ready-to-use information and activities for remedial students using simplified language and vocabulary. Students will label each part of the atom, learn what compounds are, and explore the patterns in the periodic table of elements to find calcium (Ca), chlorine (Cl), and helium (He) through hands-on activities.
Luckey, T. D.
2008-01-01
Media reports of deaths and devastation produced by atomic bombs convinced people around the world that all ionizing radiation is harmful. This concentrated attention on fear of miniscule doses of radiation. Soon the linear no threshold (LNT) paradigm was converted into laws. Scientifically valid information about the health benefits from low dose irradiation was ignored. Here are studies which show increased health in Japanese survivors of atomic bombs. Parameters include decreased mutation,...
Atomic interferometry; Interferometrie atomique
Energy Technology Data Exchange (ETDEWEB)
Baudon, J.; Robert, J. [Paris-13 Univ., 93 - Saint-Denis (France)
2004-07-01
Since the theoretical works of L. De Broglie (1924) and the famous experiment of Davisson and Germer (1927), we know that a wave is linked with any particle of mass m by the relation {lambda} = h/(mv), where {lambda} is the wavelength, v the particle velocity and h is the Planck constant. The basic principle of the interferometry of any material particle, atom, molecule or aggregate is simple: using a simple incident wave, several mutually consistent waves (with well-defined relative phases) are generated and controllable phase-shifts are introduced between them in order to generate a wave which is the sum of the previous waves. An interference figure is obtained which consists in a succession of dark and bright fringes. The atomic interferometry is based on the same principle but involves different techniques, different wave equations, but also different beams, sources and correlations which are described in this book. Because of the small possible wavelengths and the wide range of possible atomic interactions, atomic interferometers can be used in many domains from the sub-micron lithography to the construction of sensors like: inertial sensors, gravity-meters, accelerometers, gyro-meters etc. The first chapter is a preliminary study of the space and time diffraction of atoms. The next chapters is devoted to the description of slit, light separation and polarization interferometers, and the last chapter treats of the properties of Bose-Einstein condensates which are interesting in atomic interferometry. (J.S.)
Energy Technology Data Exchange (ETDEWEB)
Ichimaru, M.; Tomonaga, M.; Amenomori, T.; Matsuo, T. (Nagasaki Univ. (Japan). School of Medicine)
1991-12-01
Characteristic features of the leukemia among atomic bomb survivors were studied. Dose estimates of atomic bomb radiation were based on T65D, but the new dosimetry system DS86 was used for some analyses. The ratio of a single leukemia type to all leukemias was highest for chronic myelogenous leukemia (CML) in Hiroshima, and the occurrence of CML was thought to be most characteristic to atomic bomb radiation induced leukemia. The threshold of CML occurrence in Hiroshima is likely to be between 0.5{approx}0.09 Gy. However, the threshold of acute leukemia appears to be nearly 1 Gy. In the distribution of acute myeloid leukemia (AML) subtypes by French-American-British classification, there was no M3 case in 1 Gy or more group, although several atypical AML cases of survivors were observed. Although aplastic anemia has not increased as a late effect of the atomic bomb radiation exposure, many atypical leukemia or other myeloproliferative diseases who had been diagnosed as aplastic anemia or its related diseases have been experienced among atomic bomb survivors. Chromosome study was conducted using colony forming cells induced by hemopoietic stem cells of peripheral blood of proximal survivors. Same chromosome aberrations were observed in colony forming cells and peripheral T-cells in several atomic bomb survivors. (author).
The ALADDIN atomic physics database system
Hulse, Russell A.
1990-05-01
ALADDIN is an atomic physics database system which has been developed in order to provide a broadly-based standard medium for the exchange and management of atomic data. ALADDIN consists of a data format definition together with supporting software for both interactive searches as well as for access to the data by plasma modeling and other codes. 8AB The ALADDIN system is designed to offer maximum flexibility in the choice of data representations and labeling schemes, so as to support a wide range of atomic physics data types and allow natural evolution and modification of the database as needs change. Associated dictionary files are included in the ALADDIN system for data documentation. The importance of supporting the widest possible user community was also central to be ALADDIN design, leading to the use of straightforward text files with concatentated data entries for the file structure, and the adoption of strict FORTRAN 77 code for the supporting software. This will allow ready access to the ALADDIN system on the widest range of scientific computers, and easy interfacing with FORTRAN modeling codes, user developed atomic physics codes and database, etc. This supporting software consists of the ALADDIN interactive searching and data display code, together with the ALPACK subroutine package which provides ALADDIN datafile searching and data retrieval capabilities to user's codes. ALADDIN has been adopted as the standard international atomic physics data exchange format for magnetic confinement fusion applications by the International Atomic Energy Agency (IAEA). Entry of critically evaluated atomic data sets into ALADDIN format is to be coordinated by the IAEA atomic and Molecular Data Unit, which will also coordinate long-term development and distribution of updated software and documentation. The increasingly widespread adoption of the ALADDIN data format can be expected to greatly facilitate access to atomic data both within and outside of this original
Quantum Spin Lenses in Atomic Arrays
Directory of Open Access Journals (Sweden)
A. W. Glaetzle
2017-09-01
Full Text Available We propose and discuss quantum spin lenses, where quantum states of delocalized spin excitations in an atomic medium are focused in space in a coherent quantum process down to (essentially single atoms. These can be employed to create controlled interactions in a quantum light-matter interface, where photonic qubits stored in an atomic ensemble are mapped to a quantum register represented by single atoms. We propose Hamiltonians for quantum spin lenses as inhomogeneous spin models on lattices, which can be realized with Rydberg atoms in 1D, 2D, and 3D, and with strings of trapped ions. We discuss both linear and nonlinear quantum spin lenses: in a nonlinear lens, repulsive spin-spin interactions lead to focusing dynamics conditional to the number of spin excitations. This allows the mapping of quantum superpositions of delocalized spin excitations to superpositions of spatial spin patterns, which can be addressed by light fields and manipulated. Finally, we propose multifocal quantum spin lenses as a way to generate and distribute entanglement between distant atoms in an atomic lattice array.
Energy Technology Data Exchange (ETDEWEB)
Dudka, A. P., E-mail: dudka@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation)
2017-03-15
Accurate X-ray diffraction study of langasite (La{sub 3}Ga{sub 5}SiO{sub 14}) single crystal has been performed using the data obtained on a diffractometer equipped with a CCD area detector at 295 and 90.5 K. Within the known La{sub 3}Ga{sub 5}SiO{sub 14} model, Ga and Si cations jointly occupy the 2d site. A new model of a “multicell” consisting of two different unit cells is proposed. Gallium atoms occupy the 2d site in one of these cells, and silicon atoms occupy this site in the other cell; all other atoms correspondingly coordinate these cations. This structure implements various physical properties exhibited by langasite family crystals. The conclusions are based on processing four data sets obtained with a high resolution (sin θ/λ ≤ 1.35 Å{sup –1}), the results reproduced in repeated experiments, and the high relative precision of the study (sp. gr. P321, Z = 1; at 295 K, a = 8.1652(6) Å, c = 5.0958(5) Å, R/wR = 0.68/0.68%, 3927 independent reflections; at 90.5 K, a = 8.1559(4) Å, c = 5.0913(6) Å, R/wR = 0.92/0.93%, 3928 reflections).
Non-thermal hydrogen atoms in the terrestrial upper thermosphere.
Qin, Jianqi; Waldrop, Lara
2016-12-06
Model predictions of the distribution and dynamical transport of hydrogen atoms in the terrestrial atmosphere have long-standing discrepancies with ultraviolet remote sensing measurements, indicating likely deficiencies in conventional theories regarding this crucial atmospheric constituent. Here we report the existence of non-thermal hydrogen atoms that are much hotter than the ambient oxygen atoms in the upper thermosphere. Analysis of satellite measurements indicates that the upper thermospheric hydrogen temperature, more precisely the mean kinetic energy of the atomic hydrogen population, increases significantly with declining solar activity, contrary to contemporary understanding of thermospheric behaviour. The existence of hot hydrogen atoms in the upper thermosphere, which is the key to reconciling model predictions and observations, is likely a consequence of low atomic oxygen density leading to incomplete collisional thermalization of the hydrogen population following its kinetic energization through interactions with hot atomic or ionized constituents in the ionosphere, plasmasphere or magnetosphere.
Positronium-alkali atom scattering at medium energies
Energy Technology Data Exchange (ETDEWEB)
Chakraborty, Ajoy [Laban Hrad Vidyapith, AD-369, Salt Lake City, Kolkata 700 064 (India); Basu, Arindam [Department of Physics, Maheshtala College, Chandannagar, South 24 Parganas, Kolkata 700 140 (India); Sarkar, Nirmal K [Sodepur Chandrachur Vidyapith, 1, Desh Bandhu Nagar, Sodepur, 743 174 (India); Sinha, Prabal K [Department of Physics, Bangabasi College, 19, Raj Kumar Chakravorty Sarani, Kolkata 700 009 (India)
2004-04-28
We investigate the scattering of orthopositronium (o-Ps) atom off different atomic alkali targets (Na to Cs) at low and medium energies (up to 120 eV). Projectile-elastic and target-elastic close-coupling models have been employed to investigate the systems in addition to the static-exchange model. Elastic, excitation and total cross sections have been reported for all four systems. The magnitude of the alkali excitation cross section increases with increasing atomic number of the target atom while the position of the peak value shifts towards lower incident energies. The magnitudes of the Ps excitation and ionization cross sections increase steadily with atomic number with no change in the peak position. The reported results show regular behaviour with increasing atomic number of the target atom. Scattering parameters for the Ps-Rb and Ps-Cs systems are being reported for the first time.
Atomic clock ensemble in space
Cacciapuoti, L.; Salomon, C.
2011-12-01
Atomic Clock Ensemble in Space (ACES) is a mission using high-performance clocks and links to test fundamental laws of physics in space. Operated in the microgravity environment of the International Space Station, the ACES clocks, PHARAO and SHM, will generate a frequency reference reaching instability and inaccuracy at the 1 · 10-16 level. A link in the microwave domain (MWL) and an optical link (ELT) will make the ACES clock signal available to ground laboratories equipped with atomic clocks. Space-to-ground and ground-to-ground comparisons of atomic frequency standards will be used to test Einstein's theory of general relativity including a precision measurement of the gravitational red-shift, a search for time variations of fundamental constants, and Lorentz Invariance tests. Applications in geodesy, optical time transfer, and ranging will also be supported. ACES has now reached an advanced technology maturity, with engineering models completed and successfully tested and flight hardware under development. This paper presents the ACES mission concept and the status of its main instruments.
Dynamics in atomic signaling games
Fox, Michael J.
2015-04-08
We study an atomic signaling game under stochastic evolutionary dynamics. There are a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with high probability or mutate with low probability. We analyze the long-run distribution of states and show that, for sufficiently small mutation probability, its support is limited to efficient communication systems. We find that this behavior is insensitive to the particular choice of evolutionary dynamic, a property that is due to the game having a potential structure with a potential function corresponding to average fitness. Consequently, the model supports conclusions similar to those found in the literature on language competition. That is, we show that efficient languages eventually predominate the society while reproducing the empirical phenomenon of linguistic drift. The emergence of efficiency in the atomic case can be contrasted with results for non-atomic signaling games that establish the non-negligible possibility of convergence, under replicator dynamics, to states of unbounded efficiency loss.
Dynamics in atomic signaling games.
Fox, Michael J; Touri, Behrouz; Shamma, Jeff S
2015-07-07
We study an atomic signaling game under stochastic evolutionary dynamics. There are a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with high probability or mutate with low probability. We analyze the long-run distribution of states and show that, for sufficiently small mutation probability, its support is limited to efficient communication systems. We find that this behavior is insensitive to the particular choice of evolutionary dynamic, a property that is due to the game having a potential structure with a potential function corresponding to average fitness. Consequently, the model supports conclusions similar to those found in the literature on language competition. That is, we show that efficient languages eventually predominate the society while reproducing the empirical phenomenon of linguistic drift. The emergence of efficiency in the atomic case can be contrasted with results for non-atomic signaling games that establish the non-negligible possibility of convergence, under replicator dynamics, to states of unbounded efficiency loss. Copyright © 2015 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Bleck-Neuhaus, Joern [Bremen Univ. (Germany)
2013-07-01
The current state of knowledge of nuclear and elementary-particle physics has a checkered history, often characterized by shocking new concept formations, which also opens up to the present day students of physics only with difficulty. This book uses those controversial yet educational development in order to enable learners to improve access to the new concepts. It helps to understand how the physical picture of the smallest particles is today, and why it is so and not otherwise originated: Beginning in the detection of the atoms up to the current standard model of elementary-particle physics and the Higgs boson. So readers gain an impression of that great field, which is originated in the constant interplay between established theoretical models, confirmatory or contradictory findings, sometimes controversial new concept formations, and improved experiments - a process, that surely continues in the future. Guideline of the presentation is a comprehensible also in detail as possible reasoning argumentation. Students of physics before their B.Sc. degree will thus be able to acquire knowledge of the subatomic physics relating to general knowledge in their field. Also for physics teachers at schools or colleges, this new representation should be interesting. The second edition has been updated to the newest state of knowledge, in particular first results of the LHC have been incorporated.
Directory of Open Access Journals (Sweden)
Hiroshi Yoshii
Full Text Available Workers decommissioning the Fukushima-Daiichi nuclear power plant damaged from the Great East Japan Earthquake and resulting tsunami are at risk of injury with possible contamination from radioactive heavy atoms including actinides, such as plutonium. We propose a new methodology for on-site and rapid evaluation of heavy-atom contamination in wounds using a portable X-ray fluorescence (XRF device. In the present study, stable lead was used as the model contaminant substitute for radioactive heavy atoms. First, the wound model was developed by placing a liquid blood phantom on an epoxy resin wound phantom contaminated with lead. Next, the correlation between the concentration of contaminant and the XRF peak intensity was formulated considering the thickness of blood exiting the wound. Methods to determine the minimum detection limit (MDL of contaminants at any maximal equivalent dose to the wound by XRF measurement were also established. For example, in this system, at a maximal equivalent dose of 16.5 mSv to the wound and blood thickness of 0.5 mm, the MDL value for lead was 1.2 ppm (3.1 nmol. The radioactivity of 239Pu corresponding to 3.1 nmol is 1.7 kBq, which is lower than the radioactivity of 239Pu contaminating puncture wounds in previous severe accidents. In conclusion, the established methodology could be beneficial for future development of a method to evaluate plutonium contamination in wounds. Highlights: Methodology for evaluation of heavy-atom contamination in a wound was established. A portable X-ray fluorescence device enables on-site, rapid and direct evaluation. This method is expected to be used for evaluation of plutonium contamination in wounds.
Yoshii, Hiroshi; Yanagihara, Kouta; Imaseki, Hitoshi; Hamano, Tsuyoshi; Yamanishi, Hirokuni; Inagaki, Masayo; Sakai, Yasuhiro; Sugiura, Nobuyuki; Kurihara, Osamu; Sakai, Kazuo
2014-01-01
Workers decommissioning the Fukushima-Daiichi nuclear power plant damaged from the Great East Japan Earthquake and resulting tsunami are at risk of injury with possible contamination from radioactive heavy atoms including actinides, such as plutonium. We propose a new methodology for on-site and rapid evaluation of heavy-atom contamination in wounds using a portable X-ray fluorescence (XRF) device. In the present study, stable lead was used as the model contaminant substitute for radioactive heavy atoms. First, the wound model was developed by placing a liquid blood phantom on an epoxy resin wound phantom contaminated with lead. Next, the correlation between the concentration of contaminant and the XRF peak intensity was formulated considering the thickness of blood exiting the wound. Methods to determine the minimum detection limit (MDL) of contaminants at any maximal equivalent dose to the wound by XRF measurement were also established. For example, in this system, at a maximal equivalent dose of 16.5 mSv to the wound and blood thickness of 0.5 mm, the MDL value for lead was 1.2 ppm (3.1 nmol). The radioactivity of 239Pu corresponding to 3.1 nmol is 1.7 kBq, which is lower than the radioactivity of 239Pu contaminating puncture wounds in previous severe accidents. In conclusion, the established methodology could be beneficial for future development of a method to evaluate plutonium contamination in wounds. Highlights: Methodology for evaluation of heavy-atom contamination in a wound was established. A portable X-ray fluorescence device enables on-site, rapid and direct evaluation. This method is expected to be used for evaluation of plutonium contamination in wounds.
An interacting quantum atom study of model SN 2 reactions (X- ···CH3 X, X = F, Cl, Br, and I).
Alkorta, Ibon; Thacker, Joseph C R; Popelier, Paul L A
2017-11-10
The quantum chemical topology method has been used to analyze the energetic profiles in the X- + CH3 X → XCH3 + X- SN 2 reactions, with X = F, Cl, Br, and I. The evolution of the electron density properties at the BCPs along the reaction coordinate has been analysed. The interacting quantum atoms (IQA) method has been used to evaluate the intra-atomic and interatomic energy variations along the reaction path. The different energetic terms have been examined by the relative energy gradient method and the ANANKE program, which enables automatic and unbiased IQA analysis. Four of the six most important IQA energy contributions were needed to reproduce the reaction barrier common to all reactions. The four reactions considered share many common characteristics but when X = F a number of particularities occur. © 2017 Wiley Periodicals, Inc. © 2017 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.