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.
Hund's Rule in Two-Electron Atomic Systems
Harriman, John E.
2008-01-01
A model proposed by Rioux to explain Hund's rule is investigated. Although the largest contribution to the singlet-triplet splitting in the two-electron atomic systems is the nuclear attraction term, this arises from different optimum scale factors in the two states and that difference is driven by the electron-electron exchange term. The…
An exciton approach to the excited states of two electron atoms. I Formalism and interpretation
International Nuclear Information System (INIS)
Schipper, P.E.
1985-01-01
The exciton model is formally applied to a description of the excited states of two electron atoms with the explicit inclusion of exchange. The model leads to a conceptually simple framework for the discussion of the electronic properties of the archetypical atomic electron pair
Two-electron atomic systems confined within spheroidal boxes
Energy Technology Data Exchange (ETDEWEB)
Corella-Madueno, A.; Rosas, R.A.; Marin, J.L.; Riera, R.
2000-03-15
The direct variational method is used to estimate some interesting physical properties of the He atom and the Li{sup +} ion confined within impenetrable spheroidal boxes. A comparative investigation f the ground=state energy, pressure, polarizability, dipole, and quadrupole moments with those of the He atom inside boxes with paraboloidal walls is made. The overall results show a similar qualitative behavior. However, for Li{sup +} there are quantitative differences on such properties due to its major nuclear charge, as expected. The trial wave function is constructed as a product of two hydrogenic wave functions adapted to the geometry of the confining boxes.
Quantum mechanics of one- and two-electron atoms
Bethe, Hans A
2008-01-01
This classic of modern physics includes a vast array of approximation methods, mathematical tricks, and physical pictures that are also useful in the application of quantum mechanics to other fields. Students and professionals will find it an essential reference for calculations pertaining to hydrogen-like and helium-like atoms and their comparison with experimental results. In-depth explorations of the Dirac theory of the electron and of radiative effects include brief accounts of relevant experiments. The specific application of general field-theoretic results to atomic systems also receives
Critical screening in the one- and two-electron Yukawa atoms
Montgomery, H. E.; Sen, K. D.; Katriel, Jacob
2018-02-01
The one- and two-electron Yukawa atoms, also referred to as the Debye-Hückel or screened Coulomb atoms, have been topics of considerable interest both for intrinsic reasons and because of their relevance to terrestrial and astrophysical plasmas. At sufficiently high screening the one-electron Yukawa atom ceases to be bound. Some calculations appeared to suggest that as the screening increases in the ground state of the two-electron Yukawa atom (in which both the one-particle attraction and the interparticle repulsion are screened) the two electrons are detached simultaneously, at the same screening constant at which the one-electron atom becomes unbound. Our results rule this scenario out, offering an alternative that is not less interesting. In particular, it is found that for Z charge Zc≈0.911028 ... , at which the bare Coulomb two-electron atom becomes unbound, and even over a range of lower nuclear charges, an appropriate amount of screening gives rise to a bound two-electron system.
Photoelectron spectra as a probe of double-core resonsance in two-electron atoms
International Nuclear Information System (INIS)
Grobe, R.; Haan, S.L.; Eberly, J.H.
1996-01-01
The authors calculate photoelectron spectra for a two-electron atom under the influence of two external driving fields, using an essential states formalism. They focus on the regime of so-called coherence transfer, in which electron-electron correlation transfers field-induced photo-coherence from one electron to the other. In the case studied here, two laser fields are resonant with coupled atomic transitions, in the manner familiar from three-level dark-state spectroscopy. Dynamical two electron effects are monitored via the photoelectron energy spectrum. The authors show that the distribution of the photoelectron energies can be singly, doubly or triply peaked depending on the relative laser intensities. The electron spectra are independent of the turn-on sequence of the fields
Two-electron one-photon decay rates in doubly ionized atoms
International Nuclear Information System (INIS)
Baptista, G.B.
1984-01-01
The transion rate for the two-electron one-photon and one-electron one-photon decaying processes in atoms bearing initially two K-shell vacancies were evaluated for Ne up to Zr. The two-electron one-photon decay process is considered to be the result of the interaction between the jumping electrons and their interaction with the radiation field. The calculation is performed in second order perturbation theory and the many particle states are constructed from single particle solutions. The present approach allows one to discuss several aspects of the decaying process. The results obtained for the branching ratio between the two processes reproduces reasonably well available experimental data and show an almost linear dependence on the second power of the atomic number. A comparison with other theoretical predictions is also presented for the two decaying processes and the strong dependence of the branching ratio on the initial configuration of the decaying atom is pointed out. (Author) [pt
Rigid rotations in two-electrons atoms in a uniform magnetic field
International Nuclear Information System (INIS)
Mahecha G, J.
1991-01-01
Two exact rigid body solutions for a rotating two-electron atom under the influence of a magnetic field directed along the rotation axis were obtained using a classical approach. A solution gives at zero field the same result previously known as a rigid rotor. The other solution at zero field gives the previous result known as an asymmetric top or Langmuir solution. A stability analysis of the linearized motions near each of these equilibrium motions was made for different values of the magnetic field intensity. It was found that they are unstable but can exist during certain time for certain combinations of the magnetic field intensity and the angular momentum. The experimental realization of these classical states are the resonant states which would manifest in the spectrum as a subset of the quasi-Landau resonances. An examination of the energy levels near the ionization threshold shows that, in fact, they are similar to the quasi-Landau resonances. Also analytical expressions for the diamagnetic susceptibility of the two-excited states reported in this work were found. For the purpose of comparison, a study of the classical diamagnetism in one-electron atoms is presented. (author). 26 refs, 9 figs
Ionization of a two-electron atom in a strong electromagnetic field
International Nuclear Information System (INIS)
Ovodova, O.V.; Popov, A.M.; Tikhonova, O.V.
1997-01-01
A one-dimensional model of a helium atom in an intense field of a femtosecond electromagnetic pulse has been constructed using the Hartree technique. 'Exact' calculations have been compared to the approximations of 'frozen' and 'passive' electrons. A nonmonotonic dependence of the single-electron ionization probability on the radiation intensity has been detected. Minima in the ionization probability are due to multiphoton resonances between different atomic states due to the dynamic Stark effect. We suggest that the ionization suppression is due to the interference stabilization in this case
Peculiarities of two-electron atom ionization in strong electromagnetic field
International Nuclear Information System (INIS)
Ovodova, O.V.; Popov, A.M.; Tikhonova, O.V.
1997-01-01
One-dimensional model of helium atom in strong field of electromagnetic wave of femtosecond activity is plotted within the Hartree method frames. Comparison of 'exact' calculations with the calculations conducted within the frames of the 'frozen' and 'passive' electrons is made. The nonmonotonous dependence of one-dimensional ionization probability on the radiation intensity is found. It is shown that the ionization minima are connected with multiphoton resonances between various atomic states, originating due to the Stark effect. It is supposed that the effect of ionization suppression in this case is related to interference stabilization
International Nuclear Information System (INIS)
Macek, J.; Starace, A.F.
1985-01-01
The aim of this project is to establish the ground work for state-of-the-art calculations employing hyperspherical coordinates. Such calculations require the solution of a number of current difficulties in treating different regions of hyperspherical coordinate space. Applications have also been made to specific atomic collision processes in those cases where a hyperspherical coordinate point of view helps to understand the underlying physical mechanisms. Work on the following seven specific problems has been completed during the 3 year contract period: (1) Representation of two-electron wave functions for 1 S states in terms of a Fock expansion has been accomplished and a procedure for matching these series solutions onto an adiabatic hyperspherical representation has been developed. (2) In regions of configuration space where one electron is much further from the nucleus than the other, the R-matrix has been shown to be asymmetric. (3) Also in this region, the transformation of the coupled adiabatic hyperspherical channels to independent particle coordinates has been derived. (4) A study of the Wannier threshold law in Jacobi coordinates has been completed. (5) The electron doubly differential cross section of 0.5 MeV H - -He detachment collisions has been calculated. (6) The hyperspherical coordinate description of doubly excited states has been compared with other correlated models. (7) The length, velocity, and acceleration formulas for the electric dipole matrix element in hyperspherical coordinates have been derived. In addition, a review of the use of hyperspherical coordinate methods for atomic photoionization processes has been prepared
Two-electron time-delay interference in atomic double ionization by attosecond pulses
Energy Technology Data Exchange (ETDEWEB)
Rescigno, Thomas N
2009-10-04
A two-color two-photon atomic double ionization experiment using subfemtosecond UV pulses can be designed such that the sequential two-color process dominates and one electron is ejected by each pulse. Nonetheless, ab initio calculations show that, for sufficiently short pulses, a prominent interference pattern in the joint energy distribution of the sequentially ejected electrons can be observed that is due to their indistinguishability and the exchange symmetry of the wave function.
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…
King, Andrew W; Baskerville, Adam L; Cox, Hazel
2018-03-13
An implementation of the Hartree-Fock (HF) method using a Laguerre-based wave function is described and used to accurately study the ground state of two-electron atoms in the fixed nucleus approximation, and by comparison with fully correlated (FC) energies, used to determine accurate electron correlation energies. A variational parameter A is included in the wave function and is shown to rapidly increase the convergence of the energy. The one-electron integrals are solved by series solution and an analytical form is found for the two-electron integrals. This methodology is used to produce accurate wave functions, energies and expectation values for the helium isoelectronic sequence, including at low nuclear charge just prior to electron detachment. Additionally, the critical nuclear charge for binding two electrons within the HF approach is calculated and determined to be Z HF C =1.031 177 528.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).
Stationary Electron Atomic Model
Pressler, David E.
1998-04-01
I will present a novel theory concerning the position and nature of the electron inside the atom. This new concept is consistant with present experimental evidence and adheres strictly to the valence-shell electron-pair repulsion (VSEPR) model presently used in chemistry for predicting the shapes of molecules and ions. In addition, I will discuss the atomic model concept as being a true harmonic oscillator, periodic motion at resonant frequency which produces radiation at discrete frequencies or line spectra is possible because the electron is under the action of two restoring forces, electrostatic attraction and superconducting respulsion of the electron's magnetic field by the nucleus.
International Nuclear Information System (INIS)
Talaat, M.E.
1986-01-01
A two electron group model (bulk and tail electrons) is used to devise a theory for predicting current-voltage characteristic curves of RF discharges in helium with flow, which would agree with the experimental results of an 11 MHz RF axial discharge tests with helium flow inside a quartz tube, having an ID of 2.2 cms, at flow velocities up to μ = 485 m/s, (at reduced pressures p/sub o/ from 217 to 362 torrs). The theory assumes that the bulk electrons are Maxwellian, at a temperature T/sub b/, and have kinetic energies (1/2 mv/sup 2/ = eV) between o and eV/sub l/ (V/sub l/ = the helium metastable potential). The electrons of the depressed tail of the distribution function are also Maxwellian, at another temperature T/sub t/, and have eV > eV/sub l/
International Nuclear Information System (INIS)
Petrescu, Florian Ion
2012-01-01
The movement of an electron around the atomic nucleus has today a great importance in many engineering fields. Electronics, aeronautics, micro and nanotechnology, electrical engineering, optics, lasers, nuclear power, computing, equipment and automation, telecommunications, genetic engineering, bioengineering, special processing, modern welding, robotics, energy and electromagnetic wave field is today only a few of the many applications of electronic engineering. This book presents, shortly, a new and original relation (20 and 20') who determines the radius with that, the electron is running around the nucleus of an atom. One utilizes, two times the Lorenz relation, the Niels Bohr generalized equation, and a mass relation, which was deduced from the kinematics energy relation written in two modes: classical and Coulombian. Equalizing the mass relation with Lorenz relation one obtains a form which is a relation between the squared electron speed (v 2 ) and the radius (r). The second relation between v 2 and r was obtained by equalizing the mass of Bohr equation and the mass of Lorenz relation. For a Bohr energetically level (n=a constant value), one determines now two energetically below levels, which form an electronic layer. The author realizes by this a new atomic model, or a new quantum theory, which explains the existence of electron-clouds without spin.Writing the kinematics energy relation in two modes, classical and Coulombian one determines a relation, from which explicitely the mass of the electron is determined.
International Nuclear Information System (INIS)
Richards, J.D.; Breinig, M.; Gaither, C.C.; Berryman, J.W.; Hasson, B.F.
1993-01-01
Two electrons, excited just above the double-ionization threshold of an Ag q+ (q=5,6) core in a single collision of a 0.1-MeV/u Ag 4+ projectile ion with an Ar atom, are detected. The electron detector consists of electrically isolated anode segments located behind a microchannel-plate electron multiplier. A large electrostatic 30 degree parallel-plate analyzer is used to deflect the two free electrons, which move with approximately the projectile velocity, into the detector. The cross sections for producing final states consisting of a positively charged ionic core and two electrons just above the threshold for double ionization in ion-atom collisions have been measured. The cross sections for producing states with one electron moving with a kinetic energy less than 0.13 eV in the projectile frame and the other moving with somewhat higher kinetic energy are presented
Fisher information of two-electron systems
Saha, Aparna; Talukdar, Benoy; Sarkar, Pranab
2018-01-01
We present a theoretical model to compute numbers for position- and momentum-space Fisher information ( I_{ρ} and I_{γ} of correlated two-electron systems. The numbers for the first five members of the helium iso-electronic sequence indicate that i) values of I_{ρ} increase with the atomic number Z while those of I_{γ} decrease, and, ii) the effect of correlation reduces (increases) the bare values of I_{ρ}(I_{γ}) . The observed behavior of Fisher information in i) and ii) is opposite to that exhibited by Shannon information entropy, presumably because in describing disorder in the probability distribution, the former is convex while the latter is concave. The information measures of Fisher and of Shannon have also been found to share some common properties, the origin of which is purely physical rather than statistical.
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.
Timing analysis of two-electron photoemission
International Nuclear Information System (INIS)
Kheifets, A S; Ivanov, I A; Bray, Igor
2011-01-01
We predict a significant delay of two-electron photoemission from the helium atom after absorption of an attosecond XUV pulse. We establish this delay by solving the time-dependent Schroedinger equation and by subsequently tracing the field-free evolution of the two-electron wave packet. This delay can also be related to the energy derivative of the phase of the complex double-photoionization (DPI) amplitude which we evaluate by using the convergent close-coupling method. Our observations indicate that future attosecond time delay measurements on DPI of He can provide information on the absolute quantum phase and elucidate various mechanisms of this strongly correlated ionization process. (fast track communication)
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.
Empirical atom model of Vegard's law
International Nuclear Information System (INIS)
Zhang, Lei; Li, Shichun
2014-01-01
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
Analytical Schwartz density applied to heavy two-electron ions
Energy Technology Data Exchange (ETDEWEB)
Romera, E.; Dehesa, J.S. [Universidad de Granada (Spain); Koga, Toshikatsu [Muroran Institute of Technology (Japan)
1997-01-20
An analytical expression of the electron density function p(r) due to Schwartz for two-electron atomic systems is applied to a detailed study of density-dependent properties of relatively heavy two-electron ions. Comparison of the Schwartz results with those from accurate Hartree-Fock and Hylleraas wave functions shows that despite its simple yet analytical form, the Schwartz density has a quantitative applicability in the density study of two-electron atoms within the nonrelativistic framework. 13 refs., 4 tabs.
Nagaoka's atomic model and hyperfine interactions.
Inamura, Takashi T
2016-01-01
The prevailing view of Nagaoka's "Saturnian" atom is so misleading that today many people have an erroneous picture of Nagaoka's vision. They believe it to be a system involving a 'giant core' with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka's model is exactly the same as Rutherford's. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure.
Complex dynamics in planar two-electron quantum dots
Energy Technology Data Exchange (ETDEWEB)
Schroeter, Sebastian Josef Arthur
2013-06-25
Quantum dots play an important role in a wide range of recent experimental and technological developments. In particular they are promising candidates for realisations of quantum bits and further applications in quantum information theory. The harmonically confined Hooke's atom model is experimentally verified and separates in centre-of-mass and relative coordinates. Findings that are contradictory to this separability call for an extension of the model, in particular changing the confinement potential. In order to study effects of an anharmonic confinement potential on spectral properties of planar two-electron quantum dots a sophisticated numerical approach is developed. Comparison between the Helium atom, Hooke's atom and an anharmonic potential model are undertaken in order to improve the description of quantum dots. Classical and quantum features of complexity and chaos are investigated and used to characterise the dynamics of the system to be mixed regular-chaotic. Influence of decoherence can be described by quantum fidelity, which measures the effect of a perturbation on the time evolution. The quantum fidelity of eigenstates of the system depends strongly on the properties of the perturbation. Several methods for solving the time-dependent Schrödinger equation are implemented and a high level of accuracy for long time evolutions is achieved. The concept of offset entanglement, the entanglement of harmonic models in the noninteracting limit, is introduced. This concept explains different questions raised in the literature for harmonic quantum dot models, recently. It shows that only in the groundstate the electrons are not entangled in the fermionic sense. The applicability, validity, and origin of Hund's first rule in general quantum dot models is further addressed. In fact Hund's first rule is only applicable, and in this case also valid, for one pair of singlet and triplet states in Hooke's atom. For more realistic models of two-electron
Complex dynamics in planar two-electron quantum dots
International Nuclear Information System (INIS)
Schroeter, Sebastian Josef Arthur
2013-01-01
Quantum dots play an important role in a wide range of recent experimental and technological developments. In particular they are promising candidates for realisations of quantum bits and further applications in quantum information theory. The harmonically confined Hooke's atom model is experimentally verified and separates in centre-of-mass and relative coordinates. Findings that are contradictory to this separability call for an extension of the model, in particular changing the confinement potential. In order to study effects of an anharmonic confinement potential on spectral properties of planar two-electron quantum dots a sophisticated numerical approach is developed. Comparison between the Helium atom, Hooke's atom and an anharmonic potential model are undertaken in order to improve the description of quantum dots. Classical and quantum features of complexity and chaos are investigated and used to characterise the dynamics of the system to be mixed regular-chaotic. Influence of decoherence can be described by quantum fidelity, which measures the effect of a perturbation on the time evolution. The quantum fidelity of eigenstates of the system depends strongly on the properties of the perturbation. Several methods for solving the time-dependent Schrödinger equation are implemented and a high level of accuracy for long time evolutions is achieved. The concept of offset entanglement, the entanglement of harmonic models in the noninteracting limit, is introduced. This concept explains different questions raised in the literature for harmonic quantum dot models, recently. It shows that only in the groundstate the electrons are not entangled in the fermionic sense. The applicability, validity, and origin of Hund's first rule in general quantum dot models is further addressed. In fact Hund's first rule is only applicable, and in this case also valid, for one pair of singlet and triplet states in Hooke's atom. For more realistic models of two-electron quantum dots an
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…
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
An atomic model of the Big Bang
Lasukov, V. V.
2013-03-01
An atomic model of the Big Bang has been developed on the basis of quantum geometrodynamics with a nonzero Hamiltonian and on the concept of gravitation developed by Logunov asymptotically combined with the Gliner's idea of a material interpretation of the cosmological constant. The Lemaître primordial atom in superpace-time, whose spatial coordinate is the so-called scaling factor of the Logunov metric of the effective Riemann space, acts as the Big Bang model. The primordial atom in superspace-time corresponds to spatialtime structures(spheres, lines, and surfaces of a level) of the Minkowski spacetime real within the Logunov gravitation theory, the foregoing structures being filled with a scalar field with a negative density of potential energy.
Modeling Atom Probe Tomography: A review.
Vurpillot, F; Oberdorfer, C
2015-12-01
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. Copyright © 2015 Elsevier B.V. All rights reserved.
Modelling the Energetics of Encapsulation of Atoms and Atomic ...
Indian Academy of Sciences (India)
user
2015-07-04
July 4, 2015. Mid-year Meeting of Indian Academy of Sciences. 2. Encapsulation of atoms, clusters and molecules into carbon nanotubes: Why is it important? Carbon Nanotubes. (Discovery in 1991). Sumio Iijima. Animation Courtesy: Dr. Maruyama's CNT site. R. 0. Large aspect ratios. Precisely defined nanometer sized ...
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.
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).
Mathematical Modeling of Resonant Processes in Confined Geometry of Atomic and Atom-Ion Traps
Directory of Open Access Journals (Sweden)
Melezhik Vladimir S.
2018-01-01
Full Text Available We discuss computational aspects of the developed mathematical models for resonant processes in confined geometry of atomic and atom-ion traps. The main attention is paid to formulation in the nondirect product discrete-variable representation (npDVR of the multichannel scattering problem with nonseparable angular part in confining traps as the boundary-value problem. Computational efficiency of this approach is demonstrated in application to atomic and atom-ion confinement-induced resonances we predicted recently.
Mathematical Modeling of Resonant Processes in Confined Geometry of Atomic and Atom-Ion Traps
Melezhik, Vladimir S.
2018-02-01
We discuss computational aspects of the developed mathematical models for resonant processes in confined geometry of atomic and atom-ion traps. The main attention is paid to formulation in the nondirect product discrete-variable representation (npDVR) of the multichannel scattering problem with nonseparable angular part in confining traps as the boundary-value problem. Computational efficiency of this approach is demonstrated in application to atomic and atom-ion confinement-induced resonances we predicted recently.
Stability of two-electron diatomic molecules
International Nuclear Information System (INIS)
Ferron, Alejandro; Serra, Pablo
2007-01-01
We present a detailed study of the ground state behaviour of two-electron diatomic molecules. The ground state stability diagram for diatomic molecules in the Born-Oppenheimer approximation is obtained and the behaviour of the ground state near the stability line is studied. Two different cases are analysed: the homonuclear two-centre two-electron molecule with the internuclear distance as a free parameter and the diatomic two-electron molecule (in this case, the internuclear distance is determined by equilibrium conditions). Analytical and numerical results for these systems are presented
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.
On the correlation measure of two-electron systems
Saha, Aparna; Talukdar, Benoy; Chatterjee, Supriya
2017-05-01
We make use of a Hylleraas-type wave function to derive an exact analytical model to quantify correlation in two-electron atomic/ionic systems and subsequently employ it to examine the role of inter-electronic repulsion in affecting (i) the bare (uncorrelated) single-particle position- and momentum-space charge distributions and (ii) corresponding Shannon's information entropies. The results presented for the first five members in the helium iso-electronic sequence, on the one hand, correctly demonstrate the effect of correlation on bare charge distributions and, on the other hand, lead us to some important results for the correlated and uncorrelated values of the entropies. These include the limiting behavior of the correlated entropy sum (sum of position- and momentum-space entropies) and geometrical realization for the variation of information entropies as a function of Z. We suggest that, rather than the entropy sum, individual entropies should be regarded as better candidates for the measure of correlation.
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.
Atomic force microscopy of model lipid membranes.
Morandat, Sandrine; Azouzi, Slim; Beauvais, Estelle; Mastouri, Amira; El Kirat, Karim
2013-02-01
Supported lipid bilayers (SLBs) are biomimetic model systems that are now widely used to address the biophysical and biochemical properties of biological membranes. Two main methods are usually employed to form SLBs: the transfer of two successive monolayers by Langmuir-Blodgett or Langmuir-Schaefer techniques, and the fusion of preformed lipid vesicles. The transfer of lipid films on flat solid substrates offers the possibility to apply a wide range of surface analytical techniques that are very sensitive. Among them, atomic force microscopy (AFM) has opened new opportunities for determining the nanoscale organization of SLBs under physiological conditions. In this review, we first focus on the different protocols generally employed to prepare SLBs. Then, we describe AFM studies on the nanoscale lateral organization and mechanical properties of SLBs. Lastly, we survey recent developments in the AFM monitoring of bilayer alteration, remodeling, or digestion, by incubation with exogenous agents such as drugs, proteins, peptides, and nanoparticles.
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…
Atomic process modeling based on nearest neighbor approximation
International Nuclear Information System (INIS)
Nishikawa, Takeshi
2016-01-01
An atomic modeling based on the nearest neighbor approximation (NNA) to solove atomic process in plasmas was considered. In the atomic modeling, it includes the plasma effect to the electron state densities of the atom or ion as the potential due to the nearest neighbor atom or ion. Using the modeling, I was able to compute the ionization degrees of hydrogen plasmas without any ad hoc assumption adopted in the atomic modeling based on the plasma microfield. In order to apply the NNA to the plasmas of near and above solid density, three adequate treatments were required to obtain physically acceptable results. The first one was the Coulomb interaction between pairs of ions. The second one was the modification of the Saha equation. The third one was the adequate treatment of the neutral atom's contribution to the potential distribution as the nearest neighbor particle. (author)
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.
Murakami, I.; Sakaue, H. A.; Suzuki, C.; Kato, D.; Goto, M.; Tamura, N.; Sudo, S.; Morita, S.
2015-09-01
Quantitative tungsten study with reliable atomic modeling is important for successful achievement of ITER and fusion reactors. We have developed tungsten atomic modeling for understanding the tungsten behavior in fusion plasmas. The modeling is applied to the analysis of tungsten spectra observed from plasmas of the large helical device (LHD) with tungsten pellet injection. We found that extreme ultraviolet (EUV) emission of W24+ to W33+ ions at 1.5-3.5 nm are sensitive to electron temperature and useful to examine the tungsten behavior in edge plasmas. We can reproduce measured EUV spectra at 1.5-3.5 nm by calculated spectra with the tungsten atomic model and obtain charge state distributions of tungsten ions in LHD plasmas at different temperatures around 1 keV. Our model is applied to calculate the unresolved transition array (UTA) seen at 4.5-7 nm tungsten spectra. We analyze the effect of configuration interaction on population kinetics related to the UTA structure in detail and find the importance of two-electron-one-photon transitions between 4p54dn+1- 4p64dn-14f. Radiation power rate of tungsten due to line emissions is also estimated with the model and is consistent with other models within factor 2.
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.
Electron correlation energy in confined two-electron systems
Energy Technology Data Exchange (ETDEWEB)
Wilson, C.L. [Chemistry Program, Centre College, 600 West Walnut Street, Danville, KY 40422 (United States); Montgomery, H.E., E-mail: ed.montgomery@centre.ed [Chemistry Program, Centre College, 600 West Walnut Street, Danville, KY 40422 (United States); Sen, K.D. [School of Chemistry, University of Hyderabad, Hyderabad 500 046 (India); Thompson, D.C. [Chemistry Systems and High Performance Computing, Boehringer Ingelheim Pharamaceuticals Inc., 900 Ridgebury Road, Ridgefield, CT 06877 (United States)
2010-09-27
Radial, angular and total correlation energies are calculated for four two-electron systems with atomic numbers Z=0-3 confined within an impenetrable sphere of radius R. We report accurate results for the non-relativistic, restricted Hartree-Fock and radial limit energies over a range of confinement radii from 0.05-10a{sub 0}. At small R, the correlation energies approach limiting values that are independent of Z while at intermediate R, systems with Z{>=}1 exhibit a characteristic maximum in the correlation energy resulting from an increase in the angular correlation energy which is offset by a decrease in the radial correlation energy.
International Nuclear Information System (INIS)
Fuchs, Alain; Villani, Cedric; Guthleben, Denis; Leduc, Michele; Brenner, Anastasios; Pouthas, Joel; Perrin, Jean
2014-01-01
Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)
Stark shifting two-electron quantum dot
International Nuclear Information System (INIS)
Dineykhan, M.; Zhaugasheva, S.A.; Duysebaeva, K.S.
2003-01-01
Advances in modern technology make it possible to create semiconducting nano-structures (quantum dot) in which a finite number of electrons are 'captured' in a bounded volume. A quantum dot is associated with a quantum well formed at the interface, between two finite-size semiconductors owing to different positions of the forbidden gaps on the energy scale in these semiconductors. The possibility of monitoring and controlling the properties of quantum dots attracts considerable attention to these objects, as a new elemental basis for future generations of computers. The quantum-mechanical effects and image potential play a significant role in the description of the formation mechanism quantum dot, and determined the confinement potential in a two-electron quantum dot only for the spherical symmetric case. In the present talk, we considered the formation dynamics of two-electron quantum dot with violation of spherical symmetry. So, we have standard Stark potential. The energy spectrum two-electron quantum dot were calculated. Usually Stark interactions determined the tunneling phenomena between quantum dots
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.
"Piekara's Chair": Mechanical Model for Atomic Energy Levels.
Golab-Meyer, Zofia
1991-01-01
Uses the teaching method of models or analogies, specifically the model called "Piekara's chair," to show how teaching classical mechanics can familiarize students with the notion of energy levels in atomic physics. (MDH)
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)
Multimode quantum model of a cw atom laser
International Nuclear Information System (INIS)
Hope, J.J.; Haine, S.A.; Savage, C.M.
2002-01-01
Full text: Laser cooling allows dilute atomic gases to be cooled to within K of absolute zero. Ultracold gases were first achieved twenty years ago and have since found applications in areas such as spectroscopy, time standards, frequency standards, quantum information processing and atom optics. The atomic analogue of the lasing mode in optical lasers is Bose-Einstein Condensation (BEC), in which a cooled sample of atoms condense into the lowest energy quantum state. This new state of matter was recently achieved in dilute Bose gases in 1995. Atoms coupled out of a BEC exhibit long-range spatial coherence, and provide the coldest atomic source currently available. These atomic sources are called 'atom lasers' because the BEC is analogous to the lasing mode of an optical laser. The high spectral flux from optical lasers is caused by a process called gain-narrowing, which requires continuous wave (cw) operation. Coupling a BEC quickly into an untrapped state forms a coherent atomic beam but it has a spread in momentum as large as the trapped BEC. Coupling the atoms out more slowly reduces the output linewidth at the expense of reducing the overall flux. These atom lasers are equivalent to Q-switched optical lasers. A cw atom laser with gain-narrowing would produce an increasingly monoenergetic output as the flux increased, dramatically improving the spectral flux. A cw atom laser is therefore a major goal of the atom optics community, but there are several theoretical and practical obstacles to understanding the complexities of such a system. The main obstacle to the production of a cw atom laser is the technical difficulties involved in continuously pumping the lasing mode. No complete theory exists which describes a cw atom laser. Complete cw atom laser models require a quantum field description due to their non-Markovian dynamics, significant spatial effects and the dependence of the output on the quantum statistics of the lasing mode. The extreme dimensionality
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.
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....
Woo Kim, Hyun; Rhee, Young Min
2012-07-30
Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. Copyright © 2012 Wiley Periodicals, Inc.
Dynamics of two-electron excitations in helium
Energy Technology Data Exchange (ETDEWEB)
Caldwell, C.D.; Menzel, A.; Frigo, S.P. [Univ. of Central Florida, Orlando, FL (United States)] [and others
1997-04-01
Excitation of both electrons in helium offers a unique window for studying electron correlation at the most basic level in an atom in which these two electrons and the nucleus form a three-body system. The authors utilized the first light available at the U-8 undulator-SGM monochromator beamline to investigate the dynamic parameters, partial cross sections, differential cross sections, and photoelectron angular distribution parameters ({beta}), with a high resolving power for the photon beam and at the highly differential level afforded by the use of their electron spectrometer. In parallel, they carried out detailed calculations of the relevant properties by a theoretical approach that is based on the hyperspherical close-coupling method. Partial photoionization cross sections {sigma}{sub n}, and photoelectron angular distributions {beta}{sub n} were measured for all possible final ionic states He{sup +}(n) in the region of the double excitations N(K,T){sup A} up to the N=5 threshold. At a photon energy bandpass of 12 meV below the thresholds N=3, 4, and 5, this level of differentiation offers the most critical assessment of the dynamics of the two-electron excitations to date. The experimental data were seen to be very well described by the most advanced theoretical calculations.
Modeling HF Gain Generator F-Atom Flows
National Research Council Canada - National Science Library
Kwok, Munson
2003-01-01
Control volume analysis and one-dimensional reacting gasdynamics have been combined with a unique thermal-mechanical model of a combustor vessel to estimate production of fluorine atoms at the nozzle exit plane...
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...
Level set methods for modelling field evaporation in atom probe.
Haley, Daniel; Moody, Michael P; Smith, George D W
2013-12-01
Atom probe is a nanoscale technique for creating three-dimensional spatially and chemically resolved point datasets, primarily of metallic or semiconductor materials. While atom probe can achieve local high-level resolution, the spatial coherence of the technique is highly dependent upon the evaporative physics in the material and can often result in large geometric distortions in experimental results. The distortions originate from uncertainties in the projection function between the field evaporating specimen and the ion detector. Here we explore the possibility of continuum numerical approximations to the evaporative behavior during an atom probe experiment, and the subsequent propagation of ions to the detector, with particular emphasis placed on the solution of axisymmetric systems, such as isolated particles and multilayer systems. Ultimately, this method may prove critical in rapid modeling of tip shape evolution in atom probe tomography, which itself is a key factor in the rapid generation of spatially accurate reconstructions in atom probe datasets.
Four-parameter analytical local model potential for atoms
International Nuclear Information System (INIS)
Fei, Yu; Jiu-Xun, Sun; Rong-Gang, Tian; Wei, Yang
2009-01-01
Analytical local model potential for modeling the interaction in an atom reduces the computational effort in electronic structure calculations significantly. A new four-parameter analytical local model potential is proposed for atoms Li through Lr, and the values of four parameters are shell-independent and obtained by fitting the results of X a method. At the same time, the energy eigenvalues, the radial wave functions and the total energies of electrons are obtained by solving the radial Schrödinger equation with a new form of potential function by Numerov's numerical method. The results show that our new form of potential function is suitable for high, medium and low Z atoms. A comparison among the new potential function and other analytical potential functions shows the greater flexibility and greater accuracy of the present new potential function. (atomic and molecular physics)
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
International Nuclear Information System (INIS)
Errea, L.F.; Mendez, L.; Riera, A.
1983-01-01
In a previous paper we have pointed out that the common-translation-factor (CTF) method is the only one which, at present, and within the framework of the molecular model of atomic collisions, can be shown to be both convergent and computationally fast, even for many-electron systems. In this Communication we check that this second statement is correct, presenting, for the first time, a molecular calculation involving two-electron translation factors, for He + + H collisions. A careful study of the sensitivity of the calculated cross sections to the choice of the CTF is performed, and conclusions on that sensitivity are drawn, for several types of processes
Energy Technology Data Exchange (ETDEWEB)
Errea, L.F.; Mendez, L.; Riera, A.
1983-06-01
In a previous paper we have pointed out that the common-translation-factor (CTF) method is the only one which, at present, and within the framework of the molecular model of atomic collisions, can be shown to be both convergent and computationally fast, even for many-electron systems. In this Communication we check that this second statement is correct, presenting, for the first time, a molecular calculation involving two-electron translation factors, for He/sup +/ + H collisions. A careful study of the sensitivity of the calculated cross sections to the choice of the CTF is performed, and conclusions on that sensitivity are drawn, for several types of processes.
A crystal-chemical model of atomic interactions. Pt. 6
International Nuclear Information System (INIS)
Aslanov, L.A.; Markov, V.T.
1992-01-01
Commonly occurring structures are considered from the point of view of a crystal-chemical model of atomic interactions. It is shown that these structures sometimes contain coordination polyhedra distinct from Platonic, Archimedean and Zalgaller's polyhedra. These polyhedra have two or more groups of atoms into which all the vertices of the coordination polyhedron can be divided and which differ in distance from the central atom. The reasons for such polyhedra are considered. The crystal structure of NiTi 2 is analyzed and the causes of the quasicrystal state are revealed. (orig.)
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.
Detecting Clusters in Atom Probe Data with Gaussian Mixture Models.
Zelenty, Jennifer; Dahl, Andrew; Hyde, Jonathan; Smith, George D W; Moody, Michael P
2017-04-01
Accurately identifying and extracting clusters from atom probe tomography (APT) reconstructions is extremely challenging, yet critical to many applications. Currently, the most prevalent approach to detect clusters is the maximum separation method, a heuristic that relies heavily upon parameters manually chosen by the user. In this work, a new clustering algorithm, Gaussian mixture model Expectation Maximization Algorithm (GEMA), was developed. GEMA utilizes a Gaussian mixture model to probabilistically distinguish clusters from random fluctuations in the matrix. This machine learning approach maximizes the data likelihood via expectation maximization: given atomic positions, the algorithm learns the position, size, and width of each cluster. A key advantage of GEMA is that atoms are probabilistically assigned to clusters, thus reflecting scientifically meaningful uncertainty regarding atoms located near precipitate/matrix interfaces. GEMA outperforms the maximum separation method in cluster detection accuracy when applied to several realistically simulated data sets. Lastly, GEMA was successfully applied to real APT data.
Nagaoka’s atomic model and hyperfine interactions
INAMURA, Takashi T.
2016-01-01
The prevailing view of Nagaoka’s “Saturnian” atom is so misleading that today many people have an erroneous picture of Nagaoka’s vision. They believe it to be a system involving a ‘giant core’ with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka’s model is exactly the same as Rutherford’s. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure. PMID:27063182
Eulerian atomization modeling of a pressure-atomized spray for sprinkler irrigation
International Nuclear Information System (INIS)
Stevenin, C.; Vallet, A.; Tomas, S.; Amielh, M.; Anselmet, F.
2016-01-01
Highlights: • The atomization and dispersion of a turbulent jet of water into still air is described using an Eulerian mixture model. • The model was implemented in a parabolic code, well-suited for axisymmetric boundary-layer type flow. • The model overestimated the mean centerline velocity decrease but predicted successfully liquid fraction and droplet size. • In the far-field, the model provided auto-similar profiles close to experimental values. • In the future, turbulence anisotropy effects on droplets' dispersion will be modeled using a Reynolds Stress Model. - Abstract: The objective of this study is the modeling of the atomization and dispersion of an irrigation water jet, from the nozzle outlet to the region of full development of the spray. The use of an Eulerian model, developed for high Reynolds and Weber numbers fluid flow, provides a continuous description of the process. In this model, the conservation equations are written for a two phase mixture. A transport equation for the volume density of the interface represents fragmentation/coalescence mechanisms and gives mean liquid fragments size. The numerical results obtained by this model were compared to experimental measurements of mean velocity, turbulent kinetic energy, liquid volume fraction and Sauter Mean Diameter. The model overestimates the decrease of the longitudinal velocity on the axis, but successfully predicts the volume fraction and mean droplet size profiles.
Model for pairing phase transition in atomic nuclei
International Nuclear Information System (INIS)
Schiller, A.; Guttormsen, M.; Hjorth-Jensen, M.; Rekstad, J.; Siem, S.
2002-01-01
A model is developed which allows the investigation and classification of the pairing phase transition in atomic nuclei. The regions of the parameter space are discussed for which a pairing phase transition can be observed. The model parameters include number of particles, attenuation of pairing correlations with increasing seniority, single-particle level spacing, and pairing gap parameter
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.
Modeling noncontact atomic force microscopy resolution on corrugated surfaces
Directory of Open Access Journals (Sweden)
Kristen M. Burson
2012-03-01
Full Text Available Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid. The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.
Modelling atomic scale manipulation with the non-contact atomic force microscope
International Nuclear Information System (INIS)
Trevethan, T; Watkins, M; Kantorovich, L N; Shluger, A L; Polesel-Maris, J; Gauthier, S
2006-01-01
We present the results of calculations performed to model the process of lateral manipulation of an oxygen vacancy in the MgO(001) surface using the non-contact atomic force microscope (NC-AFM). The potential energy surfaces for the manipulation as a function of tip position are determined from atomistic modelling of the MgO(001) surface interacting with a Mg terminated MgO tip. These energies are then used to model the dynamical evolution of the system as the tip oscillates and at a finite temperature using a kinetic Monte Carlo method. The manipulation process is strongly dependent on the lateral position of the tip and the system temperature. It is also found that the expectation value of the point at which the vacancy jumps depends on the trajectory of the oscillating cantilever as the surface is approached. The effect of the manipulation on the operation of the NC-AFM is modelled with a virtual dynamic AFM, which explicitly simulates the entire experimental instrumentation and control loops. We show how measurable experimental signals can result from a single controlled atomic scale event and suggest the most favourable conditions for achieving successful atomic scale manipulation experimentally
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
The chaotic atom model via a fractal approximation of motion
International Nuclear Information System (INIS)
Agop, M; Nica, P; Gurlui, S; Focsa, C; Magop, D; Borsos, Z
2011-01-01
A new model of the atom is built based on a complete and detailed nonlinear dynamics analysis (complete time series, Poincare sections, complete phase space, Lyapunov exponents, bifurcation diagrams and fractal analysis), through the correlation of the chaotic-stochastic model with a fractal one. Some specific mechanisms that ensure the atom functionality are proposed: gun, chaotic gun and multi-gun effects for the excited states (the classical analogue of quantum absorption) and the fractalization of the trajectories for the stationary states (a natural way of introducing the quantification).
Modeling of the atomic and electronic structures of interfaces
International Nuclear Information System (INIS)
Sutton, A.P.
1988-01-01
Recent tight binding and Car-Parrinello simulations of grain boundaries in semiconductors are reviewed. A critique is given of some models of embrittlement that are based on electronic structure considerations. The structural unit model of grain boundary structure is critically assessed using some results for mixed tilt and twist grain boundaries. A new method of characterizing interfacial structure in terms of bond angle distribution functions is described. A new formulation of thermodynamic properties of interfaces is presented which focusses on the local atomic environment. Effective, temperature dependent N-body atomic interactions are derived for studying grain boundary structure at elevated temperature
International Nuclear Information System (INIS)
Gruber, B.; Thomas, M.S.
1980-01-01
In this article the symmetry chains for the atomic shell model are classified in such a way that they lead from the group SU(4l+2) to its subgroup SOsub(J)(3). The atomic configurations (nl)sup(N) transform like irreducible representations of the group SU(4l+2), while SOsub(J)(3) corresponds to total angular momentum in SU(4l+2). The defining matrices for the various embeddings are given for each symmetry chain that is obtained. These matrices also define the projection onto the weight subspaces for the corresponding subsymmetries and thus relate the various quantum numbers and determine the branching of representations. It is shown in this article that three (interrelated) symmetry chains are obtained which correspond to L-S coupling, j-j coupling, and a seniority dependent coupling. Moreover, for l<=6 these chains are complete, i.e., there are no other chains but these. In articles to follow, the symmetry chains that lead from the group SO(8l+5) to SOsub(J)(3) will be discussed, with the entire atomic shell transforming like an irreducible representation of SO(8l+5). The transformation properties of the states of the atomic shell will be determined according to the various symmetry chains obtained. The symmetry lattice discussed in this article forms a sublattice of the larger symmetry lattice with SO(8l+5) as supergroup. Thus the transformation properties of the states of the atomic configurations, according to the various symmetry chains discussed in this article, will be obtained too. (author)
Model based control of dynamic atomic force microscope
International Nuclear Information System (INIS)
Lee, Chibum; Salapaka, Srinivasa M.
2015-01-01
A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H ∞ control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments
Model based control of dynamic atomic force microscope.
Lee, Chibum; Salapaka, Srinivasa M
2015-04-01
A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.
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.
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.
NLTE atomic kinetics modeling in ICF target simulations
Patel, Mehul V.; Mauche, Christopher W.; Scott, Howard A.; Jones, Ogden S.; Shields, Benjamin T.
2017-10-01
Radiation hydrodynamics (HYDRA) simulations using recently developed 1D spherical and 2D cylindrical hohlraum models have enabled a reassessment of the accuracy of energetics modeling across a range of NIF target configurations. Higher-resolution hohlraum calculations generally find that the X-ray drive discrepancies are greater than previously reported. We identify important physics sensitivities in the modeling of the NLTE wall plasma and highlight sensitivity variations between different hohlraum configurations (e.g. hohlraum gas fill). Additionally, 1D capsule only simulations show the importance of applying a similar level of rigor to NLTE capsule ablator modeling. Taken together, these results show how improved target performance predictions can be achieved by performing inline atomic kinetics using more complete models for the underlying atomic structure and transitions. Prepared by LLNL under Contract DE-AC52-07NA27344.
Classroom: inexpensive models for teaching atomic structure and ...
African Journals Online (AJOL)
Classroom: inexpensive models for teaching atomic structure and compounds at junior secondary school level of education. WHK Hordzi, BA Mensah. Abstract. No Abstract. Global Journal of Educational Research Vol. 2(1&2) 2003: 33-40. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL ...
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
A collisional-radiative average atom model for hot plasmas
International Nuclear Information System (INIS)
Rozsnyai, B.F.
1996-01-01
A collisional-radiative 'average atom' (AA) model is presented for the calculation of opacities of hot plasmas not in the condition of local thermodynamic equilibrium (LTE). The electron impact and radiative rate constants are calculated using the dipole oscillator strengths of the average atom. A key element of the model is the photon escape probability which at present is calculated for a semi infinite slab. The Fermi statistics renders the rate equation for the AA level occupancies nonlinear, which requires iterations until the steady state. AA level occupancies are found. Detailed electronic configurations are built into the model after the self-consistent non-LTE AA state is found. The model shows a continuous transition from the non-LTE to the LTE state depending on the optical thickness of the plasma. 22 refs., 13 figs., 1 tab
Atomic Data and Modelling for Fusion: the ADAS Project
International Nuclear Information System (INIS)
Summers, H. P.; O'Mullane, M. G.
2011-01-01
The paper is an update on the Atomic Data and Analysis Structure, ADAS, since ICAM-DATA06 and a forward look to its evolution in the next five years. ADAS is an international project supporting principally magnetic confinement fusion research. It has participant laboratories throughout the world, including ITER and all its partner countries. In parallel with ADAS, the ADAS-EU Project provides enhanced support for fusion research at Associated Laboratories and Universities in Europe and ITER. OPEN-ADAS, sponsored jointly by the ADAS Project and IAEA, is the mechanism for open access to principal ADAS atomic data classes and facilitating software for their use. EXTENDED-ADAS comprises a variety of special, integrated application software, beyond the purely atomic bounds of ADAS, tuned closely to specific diagnostic analyses and plasma models.The current scientific content and scope of these various ADAS and ADAS related activities are briefly reviewed. These span a number of themes including heavy element spectroscopy and models, charge exchange spectroscopy, beam emission spectroscopy and special features which provide a broad baseline of atomic modelling and support. Emphasis will be placed on 'lifting the fundamental data baseline'--a principal ADAS task for the next few years. This will include discussion of ADAS and ADAS-EU coordinated and shared activities and some of the methods being exploited.
Interfacial Thermal Transport via One-Dimensional Atomic Junction Model
Directory of Open Access Journals (Sweden)
Guohuan Xiong
2018-03-01
Full Text Available In modern information technology, as integration density increases rapidly and the dimension of materials reduces to nanoscale, interfacial thermal transport (ITT has attracted widespread attention of scientists. This review introduces the latest theoretical development in ITT through one-dimensional (1D atomic junction model to address the thermal transport across an interface. With full consideration of the atomic structures in interfaces, people can apply the 1D atomic junction model to investigate many properties of ITT, such as interfacial (Kapitza resistance, nonlinear interface, interfacial rectification, and phonon interference, and so on. For the ballistic ITT, both the scattering boundary method (SBM and the non-equilibrium Green’s function (NEGF method can be applied, which are exact since atomic details of actual interfaces are considered. For interfacial coupling case, explicit analytical expression of transmission coefficient can be obtained and it is found that the thermal conductance maximizes at certain interfacial coupling (harmonic mean of the spring constants of the two leads and the transmission coefficient is not a monotonic decreasing function of phonon frequency. With nonlinear interaction—phonon–phonon interaction or electron–phonon interaction at interface, the NEGF method provides an efficient way to study the ITT. It is found that at weak linear interfacial coupling, the nonlinearity can improve the ITT, but it depresses the ITT in the case of strong-linear coupling. In addition, the nonlinear interfacial coupling can induce thermal rectification effect. For interfacial materials case which can be simulated by a two-junction atomic chain, phonons show interference effect, and an optimized thermal coupler can be obtained by tuning its spring constant and atomic mass.
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
First-Order Quantum Phase Transition for Dicke Model Induced by Atom-Atom Interaction
International Nuclear Information System (INIS)
Zhao Xiu-Qin; Liu Ni; Liang Jiu-Qing
2017-01-01
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. (paper)
Crystal-chemical model of atomic interactions. Pt. 1
International Nuclear Information System (INIS)
Aslanov, L.A.
1988-01-01
A crystal-chemical model of atomic interactions has been suggested to explain the diversity of inorganic structure types, their translational symmetry, and other basic characteristics. The model is based on the concepts of the minimum potential energy of a crystal and energy contributions to the total energy of a crystal which come not only from the first coordination sphere but also from the second, third and subsequent coordination spheres. The minimum potential energy is provided by coordination spheres in the shape of the Platonic regular solids or Archemedean semiregular solids and also by polyhedra having triangular faces. The model is applicable to materials with different types of chemical bonding - metals, nonmetals (diamond), ionic compounds and substances with van der Waals atomic interactions. (orig.)
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.
Atomic scale modelling of materials of the nuclear fuel cycle
International Nuclear Information System (INIS)
Bertolus, M.
2011-10-01
This document written to obtain the French accreditation to supervise research presents the research I conducted at CEA Cadarache since 1999 on the atomic scale modelling of non-metallic materials involved in the nuclear fuel cycle: host materials for radionuclides from nuclear waste (apatites), fuel (in particular uranium dioxide) and ceramic cladding materials (silicon carbide). These are complex materials at the frontier of modelling capabilities since they contain heavy elements (rare earths or actinides), exhibit complex structures or chemical compositions and/or are subjected to irradiation effects: creation of point defects and fission products, amorphization. The objective of my studies is to bring further insight into the physics and chemistry of the elementary processes involved using atomic scale modelling and its coupling with higher scale models and experimental studies. This work is organised in two parts: on the one hand the development, adaptation and implementation of atomic scale modelling methods and validation of the approximations used; on the other hand the application of these methods to the investigation of nuclear materials under irradiation. This document contains a synthesis of the studies performed, orientations for future research, a detailed resume and a list of publications and communications. (author)
Atomic structure of graphene supported heterogeneous model catalysts
International Nuclear Information System (INIS)
Franz, Dirk
2017-04-01
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 2 → sp 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, whereupon
Quantum simulation of transverse Ising models with Rydberg atoms
Schauss, Peter
2018-04-01
Quantum Ising models are canonical models for the study of quantum phase transitions (Sachdev 1999 Quantum Phase Transitions (Cambridge: Cambridge University Press)) and are the underlying concept for many analogue quantum computing and quantum annealing ideas (Tanaka et al Quantum Spin Glasses, Annealing and Computation (Cambridge: Cambridge University Press)). Here we focus on the implementation of finite-range interacting Ising spin models, which are barely tractable numerically. Recent experiments with cold atoms have reached the interaction-dominated regime in quantum Ising magnets via optical coupling of trapped neutral atoms to Rydberg states. This approach allows for the tunability of all relevant terms in an Ising spin Hamiltonian with 1/{r}6 interactions in transverse and longitudinal fields. This review summarizes the recent progress of these implementations in Rydberg lattices with site-resolved detection. Strong correlations in quantum Ising models have been observed in several experiments, starting from a single excitation in the superatom regime up to the point of crystallization. The rapid progress in this field makes spin systems based on Rydberg atoms a promising platform for quantum simulation because of the unmatched flexibility and strength of interactions combined with high control and good isolation from the environment.
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.
ADAS: Atomic data, modelling and analysis for fusion
International Nuclear Information System (INIS)
Summers, H. P.; O'Mullane, M. G.; Whiteford, A. D.; Badnell, N. R.; Loch, S. D.
2007-01-01
The Atomic Data and Analysis Structure, ADAS, comprises extensive fundamental and derived atomic data collections, interactive codes for the manipulation and generation of collisional-radiative data and models, off-line codes for large scale fundamental atomic data production and codes for diagnostic analysis in the fusion and astrophysical environments. ADAS data are organized according to precise specifications, tuned to application and are assigned to numbered ADAS data formats. Some of these formats contain very large quantities of data and some have achieved wide-scale adoption in the fusion community.The paper focuses on recent extensions of ADAS designed to orient ADAS to the needs of ITER. The issue of heavy atomic species, expected to be present as ITER wall and divertor materials, dopants or control species, will be addressed with a view to the economized handling of the emission and ionisation state data needed for diagnostic spectral analysis. Charge exchange and beam emission spectroscopic capabilities and developments in ADAS will be reviewed from an ITER perspective and in the context of a shared analysis between fusion laboratories. Finally an overview and summary of current large scale fundamental data production in the framework of the ADAS project will be given and its intended availability in both fusion and astrophysics noted
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…
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.
Multiphase Modeling of Secondary Atomization in a Shock Environment
St. Clair, Jeffrey; McGrath, Thomas; Balachandar, Sivaramakrishnan
2017-06-01
Understanding and developing accurate modeling strategies for shock-particulate interaction remains a challenging and important topic, with application to energetic materials development, volcanic eruptions, and safety/risk assessment. This work presents computational modeling of compressible multiphase flows with shock-induced droplet atomization. Droplet size has a strong influence on the interphase momentum and heat transfer. A test case is presented that is sensitive to this, requiring the dynamic modeling of the secondary atomization process occurring when the shock impacts the droplets. An Eulerian-Eulerian computational model that treats all phases as compressible, is hyperbolic and satisfies the 2nd Law of Thermodynamics is applied. Four different breakup models are applied to the test case in which a planar shock wave encounters a cloud of water droplets. The numerical results are compared with both experimental and previously-generated modeling results. The effect of the drag relation used is also investigated. The computed results indicate the necessity of using a droplet breakup model for this application, and the relative accuracy of results obtained with the different droplet breakup and drag models is discussed.
Attosecond-correlated dynamics of two electrons in argon
Indian Academy of Sciences (India)
2014-01-11
Jan 11, 2014 ... physics pp. 79–85. Attosecond-correlated dynamics of two electrons in argon. V SHARMA1,∗. , N CAMUS2, B FISCHER2, M KREMER2, ... Furthermore, a meaningful recipe for experimentally tracing the time of two elec- trons in .... tions we define the ionization time difference between the two electrons.
Macromolecular refinement by model morphing using non-atomic parameterizations.
Cowtan, Kevin; Agirre, Jon
2018-02-01
Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.
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.
Multi-atom Jaynes-Cummings model with nonlinear effects
International Nuclear Information System (INIS)
Aleixo, Armando Nazareno Faria; Balantekin, Akif Baha; Ribeiro, Marco Antonio Candido
2001-01-01
The standard Jaynes-Cummings (JC) model and its extensions, normally used in quantum optics, idealizes the interaction of matter with electromagnetic radiation by a simple Hamiltonian of a two-level atom coupled to a single bosonic mode. This Hamiltonian has a fundamental importance to the field of quantum optics and it is a central ingredient in the quantized description of any optical system involving the interaction between light and atoms. The JC Hamiltonian defines a molecule, a composite system formed from the coupling of a two-state system and a quantized harmonic oscillator. For this Hamiltonian, mostly the single-particle situation has been studied. This model can also be extended for the situation where one has N two-level systems, which interact only with the electromagnetic radiation. In this case the effects of the spatial distribution of the particles it is not taken into account and the spin angular momentum S-circumflex i of each particle contributes to form a total angular momentum J-circumflex of the system. When one considers the effects due to the spatial variation in the field intensity in a nonlinear medium it is necessary to further add a Kerr term to the standard JC Hamiltonian. This kind of nonlinear JC Hamiltonian is used in the study of micro masers. Another nonlinear variant of the JC model takes the coupling between matter and the radiation to depend on the intensity of the electromagnetic field. This model is interesting since this kind of interaction means that effectively the coupling is proportional to the amplitude of the field representing a very simple case of a nonlinear interaction corresponding to a more realistic physical situation. In this work we solve exactly the problem of the interaction of a N two-level atoms with an electromagnetic radiation when nonlinear effects due to the spatial variation in the field intensity in a nonlinear Kerr medium and the dependence on the intensity of the electromagnetic field on the matter
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...
Computational models of the single substitutional nitrogen atom in diamond
Lombardi, E B; Osuch, K; Reynhardt, E C
2003-01-01
The single substitutional nitrogen atom in diamond is apparently a very simple defect in a very simple elemental solid. It has been modelled by a range of computational models, few of which either agree with each other, or with the experimental data on the defect. If the computational models of less well understood defects in this and more complex materials are to be reliable, we should understand why the discrepancies arise and how they can be avoided in future modelling. This paper presents an all-electron, augmented plane-wave (APW) density functional theory (DFT) calculation using the modern APW with local orbitals full potential periodic approximation. This is compared to DFT, finite cluster pseudopotential calculations and a semi-empirical Hartree-Fock model. Comparisons between the results of these and previous models allow us to discuss the reliability of computational methods of this and similar defects.
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...
Model study in chemisorption: atomic hydrogen on beryllium clusters
International Nuclear Information System (INIS)
Bauschlicher, C.W. Jr.
1976-08-01
The interaction between atomic hydrogen and the (0001) surface of Be metal has been studied by ab initio electronic structure theory. Self-consistent-field (SCF) calculations have been performed using minimum, optimized minimum, double zeta and mixed basis sets for clusters as large as 22 Be atoms. The binding energy and equilibrium geometry (the distance to the surface) were determined for 4 sites. Both spatially restricted (the wavefunction was constrained to transform as one of the irreducible representations of the molecular point group) and unrestricted SCF calculations were performed. Using only the optimized minimum basis set, clusters containing as many as 22 beryllium atoms have been investigated. From a variety of considerations, this cluster is seen to be nearly converged within the model used, providing the most reliable results for chemisorption. The site dependence of the frequency is shown to be a geometrical effect depending on the number and angle of the bonds. The diffusion of atomic hydrogen through a perfect beryllium crystal is predicted to be energetically unfavorable. The cohesive energy, the ionization energy and the singlet-triplet separation were computed for the clusters without hydrogen. These quantities can be seen as a measure of the total amount of edge effects. The chemisorptive properties are not related to the total amount of edge effects, but rather the edge effects felt by the adsorbate bonding berylliums. This lack of correlation with the total edge effects illustrates the local nature of the bonding, further strengthening the cluster model for chemisorption. A detailed discussion of the bonding and electronic structure is included. The remaining edge effects for the Be 22 cluster are discussed
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.
Models of the atomic nucleus. With interactive software
International Nuclear Information System (INIS)
Cook, N.D.
2006-01-01
This book-and-CD-software package supplies users with an interactive experience for nuclear visualization via a computer-graphical interface, similar in principle to the molecular visualizations already available in chemistry. Models of the Atomic Nucleus, a largely non-technical introduction to nuclear theory, explains the nucleus in a way that makes nuclear physics as comprehensible as chemistry or cell biology. The book/software supplements virtually any of the current textbooks in nuclear physics by providing a means for 3D visual display of the diverse models of nuclear structure. For the first time, an easy-to-master software for scientific visualization of the nucleus makes this notoriously ''non-visual'' field become immediately 'visible.' After a review of the basics, the book explores and compares the competing models, and addresses how the lattice model best resolves remaining controversies. The appendix explains how to obtain the most from the software provided on the accompanying CD. (orig.)
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.
Laury, Marie L; Wang, Lee-Ping; Pande, Vijay S; Head-Gordon, Teresa; Ponder, Jay W
2015-07-23
A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model.
Terrestrial magnetospheric imaging: Numerical modeling of low energy neutral atoms
International Nuclear Information System (INIS)
Moore, K.R.; Funsten, H.O.; McComas, D.J.; Scime, E.E.; Thomsen, M.F.
1993-01-01
Imaging of the terrestrial magnetosphere can be performed by detection of low energy neutral atoms (LENAs) that are produced by charge exchange between magnetospheric plasma ions and cold neutral atoms of the Earth's geocorona. As a result of recent instrumentation advances it is now feasible to make energy-resolved measurements of LENAs from less than I key to greater than 30 key. To model expected LENA fluxes at a spacecraft, we initially used a simplistic, spherically symmetric magnetospheric plasma model. 6 We now present improved calculations of both hydrogen and oxygen line-of-sight LENA fluxes expected on orbit for various plasma regimes as predicted by the Rice University Magnetospheric Specification Model. We also estimate expected image count rates based on realistic instrument geometric factors, energy passbands, and image accumulation intervals. The results indicate that presently proposed LENA instruments are capable of imaging of storm time ring current and potentially even quiet time ring current fluxes, and that phenomena such as ion injections from the tail and subsequent drifts toward the dayside magnetopause may also be deduced
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.
Holomorphic Hartree-Fock Theory: The Nature of Two-Electron Problems.
Burton, Hugh G A; Gross, Mark; Thom, Alex J W
2018-02-13
We explore the existence and behavior of holomorphic restricted Hartree-Fock (h-RHF) solutions for two-electron problems. Through algebraic geometry, the exact number of solutions with n basis functions is rigorously identified as 1 / 2 (3 n - 1), proving that states must exist for all molecular geometries. A detailed study on the h-RHF states of HZ (STO-3G) then demonstrates both the conservation of holomorphic solutions as geometry or atomic charges are varied and the emergence of complex h-RHF solutions at coalescence points. Using catastrophe theory, the nature of these coalescence points is described, highlighting the influence of molecular symmetry. The h-RHF states of HHeH 2+ and HHeH (STO-3G) are then compared, illustrating the isomorphism between systems with two electrons and two electron holes. Finally, we explore the h-RHF states of ethene (STO-3G) by considering the π electrons as a two-electron problem and employ NOCI to identify a crossing of the lowest energy singlet and triplet states at the perpendicular geometry.
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
Analytical local electron-electron interaction model potentials for atoms
International Nuclear Information System (INIS)
Neugebauer, Johannes; Reiher, Markus; Hinze, Juergen
2002-01-01
Analytical local potentials for modeling the electron-electron interaction in an atom reduce significantly the computational effort in electronic structure calculations. The development of such potentials has a long history, but some promising ideas have not yet been taken into account for further improvements. We determine a local electron-electron interaction potential akin to those suggested by Green et al. [Phys. Rev. 184, 1 (1969)], which are widely used in atom-ion scattering calculations, electron-capture processes, and electronic structure calculations. Generalized Yukawa-type model potentials are introduced. This leads, however, to shell-dependent local potentials, because the origin behavior of such potentials is different for different shells as has been explicated analytically [J. Neugebauer, M. Reiher, and J. Hinze, Phys. Rev. A 65, 032518 (2002)]. It is found that the parameters that characterize these local potentials can be interpolated and extrapolated reliably for different nuclear charges and different numbers of electrons. The analytical behavior of the corresponding localized Hartree-Fock potentials at the origin and at long distances is utilized in order to reduce the number of fit parameters. It turns out that the shell-dependent form of Green's potential, which we also derive, yields results of comparable accuracy using only one shell-dependent parameter
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.
Development of a Kohn-Sham like potential in the Self-Consistent Atomic Deformation Model
Mehl, M. J.; Boyer, L. L.; Stokes, H. T.
1996-01-01
This is a brief description of how to derive the local ``atomic'' potentials from the Self-Consistent Atomic Deformation (SCAD) model density function. Particular attention is paid to the spherically averaged case.
Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF
Banks, Bruce A.; Degroh, Kim K.; Auer, Bruce M.; Gebauer, Linda; Edwards, Jonathan L.
1993-01-01
Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) assists in understanding of the mechanisms involved. Thus the reliability of predicting in-space durability of materials based on ground laboratory testing should be improved. A computational model which simulates atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of an assumed mechanistic behavior of atomic oxygen interaction based on in-space atomic oxygen erosion of unprotected polymers and ground laboratory atomic oxygen interaction with protected polymers, prediction of atomic oxygen interaction with protected polymers on LDEF was accomplished. However, the results of these predictions are not consistent with the observed LDEF results at defect sites in protected polymers. Improved agreement between observed LDEF results and predicted Monte Carlo modeling can be achieved by modifying of the atomic oxygen interactive assumptions used in the model. LDEF atomic oxygen undercutting results, modeling assumptions, and implications are presented.
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...... 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......, 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...
International Nuclear Information System (INIS)
Colonna, G.; Pietanza, L.D.; D’Ammando, G.
2012-01-01
Graphical abstract: Self-consistent coupling between radiation, state-to-state kinetics, electron kinetics and fluid dynamics. Highlight: ► A CR model of shock-wave in hydrogen plasma has been presented. ► All equations have been coupled self-consistently. ► Non-equilibrium electron and level distributions are obtained. ► The results show non-local effects and non-equilibrium radiation. - Abstract: A collisional-radiative model for hydrogen atom, coupled self-consistently with the Boltzmann equation for free electrons, has been applied to model a shock tube. The kinetic model has been completed considering atom–atom collisions and the vibrational kinetics of the ground state of hydrogen molecules. The atomic level kinetics has been also coupled with a radiative transport equation to determine the effective adsorption and emission coefficients and non-local energy transfer.
Binding of two-electron metastable states in semiconductor quantum dots under a magnetic field
Garagiola, Mariano; Pont, Federico M.; Osenda, Omar
2018-04-01
Applying a strong enough magnetic field results in the binding of few-electron resonant states. The mechanism was proposed many years ago but its verification in laboratory conditions is far more recent. In this work we study the binding of two-electron resonant states. The electrons are confined in a cylindrical quantum dot which is embedded in a semiconductor wire. The geometry considered is similar to the one used in actual experimental setups. The low-energy two-electron spectrum is calculated numerically from an effective-mass approximation Hamiltonian modelling the system. Methods for binding threshold calculations in systems with one and two electrons are thoroughly studied; in particular, we use quantum information quantities to assess when the strong lateral confinement approximation can be used to obtain reliable low-energy spectra. For simplicity, only cases without bound states in the absence of an external field are considered. Under these conditions, the binding threshold for the one-electron case is given by the lowest Landau energy level. Moreover, the energy of the one-electron bounded resonance can be used to obtain the two-electron binding threshold. It is shown that for realistic values of the two-electron model parameters it is feasible to bind resonances with field strengths of a few tens of tesla.
Hydrogen atom as test field of theoretical models
International Nuclear Information System (INIS)
Baiquni, A.
1976-01-01
Semi classical theory, covering Bohr atom theory, Bohr Sommerfeld theory, Sommerfeld relativistic theory, and quantum theory such as particle and complementarity dualism, wave mechanics, approximation method, relativistic quantum mechanics, and hydrogen atom fine structure, are discussed. (SMN)
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.
Atomic model for the dimeric FOregion of mitochondrial ATP synthase.
Guo, Hui; Bueler, Stephanie A; Rubinstein, John L
2017-11-17
Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F O region turns the rotor that drives ATP synthesis in the soluble F 1 region. Although crystal structures of the F 1 region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F O region. Using cryo-electron microscopy, we determined the structure of the dimeric F O complex from Saccharomyces cerevisiae at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae. Copyright © 2017, American Association for the Advancement of Science.
Clean Floquet Time Crystals: Models and Realizations in Cold Atoms
Huang, Biao; Wu, Ying-Hai; Liu, W. Vincent
2018-03-01
Time crystals, a phase showing spontaneous breaking of time-translation symmetry, has been an intriguing subject for systems far away from equilibrium. Recent experiments found such a phase in both the presence and the absence of localization, while in theories localization by disorder is usually assumed a priori. In this work, we point out that time crystals can generally exist in systems without disorder. A series of clean quasi-one-dimensional models under Floquet driving are proposed to demonstrate this unexpected result in principle. Robust time crystalline orders are found in the strongly interacting regime along with the emergent integrals of motion in the dynamical system, which can be characterized by level statistics and the out-of-time-ordered correlators. We propose two cold atom experimental schemes to realize the clean Floquet time crystals, one by making use of dipolar gases and another by synthetic dimensions.
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.
ATLAS proton-proton event containing two electrons and two muons
ATLAS Collaboration
2011-01-01
An event with two identified muons and two identified electrons from a proton- proton collision in ATLAS. This event is consistent with coming from two Z particles decaying: one Z decays to two muons, the other to two electrons. Such events are produced by Standard Model processes without Higgs particles. They are also a possible signature for Higgs particle production, but many events must be analysed together in order to tell if there is a Higgs signal. The two muons are picked out as red tracks penetrating right through the detector. The two electrons are picked out as green tracks in the central, inner detector, matching narrow green clusters of energy in the barrel part of the calorimeters. The inset at the bottom right shows a map of the energy seen in the detector: the two big yellow spikes correspond to the two electrons.
The dissipative dynamics of the Jaynes-Cummings model with degenerate atomic levels
International Nuclear Information System (INIS)
Zhou, L; Song, H S; Luo, Y X
2002-01-01
We studied the dissipative dynamics of a degenerate-level atom interacting with a single linearly polarized mode field in the dispersive approximation. It is found that the degeneracy of the atomic levels affects the dissipation of the system, of the atom and the field. The period of entanglement becomes much longer than that in the usual Jaynes-Cummings model dissipation. The degeneracy of the atomic level increases the maximum value of the degree of the statistical mixture
Attosecond-correlated dynamics of two electrons in argon
Indian Academy of Sciences (India)
2014-01-11
correlated dynamics of two electrons in argon. V Sharma N Camus B Fischer M Kremer A Rudenko B Bergues M Kuebel N G Johnson M F Kling T Pfeifer J Ullrich R Moshammer. Invited Talks Volume 82 Issue 1 January 2014 ...
International Nuclear Information System (INIS)
Khater, Antoine; Szczesniak, Dominik
2011-01-01
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.
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.
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
Crystal structures and atomic model of NADPH oxidase.
Magnani, Francesca; Nenci, Simone; Millana Fananas, Elisa; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W; Mattevi, Andrea
2017-06-27
NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.
Cholesky decomposition of the two-electron integral matrix in electronic structure calculations.
Røeggen, I; Johansen, Tor
2008-05-21
A standard Cholesky decomposition of the two-electron integral matrix leads to integral tables which have a huge number of very small elements. By neglecting these small elements, it is demonstrated that the recursive part of the Cholesky algorithm is no longer a bottleneck in the procedure. It is shown that a very efficient algorithm can be constructed when family type basis sets are adopted. For subsequent calculations, it is argued that two-electron integrals represented by Cholesky integral tables have the same potential for simplifications as density fitting. Compared to density fitting, a Cholesky decomposition of the two-electron matrix is not subjected to the problem of defining an auxiliary basis for obtaining a fixed accuracy in a calculation since the accuracy simply derives from the choice of a threshold for the decomposition procedure. A particularly robust algorithm for solving the restricted Hartree-Fock (RHF) equations can be speeded up if one has access to an ordered set of integral tables. In a test calculation on a linear chain of beryllium atoms, the advocated RHF algorithm nicely converged, but where the standard direct inversion in iterative space method converged very slowly to an excited state.
An Atomic Model for the Interaction between a ½
Hosson, J.Th.M. de
1975-01-01
The arrangement of Fe atoms around a ½<111>{110} edge dislocation in an α-Fe crystallite was calculated using the Johnson-I potential. The boundary conditions were given by anisotropic elasticity. The positions with maximum energy gain for carbon atoms were calculated.
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.
Operation of the computer model for direct atomic oxygen exposure of Earth satellites
Bourassa, R. J.; Gruenbaum, P. E.; Gillis, J. R.; Hargraves, C. R.
1995-01-01
One of the primary causes of material degradation in low Earth orbit (LEO) is exposure to atomic oxygen. When atomic oxygen molecules collide with an orbiting spacecraft, the relative velocity is 7 to 8 km/sec and the collision energy is 4 to 5 eV per atom. Under these conditions, atomic oxygen may initiate a number of chemical and physical reactions with exposed materials. These reactions contribute to material degradation, surface erosion, and contamination. Interpretation of these effects on materials and the design of space hardware to withstand on-orbit conditions requires quantitative knowledge of the atomic oxygen exposure environment. Atomic oxygen flux is a function of orbit altitude, the orientation of the orbit plan to the Sun, solar and geomagnetic activity, and the angle between exposed surfaces and the spacecraft heading. We have developed a computer model to predict the atomic oxygen exposure of spacecraft in low Earth orbit. The application of this computer model is discussed.
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.
Self-consistent assessment of Englert-Schwinger model on atomic properties.
Lehtomäki, Jouko; Lopez-Acevedo, Olga
2017-12-21
Our manuscript investigates a self-consistent solution of the statistical atom model proposed by Berthold-Georg Englert and Julian Schwinger (the ES model) and benchmarks it against atomic Kohn-Sham and two orbital-free models of the Thomas-Fermi-Dirac (TFD)-λvW family. Results show that the ES model generally offers the same accuracy as the well-known TFD-15vW model; however, the ES model corrects the failure in the Pauli potential near-nucleus region. We also point to the inability of describing low-Z atoms as the foremost concern in improving the present model.
Four shells atomic model to computer the counting efficiency of electron-capture nuclides
International Nuclear Information System (INIS)
Grau Malonda, A.; Fernandez Martinez, A.
1985-01-01
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
Two-electron Rabi oscillations in real-time time-dependent density-functional theory.
Habenicht, Bradley F; Tani, Noriyuki P; Provorse, Makenzie R; Isborn, Christine M
2014-11-14
We investigate the Rabi oscillations of electrons excited by an applied electric field in several simple molecular systems using time-dependent configuration interaction (TDCI) and real-time time-dependent density-functional theory (RT-TDDFT) dynamics. While the TDCI simulations exhibit the expected single-electron Rabi oscillations at a single resonant electric field frequency, Rabi oscillations in the RT-TDDFT simulations are a two-electron process. The existence of two-electron Rabi oscillations is determined both by full population inversion between field-free molecular orbitals and the behavior of the instantaneous dipole moment during the simulations. Furthermore, the Rabi oscillations in RT-TDDFT are subject to an intensity threshold of the electric field, below which Rabi oscillations do not occur and above which the two-electron Rabi oscillations occur at a broad range of frequencies. It is also shown that at field intensities near the threshold intensity, the field frequency predicted to induce Rabi oscillations by linear response TDDFT only produces detuned Rabi oscillations. Instead, the field frequency that yields the full two-electron population inversion and Rabi oscillation behavior is shown to be the average of single-electron transition frequencies from the ground S0 state and the doubly-excited S2 state. The behavior of the two-electron Rabi oscillations is rationalized via two possible models. The first model is a multi-photon process that results from the electric field interacting with the three level system such that three level Rabi oscillations may occur. The second model suggests that the mean-field nature of RT-TDDFT induces paired electron propagation.
Two-electron Rabi oscillations in real-time time-dependent density-functional theory
International Nuclear Information System (INIS)
Habenicht, Bradley F.; Tani, Noriyuki P.; Provorse, Makenzie R.; Isborn, Christine M.
2014-01-01
We investigate the Rabi oscillations of electrons excited by an applied electric field in several simple molecular systems using time-dependent configuration interaction (TDCI) and real-time time-dependent density-functional theory (RT-TDDFT) dynamics. While the TDCI simulations exhibit the expected single-electron Rabi oscillations at a single resonant electric field frequency, Rabi oscillations in the RT-TDDFT simulations are a two-electron process. The existence of two-electron Rabi oscillations is determined both by full population inversion between field-free molecular orbitals and the behavior of the instantaneous dipole moment during the simulations. Furthermore, the Rabi oscillations in RT-TDDFT are subject to an intensity threshold of the electric field, below which Rabi oscillations do not occur and above which the two-electron Rabi oscillations occur at a broad range of frequencies. It is also shown that at field intensities near the threshold intensity, the field frequency predicted to induce Rabi oscillations by linear response TDDFT only produces detuned Rabi oscillations. Instead, the field frequency that yields the full two-electron population inversion and Rabi oscillation behavior is shown to be the average of single-electron transition frequencies from the ground S 0 state and the doubly-excited S 2 state. The behavior of the two-electron Rabi oscillations is rationalized via two possible models. The first model is a multi-photon process that results from the electric field interacting with the three level system such that three level Rabi oscillations may occur. The second model suggests that the mean-field nature of RT-TDDFT induces paired electron propagation
Modeling Strongly Correlated Fermi Systems Using Ultra-Cold Atoms
National Research Council Canada - National Science Library
O'Hara, Kenneth M
2008-01-01
... displays, photodynamic therapy, and a pump for Cr:LiSAF lasers. This work also led to new insights into how high-power multi-longitudinal mode fiber lasers can be used for preparing quantum degenerate atomic gases...
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.
International Nuclear Information System (INIS)
Beck, W.A.
2000-01-01
The semiclassical model of atomic collisions, especially in different areas of the maximum stopping, when proton collides at the velocity of the boron order velocity, providing as the result for interactions of many bodies with an electron target, enabling application of the model with high degree of confidence to a clearly expressed experimental problem, such the antiproton capture on helium, is presented. The semiclassical collision model and stopping energy are considered. The stopping and capture of negatively-charged particles are investigated. The capture and angular moments of antiprotons, captures at the end of the collision cascade, are presented [ru
Mapping trapped atomic gas with spin-orbit coupling to quantum Rabi-like model
Hu, Haiping; Chen, Shu
2013-01-01
We construct a connection of the ultracold atomic system in a harmonic trap with Raman-induced spin-orbit coupling to the quantum Rabi-like model. By mapping the trapped atomic system to a Rabi-like model, we can get the exact solution of the Rabi-like model following the methods to solve the quantum Rabi model. The existence of such a mapping implies that we can study the basic model in quantum optics by using trapped atomic gases with spin-orbit coupling.
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
Energy Technology Data Exchange (ETDEWEB)
Brics, Martins
2016-12-09
-called renormalized natural orbitals (RNOs), TDRNOT is benchmarked with the help of a numerically exactly solvable model helium atom in laser fields. In the special case of time-dependent two-electron systems the two-particle density matrix in terms of ONs and NOs is known exactly. Hence, in this case TDRNOT is exact, apart from the unavoidable truncation of the number of RNOs per particle taken into account in the simulation. It is shown that, unlike TDDFT, TDRNOT is able to describe doubly-excited states, Fano profiles in electron and absorption spectra, auto-ionization, Rabi oscillations, high harmonic generation, non-sequential ionization, and single-photon double ionization in excellent agreement with the corresponding TDSE results.
Effect of moving away from half filling on the variational two electron ...
African Journals Online (AJOL)
In this study, the two electron interactions on one dimensional (1D) lattices is investigated in a t-U-J model where the t is the kinetic term, the U is the onsite Coulombic term and J is the nearest neighbour (NN) exchange term. Specifically, the effect of moving away from half filling (i.e. when the number of electrons Ne equals ...
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
Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.
Shen, Lin; Hu, Hao
2014-06-10
We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.
Extreme Adiabatic Expansion in Micro-gravity: Modeling for the Cold Atomic Laboratory
Sackett, C. A.; Lam, T. C.; Stickney, J. C.; Burke, J. H.
2017-12-01
The upcoming Cold Atom Laboratory mission for the International Space Station will allow the investigation of ultracold gases in a microgravity environment. Cold atomic samples will be produced using evaporative cooling in a magnetic chip trap. We investigate here the possibility to release atoms from the trap via adiabatic expansion. We discuss both general considerations and a detailed model of the planned apparatus. We find that it should be possible to reduce the mean trap confinement frequency to about 0.2 Hz, which will correspond to a three-dimensional sample temperature of about 150 pK and a mean atom velocity of 0.1 mm/s.
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
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...
Analytical model for relativistic corrections to the nuclear magnetic shielding constant in atoms
International Nuclear Information System (INIS)
Romero, Rodolfo H.; Gomez, Sergio S.
2006-01-01
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
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…
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.
Theory and computation of the rate of multiphoton two-electron ionization via the direct mechanism
Energy Technology Data Exchange (ETDEWEB)
Mercouris, Theodoros; Haritos, Costas [Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Athens (Greece)]. E-mails: thmerc@eie.gr; kharit@eie.gr; Nicolaides, Cleanthes A. [Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Athens (GR) and Physics Department, National Technical University, Athens (Greece)]. E-mail: can@eie.gr
2001-10-14
This paper discusses aspects of the physics and the computation of rates of multiphoton two-electron ionization of polyelectronic atoms within a non-perturbative, time-independent framework. A fundamental characteristic of the theory is that the physically significant features of the spectrum, of electronic structure and of free-electron channels enter systematically in an N-electron field-dressed resonance trial wavefunction. This many-electron, many-photon theory produces the rate of a particular field-induced process as the imaginary part of a frequency- and intensity-dependent complex eigenvalue obtained from the solution of a suitably constructed non-Hermitian Hamiltonian matrix. The notion of direct two-electron ionization is expressed in terms of a specific form of the trial wavefunction, which consists of configurations with real and complex square-integrable functions, subject to orthogonality constraints so as to exclude the participation of single-ionization channels, assumed to contribute mainly to the sequential path. The applications were done to the two-electron ejection from He by the direct absorption of two linearly polarized photons (photon energy in the range 35.0-55.0 eV) and to H{sup -} from the direct and the sequential absorption of four, three, two and one photons (photon energy in the range 4.08-15.00 eV). The comparison between the rates of the two paths in H{sup -}, for photon energies 7.18-10.5 eV, shows that the direct rate dominates. We also show that in the orbital Hartree-Fock approximation to the initial state, the frequency-dependent rates at the intensity of 1x10{sup 13} W cm{sup -2} differ from those obtained with a correlated wavefunction by about two orders of magnitude. (author)
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.
Molecular dynamics modeling of bonding two materials by atomic scale friction stir welding
Konovalenko S., Iv.; Konovalenko, Ig. S.; Psakhie, S. G.
2017-12-01
Molecular dynamics model of atomic scale friction stir welding has been developed. Formation of a butt joint between two crystallites was modeled by means of rotating rigid conical tool traveling along the butt joint line. The formed joint had an intermixed atomic structure composed of atoms initially belonged to the opposite mated piece of metal. Heat removal was modeled by adding the extra viscous force to peripheral atomic layers. This technique provides the temperature control in the tool-affected zone during welding. Auxiliary vibration action was added to the rotating tool. The model provides the variation of the tool's angular velocity, amplitude, frequency and direction of the auxiliary vibration action to provide modeling different welding modes.
Peng, Bo; Kowalski, Karol
2017-09-12
The representation and storage of two-electron integral tensors are vital in large-scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this work, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition of the two-electron integral tensor in our implementation. For the size of the atomic basis set, N b , ranging from ∼100 up to ∼2,000, the observed numerical scaling of our implementation shows [Formula: see text] versus [Formula: see text] cost of performing single CD on the two-electron integral tensor in most of the other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic orbital (AO) two-electron integral tensor from [Formula: see text] to [Formula: see text] with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled cluster formalism employing single and double excitations (CCSD) on several benchmark systems including the C 60 molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10 -4 to 10 -3 to give acceptable compromise between efficiency and accuracy.
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.
Gaussian-input Gaussian mixture model for representing density maps and atomic models.
Kawabata, Takeshi
2018-03-06
A new Gaussian mixture model (GMM) has been developed for better representations of both atomic models and electron microscopy 3D density maps. The standard GMM algorithm employs an EM algorithm to determine the parameters. It accepted a set of 3D points with weights, corresponding to voxel or atomic centers. Although the standard algorithm worked reasonably well; however, it had three problems. First, it ignored the size (voxel width or atomic radius) of the input, and thus it could lead to a GMM with a smaller spread than the input. Second, the algorithm had a singularity problem, as it sometimes stopped the iterative procedure due to a Gaussian function with almost zero variance. Third, a map with a large number of voxels required a long computation time for conversion to a GMM. To solve these problems, we have introduced a Gaussian-input GMM algorithm, which considers the input atoms or voxels as a set of Gaussian functions. The standard EM algorithm of GMM was extended to optimize the new GMM. The new GMM has identical radius of gyration to the input, and does not suddenly stop due to the singularity problem. For fast computation, we have introduced a down-sampled Gaussian functions (DSG) by merging neighboring voxels into an anisotropic Gaussian function. It provides a GMM with thousands of Gaussian functions in a short computation time. We also have introduced a DSG-input GMM: the Gaussian-input GMM with the DSG as the input. This new algorithm is much faster than the standard algorithm. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.
Impurity effects in two-electron coupled quantum dots: entanglement modulation
International Nuclear Information System (INIS)
Acosta Coden, Diego S; Romero, Rodolfo H; Ferrón, Alejandro; Gomez, Sergio S
2013-01-01
We present a detailed analysis of the electronic and optical properties of two-electron quantum dots with a two-dimensional Gaussian confinement potential. We study the effects of Coulomb impurities and the possibility of manipulating the entanglement of the electrons by controlling the confinement potential parameters. The degree of entanglement becomes highly modulated by both the location and charge screening of the impurity atom, resulting in two regimes: one of low entanglement and the other of high entanglement, with both of them mainly determined by the magnitude of the charge. It is shown that the magnitude of the oscillator strength of the system could provide an indication of the presence and characteristics of impurities and, therefore, the degree of entanglement. (paper)
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...
Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.
Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M
2016-09-21
We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.
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.
Energy Technology Data Exchange (ETDEWEB)
Brics, Martins; Kapoor, Varun; Bauer, Dieter [Institut fuer Physik, Universitaet Rostock, 18051 Rostock (Germany)
2013-07-01
Time-dependent density functional theory (TDDFT) with known and practicable exchange-correlation potentials does not capture highly correlated electron dynamics such as single-photon double ionization, autoionization, or nonsequential ionization. Time-dependent reduced density matrix functional theory (TDRDMFT) may remedy these problems. The key ingredients in TDRDMFT are the natural orbitals (NOs), i.e., the eigenfunctions of the one-body reduced density matrix (1-RDM), and the occupation numbers (OCs), i.e., the respective eigenvalues. The two-body reduced density matrix (2-RDM) is then expanded in NOs, and equations of motion for the NOs can be derived. If the expansion coefficients of the 2-RDM were known exactly, the problem at hand would be solved. In practice, approximations have to be made. We study the prospects of TDRDMFT following a top-down approach. We solve the exact two-electron time-dependent Schroedinger equation for a model Helium atom in intense laser fields in order to study highly correlated phenomena such as the population of autoionizing states or single-photon double ionization. From the exact wave function we calculate the exact NOs, OCs, the exact expansion coefficients of the 2-RDM, and the exact potentials in the equations of motion. In that way we can identify how many NOs and which level of approximations are necessary to capture such phenomena.
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.
Solitary Langmuir waves in two-electron temperature plasma
Prudkikh, V. V.; Prudkikh
2014-06-01
Nonlinear interaction of Langmuir and ion-acoustic waves in two-electron temperature plasma is investigated. New integrable wave interaction regime was discovered, this regime corresponds to the Langmuir soliton with three-hump amplitude, propagating with a speed close to the ion-sound speed in the conditions of strong non-isothermality of electronic components. It was discovered that besides the known analytical solution in the form of one- and two-hump waves, there exists a range of solutions in the form of solitary waves, which in the form of envelope has multi-peak structure and differs from the standard profiles described by hyperbolic functions. In case of fixed plasma parameters, different group velocities correspond to the waves with different number of peaks. It is found that the Langmuir wave package contains both even and uneven numbers of oscillations. Low-frequency potential here has uneven number of peaks. Interrelation of obtained and known earlier results are also discussed.
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.
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…
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.
A Meshless Algorithm to Model Field Evaporation in Atom Probe Tomography.
Rolland, Nicolas; Vurpillot, François; Duguay, Sébastien; Blavette, Didier
2015-12-01
An alternative approach for simulating the field evaporation process in atom probe tomography is presented. The model uses the electrostatic Robin's equation to directly calculate charge distribution over the tip apex conducting surface, without the need for a supporting mesh. The partial ionization state of the surface atoms is at the core of the method. Indeed, each surface atom is considered as a point charge, which is representative of its evaporation probability. The computational efficiency is ensured by an adapted version of the Barnes-Hut N-body problem algorithm. Standard desorption maps for cubic structures are presented in order to demonstrate the effectiveness of the method.
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.
Folding of proteins with an all-atom Go-model.
Wu, L; Zhang, J; Qin, M; Liu, F; Wang, W
2008-06-21
The Go-like potential at a residual level has been successfully applied to the folding of proteins in many previous works. However, taking into consideration more detailed structural information in the atomic level, the definition of contacts used in these traditional Go-models may not be suitable for all-atom simulations. Here, in this work, we develop a rational definition of contacts considering the screening effect in the crowded intramolecular environment. In such a scheme, a large amount of screened atom pairs are excluded and the number of contacts is decreased compared to the case of the traditional definition. These contacts defined by such a new definition are compatible with the all-atom representation of protein structures. To verify the rationality of the new definition of contacts, the folding of proteins CI2 and SH3 is simulated by all-atom molecular dynamics simulations. A high folding cooperativity and good correlation of the simulated Phi-values with those obtained experimentally, especially for CI2, are found. This suggests that the all-atom Go-model is improved compared to the traditional Go-model. Based on the comparison of the Phi-values, the roles of side chains in the folding are discussed, and it is concluded that the side-chain structures are more important for local contacts in determining the transition state structures. Moreover, the relations between side chain and backbone orderings are also discussed.
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...
Improving atomic displacement and replacement calculations with physically realistic damage models.
Nordlund, Kai; Zinkle, Steven J; Sand, Andrea E; Granberg, Fredric; Averback, Robert S; Stoller, Roger; Suzudo, Tomoaki; Malerba, Lorenzo; Banhart, Florian; Weber, William J; Willaime, Francois; Dudarev, Sergei L; Simeone, David
2018-03-14
Atomic collision processes are fundamental to numerous advanced materials technologies such as electron microscopy, semiconductor processing and nuclear power generation. Extensive experimental and computer simulation studies over the past several decades provide the physical basis for understanding the atomic-scale processes occurring during primary displacement events. The current international standard for quantifying this energetic particle damage, the Norgett-Robinson-Torrens displacements per atom (NRT-dpa) model, has nowadays several well-known limitations. In particular, the number of radiation defects produced in energetic cascades in metals is only ~1/3 the NRT-dpa prediction, while the number of atoms involved in atomic mixing is about a factor of 30 larger than the dpa value. Here we propose two new complementary displacement production estimators (athermal recombination corrected dpa, arc-dpa) and atomic mixing (replacements per atom, rpa) functions that extend the NRT-dpa by providing more physically realistic descriptions of primary defect creation in materials and may become additional standard measures for radiation damage quantification.
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...
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).
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).
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
Basharov, A. M.
2018-03-01
The Markov model of spontaneous emission of an atom localized in a spatial region with a broadband electromagnetic field with zero photon density is considered in the conditions of coupling of the electromagnetic field with the broadband field of a neighboring space. The evolution operator of the system and the kinetic equation for the atom are obtained. It is shown that the field coupling constant affects the rate of spontaneous emission of the atom, but is not manifested in the atomic frequency shift. The analytic expression for the radiative decay constant for the atom is found to be analogous in a certain sense to the expression for the decay constant for a singly excited localized ensemble of identical atoms in the conditions when the effect of stabilization of its excited state by the Stark interaction with the vacuum broadband electromagnetic field is manifested. The model is formulated based on quantum stochastic differential equations of the non- Wiener type and the generalized algebra of the Ito differential of quantum random processes.
Exactly solvable models for tri-atomic molecular Bose-Einstein condensates
Energy Technology Data Exchange (ETDEWEB)
Santos, G; Roditi, I; Santos, Z V T [CBPF-Centro Brasileiro de Pesquisas Fisicas, Rio de Janeiro RJ (Brazil); Foerster, A [Instituto de Fisica da UFRGS, Porto Alegre, RS (Brazil); Tonel, A P [CCET da Universidade Federal do Pampa/Unipampa, Bage, RS (Brazil)], E-mail: gfilho@cbpf.br
2008-07-25
We construct a family of tri-atomic models for heteronuclear and homonuclear molecular Bose-Einstein condensates. We show that these new generalized models are exactly solvable through the algebraic Bethe ansatz method and derive their corresponding Bethe ansatz equations and energies.
Interaction of attosecond electromagnetic pulses with atoms: The exactly solvable model
International Nuclear Information System (INIS)
Popov, Yu. V.; Kouzakov, K. A.; Vinitsky, S. I.; Gusev, A. A.
2007-01-01
We consider the exactly solvable model of interaction of zero-duration electromagnetic pulses with an atom. The model has a number of peculiar properties which are outlined in the cases of a single pulse and two opposite pulses. In perspective, it can be useful in different fields of physics involving interaction of attosecond laser pulses with quantum systems
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...
Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation
Willey, Ronald J.
1993-01-01
Five kinetic models are compared for their ability to predict recombination coefficients for oxygen and nitrogen atoms over high-temperature reusable surface insulation (HRSI). Four of the models are derived using Rideal-Eley or Langmuir-Hinshelwood catalytic mechanisms to describe the reaction sequence. The fifth model is an empirical expression that offers certain features unattainable through mechanistic description. The results showed that a four-parameter model, with temperature as the only variable, works best with data currently available. The model describes recombination coefficients for oxygen and nitrogen atoms for temperatures from 300 to 1800 K. Kinetic models, with atom concentrations, demonstrate the influence of atom concentration on recombination coefficients. These models can be used for the prediction of heating rates due to catalytic recombination during re-entry or aerobraking maneuvers. The work further demonstrates a requirement for more recombination experiments in the temperature ranges of 300-1000 K, and 1500-1850 K, with deliberate concentration variation to verify model requirements.
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…
Lattice location of dopant atoms: An N-body model calculation
Indian Academy of Sciences (India)
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 continuum model.
UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions
International Nuclear Information System (INIS)
Siebert, Xavier; Navaza, Jorge
2009-01-01
UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples. Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30–10 Å range and sometimes even beyond 10 Å. 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/
ATOMIC AND MOLECULAR PHYSICS: Modelling of a DNA packaging motor
Qian, Jun; Xie, Ping; Xue, Xiao-Guang; Wang, Peng-Ye
2009-11-01
During the assembly of many viruses, a powerful molecular motor packages the genome into a preassembled capsid. The Bacillus subtilis phage phi29 is an excellent model system to investigate the DNA packaging mechanism because of its highly efficient in vitro DNA packaging activity and the development of a single-molecule packaging assay. Here we make use of structural and biochemical experimental data to build a physical model of DNA packaging by the phi29 DNA packaging motor. Based on the model, various dynamic behaviours such as the packaging rate, pause frequency and slip frequency under different ATP concentrations, ADP concentrations, external loads as well as capsid fillings are studied by using Monte Carlo simulation. Good agreement is obtained between the simulated and available experimental results. Moreover, we make testable predictions that should guide future experiments related to motor function.
Pseudo potentials and model potentials in atomic collisions
International Nuclear Information System (INIS)
Reyes, O.; Jouin, H.; Fuentealba, P.
1988-01-01
In this work, it is discussed the main differences between the use of pseudo-potentials and model potentials in collision problems . It is shown the potential energy curves for distinct systems obtained with both kinds of potentials. (A.C.A.S.) [pt
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,
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
Ultracold atoms in quasi-one-dimensional traps: A step beyond the Lieb-Liniger model
Jachymski, Krzysztof; Meinert, Florian; Veksler, Hagar; Julienne, Paul S.; Fishman, Shmuel
2017-05-01
Ultracold atoms placed in a tight cigar-shaped trap are usually described in terms of the Lieb-Liniger model. We study the extensions of this model which arise when van der Waals interaction between atoms is taken into account. We find that the corrections induced by the finite range of interactions can become especially important in the vicinity of narrow Feshbach resonances and suggest realistic schemes of their experimental detection. The interplay of confinement and interactions can lead to effective transparency where the one-dimensional interactions are weak in a wide range of parameters.
Becker, A; Faisal, F
2001-03-26
Recently observed momentum distribution of doubly charged recoil-ions of atoms produced by femtosecond infrared laser pulses is analyzed using the so-called intense-field many-body S-matrix theory. Observed characteristics of the momentum distributions, parallel and perpendicular to the polarization axis, are reproduced by the theory. It is shown that correlated energy-sharing between the two electrons in the intermediate state and their 'Volkov-dressing' in the final state, can explain the origin of these characteristics.
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
2014-09-01
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.
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
2014-09-04
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.
Free-free opacity in dense plasmas with an average atom model
Shaffer, N. R.; Ferris, N. G.; Colgan, J.; Kilcrease, D. P.; Starrett, C. E.
2017-06-01
A model for the free-free opacity of dense plasmas is presented. The model uses a previously developed average atom model, together with the Kubo-Greenwood model for optical conductivity. This, in turn, is used to calculate the opacity with the Kramers-Kronig dispersion relations. Comparisons to other methods for dense deuterium results in excellent agreement with DFT-MD simulations, and reasonable agreement with a simple Yukawa screening model corrected to satisfy the conductivity sum rule. Comparisons against the very recent experiments of Kettle et al. for dense aluminum also reveal very good agreement, in contrast to existing models. Weaknesses in the model are also highlighted.
Modelling of Collisional Ionization in Laser Excited Sodium Atoms
Mahmoud, M.; Gamal, Y.
1995-12-01
The time evolution of the energy distribution of the free electrons created by collisional ionization of sodium vapor resonantly excited with cw laser due to different physical mechanisms have been studied theoretically. The calculations clarified that the distribution of the electron energy tends to become non-Maxwellian for different periods of time. Also the computational model indicated that the major processes in the different stages of the plasma creation are purely collisional for both excitation and ionization. Moreover our calculations of energy spectra of electrons have characteristic peaks corresponding to associative ionization and superelastic collisions. A reasonable agreement with experiments is obtained.
Non local thermodynamic equilibrium self-consistent average atom model for plasma physics
International Nuclear Information System (INIS)
Faussurier, G.; Blancard, Ch.; Berthier, E.
2000-01-01
A time-dependent collisional-radiative average-atom model is presented to study statistical properties of highly-charged ion plasmas in off-equilibrium conditions. Atomic structure is described either with a screened-hydrogenic model including l-splitting, or by calculating one electron states in a self-consistent average-atom potential. Collisional and radiative excitation/deexcitation and ionization/recombination rats, as well as auto-ionization and dielectronic recombination rates, are formulated within the average-configuration framework. A good agreement with experiment is found for the charge-state distribution of a gold plasma at electron and density temperature equal to 6 x 10 20 cm -3 and 2200 eV. (author)
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....... We show how the electromagnetic response of metasurfaces is related to the statistical parameters of the structure. Furthermore, we will discuss the phenomenon of anti-resonance in extracted effective parameters of metamaterials and clarify its relation to the periodicity (or amorphous nature...
Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model.
Kao, Hsiu-Fen; Lo, Ikai; Chiang, Jih-Chen; Chen, Chun-Nan; Wang, Wan-Tsang; Hsu, Yu-Chi; Ren, Chung-Yuan; Lee, Meng-En; Wu, Chieh-Lung; Gau, Ming-Hong
2012-10-17
We develop a 16-band atomic bond-orbital model (16ABOM) to compute the spin splitting induced by bulk inversion asymmetry in zincblende materials. This model is derived from the linear combination of atomic-orbital (LCAO) scheme such that the characteristics of the real atomic orbitals can be preserved to calculate the spin splitting. The Hamiltonian of 16ABOM is based on a similarity transformation performed on the nearest-neighbor LCAO Hamiltonian with a second-order Taylor expansion k at the Γ point. The spin-splitting energies in bulk zincblende semiconductors, GaAs and InSb, are calculated, and the results agree with the LCAO and first-principles calculations. However, we find that the spin-orbit coupling between bonding and antibonding p-like states, evaluated by the 16ABOM, dominates the spin splitting of the lowest conduction bands in the zincblende materials.
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.
Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former.
Kim, Jeongmin; Sung, Bong June
2015-06-17
The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.
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.
Atomic Model and Micelle Dynamics of QS-21 Saponin
Directory of Open Access Journals (Sweden)
Conrado Pedebos
2014-03-01
Full Text Available QS-21 is a saponin extracted from Quillaja saponaria, widely investigated as a vaccine immunoadjuvant. However, QS-21 use is mainly limited by its chemical instability, significant variety in molecular composition and low tolerance dose in mammals. Also, this compound tends to form micelles in a concentration-dependent manner. Here, we aimed to characterize its conformation and the process of micelle formation, both experimentally and computationally. Therefore, molecular dynamics (MD simulations were performed in systems containing different numbers of QS-21 molecules in aqueous solution, in order to evaluate the spontaneous micelle formation. The applied methodology allowed the generation of micelles whose sizes were shown to be in high agreement with small-angle X-ray scattering (SAXS. Furthermore, the ester linkage between fucose and acyl chain was less solvated in the micellar form, suggesting a reduction in hydrolysis. This is the first atomistic interpretation of previous experimental data, the first micellar characterization of saponin micelles by SAXS and first tridimensional model of a micelle constituted of saponins, contributing to the understanding of the molecular basis of these compounds.
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.
Semi-analytical wave functions in relativistic average atom model for high-temperature plasmas
International Nuclear Information System (INIS)
Guo Yonghui; Duan Yaoyong; Kuai Bin
2007-01-01
The semi-analytical method is utilized for solving a relativistic average atom model for high-temperature plasmas. Semi-analytical wave function and the corresponding energy eigenvalue, containing only a numerical factor, are obtained by fitting the potential function in the average atom into hydrogen-like one. The full equations for the model are enumerated, and more attentions are paid upon the detailed procedures including the numerical techniques and computer code design. When the temperature of plasmas is comparatively high, the semi-analytical results agree quite well with those obtained by using a full numerical method for the same model and with those calculated by just a little different physical models, and the result's accuracy and computation efficiency are worthy of note. The drawbacks for this model are also analyzed. (authors)
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/.
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.
Application of a distorted wave model to electron capture in atomic collisions
International Nuclear Information System (INIS)
Deco, G.R.; Martinez, A.E.; Rivarola, R.D.
1988-01-01
In this work, it is presented the CDW-EIS approximation applied to the description of processes of electron capture in ion-atom collisions. Differential and total cross sections are compared to results obtained by other theoretical models, as well as, to experimental data. (A.C.A.S.) [pt
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 ...
Lattice location of dopant atoms: An N-body model calculation
Indian Academy of Sciences (India)
from the concerned channelling direction. Here we applied the superior N-body model to study the yield from bismuth in silicon. The finding that bismuth atom occupies a position close to the silicon substitutional site is new. The transverse displacement of the suggested lattice site from the channelling direction is consistent ...
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.
Lattice location of dopant atoms: An N-body model calculation
Indian Academy of Sciences (India)
2015-11-27
Nov 27, 2015 ... The finding that bismuth atom occupies a position close to the silicon substitutional site is new. The transverse displacement of the suggested lattice site from the channelling direction is consistent with the experimental results. The above model is also applied to determine the location of ytterbium in silicon.
Modeling of inelastic transport in one-dimensional metallic atomic wires
DEFF Research Database (Denmark)
Frederiksen, Thomas; Brandbyge, Mads; Lorente, N
2004-01-01
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-and-springs...
A simple model for atomic layer doped field-effect transistor (ALD-FET) electronic states
International Nuclear Information System (INIS)
Mora R, M.E.; Gaggero S, L.M.
1998-01-01
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)
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
Model analysis of molecular conformations in terms of weak interactions between non bonded atoms
International Nuclear Information System (INIS)
Lombardi, E.
1988-01-01
The aim of the present paper is to establish a reliable basis for the evaluation of stable conformations and rotational barriers for molecules, with possible applications to systems of biological interest. It is proceeded in two steps: first, the effect of chemical environment on orbitals of a given atom is studied for diatomic units, adopting a valence-bond approach and considering, as prototypes, the two simplest series of diatomic molecules with one valence electron each, i.e. the alkali diatomics and the alkali hydrides. In the model, the orbital of the hydrogen atom by a simple (''1S'') gaussian function, the valence orbital of an alkali atom by a function (r 2 -a 2 ) times a simple gaussian (''2S'' gaussian). Dissociation energies D e and equilibrium distances R e are calculated using a scanning procedure. Agreement with experiment is quantitative for the alkali diatomics. For alkali hydrides, good agreement is obtained only if validity of a rule β e R e =constant, for the two atoms separately, is postulated; β e is the characteristic parameter of a ''1S'' gaussian (hydrogen) or a ''2S'' gaussian (alkali atom) function. In a second step, the authors assume validity of the same rule in conformational analysis for any single bonded A-B molecule with A=C, O, N, P, Si, Ge and B=H, or a halogen atom. Gauge β e values for H, F and C are obtained by fitting experimental rotational barriers in C 2 H 6 , C 2 F 6 and C 3 H 8 . Stable conformation of, and barriers to rotation in, ethane-like rotors are determined, applying first-order exchange perturbation theory, in terms of two- and many-center exchange interactions in cluster of non-bonded atoms. Some 60 molecules are analyzed. Agreement with experiments is strikngly good except for a few systematic deviation. Reasons for such discrepancies are discussed
Surzhykov, Andrey; Koval, Peter; Fritzsche, Stephan
2005-01-01
's standard software floating-point algorithms and on the (attempted) precision as defined by the global Digits variable. Although the default number, Digits = 10, appears sufficient for many computations, it often leads to a rather dramatic loss in the accuracy of the relativistic wave functions and integrals, mainly owing to MAPLE's imprecise internal evaluation of the corresponding special functions. Therefore, in order to avoid such computational difficulties, the Digits variable is set to 20 whenever the DIRAC program is (re-)loaded. Unusual features of the program: The DIRAC program has been designed for interactive work which, apart from the standard solutions and integrals of the hydrogen atom, also support the use of (approximate) semirelativistic wave functions for both, the bound- and continuum-states of the electron. To provide a fast and accurate access to a number of radial integrals which arise frequently in applications, the analytical expressions for these integrals have been implemented for the one-particle operators r, e, d/dr, j(kr) as well as for the (so-called) two-particle Slater integrals which are needed to describe the Coulomb repulsion among the electrons. Further procedures of the DIRAC program concern, for instance, the conversion of the physical results between different unit systems or for different sets of quantum numbers. A brief description of all procedures as available in the present version of the DIRAC program is given in the user manual Dirac-commands.pdf which is distributed together with the code. Typical running time: Although the program replies promptly on most requests, the running time also depends on the particular task. References: [1] Maple is a registered trademark of Waterloo Maple Inc. [2] H.A. Bethe and E.E. Salpeter, Quantum Mechanics of One- and Two-Electron Atoms, Springer, Berlin, 1957. [3] J. Eichler and W. Meyerhof, Relativistic Atomic Collisions, Academic Press, New York, 1995.
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.
Bai, Si-Yin; Bao, Qian-Qian; Tian, Xue-Dong; Liu, Yi-Mou; Wu, Jin-Hui
2018-04-01
We study the steady optical responses of a cold atomic ensemble driven into the three-level ladder configuration involving a Rydberg state at finite temperatures. By improving the superatom model with thermal movement included, we calculate relevant atomic coherence effects and find that the residual Doppler broadening at the mK-K temperatures will weaken the nonclassical properties of transmitted probe photons. Furthermore, propagation directions of the probe and coupling fields have a great influence on various properties related to electromagnetically induced transparency. That is, the residual Doppler effect is more destructive to relevant atomic coherence effects in the co-propagation case but can be partially eliminated in the counter-propagation case.
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.
Comparative study of dense plasma state equations obtained from different models of average-atom
International Nuclear Information System (INIS)
Fromy, Patrice
1991-01-01
This research thesis addresses the influence of temperature and density effects on magnitudes such as pressure, energy, ionisation, and on energy levels of a body described according to the approximation of an electrically neutral isolated atomic sphere. Starting from the general formalism of the functional density, with some approximations, the author deduces the Thomas-Fermi, Thomas-Fermi-Dirac, and Thomas-Fermi-Dirac-Weizsaecker models, and an average-atom approximated quantum model. For each of these models, the author presents an explicit method of resolution, as well as the determination of different magnitudes taken into account in this study. For the different studied magnitudes, the author highlights effects due to the influence of temperature and of density, as well as variations due to the different models [fr
Berry phase in a two-atom Jaynes-Cummings model with Kerr medium
International Nuclear Information System (INIS)
Bu Shenping; Zhang Guofeng; Liu Jia; Chen Ziyu
2008-01-01
The Jaynes-Cummings model (JCM) is an very important model for describing interaction between quantized electromagnetic fields and atoms in cavity quantum electrodynamics (QED). This model is generalized in many different directions since it predicts many novel quantum effects that can be verified by modern physics experimental technologies. In this paper, the Berry phase and entropy of the ground state for arbitrary photon number n of a two-atom Jaynes-Cummings model with Kerr-like medium are investigated. It is found that there is some correspondence between their images, especially the existence of a curve in the Δ-ε plane along which the energy, Berry phase and entropy all reach their special values. So it is available for detecting entanglement by applying Berry phase.
Berry phase in a two-atom Jaynes-Cummings model with Kerr medium
Energy Technology Data Exchange (ETDEWEB)
Bu Shenping; Zhang Guofeng; Liu Jia; Chen Ziyu [Department of Physics, School of Science, BeiHang University, Xueyuan Road, Beijing 100083 (China)], E-mail: chenzy@buaa.edu.cn
2008-12-15
The Jaynes-Cummings model (JCM) is an very important model for describing interaction between quantized electromagnetic fields and atoms in cavity quantum electrodynamics (QED). This model is generalized in many different directions since it predicts many novel quantum effects that can be verified by modern physics experimental technologies. In this paper, the Berry phase and entropy of the ground state for arbitrary photon number n of a two-atom Jaynes-Cummings model with Kerr-like medium are investigated. It is found that there is some correspondence between their images, especially the existence of a curve in the {delta}-{epsilon} plane along which the energy, Berry phase and entropy all reach their special values. So it is available for detecting entanglement by applying Berry phase.
The entanglement between two isolated atoms in the double mode–mode competition model
International Nuclear Information System (INIS)
Qin, Wu; Mao-Fa, Fang; Yao-Hua, Hu; Jian-Wu, Cai
2009-01-01
Extending the double Jaynes–Cummings model to a more complicated case where the mode–mode competition is considered, we investigate the entanglement character of two isolated atoms by means of concurrence, and discuss the dependence of atom–atom entanglement on the different initial state and the relative coupling strength between the atom and the corresponding cavity field. The results show that the amplitude and the period of the atom–atom entanglement evolution can be controlled by the choice of initial state and relative coupling strength, respectively. We find that the phenomenon of entanglement sudden death (ESD) is sensitive to the initial conditions. The length of the time interval for zero entanglement depends not only on the initial degree of entanglement between two atoms but also on the relative coupling strength of atom–field interaction. The ESD effect can be weakened by enhancing the mode–mode competition between the three- and single-photon processes. (classical areas of phenomenology)
International Nuclear Information System (INIS)
Rojas T, J.; Instituto Peruano de Energia Nuclear, Lima; Manrique C, E.; Torres T, E.
2002-01-01
Using monte Carlo simulation have been carried out an atomistic description of the structure and ordering processes in the system Cu-Au in a two-dimensional model. The ABV model of the alloy is a system of N atoms A and B, located in rigid lattice with some vacant sites. In the model we assume pair wise interactions between nearest neighbors with constant ordering energy J = 0,03 eV. The dynamics was introduced by means of a vacancy that exchanges of place with any atom of its neighbors. The simulations were carried out in a square lattice with 1024 and 4096 particles, using periodic boundary conditions to avoid border effects. We calculate the first two parameters of short range order of Warren-Cowley as function of the concentration and temperature. It was also studied the probabilities of formation of different atomic clusters that consist of 9 atoms as function of the concentration of the alloy and temperatures in a wide range of values. In some regions of temperature and concentration it was observed compositional and thermal polymorphism
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.
Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco
2015-09-28
An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.
Dynamic Modeling for the Design and Cyclic Operation of an Atomic Layer Deposition (ALD) Reactor
Travis, Curtisha; Adomaitis, Raymond
2013-01-01
A laboratory-scale atomic layer deposition (ALD) reactor system model is derived for alumina deposition using trimethylaluminum and water as precursors. Model components describing the precursor thermophysical properties, reactor-scale gas-phase dynamics and surface reaction kinetics derived from absolute reaction rate theory are integrated to simulate the complete reactor system. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm ...
Study of the sputtered Cu atoms and Cu+ ions in a hollow cathode glow discharge using a hybrid model
International Nuclear Information System (INIS)
Baguer, N.; Bogaerts, A.
2005-01-01
The role of the Cu atoms sputtered from the cathode material in a cylindrical hollow cathode discharge (HCD) and the corresponding Cu + ions are studied with a self-consistent model based on the principle of Monte Carlo (MC) and fluid simulations. In order to obtain a more realistic view of the discharge processes, this model is coupled with other submodels, which describe the behavior of electrons, fast Ar atoms, Ar + ions, and Ar metastable atoms, also based on the principles of MC and fluid simulations. Typical results are, among others, the thermalization profile of the Cu atoms, the fast Cu atom, the thermal Cu atom and Cu + ion fluxes and densities, and the energy distribution of the Cu + ions. It was found that the contribution of the Ar + ions to the sputtering was the most significant, followed by the fast Ar atoms. At the cathode bottom, there was no net sputtered flux but a net amount of redeposition. Throughout the discharge volume, at all the conditions investigated, the largest concentration of Cu atoms was found in the lower half of the HCD, close to the bottom. Penning ionization was found the main ionization mechanism for the Cu atoms. The ionization degree of copper atoms was found to be in the same order as for the argon atoms (10 -4 )
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.
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
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.
International Nuclear Information System (INIS)
Murakami, I.; Sakaue, H.A.; Suzuki, C.; Kato, D.; Goto, M.; Tamura, N.; Sudo, S.; Morita, S.
2014-10-01
Quantitative tungsten study with reliable atomic modeling is important for successful achievement of ITER and fusion reactors. We have developed tungsten atomic modeling for understanding the tungsten behavior in fusion plasmas. The modeling is applied to the analysis of tungsten spectra observed from currentless plasmas of the Large Helical Device (LHD) with tungsten pellet injection. We found that extreme ultraviolet (EUV) lines of W 24+ to W 33+ ions are very sensitive to electron temperature (Te) and useful to examine the tungsten behavior in edge plasmas. Based on the first quantitative analysis of measured spatial profile of W 44+ ion, the tungsten concentration is determined to be n(W 44+ )/n e = 1.4x10 -4 and the total radiation loss is estimated as ∼4 MW, of which the value is roughly half the total NBI power. (author)
A model for the stabilization of atomic hydrogen centers in borate glasses
International Nuclear Information System (INIS)
Pontuschka, W.M.; Isotani, S.; Furtado, W.W.; Piccini, A.; Rabbani, S.R.
1989-04-01
A model describing the trapping site of the interstitial atomic hydrogen (H sup(0) sub(i) in borate glasses x-irradiated at 77 K is proposed. The hydrogen atom is stabilized at the centers of oxygen polygons belonging to B-O ring structures in the glass network by van der Waals forces. The previously reported H sup(0) sub(i) isothermal decay experimental data are discussed in the light of this microscopic model. A coupled differential equation system describing the possible reactions was numerically solved by means of Runge-Kutta's method. The parameter best fit was found by trial and error. The untrapping parameter provided an activation energy of 0.7 x 10 sup(-19) J, in good agreement with the calculated results for dispersion interactions between the stabilized atomic hydrogen and the neighbouring oxygen atoms at the vertices of hexagonal and heptagonal structures. The retrapping and recombination parameters were found to be correlated to (T sup1/2) - T sup(1/2) sub(0)) where t sub(0)=179 K is a cutoff temperature for the kinetics process. (author)
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.
Klocke, Michael; Wolf, Dietrich E
2016-01-01
A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.
A computer code for calculations in the algebraic collective model of the atomic nucleus
Welsh, T. A.; Rowe, D. J.
2014-01-01
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1,1) x SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functi...
Alternatives to the BEIR relative risk model for explaining atomic-bomb survivor cancer mortality
International Nuclear Information System (INIS)
Cohen, B.L.
1987-01-01
The apparent failure of the BEIR absolute risk model to explain the data on the Japanese atomic-bomb survivors does not imply that the BEIR relative risk model (RRM) is correct. RRM is objectionable in that it fits the data only in conjunction with an assumption not in accord with current knowledge and thinking. Contrary to what is widely believed, RRM is not a consequence of, or consistent with, initiator-promoter theories; models derived from initiator-promoter theories fit the data with fewer adjustable parameters and without requiring unpalatable assumptions. The preferable models give substantially lower radiation risks
A phenomenological model of the growth of two-species atomic Bose-Einstein condensates
International Nuclear Information System (INIS)
Pattinson, R W; Parker, N G; Proukakis, N P
2014-01-01
We introduce a phenomenological mean-field model to describe the growth of immiscible two-species atomic Bose-Einstein condensates towards some equilibrium. Our model is based on the coupled Gross-Pitaevskii equations with the addition of dissipative terms to account for growth. While our model may be applied generally, we take a recent Rb-Cs experiment [McCarron et al., Phys. Rev. A 84 011603(R) (2011)] as a case study. As the condensates grow, they can pass through ranging transient density structures which can be distinct from the equilibrium states, although such a model always predicts the predominance of one condensate species over longer evolution times.
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.
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
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.
Xu, Dong; Zhang, Yang
2011-01-01
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. PMID:22098752
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.
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).
Long-range interactions and the sign of natural amplitudes in two-electron systems
Giesbertz, K.J.H.; Van Leeuwen, R.
In singlet two-electron systems, the natural occupation numbers of the one-particle reduced density matrix are given as squares of the natural amplitudes which are defined as the expansion coefficients of the two-electron wave function in a natural orbital basis. In this work, we relate the sign of
Stimulated transitions in resonant atom Majorana mixing
Bernabéu, José; Segarra, Alejandro
2018-02-01
Massive neutrinos demand to ask whether they are Dirac or Majorana particles. Majorana neutrinos are an irrefutable proof of physics beyond the Standard Model. Neutrinoless double electron capture is not a process but a virtual Δ L = 2 mixing between a parent A Z atom and a daughter A ( Z - 2) excited atom with two electron holes. As a mixing between two neutral atoms and the observable signal in terms of emitted two-hole X-rays, the strategy, experimental signature and background are different from neutrinoless double beta decay. The mixing is resonantly enhanced for almost degeneracy and, under these conditions, there is no irreducible background from the standard two-neutrino channel. We reconstruct the natural time history of a nominally stable parent atom since its production either by nature or in the laboratory. After the time periods of atom oscillations and the decay of the short-lived daughter atom, at observable times the relevant "stationary" states are the mixed metastable long-lived state and the non-orthogonal short-lived excited state, as well as the ground state of the daughter atom. We find that they have a natural population inversion which is most appropriate for exploiting the bosonic nature of the observed atomic transitions radiation. Among different observables of the atom Majorana mixing, we include the enhanced rate of stimulated X-ray emission from the long-lived metastable state by a high-intensity X-ray beam: a gain factor of 100 can be envisaged at current XFEL facilities. On the other hand, the historical population of the daughter atom ground state can be probed by exciting it with a current pulsed optical laser, showing the characteristic absorption lines: the whole population can be excited in a shorter time than typical pulse duration.
International Nuclear Information System (INIS)
Auger, P.; Pareige, P.; Akamatsu, M.; Van Duysen, J.C.
1993-01-01
In order to characterize the microstructural evolution of iron solid solution under irradiation, two pressure vessel steels irradiated in service conditions, and, for comparison, low copper model alloys irradiated with neutrons and electrons, have been studied through small angle neutron scattering and atom probe experiments. In Fe-Cu model alloys, copper clusters are formed containing uncertain proportions of iron. In the low copper industrial steels, the feature is more complex; solute atoms such as Ni, Mn and Si, sometimes associated with Cu, segregate as ''clouds'' more or less condensed in the iron solid solution. These silicides, or at least Si, Ni, Mn association, may facilitate the copper segregation although the initial iron matrix contains a low copper concentration. (authors). 24 refs., 3 figs., 2 tabs
Characterization of atom clusters in irradiated pressure vessel steels and model alloys
International Nuclear Information System (INIS)
Auger, P.; Pareige, P.; Akamatsu, M.; Van Duysen, J.C.
1993-12-01
In order to characterize the microstructural evolution of the iron solid solution under irradiation, two pressure vessel steels irradiated in service conditions and, for comparison, low copper model alloys irradiated with neutrons and electrons have been studied. The characterization has been carried out mainly thanks to small angle neutron scattering and atom probe experiments. Both techniques lead to the conclusion that clusters develop with irradiations. In Fe-Cu model alloys, copper clusters are formed containing uncertain proportions of iron. In the low copper industrial steels, the feature is more complex. Solute atoms like Ni, Mn and Si, sometimes associated with Cu, segregate as ''clouds'' more or less condensed in the iron solid solution. These silicides, or at least Si, Ni, Mn association, may facilitate the copper segregation although the initial iron matrix contains a low copper concentration. (authors). 24 refs., 3 figs., 2 tabs
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...
Bakowies, Dirk
2009-04-01
A theoretical composite approach, termed ATOMIC for Ab initio Thermochemistry using Optimal-balance Models with Isodesmic Corrections, is introduced for the calculation of molecular atomization energies and enthalpies of formation. Care is taken to achieve optimal balance in accuracy and cost between the various components contributing to high-level estimates of the fully correlated energy at the infinite-basis-set limit. To this end, the energy at the coupled-cluster level of theory including single, double, and quasiperturbational triple excitations is decomposed into Hartree-Fock, low-order correlation (MP2, CCSD), and connected-triples contributions and into valence-shell and core contributions. Statistical analyses for 73 representative neutral closed-shell molecules containing hydrogen and at least three first-row atoms (CNOF) are used to devise basis-set and extrapolation requirements for each of the eight components to maintain a given level of accuracy. Pople's concept of bond-separation reactions is implemented in an ab initio framework, providing for a complete set of high-level precomputed isodesmic corrections which can be used for any molecule for which a valence structure can be drawn. Use of these corrections is shown to lower basis-set requirements dramatically for each of the eight components of the composite model. A hierarchy of three levels is suggested for isodesmically corrected composite models which reproduce atomization energies at the reference level of theory to within 0.1 kcal/mol (A), 0.3 kcal/mol (B), and 1 kcal/mol (C). Large-scale statistical analysis shows that corrections beyond the CCSD(T) reference level of theory, including coupled-cluster theory with fully relaxed connected triple and quadruple excitations, first-order relativistic and diagonal Born-Oppenheimer corrections can normally be dealt with using a greatly simplified model that assumes thermoneutral bond-separation reactions and that reduces the estimate of these
A model to predict image formation in Atom probeTomography
International Nuclear Information System (INIS)
Vurpillot, F.; Gaillard, A.; Da Costa, G.; Deconihout, B.
2013-01-01
A model devoted to the modelling of the field evaporation of a tip is presented in this paper. The influence of length scales from the atomic scale to the macroscopic scale is taken into account in this approach. The evolution of the tip shape is modelled at the atomic scale in a three dimensional geometry with cylindrical symmetry. The projection law of ions is determined using a realistic representation of the tip geometry including the presence of electrodes in the surrounding area of the specimen. This realistic modelling gives a direct access to the voltage required to field evaporate, to the evolving magnification in the microscope and to the understanding of reconstruction artefacts when the presence of phases with different evaporation fields and/or different dielectric permittivity constants are modelled. This model has been applied to understand the field evaporation behaviour in bulk dielectric materials. In particular the role of the residual conductivity of dielectric materials is addressed. - Highlights: ► Modelling tool for the evaporation of a tip under field evaporation. ► Model applied to understand the field evaporation behaviour in bulk dielectric materials. ► Residual conductivity is shown to be of great influence
International Nuclear Information System (INIS)
Errea, L.F.; Mendez, L.; Riera, A.
1991-01-01
To offset the defective behavior of the molecular method of atomic collisions at intermediate energies, we propose a method to approximate the probability flux towards continuum and discrete states not included in the molecular basis. We check the degree of accuracy and limitations of the method for a model case where transition probabilities can be calculated exactly. An application to the benchmark case of He + +H + collisions is also presented, and yields complementary information on the properties of this approach
Modeling inelastic phonon scattering in atomic- and molecular-wire junctions
DEFF Research Database (Denmark)
Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads
2005-01-01
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....
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
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.
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...... 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. © 2013 Wiley Periodicals, Inc....
An improved model of fission gas atom transport in irradiated uranium dioxide
Shea, J. H.
2018-04-01
The hitherto standard approach to predicting fission gas release has been a pure diffusion gas atom transport model based upon Fick's law. An additional mechanism has subsequently been identified from experimental data at high burnup and has been summarised in an empirical model that is considered to embody a so-called fuel matrix 'saturation' phenomenon whereby the fuel matrix has become saturated with fission gas so that the continued addition of extra fission gas atoms results in their expulsion from the fuel matrix into the fuel rod plenum. The present paper proposes a different approach by constructing an enhanced fission gas transport law consisting of two components: 1) Fick's law and 2) a so-called drift term. The new transport law can be shown to be effectively identical in its predictions to the 'saturation' approach and is more readily physically justifiable. The method introduces a generalisation of the standard diffusion equation which is dubbed the Drift Diffusion Equation. According to the magnitude of a dimensionless Péclet number, P, the new equation can vary from pure diffusion to pure drift, which latter represents a collective motion of the fission gas atoms through the fuel matrix at a translational velocity. Comparison is made between the saturation and enhanced transport approaches. Because of its dependence on P, the Drift Diffusion Equation is shown to be more effective at managing the transition from one type of limiting transport phenomenon to the other. Thus it can adapt appropriately according to the reactor operation.
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...
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.
Incorporation of defects into the central atoms model of a metallic glass
International Nuclear Information System (INIS)
Lass, Eric A.; Zhu Aiwu; Shiflet, G.J.; Joseph Poon, S.
2011-01-01
The central atoms model (CAM) of a metallic glass is extended to incorporate thermodynamically stable defects, similar to vacancies in a crystalline solid, within the amorphous structure. A bond deficiency (BD), which is the proposed defect present in all metallic glasses, is introduced into the CAM equations. Like vacancies in a crystalline solid, BDs are thermodynamically stable entities because of the increase in entropy associated with their creation, and there is an equilibrium concentration present in the glassy phase. When applied to Cu-Zr and Ni-Zr binary metallic glasses, the concentration of thermally induced BDs surrounding Zr atoms reaches a relatively constant value at the glass transition temperature, regardless of composition within a given glass system. Using this 'critical' defect concentration, the predicted temperatures at which the glass transition is expected to occur are in good agreement with the experimentally determined glass transition temperatures for both alloy systems.
Stauffer, D; Dragneva, N; Floriano, W B; Mawhinney, R C; Fanchini, G; French, S; Rubel, O
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.
Testing the validity of the International Atomic Energy Agency (IAEA) safety culture model.
López de Castro, Borja; Gracia, Francisco J; Peiró, José M; Pietrantoni, Luca; Hernández, Ana
2013-11-01
This paper takes the first steps to empirically validate the widely used model of safety culture of the International Atomic Energy Agency (IAEA), composed of five dimensions, further specified by 37 attributes. To do so, three independent and complementary studies are presented. First, 290 students serve to collect evidence about the face validity of the model. Second, 48 experts in organizational behavior judge its content validity. And third, 468 workers in a Spanish nuclear power plant help to reveal how closely the theoretical five-dimensional model can be replicated. Our findings suggest that several attributes of the model may not be related to their corresponding dimensions. According to our results, a one-dimensional structure fits the data better than the five dimensions proposed by the IAEA. Moreover, the IAEA model, as it stands, seems to have rather moderate content validity and low face validity. Practical implications for researchers and practitioners are included. Copyright © 2013 Elsevier Ltd. All rights reserved.
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.
Dynamics and post-collision interaction effects in two electron decay from the Xenon 4d hole.
Lablanquie, P; Sheinerman, S; Penent, F; Hall, R I; Ahmad, M; Hikosaka, Y; Ito, K
2001-07-30
Two Auger electrons, one very slow, one fast, have been detected in coincidence following near threshold 4d photoionization of the Xe atom. The distribution in the energy the two electrons share has been measured for the first time revealing the presence of post-collision interaction effects that provide unique information on the decay dynamics of the 4d hole. Analysis of the distorted line shapes indicates that the dominant process is decay of Xe+(4d(-1)) to Xe3+ through cascade emission of a zero kinetic energy Auger electron followed by a fast Auger electron. The widths of the intermediate Xe2+* states are estimated to be about 60 meV.
The A Theory Of Magnitude (ATOM) model in temporal perception and reproduction tasks.
Fabbri, Marco; Cancellieri, Jennifer; Natale, Vincenzo
2012-01-01
According to the A Theory of Magnitude (ATOM) model, time, numbers and space are processed by a common analog magnitude system. The model proposes that time, numbers and space are influenced by each other. Indeed, spatial-temporal (STEARC effect), spatial-numerical (SNARC effect) and temporal-numerical (TiNARC effect) interactions have been observed. However, the processing of time, numbers and space has not yet been studied within the same experimental procedure. The goal of this study is to test the ATOM model using a procedure in which time, numbers and space are all present. The participants were asked to perform temporal estimation (Experiment 1) and reproduction (Experiment 2) tasks in two different conditions, with either numbers or letters as stimuli. In Experiment 1, significant STEARC, SNARC and TiNARC effects were found in general and when numbers were presented. Moreover, a significant triple interaction between space, time and magnitude was observed, indicating associations between the left key, short duration and small magnitudes, as well as between the right key, long duration and large magnitudes. These results were similar in reaction times and accuracy. In Experiment 2, the results of reproduction times mirrored the previous data but the triple interaction was not found on reproduction times. Considering the temporal accuracy, the STEARC, SNARC and TiNARC effects as well as triple interaction were found. The results seem to partially confirm the ATOM model, even if differences between temporal tasks should be posited. Copyright © 2011 Elsevier B.V. All rights reserved.
Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.
Ni, Boris; Baumketner, Andrij
2013-02-14
Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.
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.
Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.
Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi
2015-03-17
Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.
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
International Nuclear Information System (INIS)
Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; Fraser, James S.; Adams, Paul D.
2015-01-01
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.
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.
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...
Realistic Gamow shell model for resonance and continuum in atomic nuclei
Xu, F. R.; Sun, Z. H.; Wu, Q.; Hu, B. S.; Dai, S. J.
2018-02-01
The Gamow shell model can describe resonance and continuum for atomic nuclei. The model is established in the complex-moment (complex-k) plane of the Berggren coordinates in which bound, resonant and continuum states are treated on equal footing self-consistently. In the present work, the realistic nuclear force, CD Bonn, has been used. We have developed the full \\hat{Q}-box folded-diagram method to derive the realistic effective interaction in the model space which is nondegenerate and contains resonance and continuum channels. The CD-Bonn potential is renormalized using the V low-k method. With choosing 16O as the inert core, we have applied the Gamow shell model to oxygen isotopes.
Rolland, N; Larson, D J; Geiser, B P; Duguay, S; Vurpillot, F; Blavette, D
2015-12-01
An analytical model describing the field evaporation dynamics of a tip made of a thin layer deposited on a substrate is presented in this paper. The difference in evaporation field between the materials is taken into account in this approach in which the tip shape is modeled at a mesoscopic scale. It was found that the non-existence of sharp edge on the surface is a sufficient condition to derive the morphological evolution during successive evaporation of the layers. This modeling gives an instantaneous and smooth analytical representation of the surface that shows good agreement with finite difference simulations results, and a specific regime of evaporation was highlighted when the substrate is a low evaporation field phase. In addition, the model makes it possible to calculate theoretically the tip analyzed volume, potentially opening up new horizons for atom probe tomographic reconstruction. Copyright © 2015 Elsevier B.V. All rights reserved.
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.
Caffau, E.; Ludwig, H.-G.; Steffen, M.; Ayres, T. R.; Bonifacio, P.; Cayrel, R.; Freytag, B.; Plez, B.
2008-09-01
Context: The solar oxygen abundance has undergone a major downward revision in the past decade, the most noticeable one being the update including 3D hydrodynamical simulations to model the solar photosphere. Up to now, such an analysis has only been carried out by one group using one radiation-hydrodynamics code. Aims: We investigate the photospheric oxygen abundance considering lines from atomic transitions. We also consider the relationship between the solar model used and the resulting solar oxygen abundance, to understand whether the downward abundance revision is specifically related to 3D hydrodynamical effects. Methods: We performed a new determination of the solar photospheric oxygen abundance by analysing different high-resolution high signal-to-noise ratio atlases of the solar flux and disc-centre intensity, making use of the latest generation of CO5BOLD 3D solar model atmospheres. Results: We find 8.73 ≤ log (N_O/N_H) +12 ≤ 8.79. The lower and upper values represent extreme assumptions on the role of collisional excitation and ionisation by neutral hydrogen for the NLTE level populations of neutral oxygen. The error of our analysis is ± (0.04± 0.03) dex, the last being related to NLTE corrections, the first error to any other effect. The 3D “granulation effects” do not play a decisive role in lowering the oxygen abundance. Conclusions: Our recommended value is log (N_O/N_H) = 8.76 ± 0.07, considering our present ignorance of the role of collisions with hydrogen atoms on the NLTE level populations of oxygen. The reasons for lower O abundances in the past are identified as (1) the lower equivalent widths adopted and (2) the choice of neglecting collisions with hydrogen atoms in the statistical equilibrium calculations for oxygen. This paper is dedicated to the memory of Hartmut Holweger.
Antropov, A. S.; Fidanyan, K. S.; Stegailov, V. V.
2018-01-01
An accurate computation of the vibrational properties of a crystal lattice, such as phonon density of states and dispersion curves, is necessary for the description of thermodynamic properties of the solid state as well as defect migration rates. In this work, we use a simple embedded atom model classical interatomic potential. The phonon density of states for the α and γ phases of uranium at different temperatures was calculated by three methods: the lattice dynamics approach, the Fourier transformation of the velocity autocorrelation function and the Green’s function method for lattice dynamics.
Final technical report for DE-SC00012633 AToM (Advanced Tokamak Modeling)
Energy Technology Data Exchange (ETDEWEB)
Holland, Christopher [Univ. of California, San Diego, CA (United States); Orlov, Dmitri [Univ. of California, San Diego, CA (United States); Izzo, Valerie [Univ. of California, San Diego, CA (United States)
2018-02-05
This final report for the AToM project documents contributions from University of California, San Diego researchers over the period of 9/1/2014 – 8/31/2017. The primary focus of these efforts was on performing validation studies of core tokamak transport models using the OMFIT framework, including development of OMFIT workflow scripts. Additional work was performed to develop tools for use of the nonlinear magnetohydrodynamics code NIMROD in OMFIT, and its use in the study of runaway electron dynamics in tokamak disruptions.
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.
Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge
2015-07-21
In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.
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.
Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2013-09-13
Recently, the possibility of quantum simulation of dynamical gauge fields was pointed out by using a system of cold atoms trapped on each link in an optical lattice. However, to implement exact local gauge invariance, fine-tuning the interaction parameters among atoms is necessary. In the present Letter, we study the effect of violation of the U(1) local gauge invariance by relaxing the fine-tuning of the parameters and showing that a wide variety of cold atoms is still a faithful quantum simulator for a U(1) gauge-Higgs model containing a Higgs field sitting on sites. The clarification of the dynamics of this gauge-Higgs model sheds some light upon various unsolved problems, including the inflation process of the early Universe. We study the phase structure of this model by Monte Carlo simulation and also discuss the atomic characteristics of the Higgs phase in each simulator.
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
Quantum electron-acoustic double layers in two electron species quantum plasma
Sah, Om Prakash
2009-01-01
The existence and the characteristic properties of electron-acoustic double layers are investigated in three component unmagnetized dense quantum plasmas consisting of stationary background ions and two electron populations: one "cold" and the other "hot." Using the one-dimensional quantum hydrodynamic model and the reductive perturbation technique, a generalized form of nonlinear quantum Korteweg-de Vries equation governing the dynamics of weak electron acoustic double layers is derived. A stationary solution of this equation is obtained to discuss the existence criteria of different types of double layers and their characteristic properties. It is shown that two types of compressive double layers: one in the lower δ-parameter region and the other at the higher δ-parameter region, along with rarefactive double layers in the intermediate region, may exist, where δ =nec0/neh0 is the ratio of unperturbed cold to hot electron densities. The width, the amplitude, and the velocity of these double layers are significantly affected by the δ-parameter. The relevance of the present investigation is also discussed.
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.
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.
Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji
2016-12-13
Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.
Atomic model for the membrane-embedded VOmotor of a eukaryotic V-ATPase.
Mazhab-Jafari, Mohammad T; Rohou, Alexis; Schmidt, Carla; Bueler, Stephanie A; Benlekbir, Samir; Robinson, Carol V; Rubinstein, John L
2016-11-03
Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V 1 region drives proton translocation through the membrane-embedded V O region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V 1 and V O regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the V O complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits ac 8 c'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.
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
Rényi Entropies from Random Quenches in Atomic Hubbard and Spin Models.
Elben, A; Vermersch, B; Dalmonte, M; Cirac, J I; Zoller, P
2018-02-02
We present a scheme for measuring Rényi entropies in generic atomic Hubbard and spin models using single copies of a quantum state and for partitions in arbitrary spatial dimensions. Our approach is based on the generation of random unitaries from random quenches, implemented using engineered time-dependent disorder potentials, and standard projective measurements, as realized by quantum gas microscopes. By analyzing the properties of the generated unitaries and the role of statistical errors, with respect to the size of the partition, we show that the protocol can be realized in existing quantum simulators and used to measure, for instance, area law scaling of entanglement in two-dimensional spin models or the entanglement growth in many-body localized systems.
Optical and atomic stochastic resonances in the driven dissipative Jaynes-Cummings model
Qiu, Qingyang; Tao, Shengdan; Liu, Cunjin; Guan, Shengguo; Xie, Min; Fan, Bixuan
2017-12-01
In this paper, we study the stochastic resonance (SR) effect in a driven dissipative Jaynes-Cummings model. The SR effect is systematically investigated in the semiclassical and full quantum frameworks, and in both cases we find that SRs simultaneously occur for optical and atomic degrees of freedom. In particular, at zero temperature, quantum SR can be induced merely by vacuum fluctuations. Although the qualitative features of semiclassical SR and quantum SR are similar, their mechanisms are completely different: semiclassical SR is induced by thermal activation while quantum SR is induced by quantum-tunneling-assisted transitions. Our results provide a theoretical basis for experimentally observing and studying the SR phenomenon of the Jaynes-Cummings model in the quantum regime.
Rényi Entropies from Random Quenches in Atomic Hubbard and Spin Models
Elben, A.; Vermersch, B.; Dalmonte, M.; Cirac, J. I.; Zoller, P.
2018-02-01
We present a scheme for measuring Rényi entropies in generic atomic Hubbard and spin models using single copies of a quantum state and for partitions in arbitrary spatial dimensions. Our approach is based on the generation of random unitaries from random quenches, implemented using engineered time-dependent disorder potentials, and standard projective measurements, as realized by quantum gas microscopes. By analyzing the properties of the generated unitaries and the role of statistical errors, with respect to the size of the partition, we show that the protocol can be realized in existing quantum simulators and used to measure, for instance, area law scaling of entanglement in two-dimensional spin models or the entanglement growth in many-body localized systems.
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.
An atomic model of the tropomyosin cable on F-actin.
Orzechowski, Marek; Li, Xiaochuan Edward; Fischer, Stefan; Lehman, William
2014-08-05
Tropomyosin regulates a wide variety of actin filament functions and is best known for the role that it plays together with troponin in controlling muscle activity. For effective performance on actin filaments, adjacent 42-nm-long tropomyosin molecules are joined together by a 9- to 10-residue head-to-tail overlapping domain to form a continuous cable that wraps around the F-actin helix. Yet, despite the apparent simplicity of tropomyosin's coiled-coil structure and its well-known periodic association with successive actin subunits along F-actin, the structure of the tropomyosin cable on actin is uncertain. This is because the conformation of the overlap region that joins neighboring molecules is poorly understood, thus leaving a significant gap in our understanding of thin-filament structure and regulation. However, recent molecular-dynamics simulations of overlap segments defined their overall shape and provided unique and sufficient cues to model the whole actin-tropomyosin filament assembly in atomic detail. In this study, we show that these MD structures merge seamlessly onto the ends of tropomyosin coiled-coils. Adjacent tropomyosin molecules can then be joined together to provide a comprehensive model of the tropomyosin cable running continuously on F-actin. The resulting complete model presented here describes for the first time (to our knowledge) an atomic-level structure of αα-striated muscle tropomyosin bound to an actin filament that includes the critical overlap domain. Thus, the model provides a structural correlate to evaluate thin-filament mechanics, self-assembly mechanisms, and the effect of disease-causing mutations. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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…
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.
International Nuclear Information System (INIS)
Braams, B.J.
2012-03-01
The Joint ICTP-IAEA Workshop on Fusion Plasma Modelling using Atomic and Molecular Data was held from 23-27 January 2012 at Abdus Salam International Centre for Theoretical Physics in Trieste, Italy. Ten lecturers presented tutorials and reviews on topics in fusion plasma modelling and atomic, molecular and plasma-material interaction processes. There were 20 participants, generally early-career researchers in the area of A+M+PMI processes and also plasma modellers. The participants presented their work in short talks and a poster session. The proceedings of the workshop are summarized here. (author)
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…
Deformed model Sp(4) model for studying pairing correlations in atomic nuclei
Georgieva, A I; Sviratcheva, K
2002-01-01
A fermion representation of the compact symplectic sp(4) algebra introduces a theoretical framework for describing pairing correlations in atomic nuclei. The important non-deformed and deformed subalgebras of sp sub ( sub q sub ) (4) and the corresponding reduction chains are explored for the multiple orbit problem. One realization of the u sub ( sub q sub ) (2) subalgebra is associated with the valence isospin, other reductions describe coupling between identical nucleons or proton-neutron pairs. Microscopic non-deformed and deformed Hamiltonians are expressed in terms of the generators of the sp(4) and sp sub q (4) algebras. In both cases eigenvalues of the isospin breaking Hamiltonian are fit to experimental ground state energies. The theory can be used to investigate the origin of the deformation and predict binding energies of nuclei in proton-rich regions. The q-deformation parameter changes the pairing strength and in so doing introduces a non-linear coupling into the collective degree of freedom
An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.
Schur, Florian K M; Obr, Martin; Hagen, Wim J H; Wan, William; Jakobi, Arjen J; Kirkpatrick, Joanna M; Sachse, Carsten; Kräusslich, Hans-Georg; Briggs, John A G
2016-07-29
Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1. Copyright © 2016, American Association for the Advancement of Science.
Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA.
Fojan, Peter; Gurevich, Leonid
2017-01-01
The cell membrane is the first barrier and quite often the primary target that antimicrobial peptides (AMPs) have to destroy or penetrate to fulfill their mission. Upon penetrating through the membrane, the peptides can further attack intracellular targets, in particular DNA. Studying the interaction of an antimicrobial peptide with a cell membrane and DNA holds keys to understanding its killing mechanisms. Commonly, these interactions are studied by using optical or scanning electron microscopy and appropriately labeled peptides. However, labeling can significantly affect the hydrophobicity, conformation, and size of the peptide, hence altering the interaction significantly. Here, we describe the use of atomic force microscopy (AFM) for a label-free study of the interactions of peptides with model membranes under physiological conditions and DNA as a possible intracellular target.
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.
The Challenge of Teaching Blind Students Atomic Models and the Process of Teacher Education
Directory of Open Access Journals (Sweden)
Renata Cardoso de Sá Ribeiro Razuck
2014-04-01
Full Text Available Based on the National Special Education in the Perspective of Inclusive Education (2008, students with special educational needs have to be included in the regular schools. Specifically blind students, because of their specific characteristics, they need necessary resources and suitable materials that can provide overcoming the lack of visualization. In this context, chemistry has a great visual appeal and provides a huge challenge for the acquisition of its concepts by the blinds. In order to try to fill some gaps in Chemistry contents with great visual appeal, this paper proposes a discussion on the importance of applying alternative pedagogical resources that enable visually impaired to understand and construct this imaginary science, working to this with prototypes of atomic models. This work is intended not only to contribute to the teaching-learning process, but also for the training of undergraduate courses to work towards inclusion.
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...
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 ......, the model predicts the effect of process parameters on the size distribution, temperature, velocity histories, fraction-solid and cooling rate for all droplet sizes characterizing the complete droplet size distribution....
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.
Two-electron Oxidation of a Twisted Non Anti-aromatic 40π ...
Indian Academy of Sciences (India)
Abstract. Expanded isophlorins are typical examples for stable anti-aromatic systems. Paratropic ring cur- rent effects are observed in their NMR spectra mainly due to their planar conformation. Herein we report the synthesis of the first twisted 40π expanded isophlorin and also its two-electron oxidation to a 38π dication.
Two-electron Oxidation of a Twisted Non Anti-aromatic 40π ...
Indian Academy of Sciences (India)
PRACHI GUPTA, SANTOSH P PANCHAL and VENKATARAMANARAO G ANAND. ∗. Department of Chemistry ... synthesis of the first twisted 40π expanded isophlorin and also its two-electron oxidation to a 38π dication. It sustains the twisted .... Tanaka T, Aratani N, Lim J M, Kim K S, Kim D and. Osuka A 2011 Chem. Sci.
Bridge mediated two-electron transfer reactions: Analysis of stepwise and concerted pathways
International Nuclear Information System (INIS)
Petrov, E.G.; May, V.
2004-01-01
A theory of nonadiabatic donor (D)-acceptor (A) two-electron transfer (TET) mediated by a single regular bridge (B) is developed. The presence of different intermediate two-electron states connecting the reactant state D -- BA with the product state DBA -- results in complex multiexponential kinetics. The conditions are discussed at which a reduction to two-exponential as well as single-exponential kinetics becomes possible. For the latter case the rate K TET is calculated, which describes the bridge-mediated reaction as an effective two-electron D-A transfer. In the limit of small populations of the intermediate TET states D - B - A, DB -- A, D - BA - , and DB - A - , K TET is obtained as a sum of the rates K TET (step) and K TET (sup) . The first rate describes stepwise TET originated by transitions of a single electron. It starts at D -- BA and reaches DBA -- via the intermediate state D - BA - . These transitions cover contributions from sequential as well as superexchange reactions all including reduced bridge states. In contrast, a specific two-electron superexchange mechanism from D -- BA to DBA -- defines K TET (sup) . An analytic dependence of K TET (step) and K TET (sup) on the number of bridging units is presented and different regimes of D-A TET are studied
International Nuclear Information System (INIS)
Tieleman, D Peter; MacCallum, Justin L; Ash, Walter L; Kandt, Christian; Xu Zhitao; Monticelli, Luca
2006-01-01
We have reparameterized the dihedral parameters in a commonly used united-atom lipid force field so that they can be used with the all-atom OPLS force field for proteins implemented in the molecular dynamics simulation software GROMACS. Simulations with this new combination give stable trajectories and sensible behaviour of both lipids and protein. We have calculated the free energy of transfer of amino acid side chains between water and 'lipid-cyclohexane', made of lipid force field methylene groups, as a hydrophobic mimic of the membrane interior, for both the OPLS-AA and a modified OPLS-AA force field which gives better hydration free energies under simulation conditions close to those preferred for the lipid force field. The average error is 4.3 kJ mol -1 for water-'lipid-cyclohexane' compared to 3.2 kJ mol -1 for OPLS-AA cyclohexane and 2.4 kJ mol -1 for the modified OPLS-AA water-'lipid-cyclohexane'. We have also investigated the effect of different methods to combine parameters between the united-atom lipid force field and the united-atom protein force field ffgmx. In a widely used combination, the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering. Using straight combination rules improves the results. Combined, we suggest that using OPLS-AA together with the united-atom lipid force field implemented in GROMACS is a reasonable approach to membrane protein simulations. We also suggest that using partial volume information and free energies of transfer may help to improve the parameterization of lipid-protein interactions and point out the need for accurate experimental data to validate and improve force field descriptions of such interactions
Analysis of phase transitions in spin-crossover compounds by using atom - phonon coupling model
International Nuclear Information System (INIS)
Gindulescu, A; Linares, J; Rotaru, A; Dimian, M; Nasser, J
2011-01-01
The spin - crossover compounds (SCO) have become of great interest recently due to their potential applications in memories, sensors, switches, and display devices. These materials are particularly interesting because upon application of heat, light, pressure or other physical stimulus, they feature a phase transition between a low-spin (LS) diamagnetic ground state and a high-spin (HS) paramagnetic state, accompanied in some cases by color change. The phase transition can be discontinuous (with hysteresis), in two steps or gradual. Our analysis is performed by using the atom - phonon coupling (APC) model which considers that neighboring molecules are connected through a spring characterized by an elastic constant depending on molecules electronic state. By associating a fictitious spin to each molecule that has -1 and +1 eigenvalues corresponding to LS and HS levels respectively, an Ising type model can be developed for the analysis of metastable states and phase transitions in spin-crossover compounds. This contribution is aimed at providing a review of our recent results in this area, as well as novel aspects related to SCO compounds behavior at low temperature. In the framework of the APC model, we will discuss about the existence of metastable and unstable states, phase transitions and hysteresis phenomena, as well as their dependence on sample size.
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-10-29
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.
Bag-model analyses of proton-antiproton scattering and atomic bound states
International Nuclear Information System (INIS)
Alberg, M.A.; Freedman, R.A.; Henley, E.M.; Hwang, W.P.; Seckel, D.; Wilets, L.
1983-01-01
We study proton-antiproton (pp-bar ) scattering using the static real potential of Bryan and Phillips outside a cutoff radius rsub0 and two different shapes for the imaginary potential inside a radius R*. These forms, motivated by bag models, are a one-gluon-annihilation potential and a simple geometric-overlap form. In both cases there are three adjustable parameters: the effective bag radius R*, the effective strong coupling constant αsubssup*, and rsub0. There is also a choice for the form of the real potential inside the cutoff radius rsub0. Analysis of the pp-bar scattering data in the laboratory-momentum region 0.4--0.7 GeV/c yields an effective nucleon bag radius R* in the range 0.6--1.1 fm, with the best fit obtained for R* = 0.86 fm. Arguments are presented that the deduced value of R* is likely to be an upper bound on the isolated nucleon bag radius. The present results are consistent with the range of bag radii in current bag models. We have also used the resultant optical potential to calculate the shifts and widths of the sup3Ssub1 and sup1Ssub0 atomic bound states of the pp-bar system. For both states we find upward (repulsive) shifts and widths of about 1 keV. We find no evidence for narrow, strongly bound pp-bar states in our potential model
International Nuclear Information System (INIS)
Collins, R.; Perez-Martin, A.M.C.; Dominguez-Vazquez, J.; Jimenez-Rodriguez, J.J.
1994-01-01
A simple model for three-dimensional material relaxation associated with atomic mixing is presented. The relaxation of the solid to accommodate the extra effective displacement volume Ω of an implanted or relocated atom is modelled by treating the surrounding solid as an incompressible medium. This leads to a tractable general formalism which can be used to predict implant distribution and changes in surface topography induced by ion beams, both in monatomic and multicomponent targets. The two-component case is discussed in detail. (orig.)
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.
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.
International Nuclear Information System (INIS)
Colgan, J.; Judge, E.J.; Kilcrease, D.P.; Barefield, J.E.
2014-01-01
We report on efforts to model the Fe emission spectrum generated from laser-induced breakdown spectroscopy (LIBS) measurements on samples of pure iron oxide (Fe 2 O 3 ). Our modeling efforts consist of several components. We begin with ab-initio atomic structure calculations performed by solving the Hartree–Fock equations for the neutral and singly ionized stages of Fe. Our energy levels are then adjusted to their experimentally known values. The atomic transition probabilities and atomic collision quantities are also computed in an ab-initio manner. We perform LTE or non-LTE calculations that generate level populations and, subsequently, an emission spectrum for the iron plasma for a range of electron temperatures and electron densities. Such calculations are then compared to the experimental spectrum. We regard our work as a preliminary modeling effort that ultimately strives towards the modeling of emission spectra from even more complex samples where less atomic data are available. - Highlights: • LIBS plasma of iron oxide • Ab-initio theoretical Modeling • Discussion of LTE versus non-LTE criteria and assessment • Boltzmann plots for Fe—determination of when LTE is a valid assumption • Emission spectra for Fe—comparison of theoretical modeling and measurement: good agreement obtained
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.
Elementary particles. Modern physics from the atoms to the standard model
International Nuclear Information System (INIS)
Bleck-Neuhaus, Joern
2010-01-01
The actual state of knowledge of nuclear and elementary-particle physics has a fluctuating history of origin, often characterized by shockingly new formations of terms, which until today are for studyings of physics often only under difficulties accessible. This books uses the controverse and at the same time instructive development processes themselves for the access to the difficult new concepts. It makes understandable, how the physical picture of the smallest particles looks today und why it has arised so and not otherwise: From the detection of the existence of the atoms up to the present standard model of elementary-particle physics, in a steady exchange between established theoretical models, confirming and contradicting experimental findings, sometimes controversial new formations of terms, improved experiments etc. - a process, which certainly continues in the future. Guidance of the presentation is an also in the detail reproducible argumentation. Studyings of physics before their B.Sc. examination will get knowledges about subatomar physics, which belong to the genralknowledge of their field. Also for teachings of physics at schools or universities this new presentation might be interesting. [de
Cui, Jian; Zhao, Xue-Hong; Wang, Yan; Xiao, Ya-Bing; Jiang, Xue-Hui; Dai, Li
2014-01-01
Flow injection-hydride generation-atomic fluorescence spectrometry was a widely used method in the industries of health, environmental, geological and metallurgical fields for the merit of high sensitivity, wide measurement range and fast analytical speed. However, optimization of this method was too difficult as there exist so many parameters affecting the sensitivity and broadening. Generally, the optimal conditions were sought through several experiments. The present paper proposed a mathematical model between the parameters and sensitivity/broadening coefficients using the law of conservation of mass according to the characteristics of hydride chemical reaction and the composition of the system, which was proved to be accurate as comparing the theoretical simulation and experimental results through the test of arsanilic acid standard solution. Finally, this paper has put a relation map between the parameters and sensitivity/broadening coefficients, and summarized that GLS volume, carrier solution flow rate and sample loop volume were the most factors affecting sensitivity and broadening coefficients. Optimizing these three factors with this relation map, the relative sensitivity was advanced by 2.9 times and relative broadening was reduced by 0.76 times. This model can provide a theoretical guidance for the optimization of the experimental conditions.
Electron spectroscopy of collisional excited atoms
International Nuclear Information System (INIS)
Straten, P. van der.
1987-01-01
In this thesis measurements are described in which coincidences are detected between scattered projectiles and emitted electrons. This yields information on two-electron excitation processes. In order to show what can be learnt from coincidence experiments a detailed theoretical analysis is given. The transition amplitudes, which contain all the information, are introduced (ch.2). In ch.3 the experimental set-up is shown. The results for the Li + -He system are shown in ch. 7 and are compared with predictions based on the Molecular-Orbitalmodel which however does not account for two-excitation mechanisms. With the transition amplitudes also the wave function of the excited atom has been completely determined. In ch.8 the shape of the electron cloud, induced by the collision, is derived from the amplitudes. The relation between the oscillatory motion of this cloud after the collision and the correlation between the two electrons of the excited atom is discussed. In ch. 6 it is shown that the broad structures in the non-coincident energy spectra of the Li + -He system are erroneously interpretated as a result of electron emission from the (Li-He) + -quasimolecule. A model is presented which explains, based on the results obtained from the coincidence measurements, these broad structures. In ch. 4 the Post-Collision Interaction process is treated. It is shown that for high-energy collisions, in contrast with general assumptions, PCI is important. In ch. 5 the importance of PCI-processes in photoionization of atoms, followed by Auger decay, are studied. From the formulas derived in ch. 4 simple analytical results are obtained. These are applied to recent experiments and good agreement is achieved. 140 refs.; 55 figs.; 9 tabs
Energy Technology Data Exchange (ETDEWEB)
Cleaves, Peter A.; King, David M.; McMaster, Jonathan; Lewis, William; Blake, Alexander J.; Liddle, Stephen T. [Nottingham Univ. (United Kingdom). School of Chemistry; Kefalidis, Christos E.; Maron, Laurent [Paul Sabatier Univ., Toulouse (France). LPCNO, CNRS et INSA; Tuna, Floriana; McInnes, Eric J.L. [Manchester Univ. (United Kingdom). School of Chemistry
2014-09-22
Two-electron reductive carbonylation of the uranium(VI) nitride [U(Tren{sup TIPS})(N)] (2, Tren{sup TIPS}=N(CH{sub 2}CH{sub 2}NSiiPr{sub 3}){sub 3}) with CO gave the uranium(IV) cyanate [U(Tren{sup TIPS})(NCO)] (3). KC{sub 8} reduction of 3 resulted in cyanate dissociation to give [U(Tren{sup TIPS})] (4) and KNCO, or cyanate retention in [U(Tren{sup TIPS})(NCO)][K(B15C5){sub 2}] (5, B15C5=benzo-15-crown-5 ether) with B15C5. Complexes 5 and 4 and KNCO were also prepared from CO and the uranium(V) nitride [{U(Tren"T"I"P"S)(N)K}{sub 2}] (6), with or without B15C5, respectively. Complex 5 can be prepared directly from CO and [U(Tren{sup TIPS})(N)][K(B15C5){sub 2}] (7). Notably, 7 reacts with CO much faster than 2. This unprecedented f-block reactivity was modeled theoretically, revealing nucleophilic attack of the π* orbital of CO by the nitride with activation energy barriers of 24.7 and 11.3 kcal mol{sup -1} for uranium(VI) and uranium(V), respectively. A remarkably simple two-step, two-electron cycle for the conversion of azide to nitride to cyanate using 4, NaN{sub 3} and CO is presented.
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.
International Nuclear Information System (INIS)
Yang Tianxing; Ye Xiang; Huang Lei; Xie Yiqun; Ke Sanhuang
2012-01-01
Highlights: ► We simulate the reversible vertical single-atom manipulations on several metal surfaces. ► We propose a method to predict whether a reversible vertical single-atom manipulation can be successful on several metal surfaces. ► A 3-dimensional Ni nanocluster is assembled on the Ni(1 1 1) surface using a Ni trimer-apex tip. - Abstract: We propose a theoretical model to show that pulling up an adatom from an atomic step requires a weaker force than from the flat surfaces of Al(0 0 1), Ni(1 1 1), Pt(1 1 0) and Au(1 1 0). Single adatom in the atomic step can be extracted vertically by a trimer-apex tip while can be released to the flat surface. This reversible vertical manipulation can then be used to fabricate a supported three-dimensional (3D) nanostructure on the Ni(1 1 1) surface. The present modeling can be used to predict whether the reversible vertical single-atom manipulation and thus the assembling of 3D nanostructures can be achieved on a metal surface.
Surface structure of polymers and their model compounds observed by atomic force microscopy
Stocker, W.; Bickmann, B.; Magonov, S.N.; Cantow, H.J.; Lotz, B.; Wittmann, J.C.; Moller, M.; Möller, M.
1992-01-01
Results of atomic force microscopy (AFM) of normal alkanes, polyethylene, isotactic polypropylene and of a diblock copolymer are presented. Various types of surfaces - naturally and epitaxially grown on different substrates - have been examined from hundreds of nanometers down to the atomic scale.
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...
A model for the interaction between F centers and H atoms in ionic crystals
International Nuclear Information System (INIS)
Dumke, V.R.; Souza, M. de
1975-01-01
The interaction between an F center and neutral hydrogen atoms, the most simple paramagnetic defects in ionic crystals, is described in terms of a perturbation theory of two square potential wells. The good agreement with experimental data indicates that lattice distortion due to the presence of the hydrogen atoms is negligible [pt
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.
Space-group approach to two-electron states in unconventional superconductors
International Nuclear Information System (INIS)
Yarzhemsky, V. G.
2008-01-01
The direct application of the space-group representation theory, makes possible to obtain limitations for the symmetry of SOP on lines and planes of symmetry in one-electron Brillouin zone. In the case of highly symmetric UPt 3 only theoretical nodal structure of IR E 2u is in agreement with all the experimental results. On the other hand, in the case of high-T c superconductors the two electron description of Cooper pairs in D 2h symmetry is not sufficient to describe experimental nodal structure. It was shown that in this case, the nodal structure is the result of underlying interactions between two-electron states and hidden symmetry D-4 h . (author)
Two-electron electrochemical oxidation of quercetin and kaempferol changes only the flavonoid C-ring
DEFF Research Database (Denmark)
Jørgensen, Lars; Cornett, Claus; Justesen, Ulla
1998-01-01
Bulk electrolysis of the antioxidant flavonoids quercetin and kaempferol in acetonitrile both yield a single oxidation product in two-electron processes. The oxidation products are more polar than their parent compounds, with an increased molecular weight of 16g/mol, and were identified as 2......-(3,4-dihydroxybenzoyl)-2,4,6-trihydroxy-3 (2H)-benzofuranone and 2-(4-hydroxybenzoyl)-2,4,6-trihydroxy-3(2H)-benzofuranone for quercetin and kaempferol, respectively. Two-electron oxidation of the parent flavonoid is suggested to yield a 3,4-flavandione with unchanged substitution pattern in the A- and B-ring, which...... (lacking the 3-OH group) could be isolated despite rather similar half-peak potentials: E-p/2 = 0.97 V, 0.98 V and 1.17 V vs. NHE for quercetin, kaempferol and luteolin, respectively, as measured by cyclic voltammetry in acetonitrile....
Energy Technology Data Exchange (ETDEWEB)
Zhang, Peng; Yuly, Jonathon L.; Lubner, Carolyn E. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Mulder, David W. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; King, Paul W. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Peters, John W. [Institute; Beratan, David N. [Department
2017-08-23
How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation.
Mixed-precision evaluation of two-electron integrals by Rys quadrature
Asadchev, Andrey; Gordon, Mark S.
2012-08-01
A mixed precision implementation of two-electron integrals is demonstrated to have two benefits: (a) computations can be performed reliably in 32-bit precision on architectures for which 32-bit precision is significantly faster than 64-bit precision (e.g. graphical processing units), and (b) numerical results that match those using higher than 64-bit precision can be recovered without a significant penalty associated with performing the entire computation in higher precision. A justification is presented for using mixed precision in the Rys two-electron integral quadrature algorithm, together with timings and numerical results using a variety of floating-point types. The code discussed here presents a systematic way to control the accuracy of the Rys algorithm, regardless of the types and numbers of integrals.
Dynamical localization of two electrons in triple-quantum-dot shuttles
International Nuclear Information System (INIS)
Qu, Jinxian; Duan, Suqing; Yang, Ning
2012-01-01
The dynamical localization phenomena in two-electron quantum-dot shuttles driven by an ac field have been investigated and analyzed by the Floquet theory. The dynamical localization occurs near the anti-crossings in Floquet eigenenergy spectrum. The oscillation of the quantum-dot shuttles may increase the possibility of the dynamical localization. Especially, even if the two electrons are initialized in two neighbor dots, they can be localized there for appropriate intensity of the driven field. The studies may help the understanding of dynamical localization in electron shuttles and expand the application potential of nanoelectromechanical devices. -- Highlights: ► The dynamical localization in electron shuttle is studied by Floquet theory. ► There is a relation between quasi-energy anti-crossings and dynamical localization. ► The oscillation of quantum dot increases the dynamical localization. ► Even the electrons are initialized in different dots, the localization can occur.
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…
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…
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…
Farina, William J., Jr.; Bodzin, Alec M.
2018-01-01
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…
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…
Steffy, S. V.; Ghosh, S. S.
2018-01-01
The emergence of the compressive ion acoustic double layer has been investigated for a two electron temperature warm, multi-ion plasma by the Sagdeev pseudopotential technique. It shows that the ambient cooler electron concentration plays a deterministic role in initiating the transition process of a compressive ion acoustic solitary wave to its double layer. Incorporating the derivative analysis for the pseudopotential, the transitional phase was further quantified by assigning a critical value for the ambient cooler electron concentration. It has been observed that, beyond that critical value, the width of the solitary wave increases rapidly with the increasing amplitude which coincides with the aforementioned transitional phase, manifesting a change in the internal microphysics of the structure for that region. A comparison with the satellite observation revealed good agreement validating the present model. The model will be useful in interpreting the observed monopolar structures in the auroral acceleration region.
DePrince, A. Eugene; Mazziotti, David A.
2010-01-01
The parametric variational two-electron reduced-density-matrix (2-RDM) method is applied to computing electronic correlation energies of medium-to-large molecular systems by exploiting the spatial locality of electron correlation within the framework of the cluster-in-molecule (CIM) approximation [S. Li et al., J. Comput. Chem. 23, 238 (2002); J. Chem. Phys. 125, 074109 (2006)]. The 2-RDMs of individual molecular fragments within a molecule are determined, and selected portions of these 2-RDMs are recombined to yield an accurate approximation to the correlation energy of the entire molecule. In addition to extending CIM to the parametric 2-RDM method, we (i) suggest a more systematic selection of atomic-orbital domains than that presented in previous CIM studies and (ii) generalize the CIM method for open-shell quantum systems. The resulting method is tested with a series of polyacetylene molecules, water clusters, and diazobenzene derivatives in minimal and nonminimal basis sets. Calculations show that the computational cost of the method scales linearly with system size. We also compute hydrogen-abstraction energies for a series of hydroxyurea derivatives. Abstraction of hydrogen from hydroxyurea is thought to be a key step in its treatment of sickle cell anemia; the design of hydroxyurea derivatives that oxidize more rapidly is one approach to devising more effective treatments.
Gillen, D R; Goelich,
2002-01-01
Non-resonant multiphoton ionisation combined with quadrupole and time-of-flight analysis has been used to measure energy distributions of sputtered copper atoms. The sputtering of a polycrystalline copper target by 3.6 keV Ar sup + , N sup + and CF sub 2 sup + and 1.8 keV N sup + and CF sub 2 sup + ion bombardment at 45 deg. has been investigated. The linear collision model in the isotropic limit fails to describe the high energy tail of the energy distributions. However the TRIM.SP computer simulation has been shown to provide a good description. The results indicate that an accurate description of sputtering by low energy, molecular ions requires the use of computer simulation rather than analytical approaches. This is particularly important when considering plasma-surface interactions in plasma etching and deposition systems.
Evidence for Single Metal Two Electron Oxidative Addition and Reductive Elimination at Uranium
Gardner, Benedict M; Kefalidis, Christos E; Lu, Erli; Patel, Dipti; Mcinnes, Eric; Tuna, Floriana; Wooles, Ashley; Maron, Laurent; Liddle, Stephen
2017-01-01
Reversible single-metal two-electron oxidative addition and reductive elimination are common fundamental reactions for transition metals that underpin major catalytic transformations. However, these reactions have never been observed together in the f-block because these metals exhibit irreversible one- or multi-electron oxidation or reduction reactions. Here, we report that azobenzene oxidises sterically and electronically unsaturated uranium(III) complexes to afford a uranium(V)-imido compl...
Spectral measurements of a 2D cyclotron-resonance maser array with two electron beams
Lei, Li; Jerby, Eli
1997-10-01
The cyclotron resonance maser (CRM) array was proposed recently by our group as a compact high-power microwave source operating at low-voltages. In this paper, we present a CRM array experiment with two electron beams, in a 2D array periodic-waveguide. Spectral measurements are displayed for fast- and slow-wave interactions. This two- beam experiment leads to the construction of a multi-beam CRM array at Tel Aviv University.
Modeling and simulation of the atomization process in the ceramic tile industry
International Nuclear Information System (INIS)
Favalli, Renata Cristina
2002-01-01
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 given by
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
Energy Technology Data Exchange (ETDEWEB)
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
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.
A Hartree–Fock study of the confined helium atom: Local and global basis set approaches
Energy Technology Data Exchange (ETDEWEB)
Young, Toby D., E-mail: tyoung@ippt.pan.pl [Zakład Metod Komputerowych, Instytut Podstawowych Prolemów Techniki Polskiej Akademia Nauk, ul. Pawińskiego 5b, 02-106 Warszawa (Poland); Vargas, Rubicelia [Universidad Autónoma Metropolitana Iztapalapa, División de Ciencias Básicas e Ingenierías, Departamento de Química, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, D.F. C.P. 09340, México (Mexico); Garza, Jorge, E-mail: jgo@xanum.uam.mx [Universidad Autónoma Metropolitana Iztapalapa, División de Ciencias Básicas e Ingenierías, Departamento de Química, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, D.F. C.P. 09340, México (Mexico)
2016-02-15
Two different basis set methods are used to calculate atomic energy within Hartree–Fock theory. The first is a local basis set approach using high-order real-space finite elements and the second is a global basis set approach using modified Slater-type orbitals. These two approaches are applied to the confined helium atom and are compared by calculating one- and two-electron contributions to the total energy. As a measure of the quality of the electron density, the cusp condition is analyzed. - Highlights: • Two different basis set methods for atomic Hartree–Fock theory. • Galerkin finite element method and modified Slater-type orbitals. • Confined atom model (helium) under small-to-extreme confinement radii. • Detailed analysis of the electron wave-function and the cusp condition.
Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A
2016-06-24
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.
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.
Phase transitions in an Ising model for monolayers of coadsorbed atoms
International Nuclear Information System (INIS)
Lee, H.H.; Landau, D.P.
1979-01-01
A Monte Carlo method is used to study a simple S=1 Ising (lattice-gas) model appropriate for monolayers composed of two kinds of atoms on cubic metal substrates H = K/sub nn/ Σ/sub nn/ S 2 /sub i/zS 2 /sub j/z + J/sub nnn/ Σ/sub nnn/ S/sub i/zS/sub j/z + Δ Σ/sub i/ S 2 /sub i/z (where nn denotes nearest-neighbor and nnn next-nearest-neighbor pairs). The phase diagram is determined over a wide range of Δ and T for K/sub nn//J/sub nnn/=1/4. For small (or negative) Δ we find an antiferromagnetic 2 x 1 ordered phase separated from the disordered state by a line of second-order phase transitions. The 2 x 1 phase is separated by a line of first-order transitions from a c (2 x 2) phase which appears for larger Δ. The 2 x 1 and c (2 x 2) phases become simultaneously critical at a bicritical point and the phase boundary of the c (2 x 2) → disordered transition shows a tricritical point
Atomic Scale Modeling of Laser Shock induced Spallation of FCC Metals
Galitskiy, Sergey; Ivanov, Dmitry; Dongare, Avinash
2017-06-01
An atomistic-continuum approach combining the molecular dynamics (MD) simulations with a two temperature model (TTM) was used to simulate the laser induced shock loading and spall failure in FCC metals. The combined TTM-MD approach incorporates the laser energy absorption, fast electron heat conduction, and the electron-phonon non-equilibrium interaction, as well as the shock wave propagation, plastic deformation, and failure processes (spallation) in metals at atomic scales. The simulations are carried out for systems corresponding to dimensions of up to 500 nm in the loading direction for various Cu and Al microstructures and laser loading conditions (intensity and pulse durations). The front end of the metal that absorbs the laser energy is observed to undergo melting and a shock wave is generated that travels towards the rear surface. The shock wave reaches the rear surface, reflects, and interacts with the its tail to create a high triaxial tensile stress region and initiates spall failure (void nucleation). The predicted values of spall strength and wave velocities of shock waves compare very well with experimentally reported values at these dimensions and laser loading conditions. The effect of microstructure and the defect evolution in the system on the predicted spall failure behavior will be presented.
Snyder, Aaron; Banks, Bruce; Miller, Sharon; Stueber, Thomas; Sechkar, Edward
2001-01-01
A numerical procedure is presented to calculate transmittance degradation caused by contaminant films on spacecraft surfaces produced through the interaction of orbital atomic oxygen (AO) with volatile silicones and hydrocarbons from spacecraft components. In the model, contaminant accretion is dependent on the adsorption of species, depletion reactions due to gas-surface collisions, desorption, and surface reactions between AO and silicone producing SiO(x), (where x is near 2). A detailed description of the procedure used to calculate the constituents of the contaminant layer is presented, including the equations that govern the evolution of fractional coverage by specie type. As an illustrative example of film growth, calculation results using a prototype code that calculates the evolution of surface coverage by specie type is presented and discussed. An example of the transmittance degradation caused by surface interaction of AO with deposited contaminant is presented for the case of exponentially decaying contaminant flux. These examples are performed using hypothetical values for the process parameters.
Viewing dynamic interactions of proteins and a model lipid membrane with atomic force microscopy.
Quinn, Anthony S; Rand, Jacob H; Wu, Xiao-Xuan; Taatjes, Douglas J
2013-01-01
The information covered in this chapter will present a model homogenous membrane preparation technique and dynamic imaging procedure that can be successfully applied to more than one type of lipid study and atomic force microscope (AFM) instrument setup. The basic procedural steps have been used with an Asylum Research MFP-3D BIO and the Bruker (formerly, Veeco) BioScope. The AFM imaging protocol has been supplemented by procedures (not to be presented in this chapter) of ellipsometry, standardized western blotting, and dot-blots to verify appropriate purity and activity of all experimental molecular components; excellent purity and activity level of the lipids, proteins, and drug(s) greatly influence the success of imaging experiments in the scanning probe microscopy field. The major goal of the chapter is to provide detailed procedures for sample preparation and operation of the Asylum Research MFP-3D BIO AFM. In addition, one should be cognizant that our comprehensive description in the use of the MFP-3D BIO's functions for successful image acquisitions and analyses is greatly enhanced by Asylum Research's (AR's) accompanying extensive manual(s), technical notes, and AR's users forum. Ultimately, the stepwise protocol and information will allow novice personnel to begin acquiring quality images for processing and analysis with minimal supervision.
Optimized Model Surfaces for Advanced Atomic Force Microscopy Studies of Surface Nanobubbles.
Song, Bo; Zhou, Yi; Schönherr, Holger
2016-11-01
The formation of self-assembled monolayers (SAMs) of binary mixtures of 16-mercaptohexadecanoic acid (MHDA) and 1-octadecanethiol (ODT) on ultraflat template-stripped gold (TSG) surfaces was systematically investigated to clarify the assembly behavior, composition, and degree of possible phase segregation in light of atomic force microscopy (AFM) studies of surface nanobubbles on these substrates. The data for SAMs on TSG were compared to those obtained by adsorption on rough evaporated gold, as reported in a previous study. Quartz crystal microbalance and surface plasmon resonance data acquired in situ on TSG indicate that similar to SAM formation on conventional evaporated gold substrates ODT and MHDA form monolayers and bilayers, respectively. The second layer on MHDA, whose formation is attributed to hydrogen bonding, can be easily removed by adequate rinsing with water. The favorable agreement of the grazing incidence reflection Fourier transform infrared (GIR FTIR) spectroscopy and contact angle data analyzed with the Israelachvili-Gee model suggests that the binary SAMs do not segregate laterally. This conclusion is fully validated by high-resolution friction force AFM observations down to a length scale of 8-10 nm, which is much smaller than the typical observed surface nanobubble radii. Finally, correspondingly functionalized TSG substrates are shown to be valuable supports for studying surface nanobubbles by AFM in water and for addressing the relation between surface functionality and nanobubble formation and properties.
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.
International Nuclear Information System (INIS)
Mueller, A.; Wickart, M.; Van Nieuwkoop, R.
2001-01-01
This article is a short version of the ENET number 210359. This report for the Swiss Federal Office of Energy (SFOE) presents the results of a study made to assess the economic consequences of two models for the opting out of nuclear energy in Switzerland, as proposed in two popular initiatives. The 'Strom ohne Atom' (electricity without atomic power) initiative calls for the shutting down of the existing nuclear power stations and the 'Moratorium Plus' initiative calls for a stop on the building of new atomic power stations for 10 years. The method used for assessing the costs and benefits resulting if the initiatives were accepted in a public vote is described. Basic assumptions made on further factors concerning the electricity and energy markets are discussed. Results of analyses made for various scenarios with respect to CO 2 emissions are presented and include discussions on risk costs, effects on employment and welfare aspects
de Léséleuc, Sylvain; Weber, Sebastian; Lienhard, Vincent; Barredo, Daniel; Büchler, Hans Peter; Lahaye, Thierry; Browaeys, Antoine
2018-03-01
We study a system of atoms that are laser driven to n D3 /2 Rydberg states and assess how accurately they can be mapped onto spin-1 /2 particles for the quantum simulation of anisotropic Ising magnets. Using nonperturbative calculations of the pair potentials between two atoms in the presence of electric and magnetic fields, we emphasize the importance of a careful selection of experimental parameters in order to maintain the Rydberg blockade and avoid excitation of unwanted Rydberg states. We benchmark these theoretical observations against experiments using two atoms. Finally, we show that in these conditions, the experimental dynamics observed after a quench is in good agreement with numerical simulations of spin-1 /2 Ising models in systems with up to 49 spins, for which numerical simulations become intractable.
A phenomenological model for collisional coherence transfer in an optically pumped atomic system
Energy Technology Data Exchange (ETDEWEB)
Khanbekyan, K; Bevilaqua, G; Mariotti, E; Moi, L [Universita degli Studi di Siena, Siena, 53100 (Italy); Khanbekyan, A; Papoyan, A, E-mail: karen.khanbekyan@gmail.com [Institute for Physical Research, National Academy of Sciences, Ashtarak 2 (Armenia)
2011-03-14
We consider a dual {Lambda}-system under double laser excitation to investigate the possibility of indirect coherence transfer between atomic ground states through an excited state. The atomic system is excited by a frequency modulated pump laser and probed by a low-power cw laser. All the decoherence mechanisms are discussed and taken into account. Adjustment of parameters of the two radiations aimed at maximization of coherence transfer is addressed. The study can help to understand the phenomena as collisional transfer of coherence and can find application in the experimental realization of atomic sensors.
First observation of two-electron one-photon transitions in single-photon K-shell double ionization.
Hoszowska, J; Dousse, J-Cl; Szlachetko, J; Kayser, Y; Cao, W; Jagodziński, P; Kavčič, M; Nowak, S H
2011-07-29
Experimental evidence for the correlated two-electron one-photon transitions (1s(-2)→2s(-1)2p(-1)) following single-photon K-shell double ionization is reported. The double K-shell vacancy states in solid Mg, Al, and Si were produced by means of monochromatized synchrotron radiation, and the two-electron one-photon radiative transitions were observed by using a wavelength dispersive spectrometer. The two-electron one-photon transition energies and the branching ratios of the radiative one-electron to two-electron transitions were determined and compared to available perturbation theory predictions and configuration interaction calculations.
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.
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......Presents the solution of a special scattering problem which may be important in the theory of slowing-down of atomic particles in crystals. A projectile moves along the centre axis of a regular ring of n equal atoms which are free and do not interact with each other. The interaction between...... the asymptotic velocities of the ring atoms as well as the energy loss of the projectile. Furthermore, it can be decided whether the projectile is reflected by the ring. Both the feasibility of assumptions specifying the problem and the validity of different approximations made in the transformation from...
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
2014-05-01
We report on numerical simulations of a zincblende InP surface quantum dot (QD) on \\text{I}{{\\text{n}}_{0.48}}\\text{G}{{\\text{a}}_{0.52}}\\text{P} buffer. Our model is strictly based on experimental structures, since we extrapolated a three-dimensional dot directly by atomic force microscopy results. Continuum electromechanical, \\vec{k}\\;\\cdot \\;\\vec{p} 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 \\vec{k}\\;\\cdot \\;\\vec{p} 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
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
An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.
Förster, Friedrich; Lasker, Keren; Beck, Florian; Nickell, Stephan; Sali, Andrej; Baumeister, Wolfgang
2009-10-16
The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) is in excellent agreement with the recently identified base-precursor complexes formed during the assembly of the RP. Furthermore, the atomic CP-AAA-ATPase model suggests that the assembly chaperone Nas6 facilitates CP-RP association by enhancing the shape complementarity between Rpt3 and its binding CP alpha subunits partners.
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.
Pan, Jianjun; Khadka, Nawal K
2016-05-26
Quantitative characterization of membrane defects (pores) is important for elucidating the molecular basis of many membrane-active peptides. We study kinetic defects induced by melittin in vesicular and planar lipid bilayers. Fluorescence spectroscopy measurements indicate that melittin induces time-dependent calcein leakage. Solution atomic force microscopy (AFM) is used to visualize melittin-induced membrane defects. After initial equilibration, the most probable defect radius is ∼3.8 nm in 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) bilayers. Unexpectedly, defects become larger with longer incubation, accompanied by substantial shape transformation. The initial defect radius is ∼4.7 nm in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. Addition of 30 mol % cholesterol to DOPC bilayers suppresses defect kinetics, although the inhibitory impact is negated by longer incubation. Overall, the kinetic rate of defect development follows DLPC > DOPC > DOPC/cholesterol. Kinetic defects are also observed when anionic lipids are present. Based on the observation that defects can occupy as large as 40% of the bilayer surface, we propose a kinetic defect growth model. We also study the effect of melittin on the phase behavior of DOPC/egg-sphingomyelin/cholesterol bilayers. We find that melittin initially suppresses or eliminates liquid-ordered (Lo) domains; Lo domains gradually emerge and become the dominant species with longer incubation; and defects in phase-coexisting bilayers have a most probable radius of ∼5 nm and are exclusively localized in the liquid-disordered (Ld) phase. Our experimental data highlight that melittin-induced membrane defects are not static; conversely, spontaneous defect growth is intrinsically associated with membrane permeabilization exerted by melittin.
Anisotropic atomic packing model for abnormal grain growth mechanism of WC-25 wt.% Co alloy
International Nuclear Information System (INIS)
Ryoo, H.S.; Hwang, S.K.
1998-01-01
During liquid phase sintering, cemented carbide particles grow into either faceted or non-faceted grain shapes depending on ally system. In case of WC-Co alloy, prism-shape faceted grains with (0001) planes and {1 bar 100} planes on each face are observed, and furthermore an abnormal grain growth has been reported to occur. When abnormal grain growth occurs in WC crystals, dimension ratio, R, of the length of the side of the triangular prism face to the height of the prism is higher than 4 whereas that for normal grains is approximately 2. Abnormal grain growth in this alloy is accelerated by the fineness of starting powders and by high sintering temperature. To account for the mechanism of the abnormal grain growth, there are two proposed models which drew much research attention: nucleation and subsequent carburization and transformation of η (W 3 Co 3 C) phase into WC, and coalescence of coarse WC grains through dissolution and re-precipitation. Park et al. proposed a two-dimensional nucleation theory to explain the abnormal grain growth of faceted grains. There are questions, however, on the role of η phase on abnormal grain growth. The mechanism of coalescence of spherical grains as proposed by Kingery is also unsuitable for faceted grains. So far theories on abnormal grain growth do not provide a satisfactory explanation on the change of R value during the growth process. In the present work a new mechanism of nucleation and growth of faceted WC grains is proposed on the ground of anisotropic packing sequence of each atom
Two-electron double quantum dot coupled to coherent photon and phonon fields
Sato, Yuya; Chen, Jason C. H.; Hashisaka, Masayuki; Muraki, Koji; Fujisawa, Toshimasa
2017-09-01
Two-electron states of a double quantum dot (DQD) under irradiation of coherent boson (photon and phonon) fields are studied by measuring spin-flip tunneling current in the Pauli spin blockade regime. This measurement scheme allows us to investigate Rabi splitting and associated boson dressed states particularly in the deep dispersive regime where the detuning δ ≡ℏ ω -EAB between the boson energy ℏ ω and energy spacing EAB of the two-level system is significantly large (δ ˜ℏ ω ), where the permanent dipole moment in the DQD plays a significant role in the hybridization.
Variational Calculations for a Two-Electron Quantum Dot Interacting with a Magnetic Field
International Nuclear Information System (INIS)
Nader, D. J.; Alvarez-Jiménez, J.; Mejía-Díaz, H.
2017-01-01
The behavior of the two-electron quantum dot interacting with a uniform magnetic field is not fully understood yet. This lack of clarity arises from the fact that the mixed, spherical and cylindrical, coordinates do not allow the system to be separable. In this paper, we applied an standard variational method, with a physical recipe for choosing compact trial functions. In order to solve the six dimensional integrals necessary to compute the expectation value of the Hamiltonian, we used a Monte Carlo routine. The energy values obtained are in agreement with the ones presented in previous literature. (author)
Two-electron states in double quantum dot in direct electric field
International Nuclear Information System (INIS)
Burdov, V.A.
2001-01-01
One determined analytically the wave functions of stationary states and the spectrum of two-electron system in symmetric binary quantum point. It is shown that in the normal state at the absence of external electric field the electrons due to the Coulomb blockade can not be collectively in one quantum point. In the external electric field the situation changes. When a certain critical value of field intensity is reached the probability of detection of both electrons in one quantum point by a jump increases from zero up to 1 [ru
Relaxation and Dephasing in a Two-Electron 13C Nanotube Double Quantum Dot
DEFF Research Database (Denmark)
Churchill, H O H; Kuemmeth, Ferdinand; Harlow, J W
2009-01-01
We use charge sensing of Pauli blockade (including spin and isospin) in a two-electron 13C nanotube double quantum dot to measure relaxation and dephasing times. The relaxation time T1 first decreases with a parallel magnetic field and then goes through a minimum in a field of 1.4 T. We attribute...... both results to the spin-orbit-modified electronic spectrum of carbon nanotubes, which at high field enhances relaxation due to bending-mode phonons. The inhomogeneous dephasing time T2* is consistent with previous data on hyperfine coupling strength in 13C nanotubes....
Critical density for Landau damping in a two-electron-component plasma
Energy Technology Data Exchange (ETDEWEB)
Rupp, Constantin F.; López, Rodrigo A.; Araneda, Jaime A. [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Concepción (Chile)
2015-10-15
The asymptotic evolution of an initial perturbation in a collisionless two-electron-component plasma with different temperatures is studied numerically. The transition between linear and nonlinear damping regimes is determined by slowly varying the density of the secondary electron-component using high-resolution Vlasov-Poisson simulations. It is shown that, for fixed amplitude perturbations, this transition behaves as a critical phenomenon with time scales and field amplitudes exhibiting power-law dependencies on the threshold density, similar to the critical amplitude behavior in a single-component plasma.
International Nuclear Information System (INIS)
Schlegel, H.B.; Binkley, J.S.; Pople, J.A.
1984-01-01
Formulas are developed for the first and second derivatives of two electron integrals over Cartesian Gaussians. Integrals and integral derivatives are evaluated by the Rys polynomial method. Higher angular momentum functions are not used to calculate the integral derivatives; instead the integral formulas are differentiated directly to produce compact and efficient expressions for the integral derivatives. The use of this algorithm in the ab initio molecular orbital programs gaussIan 80 and gaussIan 82 is discussed. Representative timings for some small molecules with several basis sets are presented. This method is compared with previously published algorithms and its computational merits are discussed
Theory of Square-Wave Voltammetry of Two-Electron Reduction with the Adsorption of Intermediate
Directory of Open Access Journals (Sweden)
Milivoj Lovric
2012-01-01
Full Text Available Thermodynamically unstable intermediate of fast and reversible two-electron electrode reaction can be stabilized by the adsorption to the electrode surface. In square-wave voltammetry of this reaction mechanism, the split response may appear if the electrode surface is not completely covered by the adsorbed intermediate. The dependence of the difference between the net peak potentials of the prepeak and postpeak on the square-wave frequency is analyzed theoretically. This relationship can be used for the estimation of adsorption constant.
Energy Technology Data Exchange (ETDEWEB)
McCurdy, C. William [Univ. of California, Davis, CA (United States). Dept. of
2017-12-14
This project made use of Multiconfiguration Time-Dependent Hartree-Fock method developed earlier in the McCurdy group in a series of novel applications of the method to ultrafast spectroscopic processes. MCTDHF treats the dynamics of a molecule or atom under the influence of an external field in manner that has all electrons active. That property distinguishes this method from the more popular (and much less computationally demanding) approaches for treating the electron dynamics of atoms and molecules in fields, such as the time-dependent “Configuration Interaction Singles” approximation or approaches that limit the treatment to either one or two-electron models.
Atomic Fisher information versus atomic number
International Nuclear Information System (INIS)
Nagy, A.; Sen, K.D.
2006-01-01
It is shown that the Thomas-Fermi Fisher information is negative. A slightly more sophisticated model proposed by Gaspar provides a qualitatively correct expression for the Fisher information: Gaspar's Fisher information is proportional to the two-third power of the atomic number. Accurate numerical calculations show an almost linear dependence on the atomic number
Using Balls of Different Sports To Model the Variation of Atomic Sizes
Pinto, Gabriel
1998-06-01
In this article, an analogy is described about the order of magnitude of the variation of atomic sizes that can be used for discussion in introductory chemistry classes. The order of magnitude of this variation, involving microscopic magnitudes, is difficult for students to imagine. For the most part, the students are very familiar with the world of sports. In any case for example, the teacher can make use of the wide, informative coverage given to the olympic games or similar events, where different sports are televised in a few days. The radii of official balls for seven well-known sports are given, and students must assign an atom to each ball by using tabulated single-bond, covalent radii and by assigning the smallest ball (i.e., corresponding to ping-pong) to the smallest atom (i.e., hydrogen). The balls can also be used to show how the ionic radii change upon ionization.
Assessment of ion-atom collision data for magnetic fusion plasma edge modelling
International Nuclear Information System (INIS)
Phaneuf, R.A.
1990-01-01
Cross-section data for ion-atom collision processes which play important roles in the edge plasma of magnetically-confined fusion devices are surveyed and reviewed. The species considered include H, He, Li, Be, C, O, Ne, Al, Si, Ar, Ti, Cr, Fe, Ni, Cu, Mo, W and their ions. The most important ion-atom collision processes occurring in the edge plasma are charge-exchange reactions. Excitation and ionization processes are also considered. The scope is limited to atomic species and to collision velocities corresponding to plasma ion temperatures in the 2-200 eV range. Sources of evaluated or recommended data are presented where possible, and deficiencies in the data base are indicated. 42 refs., 1 fig., 4 tabs
Energy Technology Data Exchange (ETDEWEB)
Cleaves, Peter A.; King, David M.; McMaster, Jonathan; Lewis, William; Blake, Alexander J.; Liddle, Stephen T. [School of Chemistry, University of Nottingham (United Kingdom); Kefalidis, Christos E.; Maron, Laurent [LPCNO, CNRS and INSA, Universite Paul Sabatier, Toulouse (France); Tuna, Floriana; McInnes, Eric J.L. [School of Chemistry and Photon Science Institute, University of Manchester (United Kingdom)
2014-09-22
Two-electron reductive carbonylation of the uranium(VI) nitride [U(Tren{sup TIPS})(N)] (2, Tren{sup TIPS}=N(CH{sub 2}CH{sub 2}NSiiPr{sub 3}){sub 3}) with CO gave the uranium(IV) cyanate [U(Tren{sup TIPS})(NCO)] (3). KC{sub 8} reduction of 3 resulted in cyanate dissociation to give [U(Tren{sup TIPS})] (4) and KNCO, or cyanate retention in [U(Tren{sup TIPS})(NCO)][K(B15C5){sub 2}] (5, B15C5=benzo-15-crown-5 ether) with B15C5. Complexes 5 and 4 and KNCO were also prepared from CO and the uranium(V) nitride [{U(Tren"T"I"P"S)(N)K}{sub 2}] (6), with or without B15C5, respectively. Complex 5 can be prepared directly from CO and [U(Tren{sup TIPS})(N)][K(B15C5){sub 2}] (7). Notably, 7 reacts with CO much faster than 2. This unprecedented f-block reactivity was modeled theoretically, revealing nucleophilic attack of the π* orbital of CO by the nitride with activation energy barriers of 24.7 and 11.3 kcal mol{sup -1} for uranium(VI) and uranium(V), respectively. A remarkably simple two-step, two-electron cycle for the conversion of azide to nitride to cyanate using 4, NaN{sub 3} and CO is presented. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
International Nuclear Information System (INIS)
Luan, P; Knoll, A J; Wang, H; Oehrlein, G S; Kondeti, V S S K; Bruggeman, P J
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% O 2 and 1% air plasma and OH for Ar/1% H 2 O plasma, play an essential role for polymer etching. For O 2 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 O 2 and H 2 O simultaneously into Ar feed gas quenches polymer etching compared to adding them separately which suggests the reduction of O and OH density in Ar/O 2 /H 2 O plasma. (letter)
Santangelo, Paolo E.
2012-12-01
Pressure-swirl atomizers are often employed to generate a water-mist spray, typically employed in fire suppression. In the present study, an experimental characterization of dispersion (velocity and cone angle) and atomization (drop-size axial evolution) was carried out following a previously developed methodology, with specific reference to the initial region of the spray. Laser-based techniques were used to quantitatively evaluate the considered phenomena: velocity field was reconstructed through a Particle Image Velocimetry analysis; drop-size distribution was measured by a Malvern Spraytec device, highlighting secondary atomization and subsequent coalescence along the spray axis. Moreover, a comprehensive set of relations was validated as predictive of the involved parameters, following an inviscid-fluid approach. The proposed model pertains to early studies on pressure-swirl atomizers and primarily yields to determine both initial velocity and cone angle. The spray thickness is also predicted and a classic correlation for Sauter Mean Diameter is shown to provide good agreement with experimental results. The analysis was carried out at the operative pressure of 80 bar; two injectors were employed featuring different orifice diameters and flow numbers, as a sort of parametric approach to this spray typology.
Sattonnay, G; Tétot, R
2014-02-05
Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd2Ti2O7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd2Zr2O7. Therefore, the defect stability in A2B2O7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd2Ti2O7 amorphization induced by irradiation.
Projectile K-Auger-electron production by bare, one-, and two-electron ions
International Nuclear Information System (INIS)
Dillingham, T.R.; Newcomb, J.; Hall, J.; Pepmiller, P.L.; Richard, P.
1984-01-01
Projectile K-Auger-electron production measurements were performed for the bare, one-, and two-electron ions of C, N, O, and F incident on He, Ne, Ar, and Kr gases. The measurements were taken over an energy range of (1/4) to (2/3) MeV/amu using a cylindrical mirror analyzer. For the incident two-electron ions, single-electron capture to excited states of the (1s2s) 3 S metastable component of the incident beam was the principal mechanism giving rise to the observed K-Auger transitions. For the bare and one-electron ions, double electron capture to excited states was the dominant mechanism leading to K-Auger-electron production. In addition to Auger-spectroscopy measurements, total K-Auger production cross sections were determined as well as the partial cross sections for electron capture to specific n levels of the projectile. The n distributions were also measured for double electron capture to excited states of the bare and one-electron ions
Systematics of projectile K-Auger electron production by bare, one, and two electron ions
International Nuclear Information System (INIS)
Dillingham, T.R.
1983-01-01
Projectile K-Auger electron production measurements were performed for the bare, one, and two electron ions of C, N, O, and F incident on He, Ne, Ar, and Kr gases. The measurements were taken over an energy range of 1/4 to 2/3 MeV/amu using a cylindrical mirror analyzer. For the incident two electron ions, single electron capture to excited states of the (1s2s) 3 S metastable component of the incident beam was the principal mechanism giving rise to the observed K-Auger transitions. For the bare and one electron ions, double electron capture to excited states was the dominant mechanism leading to K-Auger electron production. In addition to Auger spectroscopy measurements, total K-Auger production cross sections were determined as well as the partial cross sections for electron capture to specific n-levels of the projectile. The n-distribution for single electron capture was observed to follow a 1/n 3 dependence. The n-distributions were also measured for double electron capture to excited states of the bare and one electron ions
Evidence for single metal two electron oxidative addition and reductive elimination at uranium.
Gardner, Benedict M; Kefalidis, Christos E; Lu, Erli; Patel, Dipti; McInnes, Eric J L; Tuna, Floriana; Wooles, Ashley J; Maron, Laurent; Liddle, Stephen T
2017-12-01
Reversible single-metal two-electron oxidative addition and reductive elimination are common fundamental reactions for transition metals that underpin major catalytic transformations. However, these reactions have never been observed together in the f-block because these metals exhibit irreversible one- or multi-electron oxidation or reduction reactions. Here we report that azobenzene oxidises sterically and electronically unsaturated uranium(III) complexes to afford a uranium(V)-imido complex in a reaction that satisfies all criteria of a single-metal two-electron oxidative addition. Thermolysis of this complex promotes extrusion of azobenzene, where H-/D-isotopic labelling finds no isotopomer cross-over and the non-reactivity of a nitrene-trap suggests that nitrenes are not generated and thus a reductive elimination has occurred. Though not optimally balanced in this case, this work presents evidence that classical d-block redox chemistry can be performed reversibly by f-block metals, and that uranium can thus mimic elementary transition metal reactivity, which may lead to the discovery of new f-block catalysis.
Double-continuum wave functions and double-photoionization cross sections of two-electron systems
International Nuclear Information System (INIS)
Tiwary, S.N.
1996-09-01
The present review briefly presents the growing experimental as well as theoretical interests in recent years in the double-continuum wave functions and double-photoionization cross sections of two-electron systems. The validity of existing double-continuum wave functions is analyzed and the importance of electronic correlations in both the initial as well as final states wave functions involved in the transition amplitude for double-photoionization process is demonstrated. At present, we do not have comprehensive and practical double-continuum wave functions which account the full correlation of two-electron in the continuum. Basic difficulties in making accurate theoretical calculations of double ionization by a single high energy photon especially in the vicinity of the threshold, where the correlation plays an important role, are discussed. Illuminating, illustrative and representative examples are presented in order to show the present status and the progress in this field. Future challenges and directions, in high-precision double-photoionization cross sections calculations, have been discussed and suggested. (author). 133 refs, 9 figs
Numerical and experimental modelling of back stream flow during close-coupled gas atomization
Motaman, S; Mullis, AM; Borman, DJ; Cochrane, RF; McCarthy, IN
2013-01-01
This paper reports the numerical and experimental investigation into the effects of different gas jet mis-match angles (for an external melt nozzle wall) on the back-stream flow in close coupled gas atomization. The Pulse Laser Imaging (PLI) technique was applied for visualising the back-stream melt flow phenomena with an analogue water atomizer and the associated PLI images compared with numerical results. In the investigation a Convergent–Divergent (C–D) discrete gas jet die at five differe...
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...
Babilas, Rafał; Łukowiec, Dariusz; Temleitner, Laszlo
2017-01-01
The structure of a multicomponent metallic glass, Mg 65 Cu 20 Y 10 Ni 5 , was investigated by the combined methods of neutron diffraction (ND), reverse Monte Carlo modeling (RMC) and high-resolution transmission electron microscopy (HRTEM). The RMC method, based on the results of ND measurements, was used to develop a realistic structure model of a quaternary alloy in a glassy state. The calculated model consists of a random packing structure of atoms in which some ordered regions can be indicated. The amorphous structure was also described by peak values of partial pair correlation functions and coordination numbers, which illustrated some types of cluster packing. The N = 9 clusters correspond to the tri-capped trigonal prisms, which are one of Bernal's canonical clusters, and atomic clusters with N = 6 and N = 12 are suitable for octahedral and icosahedral atomic configurations. The nanocrystalline character of the alloy after annealing was also studied by HRTEM. The selected HRTEM images of the nanocrystalline regions were also processed by inverse Fourier transform analysis. The high-angle annular dark-ﬁeld (HAADF) technique was used to determine phase separation in the studied glass after heat treatment. The HAADF mode allows for the observation of randomly distributed, dark contrast regions of about 4-6 nm. The interplanar spacing identified for the orthorhombic Mg 2 Cu crystalline phase is similar to the value of the first coordination shell radius from the short-range order.
Random model of two-level atoms interacting with electromagnetic field
International Nuclear Information System (INIS)
Kireev, A.N.; Meleshko, A.N.
1983-12-01
A phase transition has been studied in a random system of two-level atoms interacting with an electromagnetic field. It is shown that superradiation can arise when there is short-range order in a spin-subsystem. The existence of long-range order is irrelevant for this phase transition
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
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…
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...
Khuseynov, Dmitry; Blackstone, Christopher C; Culberson, Lori M; Sanov, Andrei
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(-) 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.
Martinez, G T; Rosenauer, A; De Backer, A; Verbeeck, J; Van Aert, S
2014-02-01
High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed. © 2013 Published by Elsevier B.V. All rights reserved.
International Nuclear Information System (INIS)
Balykin, V. I.; Jhe, W.
1999-01-01
Atom optics, in analogy to neutron and electron optics, deals with the realization of as a traditional elements, such as lenes, mirrors, beam splitters and atom interferometers, as well as a new 'dissipative' elements such as a slower and a cooler, which have no analogy in an another types of optics. Atom optics made the development of atom interferometer with high sensitivity for measurement of acceleration and rotational possible. The practical interest in atom optics lies in the opportunities to create atom microprobe with atom-size resolution and minimum damage of investigated objects. (Cho, G. S.)
Cieplak, Andrzej Stanisław
2017-01-01
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates' morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer's and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer's amyloid β and tau, Parkinson's α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid
Levashov, V A
2016-03-07
It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.
De Backer, A; van den Bos, K H W; Van den Broek, W; Sijbers, J; Van Aert, S
2016-12-01
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. Copyright © 2016 Elsevier B.V. All rights reserved.
Visible-light-induced two-electron-transfer photoreductions on CdS: Effects of morphology
Energy Technology Data Exchange (ETDEWEB)
Shiragami, Tsutomu; Pac, Chyongjin; Yanagida, Shozo (Osaka Univ. (Japan))
1990-01-25
Freshly prepared CdS suspensions (CdS-O) consisting of quantized particles and their loose aggregation catalyze photoreductions of aromatic ketones and olefins in methanol under visible light irradiation using triethylamine as sacrificial electron donor, yielding alcohols and dihydro compounds, respectively, which are more selective than photocatalysis of commercially available crystalline CdS (Aldrich) (CdS-Ald). Deuterium incorporation experiments in photolysis of dimethyl maleate in methanol-O-D revealed that CdS-O catalyzes sequential two-electron-transfer photoreduction, affording dideuterated dimethyl succinate, while CdS-Ald induces both photoreduction and photoisomerization through disproportionation between one-electron-transfer-reduction intermediates, yielding much trideuterated dimethyl succinate and monodeuterated dimethyl fumarate and maleate.
Zhang, Peng; Yuly, Jonathon L; Lubner, Carolyn E; Mulder, David W; King, Paul W; Peters, John W; Beratan, David N
2017-09-19
How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation. Remarkably, bifurcating electron transfer (ET) proteins typically send one electron uphill and one electron downhill by similar energies, such that the overall reaction is spontaneous, but not profligate. Electron bifurcation in the NADH-dependent reduced ferredoxin: NADP + oxidoreductase I (Nfn) is explored in detail here. Recent experimental progress in understanding the structure and function of Nfn allows us to dissect its workings in the framework of modern ET theory. The first electron that leaves the two-electron donor flavin (L-FAD) executes a positive free energy "uphill" reaction, and the departure of this electron switches on a second thermodynamically spontaneous ET reaction from the flavin along a second pathway that moves electrons in the opposite direction and at a very different potential. The singly reduced ET products formed from the bifurcating flavin are more than two nanometers distant from each other. In Nfn, the second electron to leave the flavin is much more reducing than the first: the potentials are said to be "crossed." The eventually reduced cofactors, NADH and ferredoxin in the case of Nfn, perform crucial downstream redox
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.
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.
Sun, Shoutian; Ramachandran, Bala Ramu; Wick, Collin D
2018-02-21
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.
International Nuclear Information System (INIS)
Paziresh, M.; Kingston, A. M.; Latham, S. J.; Fullagar, W. K.; Myers, G. M.
2016-01-01
Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073–2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127–135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260–1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (
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.
A simple reductionist model for cancer risk in atom bomb survivors
International Nuclear Information System (INIS)
Mendelsohn, M.L.
1995-01-01
1) In data from the atom bomb survivors of Hiroshima and Nagasaki, the roughly linear-quadratic radiation dose responses for chromosome aberration and leukemia correspond closely to each other, as do the linear dose responses for gene mutation and solid cancer incidence. 2) In view of the increasing evidence for multiple oncogene and suppressor gene changes in human cancer, as well as the evidence that human cancer rate is often proportional to age to the power of 6 or so, it is postulated that the radiation has contributed one and only one oncogenic mutational event to the radiation induced cancers. 3) The radiation induced cancers should therefore display a cancer rate versus age relationship that has a power of n-1, where n is the power for the corresponding background cancers. 4) It is shown that this is precisely what is happening in the collective solid cancer incidence of the atom bomb survivors. (author)
International Nuclear Information System (INIS)
Hla, Saw Wai
2014-01-01
Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to ‘see’ individual atoms by means of imaging, but is also a tool that is used to ‘touch’ and ‘take’ the atoms, or to ‘hear’ their movements. Therefore, the STM can be considered as the ‘eyes’, ‘hands’ and ‘ears’ of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed. (review article)
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.
Ab initio and Atomic kinetic Monte Carlo modelling of segregation in concentrated FeCrNi alloys
Piochaud, J. B.; Becquart, C. S.; Domain, C.
2014-06-01
Internal structure of pressurised water reactors are made of austenitic materials. Under irradiation, the microstructure of these concentrated alloys evolves and solute segregation on grain boundaries or irradiation defects such as dislocation loops are observed to take place. In order to model and predict the microstructure evolution, a multiscale modelling approach needs to be developed, which starts at the atomic scale. Atomic Kinetic Monte Carlo (AKMC) modelling is the method we chose to provide an insight on defect mediated diffusion under irradiation. In that approach, we model the concentrated commercial steel as a FeCrNi alloy (γ-Fe70Cr20Ni10). As no reliable empirical potential exists at the moment to reproduce faithfully the phase diagram and the interactions of the elements and point defects, we have adjusted a pair interaction model on large amount of DFT calculations. The point defect properties in the Fe70Cr20Ni10, and more precisely, how their formation energy depends on the local environment will be presented and some AKMC results on thermal non equilibrium segregation and radiation induce segregation will be presented. The effect of Si on the segregation will also be discussed.
Ab initio and atomic kinetic Monte Carlo modelling of segregation in concentrated FeCrNi alloys
International Nuclear Information System (INIS)
Piochaud, J.B.; Becquart, C.S.; Domain, C.
2013-01-01
Internal structure of pressurised water reactors are made of austenitic materials. Under irradiation, the microstructure of these concentrated alloys evolves and solute segregation on grain boundaries or irradiation defects such as dislocation loops are observed to take place. In order to model and predict the microstructure evolution, a multi-scale modelling approach needs to be developed, which starts at the atomic scale. Atomic Kinetic Monte Carlo (AKMC) modelling is the method we chose to provide an insight on defect mediated diffusion under irradiation. In that approach, we model the concentrated commercial steel as a FeCrNi alloy (γ-Fe 70 Cr 20 Ni 10 ). As no reliable empirical potential exists at the moment to reproduce faithfully the phase diagram and the interactions of the elements and point defects, we have adjusted a pair interaction model on large amount of DFT (Density Functional Theory) calculations. The point defect properties in the Fe 70 Cr 20 Ni 10 , and more precisely, how their formation energy depends on the local environment will be presented and some AKMC results on thermal non equilibrium segregation (TNES) and radiation induce segregation will be presented. The effect of Si on the segregation will also be discussed. Preliminary results show that it is the solute- grain boundaries interactions which drive TNES
Excitation and charge transfer in low-energy hydrogen atom collisions with neutral oxygen
Barklem, P. S.
2018-02-01
Excitation and charge transfer in low-energy O+H collisions is studied; it is a problem of importance for modelling stellar spectra and obtaining accurate oxygen abundances in late-type stars including the Sun. The collisions have been studied theoretically using a previously presented method based on an asymptotic two-electron linear combination of atomic orbitals (LCAO) model of ionic-covalent interactions in the neutral atom-hydrogen-atom system, together with the multichannel Landau-Zener model. The method has been extended to include configurations involving excited states of hydrogen using an estimate for the two-electron transition coupling, but this extension was found to not lead to any remarkably high rates. Rate coefficients are calculated for temperatures in the range 1000-20 000 K, and charge transfer and (de)excitation processes involving the first excited S-states, 4s.5So and 4s.3So, are found to have the highest rates. Data are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/vizbin/qcat?J/A+A/610/A57. The data are also available at http://https://github.com/barklem/public-data
Ivanovic, Milos T; Bruetzel, Linda K; Lipfert, Jan; Hub, Jochen S
2018-03-13
Surfactants have found a wide range of industrial and scientific applications. In particular, detergent micelles are used as lipid membrane mimics to solubilize membrane proteins for functional and structural characterisation. However, an atomic-level understanding of surfactants remains limited because many experiments provide only low-resolution structural information on surfactant aggregates. Here, we combine small-angle X-ray scattering with molecular dynamics simulations to derive fully atomic models of two maltoside micelles, at temperatures between 10°C and 70°C. We find that the micelles take the shape of general tri-axial ellipsoids and decrease in size and aggregation number with increasing temperature. Density profiles of hydrophobic groups and water along the three principal axes reveal that the minor micelle axis closely mimics lipid membranes. Our results suggest that coupling atomic simulations with low-resolution data allows for a structural characterisation of surfactant aggregates. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Jin, Lin; Auerbach, Scott M; Monson, Peter A
2012-03-15
The potential of tailored nanopores to transform technologies such as drug delivery, biofuel production, and optical-electronic devices depends on fundamental knowledge of the self-assembly of ordered nanoporous solids. Atomic-level geometries of critical nuclei that lead to such solids have remained hidden in the nanoscale blind spot between local (5 nm) probes of structure. Heroic efforts at molecular simulation of nanopore formation have provided massive libraries of hypothetical structures; (1-5) however, to date no statistical simulation has generated a crystallization pathway from random initial condition to ordered nanoporous solid, until now. In this work, we show that a recently developed atomic lattice model of silica and related materials can form ordered nanoporous solids with a rich variety of structures including known chalcogenides, zeolite analogs, and layered materials. We find that whereas canonical Monte Carlo simulations of the model consistently produce the amorphous solids studied in our previous work, parallel tempering Monte Carlo gives rise to ordered nanoporous solids. The utility of parallel tempering highlights the existence of barriers between amorphous and crystalline phases of our model. Moreover, the self-assembly or nanoporous crystalline phases in the model open the door to detailed understanding of nanopore nucleation.
Lunin, V Y; Lunina, N L; Petrova, T E; Vernoslova, E A; Urzhumtsev, A G; Podjarny, A D
1995-11-01
A method is proposed for the solution of the phase problem at very low resolution for macromolecules. It generates randomly a very large number of models, each consisting of a few (two to ten) pseudo-atoms. The corresponding amplitudes are used for selecting a subset of 'best' models by choosing those with the highest correlation with experimental values. The phases calculated from these 'best' models are analysed by a clusterization procedure leading to a few possible solutions, from which the correct one can be recognized by simple additional criteria. This method has been successfully applied to the neutron diffraction data of the AspRS-tRNA(Asp) complex at 50 A resolution and to data calculated from a model ribosome crystal at 60 A resolution.
Directory of Open Access Journals (Sweden)
Andrzej Stanisław Cieplak
Full Text Available Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates' morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer's and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer's amyloid β and tau, Parkinson's α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and
International Nuclear Information System (INIS)
Meinhold, H.
1980-01-01
This book is a popular introduction into the foundations of atomic physics und quantum mechanics. Starting from some phenomenological concepts Bohr's model and the construction of the periodic system regarding the shell structure of atoms are introduced. In this framework the selection rules and magnetic moments of atomic electrons are considered. Finally the wave-particle dualism is considered. In the appendix some mathematical methods are described which are useful for a deeper penetration into the considered ideas. (HSI)
How far can radiation from atoms be represented by classical models
International Nuclear Information System (INIS)
Haar, D. Ter; Wergeland, H.
1978-01-01
In recent years some phenomena currently assumed to be essentially quantal have found an accurate description in classical terms. An example is Lamb's semiclassical theory of the laser. Consequently many physicists are discussing in how far a full quantum mechanical treatment is necessary. A good many of the formulae for the radiation from atoms can certainly be obtained by classical methods. But these methods fail already at the question of the line profiles. Even though the damping is a simple mechanism - classically speaking. It seems inevitible that the semi-classical formulae must be limited to those phenomena which essentially only involve the averages of photon numbers. (JIW)
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.
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...
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.
Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.
2013-04-01
Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.
Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan.
Schanda, Paul; Triboulet, Sébastien; Laguri, Cédric; Bougault, Catherine M; Ayala, Isabel; Callon, Morgane; Arthur, Michel; Simorre, Jean-Pierre
2014-12-24
The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains-the catalytic domain as well as the proposed peptidoglycan recognition domain-are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein-peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.
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.
Munoz Burgos, Jorge Manuel
Accurate knowledge of atomic processes plays a key role in modeling the emission in laboratory as well as in astrophysical plasmas. These processes are included in a collisional-radiative model and the results are compared with experimental measurements for Ar and Ne ions from the ASTRAL (Auburn Steady sTate Research fAciLity) experiment. The accuracy of our model depends upon the quality of the atomic data we use. Atomic data for near neutral systems present a challenge due to the low accuracy of perturbative methods for these systems. In order to improve our model we rely on non-perturbative methods such as R - Matrix and RMPS ( R -Matrix with Pseudo-States) to include correlation in the collision cross-sections. In the case of Ar + we compared R -Matrix electron-impact excitation data against the results from a new RMPS calculation. The aim was to assess the effects of continuum-coupling effects on the atomic data and the resulting spectrum. We do our spectral modeling using the ADAS suite of codes. Our collisional-radiative formalism assumes that the excited levels are in quasi- static equilibrium with the ground and metastable populations. In our model we allow for N e and T e variation along the line of sight by fitting our densities and temperature profiles with those measured within the experiment. The best results so far have been obtained by the fitting of the experimental temperature and density profiles with Gaussian and polynomial distribution functions. The line of sight effects were found to have a significant effect on the emission modeling. The relative emission rates were measured in the ASTRAL helicon plasma source. A spectrometer which features a 0.33 m Criss-Cross Scanning monochromator and a CCD camera is used for this study. ASTRAL produces bright intense Ar and Ne plasmas with n e = 10 11 to 10 13 cm -3 and T e = 2 to 10 eV. A series of 7 large coils produce an axial magnetic field up to 1.3 kGauss. A fractional helix antenna is used to
Excitation and decay of correlated atomic states
International Nuclear Information System (INIS)
Rau, A.R.P.
1992-01-01
Doubly excited states of atoms and ions in which two electrons are excited from the ground configuration display strong radial and angular electron correlations. They are prototypical examples of quantum-mechanical systems with strong coupling. Two distinguishing characteristics of these states are: (1) their organization into successive families, with only weak coupling between families, and (2) a hierarchical nature of this coupling, with states from one family decaying primarily to those in the next lower family. A view of the pair of electrons as a single entity, with the electron-electron repulsion between them divided into a adiabatic and nonadiabatic piece, accounts for many of the dominant features. The stronger, adiabatic part determines the family structure and the weaker, nonadiabatic part the excitation and decay between successive families. Similar considerations extend to three-electron atomic states, which group into five different classes. They are suggestive of composite models for quarks in elementary particle physics, which exhibit analogous groupings into families with a hierarchical arrangement of masses and electroweak decays. 49 refs., 6 figs., 2 tabs
Atomic compressibility and reversible insertion of atoms into solids
International Nuclear Information System (INIS)
Connerade, J.P.; Semaoune, R.
2000-01-01
We developed a theoretical model to investigate the compressibility of atoms. Atoms are confined inside a spherical cavity, simulated numerically by a finite repulsive potential barrier. The energy levels and wavefunctions of confined atoms are determined by solving, for different cavity radii, the relativistic Dirac-Fock equations, including formally the repulsive barrier. The changes in the atomic size and in the ground-state energy level allow one to define a positive isotropic pressure exerted on the confined atom. The model is applied to atomic caesium and it is demonstrated quantitatively that the remarkable compressibility of caesium originates from a purely atomic mechanism, namely the pressure-induced collapse of the 5d orbital. We propose that this mechanism can also drive, at an atomic level, a reversible insertion of atoms into solids. Applications to lithium-ion batteries are briefly discussed at the end of this paper. (author)
High-frequency two-electron photoionization cross section of triplet states
International Nuclear Information System (INIS)
Krivec, R.; Amusia, M.Ya.; Mandelzweig, V.B.
2003-01-01
Using high precision wave functions describing the triplet ground and excited 3 S states of the He atom and heliumlike ions, the cross sections of single- and double-electron photoionization are calculated. The dependence of the ratio R of the double and single ionization cross sections on the nuclear charge Z and the principal quantum number of excitation n is studied. The results obtained are compared to those for previously studied singlet states
International Nuclear Information System (INIS)
Safronova, M. S.; Mitroy, J.; Clark, Charles W.; Kozlov, M. G.
2015-01-01
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
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.
Schöllnberger, H; Kaiser, J C; Jacob, P; Walsh, L
2012-05-01
The non-cancer mortality data for cerebrovascular disease (CVD) and cardiovascular diseases from Report 13 on the atomic bomb survivors published by the Radiation Effects Research Foundation were analysed to investigate the dose-response for the influence of radiation on these detrimental health effects. Various parametric and categorical models (such as linear-no-threshold (LNT) and a number of threshold and step models) were analysed with a statistical selection protocol that rated the model description of the data. Instead of applying the usual approach of identifying one preferred model for each data set, a set of plausible models was applied, and a sub-set of non-nested models was identified that all fitted the data about equally well. Subsequently, this sub-set of non-nested models was used to perform multi-model inference (MMI), an innovative method of mathematically combining different models to allow risk estimates to be based on several plausible dose-response models rather than just relying on a single model of choice. This procedure thereby produces more reliable risk estimates based on a more comprehensive appraisal of model uncertainties. For CVD, MMI yielded a weak dose-response (with a risk estimate of about one-third of the LNT model) below a step at 0.6 Gy and a stronger dose-response at higher doses. The calculated risk estimates are consistent with zero risk below this threshold-dose. For mortalities related to cardiovascular diseases, an LNT-type dose-response was found with risk estimates consistent with zero risk below 2.2 Gy based on 90% confidence intervals. The MMI approach described here resolves a dilemma in practical radiation protection when one is forced to select between models with profoundly different dose-responses for risk estimates.
Energy Technology Data Exchange (ETDEWEB)
Schoellnberger, H.; Kaiser, J.C.; Jacob, P. [Institute of Radiation Protection, Helmholtz Zentrum Muenchen, Department of Radiation Sciences, Neuherberg (Germany); Walsh, L. [BfS-Federal Office for Radiation Protection, Neuherberg (Germany)
2012-05-15
The non-cancer mortality data for cerebrovascular disease (CVD) and cardiovascular diseases from Report 13 on the atomic bomb survivors published by the Radiation Effects Research Foundation were analysed to investigate the dose-response for the influence of radiation on these detrimental health effects. Various parametric and categorical models (such as linear-no-threshold (LNT) and a number of threshold and step models) were analysed with a statistical selection protocol that rated the model description of the data. Instead of applying the usual approach of identifying one preferred model for each data set, a set of plausible models was applied, and a sub-set of non-nested models was identified that all fitted the data about equally well. Subsequently, this sub-set of non-nested models was used to perform multi-model inference (MMI), an innovative method of mathematically combining different models to allow risk estimates to be based on several plausible dose-response models rather than just relying on a single model of choice. This procedure thereby produces more reliable risk estimates based on a more comprehensive appraisal of model uncertainties. For CVD, MMI yielded a weak dose-response (with a risk estimate of about one-third of the LNT model) below a step at 0.6 Gy and a stronger dose-response at higher doses. The calculated risk estimates are consistent with zero risk below this threshold-dose. For mortalities related to cardiovascular diseases, an LNT-type dose-response was found with risk estimates consistent with zero risk below 2.2 Gy based on 90% confidence intervals. The MMI approach described here resolves a dilemma in practical radiation protection when one is forced to select between models with profoundly different dose-responses for risk estimates. (orig.)
International Nuclear Information System (INIS)
Armbruster, P.; Beyer, H.; Bosch, F.; Dohmann, H.D.; Kozhuharov, C.; Liesen, D.; Mann, R.; Mokler, P.H.
1984-01-01
The heavy ion accelerator UNILAC is well suited to experiments in the field of atomic physics because, with the aid of high-energy heavy ions atoms can be produced in exotic states - that is, heavy atoms with only a few electrons. Also, in close collisions of heavy ions (atomic number Z 1 ) and heavy target atoms (Z 2 ) short-lived quasi-atomic 'superheavy' systems will be formed - huge 'atoms', where the inner electrons are bound in the field of the combined charge Z 1 + Z 2 , which exceeds by far the charge of the known elements (Z <= 109). Those exotic or transient superheavy atoms delivered from the heavy ion accelerator make it possible to study for the first time in a terrestrial laboratory exotic, but fundamental, processes, which occur only inside stars. Some of the basic research carried out with the UNILAC is discussed. This includes investigation of highly charged heavy atoms with the beam-foil method, the spectroscopy of highly charged slow-recoil ions, atomic collision studies with highly ionised, decelerated ions and investigations of super-heavy quasi-atoms. (U.K.)
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.
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...
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.
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...
Evaporative cooling of trapped atoms
International Nuclear Information System (INIS)
Ketterle, W.; Van Druten, N.J.
1996-01-01
This report discusses the following topics on evaporative cooling of trapped atoms: Theoretical models for evaporative cooling; the role of collisions for real atoms; experimental techniques and summary of evaporative cooling experiments. 166 refs., 6 figs., 3 tabs
International Nuclear Information System (INIS)
Apetrei, Alin Marian; Enachescu, Cristian; Tanasa, Radu; Stoleriu, Laurentiu; Stancu, Alexandru
2010-01-01
We apply here the Monte Carlo Metropolis method to a known atom-phonon coupling model for 1D spin transition compounds (STC). These inorganic molecular systems can switch under thermal or optical excitation, between two states in thermodynamical competition, i.e. high spin (HS) and low spin (LS). In the model, the ST units (molecules) are linked by springs, whose elastic constants depend on the spin states of the neighboring atoms, and can only have three possible values. Several previous analytical papers considered a unique average value for the elastic constants (mean-field approximation) and obtained phase diagrams and thermal hysteresis loops. Recently, Monte Carlo simulation papers, taking into account all three values of the elastic constants, obtained thermal hysteresis loops, but no phase diagrams. Employing Monte Carlo simulation, in this work we obtain the phase diagram at T=0 K, which is fully consistent with earlier analytical work; however it is more complex. The main difference is the existence of two supplementary critical curves that mark a hysteresis zone in the phase diagram. This explains the pressure hysteresis curves at low temperature observed experimentally and predicts a 'chemical' hysteresis in STC at very low temperatures. The formation and the dynamics of the domains are also discussed.
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.
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.
One- and two-electron reduction of quinizarin and 5-methoxyquinizarin: a pulse radiolysis study
Energy Technology Data Exchange (ETDEWEB)
Mukherjee, Tulsi; Swallow, A.J. (Christie Hospital and Holt Radium Inst., Manchester (UK). Paterson Labs.); Guyan, P.M.; Bruce, J.M. (Manchester Univ. (UK). Dept. of Chemistry)
1990-01-01
Absorption characteristics of the semiquinone free radicals formed by one-electron reduction of quinizarin (QH{sub 2}), 5-methoxyquinizarin (MQH{sub 2}) and quinizarin 2-sulphonate (QSH{sub 2}) have been studied by pulse radiolysis in a mixed solvent system consisting of water, isopropyl alcohol and acetone. Second-order rate constants have been determined for the reactions of (CH{sub 3}){sub 2}COH with the quinones, of the semiquinones with O{sub 2} and of the semiquinones with each other. The one-electron reduction potentials (vs. NHE) are E{sub 7}{sup 1} = -269 mV for QH{sub 2}, -333 mV for MQH{sub 2} and -298 mV for QSH{sub 2}. They vary with pH in accordance with the pK{sub a} values of the parent quinones and the semiquinones. The radicals are stable within the approximate pH range 5-11. The stability constant is highest at pH 8.5 (K{sub 2} {approx equal} 0.09) for QH{sub 2}, at pH {approx equal} 9.5 for QSH{sub 2} (K{sub s} {approx equal}10) and pH {approx equal} 10.8 for MQH{sub 2} (K{sub s} {approx equal} 4.8), respectively. The one-electron reduction potentials of the semiquinones and the two-electron reduction potentials of the quinones are calculated to be E{sub 7}{sup 2} = -188, -192 and -216 mV, and E{sub 7}{sup m} = -229, -263 and -257 mV for QH{sub 2}, MQH{sub 2} and QSH{sub 2}, respectively. The effect of solvent on the properties of the semiquinones is discussed. (author).
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.
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...
Gleadall, Andrew; Pan, Jingzhe; Kruft, Marc-Anton
2015-11-01
Atomic simulations were undertaken to analyse the effect of polymer chain scission on amorphous poly(lactide) during degradation. Many experimental studies have analysed mechanical properties degradation but relatively few computation studies have been conducted. Such studies are valuable for supporting the design of bioresorbable medical devices. Hence in this paper, an Effective Cavity Theory for the degradation of Young's modulus was developed. Atomic simulations indicated that a volume of reduced-stiffness polymer may exist around chain scissions. In the Effective Cavity Theory, each chain scission is considered to instantiate an effective cavity. Finite Element Analysis simulations were conducted to model the effect of the cavities on Young's modulus. Since polymer crystallinity affects mechanical properties, the effect of increases in crystallinity during degradation on Young's modulus is also considered. To demonstrate the ability of the Effective Cavity Theory, it was fitted to several sets of experimental data for Young's modulus in the literature. Copyright © 2015 Elsevier Ltd. All rights reserved.
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.
International Nuclear Information System (INIS)
Silva, Pedro Maffia da
2017-01-01
The International Atomic Energy Agency's Technical Cooperation Program is the main mechanism through which services are provided to its member states to help them build, strengthen and maintain their capabilities in the safe use of nuclear technology in support of socio-economic development. The technical cooperation program operates in four geographical regions, each regional program helps Member States to meet their specific needs, taking into account existing capacities and different operating conditions. The technical cooperation regions are Asia and the Pacific, Europe, Africa and Latin America and the Caribbean. Developing activities together with the technical cooperation program we have the Regional Cooperation Agreement for the Promotion of Nuclear Science and Technology in Latin America and the Caribbean (ARCAL), which involves the majority of the members of the International Atomic Energy Agency of that region, for Technical Cooperation. All ARCAL's work is guided by the Regional Strategic Profile, which identifies the needs and problems of the region that require support projects. In the technical meeting of the Regional Strategic Profile, the needs and problems that are analyzed through indexes associated with severity, urgency, extension, relevance and difficulty are listed by different thematic areas. To these indexes, values are established by the technical staff on a continuous scale between 1 and 5. From these values an expression is used to arrive at a priority number for the needs and problems. In the face of many criticisms associated with similar approaches, such as Failure Modes and Effects Analysis, and Timing, Trend and Impact Matrix, the aim of this thesis is to propose a methodological approach that can assist in the prioritization of investments of technical cooperation projects and programs that take into account the budget available and the technical and strategic visions of the parties involved. For this, the Probabilistic
Atom-atom collision cascades localization
International Nuclear Information System (INIS)
Kirsanov, V.V.
1980-01-01
The presence of an impurity and thermal vibration influence on the atom-atom collision cascade development is analysed by the computer simulation method (the modificated dynamic model). It is discovered that the relatively low energetic cascades are localized with the temperature increase of an irradiated crystal. On the basis of the given effect the mechanism of splitting of the high energetic cascades into subcascades is proposed. It accounts for two factors: the primary knocked atom energy and the irradiated crystal temperature. Introduction of an impurity also localizes the cascades independently from the impurity atom mass. The cascades localization leads to intensification of the process of annealing in the cascades and reduction of the post-cascade vacancy cluster sizes. (author)
Improving Atomic Force Microscopy Imaging by a Direct Inverse Asymmetric PI Hysteresis Model
Directory of Open Access Journals (Sweden)
Dong Wang
2015-02-01
Full Text Available A modified Prandtl–Ishlinskii (PI model, referred to as a direct inverse asymmetric PI (DIAPI model in this paper, was implemented to reduce the displacement error between a predicted model and the actual trajectory of a piezoelectric actuator which is commonly found in AFM systems. Due to the nonlinearity of the piezoelectric actuator, the standard symmetric PI model cannot precisely describe the asymmetric motion of the actuator. In order to improve the accuracy of AFM scans, two series of slope parameters were introduced in the PI model to describe both the voltage-increase-loop (trace and voltage-decrease-loop (retrace. A feedforward controller based on the DIAPI model was implemented to compensate hysteresis. Performance of the DIAPI model and the feedforward controller were validated by scanning micro-lenses and standard silicon grating using a custom-built AFM.
Improving atomic force microscopy imaging by a direct inverse asymmetric PI hysteresis model.
Wang, Dong; Yu, Peng; Wang, Feifei; Chan, Ho-Yin; Zhou, Lei; Dong, Zaili; Liu, Lianqing; Li, Wen Jung
2015-02-03
A modified Prandtl-Ishlinskii (PI) model, referred to as a direct inverse asymmetric PI (DIAPI) model in this paper, was implemented to reduce the displacement error between a predicted model and the actual trajectory of a piezoelectric actuator which is commonly found in AFM systems. Due to the nonlinearity of the piezoelectric actuator, the standard symmetric PI model cannot precisely describe the asymmetric motion of the actuator. In order to improve the accuracy of AFM scans, two series of slope parameters were introduced in the PI model to describe both the voltage-increase-loop (trace) and voltage-decrease-loop (retrace). A feedforward controller based on the DIAPI model was implemented to compensate hysteresis. Performance of the DIAPI model and the feedforward controller were validated by scanning micro-lenses and standard silicon grating using a custom-built AFM.
Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach
International Nuclear Information System (INIS)
Yakubovich, Alexander V.; Solov'yov, Andrey V.; Surdutovich, Eugene
2011-01-01
We present a brief overview of the multiscale approach towards understanding of the processes responsible for the radiation damage caused by energetic ions. This knowledge is very important, because it can be utilized in the ion-beam cancer therapy, which is one of the most advanced modern techniques to cure certain type of cancer. The central element of the multiscale approach is the theoretical evaluation and quantification of the DNA damage within cell environment. To achieve this goal one needs a significant amount of data on various atomic and molecular processes involved into the cascade of events starting with the ion entering and propagation in the biological medium and resulting in the DNA damage. The discussion of the follow up biological processes are beyond the scope of this brief overview. We consider different paths of the DNA damage and focus on the the illustration of the thermo-mechanical effects caused by the propagation of ions through the biological environment and in particular on the possibility of the creation of the shock waves in the vicinity of the ion tracks. We demonstrate that at the initial stages after ion's passage the shock wave is so strong that it can contribute to the DNA damage due to large pressure gradients developed at the distances of a few nanometers from the ionic tracks. This novel mechanism of the DNA damage provides an important contribution to the cumulative biodamage caused by low-energy secondary electrons, holes and free radicals.
Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach
Yakubovich, Alexander V.; Surdutovich, Eugene; Solov'yov, Andrey V.
2011-05-01
We present a brief overview of the multiscale approach towards understanding of the processes responsible for the radiation damage caused by energetic ions. This knowledge is very important, because it can be utilized in the ion-beam cancer therapy, which is one of the most advanced modern techniques to cure certain type of cancer. The central element of the multiscale approach is the theoretical evaluation and quantification of the DNA damage within cell environment. To achieve this goal one needs a significant amount of data on various atomic and molecular processes involved into the cascade of events starting with the ion entering and propagation in the biological medium and resulting in the DNA damage. The discussion of the follow up biological processes are beyond the scope of this brief overview. We consider different paths of the DNA damage and focus on the the illustration of the thermo-mechanical effects caused by the propagation of ions through the biological environment and in particular on the possibility of the creation of the shock waves in the vicinity of the ion tracks. We demonstrate that at the initial stages after ion's passage the shock wave is so strong that it can contribute to the DNA damage due to large pressure gradients developed at the distances of a few nanometers from the ionic tracks. This novel mechanism of the DNA damage provides an important contribution to the cumulative biodamage caused by low-energy secondary electrons, holes and free radicals.
International Nuclear Information System (INIS)
Anon.
1976-01-01
Research activities in atomic physics at Lawrence Berkeley Laboratory during 1976 are described. Topics covered include: experiments on stored ions; test for parity violation in neutral weak currents; energy conservation and astrophysics; atomic absorption spectroscopy, atomic and molecular detectors; theoretical studies of quantum electrodynamics and high-z ions; atomic beam magnetic resonance; radiative decay from the 2 3 Po, 2 levels of helium-like argon; quenching of the metastable 2S/sub 1/2/ state of hydrogen-like argon in an external electric field; and lifetime of the 2 3 Po level of helium-like krypton
Quantum Simulation of the Hubbard Model Using Ultra-Cold Atoms
2008-11-01
Hubbard model. The SU(3) Hubbard model has been proposed as a model system for studying different phases of matter expected to occur in quantum...chromodynamics (QCD): the color superconducting phase and the formation of baryons . Our initial investigations have focused on understanding three-body...density quark matter described by quantum chromodynamics . We have been investigating the stability of the 3-state Fermi gas with respect to decay due
Reconstructive approaches to one- and two-electron density matrix theory
Herbert, John Michael
Novel computational methods for electronic structure theory are explored, in which the fundamental variable is either the one- or the two-electron reduced density matrix (1- or 2-RDM), rather than the electronic wavefunction. A unifying theme among these methods is density matrix reconstruction, that is, decoupling approximations that express higher-order density matrices as functionals of lower-order ones. On the 2-RDM side, a connected (extensive) version of the Contracted Schrodinger Equation (CSE) is developed, in which the basic unknowns are the RDM cumulants through order four. Reconstruction functionals that neglect the 3- and 4-RDM cumulants are examined and revealed to be significantly less accurate than suggested by previous minimal-basis results. Exact 3-RDM cumulants for some four-electron systems are calculated and found to be comparable in importance to unconnected products of lower-order cumulants. Decoupling approximations for the 3- and 4-RDM cumulants are developed based upon a renormalized, diagrammatic perturbation theory for the three- and four-particle Green's functions, in which the effective, pairwise interaction is extracted from the two-particle cumulant. Diagram rules suitable for both the time-dependent and time-independent versions of this perturbation theory are derived. Reconstructive approaches to natural orbital (1-RDM) functional theory are also examined, wherein the 2-RDM is parametrized in terms of the natural orbitals and their (generally fractional) occupancies. It is demonstrated, at the theorem level, that proposed "corrected Hartree" and "corrected Hartree-Fock" natural orbital functionals necessarily violate positivity of the 2-RDM, which is closely related to their failure to respect antisymmetry. Calculations demonstrate that negative eigenvalues of the 2-RDM are associated with a large, stabilizing (but ultimately spurious) contribution to the energy. Nevertheless, a partially self-interaction-corrected version of the
Levashov, V A; Stepanov, M G
2016-01-01
Considerations of local atomic-level stresses associated with each atom represent a particular approach to address structures of disordered materials at the atomic level. We studied structural correlations in a two-dimensional model liquid using molecular dynamics simulations in the following way. We diagonalized the atomic-level stress tensor of every atom and investigated correlations between the eigenvalues and orientations of the eigenvectors of different atoms as a function of distance between them. It is demonstrated that the suggested approach can be used to characterize structural correlations in disordered materials. In particular, we found that changes in the stress correlation functions on decrease of temperature are the most pronounced for the pairs of atoms with separation distance that corresponds to the first minimum in the pair density function. We also show that the angular dependencies of the stress correlation functions previously reported by Wu et al. [Phys. Rev. E 91, 032301 (2015)10.1103/PhysRevE.91.032301] do not represent the anisotropic Eshelby's stress fields, as it is suggested, but originate in the rotational properties of the stress tensors.
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.
International Nuclear Information System (INIS)
Heidenreich, W.F.; Jacob, P.; Paretzke, H.G.
1997-01-01
We derive explizit hazard functions for the clonal expansion model in the ''exact formulation'' and in the ''epidemiological approximation'' for the spontaneous rate and for short-time exposure. We investigate which combination of the biological parameters can be determined from the incidence function, and which cannot. We then analyze the incidence data of all solid tumors of atomic bomb survivors (1958-1987). We restrict ourselves to adults at exposure (>20 years) and to attained age <80 years, and we consider the two cities (Hiroshima and Nagasaki) and the two sexes separately. With four parameters, we find good fits in each case, comparable to the quality of fit of epidemiological age-at-exposure and age-attained models used for comparison. The parameters which describe the spontaneous risk agree very well for the two cities, while they are quite different for the two sexes. The apparent flattening of the risk for elderly men can be described with the exact formulation of the clonal expansion model, but may be due to other causes than the mechanisms modeled. The dose-response parameters differ by more than two standard deviations (factor 2 to 3) between the two cities, when considering the same sex. They are bigger for the men of Nagasaki and the women of Hiroshima. One example for model application to tumors of specific organs (men's lung tumor) is considered. (orig.). With 15 figs., 4 tabs
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
Energy Technology Data Exchange (ETDEWEB)
Bordovsky, G. A. [Alexander Herzen State Pedagogical University of Russia (Russian Federation); Nemov, S. A. [St Petersburg State Polytechnical University (Russian Federation); Marchenko, A. V.; Seregin, P. P., E-mail: ppseregin@mail.ru [Alexander Herzen State Pedagogical University of Russia (Russian Federation)
2012-01-15
The results of the study of donor U{sup -}-centers of tin and germanium in lead chalcogenides by Moessbauer emission spectroscopy are discussed. The published data regarding the identification of amphoteric U{sup -}-centers of tin in glassy binary arsenic and germanium chalcogenides using Moessbauer emission spectroscopy, and in multicomponent chalcogenide glasses using Moessbauer absorption spectroscopy are considered. Published data concerning the identification of two-atom U{sup -}-centers of copper in lattices of semimetal copper oxides by Moessbauer emission spectroscopy are analyzed. The published data on the detection of spatial inhomogeneity of the Bose-Einstein condensate in superconducting semiconductors and semimetal compounds, and on the existence of the correlation between the electron density in lattice sites and the superconducting transition temperature are presented. The principal possibility of using Moessbauer U{sup -}-centers as a tool for studying the Bose-Einstein condensation of electron pairs during the superconducting phase transition in semiconductors and semimetals is considered.
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.
Indian Academy of Sciences (India)
https://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, ...
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.
International Nuclear Information System (INIS)
Backenstoss, G.
1986-01-01
Recent developments in the field of exotic atoms are presented. The improved quality of accelerator facilities and experimental techniques leads to a more precise determination of data. This opens new fields in nuclear and particle physics to which exotic atoms may contribute valuable knowledge. (author)