ERIC Educational Resources Information Center
Willden, Jeff
2001-01-01
"Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…
Computer Modeling Of Atomization
NASA Technical Reports Server (NTRS)
Giridharan, M.; Ibrahim, E.; Przekwas, A.; Cheuch, S.; Krishnan, A.; Yang, H.; Lee, J.
1994-01-01
Improved mathematical models based on fundamental principles of conservation of mass, energy, and momentum developed for use in computer simulation of atomization of jets of liquid fuel in rocket engines. Models also used to study atomization in terrestrial applications; prove especially useful in designing improved industrial sprays - humidifier water sprays, chemical process sprays, and sprays of molten metal. Because present improved mathematical models based on first principles, they are minimally dependent on empirical correlations and better able to represent hot-flow conditions that prevail in rocket engines and are too severe to be accessible for detailed experimentation.
Pearson, Ralph G.
1981-01-01
The energies of several two- and three-electron atoms, in both ground states and excited states, are calculated by a very simple semiclassical model. The only change from Bohr's original method is to replace definite orbits by probability distribution functions based on classical dynamics. The energies are better than Hartree-Fock values. There is still a need for an exchange-energy correction. Images PMID:16593047
Stochastic models for atomic clocks
NASA Technical Reports Server (NTRS)
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.
A Quantum Model of Atoms (the Energy Levels of Atoms).
ERIC Educational Resources Information Center
Rafie, Francois
2001-01-01
Discusses the model for all atoms which was developed on the same basis as Bohr's model for the hydrogen atom. Calculates the radii and the energies of the orbits. Demonstrates how the model obeys the de Broglie's hypothesis that the moving electron exhibits both wave and particle properties. (Author/ASK)
"Electronium": A Quantum Atomic Teaching Model.
ERIC Educational Resources Information Center
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)
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
The Hydrogen Atom: The Rutherford Model
NASA Astrophysics Data System (ADS)
Tilton, Homer Benjamin
1996-06-01
Early this century Ernest Rutherford established the nuclear model of the hydrogen atom, presently taught as representing the best visual model after modification by Niels Bohr and Arnold Sommerfeld. It replaced the so-called "plum pudding" model of J. J. Thomson which held sway previously. While the Rutherford model represented a large step forward in our understanding of the hydrogen atom, questions remained, and still do.
The Completeness Criterion in Atomic Modeling
NASA Astrophysics Data System (ADS)
Liedahl, Duane A.
2000-10-01
I discuss two variations on the completeness theme in atomic modeling; missing lines as they affect the performance of spectral synthesis codes, and missing configurations as they affect the theoretical emissivities of bright lines, with emphasis on the latter. It is shown that the detrimental effects of working with incomplete atomic models can overshadow those brought about by working with less-than-perfect atomic rates. Atomic models can be brought up to an acceptable level of completeness in a fairly straightforward manner, and on a reasonably short timescale, whereas the long-term goal of comprehensive accuracy is unlikely to be reached on the timescale of the current generation of X-ray observatories. A near-term, albeit imperfect, solution is to hybridize atomic models used to synthesize spectra. A hybrid atomic model is one for which a large-scale atomic model, in which completeness is achieved at the expense of accuracy, is augmented with more accurate atomic quantities as they become available.
Atomic modeling of the plasma EUV sources
NASA Astrophysics Data System (ADS)
Sasaki, Akira; Sunahara, Atsushi; Furukawa, Hiroyuki; Nishihara, Katsunobu; Nishikawa, Takeshi; Koike, Fumihiro; Tanuma, Hajime
2009-09-01
We present the development of population kinetics models for tin plasmas that can be employed to design an EUV source for microlithography. The atomic kinetic code is constrained for the requirement that the model must be able to calculate spectral emissivity and opacity that can be used in radiation hydrodynamic simulations. Methods to develop compact and reliable atomic model with an appropriate set of atomic states are discussed. Specifically, after investigation of model dependencies and comparison experiment, we improve the effect of configuration interaction and the treatment of satellite lines. Using the present atomic model we discuss the temperature and density dependencies of the emissivity, as well as conditions necessary to obtain high efficiency EUV power at λ = 13.5 nm.
Ion-Atom and Atom-Atom Collisional Processes and Modeling of Stellar Atmospheres
NASA Astrophysics Data System (ADS)
Mihajlov, A. A.; Ignjatovic, Lj. M.; Sreckovic, V. A.; Dimitrijevic, M. S.; Dimitrijevic, M. S.
2015-09-01
We report the results obtained in our previous works on the influence of two groups of collisional processes (ion--atom and atom--atom) on the optical and kinetic properties of weakly ionised plasma. The first group includes radiative processes of the photodissociation/association type and radiative charge exchange, the second one -- chemi-ionisation/recombination processes. The effect of the radiative processed is assessed by comparing their intensities with those of the known competing processed in application to the solar photosphere and to the photospheres of DB white dwarfs. The studied chemi-ionisation/recombination processes are considered from the viewpoint of their influence on the populations of the excited states of the hydrogen atom (the Sun and an M-type red dwarf with an effective temperature of 3800~K) and helium atom (DB white dwarfs). The effect of these processes on the populations of the excited states of the hydrogen atom has been studied using the PHOENIX code, which generates the model of the considered atmosphere. The reported results demonstrate the unquestionable influence of the considered radiative and chemi- ionisation/recombination processes on the optical properties and on the kinetics of the weakly ionised layers in stellar atmospheres. It can be expected that the reported results will be a sufficient reason for including these processes in the models of stellar atmospheres.
Tight Binding Models in Cold Atoms Physics
NASA Astrophysics Data System (ADS)
Zakrzewski, J.
2007-05-01
Cold atomic gases placed in optical lattice potentials offer a unique tool to study simple tight binding models. Both the standard cases known from the condensed matter theory as well as novel situations may be addressed. Cold atoms setting allows for a precise control of parameters of the systems discussed, stimulating new questions and problems. The attempts to treat disorder in a controlled fashion are addressed in detail.
A Newtonian Model of the Hydrogen Atom
NASA Astrophysics Data System (ADS)
Espinosa, James; Woodyard, James
2010-03-01
Classical physics was deemed useless in atomic physics in the early 1900's by the vast majority of the physics community. There were multiple problems that were believed to be insoluble, such as blackbody radiation and the photoelectric and Compton effects. Another outstanding problem had been the explanation of atomic spectra. By the 1920's, a very powerful theory called quantum mechanics was created which explained all atomic experiments. Nevertheless, a few physicists, most notably Albert Einstein, rejected this theory on the grounds that it did not give a complete description of the microscopic world. Another more radical view held by Walter Ritz is that Newtonian physics is applicable to all of atomic physics. Over the last couple of years, we have presented classical explanations of many of the ``insoluble'' problems given by textbooks. We will present a model of the hydrogen atom that stays within the framework of Newton. Using only the assumption that the stable building blocks of matter are the electron, positron, and neutrino, we will deduce the following results from our model: orbital stability, line spectra, and scattering cross sections for electrons and protons. We will also qualitatively demonstrate how to explain the lifetime of excited states.
Atomic Data Applications for Supernova Modeling
NASA Astrophysics Data System (ADS)
Fontes, Christopher J.
2013-06-01
The modeling of supernovae (SNe) incorporates a variety of disciplines, including hydrodynamics, radiation transport, nuclear physics and atomic physics. These efforts require numerical simulation of the final stages of a star's life, the supernova explosion phase, and the radiation that is subsequently emitted by the supernova remnant, which can occur over a time span of tens of thousands of years. While there are several different types of SNe, they all emit radiation in some form. The measurement and interpretation of these spectra provide important information about the structure of the exploding star and the supernova engine. In this talk, the role of atomic data is highlighted as iit pertains to the modeling of supernova spectra. Recent applications [1,2] involve the Los Alamos OPLIB opacity database, which has been used to provide atomic opacities for modeling supernova plasmas under local thermodynamic equilibrium (LTE) conditions. Ongoing work includes the application of atomic data generated by the Los Alamos suite of atomic physics codes under more complicated, non-LTE conditions [3]. As a specific, recent example, a portion of the x-ray spectrum produced by Tycho's supernova remnant (SN 1572) will be discussed [4]. [1] C.L. Fryer et al, Astrophys. J. 707, 193 (2009). [2] C.L. Fryer et al, Astrophys. J. 725, 296 (2009). [3] C.J. Fontes et al, Conference Proceedings for ICPEAC XXVII, J. of Phys: Conf. Series 388, 012022 (2012). [4] K.A. Eriksen et al, Presentation at the 2012 AAS Meeting (Austin, TX). (This work was performed under the auspices of the U.S. Department of Energy by Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396.)
Optical analogs of model atoms in fields
Milonni, P.W.
1991-05-02
The equivalence of the paraxial wave equation to a time-dependent Schroedinger equation is exploited to construct optical analogs of model atoms in monochromatic fields. The approximation of geometrical optics provides the analog of the corresponding classical mechanics. Optical analogs of Rabi oscillations, photoionization, stabilization, and the Kramers-Henneberger transformation are discussed. One possibility for experimental realization of such optical analogs is proposed. These analogs may be useful for studies of quantum chaos'' when the ray trajectories are chaotic. 9 refs.
A Green's function quantum average atom model
Starrett, Charles Edward
2015-05-21
A quantum average atom model is reformulated using Green's functions. This allows integrals along the real energy axis to be deformed into the complex plane. The advantage being that sharp features such as resonances and bound states are broadened by a Lorentzian with a half-width chosen for numerical convenience. An implementation of this method therefore avoids numerically challenging resonance tracking and the search for weakly bound states, without changing the physical content or results of the model. A straightforward implementation results in up to a factor of 5 speed-up relative to an optimized orbital based code.
Atom-Role-Based Access Control Model
NASA Astrophysics Data System (ADS)
Cai, Weihong; Huang, Richeng; Hou, Xiaoli; Wei, Gang; Xiao, Shui; Chen, Yindong
Role-based access control (RBAC) model has been widely recognized as an efficient access control model and becomes a hot research topic of information security at present. However, in the large-scale enterprise application environments, the traditional RBAC model based on the role hierarchy has the following deficiencies: Firstly, it is unable to reflect the role relationships in complicated cases effectively, which does not accord with practical applications. Secondly, the senior role unconditionally inherits all permissions of the junior role, thus if a user is under the supervisor role, he may accumulate all permissions, and this easily causes the abuse of permission and violates the least privilege principle, which is one of the main security principles. To deal with these problems, we, after analyzing permission types and role relationships, proposed the concept of atom role and built an atom-role-based access control model, called ATRBAC, by dividing the permission set of each regular role based on inheritance path relationships. Through the application-specific analysis, this model can well meet the access control requirements.
NASA Technical Reports Server (NTRS)
Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.
1992-01-01
The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.
Making It Visual: Creating a Model of the Atom
ERIC Educational Resources Information Center
Pringle, Rose M.
2004-01-01
This article describes a lesson in which students construct Bohr's planetary model of the atom. Niels Bohr's atomic model provides a framework for discussing with middle and high school students the historical development of our understanding of the structure of the atom. The model constructed in this activity will enable students to visualize the…
Computer Model Of Fragmentation Of Atomic Nuclei
NASA Technical Reports Server (NTRS)
Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.
1995-01-01
High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.
Atomic Models for Motional Stark Effects Diagnostics
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.
Operation of the computer model for microenvironment atomic oxygen exposure
NASA Technical Reports Server (NTRS)
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.
Atomic Oscillator Strengths for Stellar Atmosphere Modeling
NASA Astrophysics Data System (ADS)
Ruffoni, Matthew; Pickering, Juliet C.
2015-08-01
In order to correctly model stellar atmospheres, fundamental atomic data must be available to describe atomic lines observed in their spectra. Accurate, laboratory-measured oscillator strengths (f-values) for Fe peak elements in neutral or low-ionisation states are particularly important for determining chemical abundances.However, advances in astronomical spectroscopy in recent decades have outpaced those in laboratory astrophysics, with the latter frequently being overlooked at the planning stages of new projects. As a result, numerous big-budget astronomy projects have been, and continue to be hindered by a lack of suitable, accurately-measured reference data to permit the analysis of expensive astronomical spectra; a problem only likely to worsen in the coming decades as spectrographs at new facilities increasingly move to infrared wavelengths.At Imperial College London - and in collaboration with NIST, Wisconsin University and Lund University - we have been working with the astronomy community in an effort to provide new accurately-measured f-values for a range of projects. In particular, we have been working closely with the Gaia-ESO (GES) and SDSS-III/APOGEE surveys, both of which have discovered that many lines that would make ideal candidates for inclusion in their analyses have poorly defined f-values, or are simply absent from the database. Using high-resolution Fourier transform spectroscopy (R ~ 2,000,000) to provide atomic branching fractions, and combining these with level lifetimes measured with laser induced fluorescence, we have provided new laboratory-measured f-values for a range of Fe-peak elements, most recently including Fe I, Fe II, and V I. For strong, unblended lines, uncertainties are as low as ±0.02 dex.In this presentation, I will describe how experimental f-values are obtained in the laboratory and present our recent work for GES and APOGEE. In particular, I will also discuss the strengths and limitations of current laboratory
Project Physics Text 5, Models of the Atom.
ERIC Educational Resources Information Center
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…
An atomic model for neutral and singly ionized uranium
NASA Technical Reports Server (NTRS)
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.
Two Dimensional Non-commutative Space and Rydberg Atom Model
NASA Astrophysics Data System (ADS)
Chung, Won Sang
2015-06-01
In this paper we consider the case of only space-space non-commutativity in two dimension. We also discuss the Rydberg atom model in this space and use the linear realization of the coordinate and momentum operators to solve the Schrödinger equation for the Rydberg atom through the standard perturbation method. Finally, the thermodynamics for the Rydberg atom model is discussed.
Perturbed atoms in molecules and solids: The PATMOS model
NASA Astrophysics Data System (ADS)
Røeggen, Inge; Gao, Bin
2013-09-01
A new computational method for electronic-structure studies of molecules and solids is presented. The key element in the new model - denoted the perturbed atoms in molecules and solids model - is the concept of a perturbed atom in a complex. The basic approximation of the new model is unrestricted Hartree Fock (UHF). The UHF orbitals are localized by the Edmiston-Ruedenberg procedure. The perturbed atoms are defined by distributing the orbitals among the nuclei in such a way that the sum of the intra-atomic UHF energies has a minimum. Energy corrections with respect to the UHF energy, are calculated within the energy incremental scheme. The most important three- and four-electron corrections are selected by introducing a modified geminal approach. Test calculations are performed on N2, Li2, and parallel arrays of hydrogen atoms. The character of the perturbed atoms is illustrated by calculations on H2, CH4, and C6H6.
Perturbed atoms in molecules and solids: The PATMOS model.
Røeggen, Inge; Gao, Bin
2013-09-01
A new computational method for electronic-structure studies of molecules and solids is presented. The key element in the new model - denoted the perturbed atoms in molecules and solids model - is the concept of a perturbed atom in a complex. The basic approximation of the new model is unrestricted Hartree Fock (UHF). The UHF orbitals are localized by the Edmiston-Ruedenberg procedure. The perturbed atoms are defined by distributing the orbitals among the nuclei in such a way that the sum of the intra-atomic UHF energies has a minimum. Energy corrections with respect to the UHF energy, are calculated within the energy incremental scheme. The most important three- and four-electron corrections are selected by introducing a modified geminal approach. Test calculations are performed on N2, Li2, and parallel arrays of hydrogen atoms. The character of the perturbed atoms is illustrated by calculations on H2, CH4, and C6H6. PMID:24028099
"Piekara's Chair": Mechanical Model for Atomic Energy Levels.
ERIC Educational Resources Information Center
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
NASA Technical Reports Server (NTRS)
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.
ERIC Educational Resources Information Center
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Focuses on the quantum atomic model Electronium. Outlines the Bremen teaching approach in which this model is used, and analyzes the learning of two students as they progress through the teaching unit. (Author/MM)
Developing Models: What is the Atom Really Like?
ERIC Educational Resources Information Center
Records, Roger M.
1982-01-01
Five atomic theory activities feasible for high school students to perform are described based on the following models: (1) Dalton's Uniform Sphere Model; (2) Thomson's Raisin Pudding Model; (3) Rutherford's Nuclear Model; (4) Bohr's Energy Level Model, and (5) Orbital Model from quantum mechanics. (SK)
Early atomic models - from mechanical to quantum (1904-1913)
NASA Astrophysics Data System (ADS)
Baily, C.
2013-01-01
A complete history of early atomic models would fill volumes, but a reasonably coherent tale of the path from mechanical atoms to the quantum can be told by focusing on the relevant work of three great contributors to atomic physics, in the critically important years between 1904 and 1913: J.J. Thomson, Ernest Rutherford and Niels Bohr. We first examine the origins of Thomson's mechanical atomic models, from his ethereal vortex atoms in the early 1880's, to the myriad "corpuscular" atoms he proposed following the discovery of the electron in 1897. Beyond qualitative predictions for the periodicity of the elements, the application of Thomson's atoms to problems in scattering and absorption led to quantitative predictions that were confirmed by experiments with high-velocity electrons traversing thin sheets of metal. Still, the much more massive and energetic α-particles being studied by Rutherford were better suited for exploring the interior of the atom, and careful measurements on the angular dependence of their scattering eventually allowed him to infer the existence of an atomic nucleus. Niels Bohr was particularly troubled by the radiative instability inherent to any mechanical atom, and succeeded in 1913 where others had failed in the prediction of emission spectra, by making two bold hypotheses that were in contradiction to the laws of classical physics, but necessary in order to account for experimental facts.
Project Physics Tests 5, Models of the Atom.
ERIC Educational Resources Information Center
Harvard Univ., Cambridge, MA. Harvard Project Physics.
Test items relating to Project Physics Unit 5 are presented in this booklet. Included are 70 multiple-choice and 23 problem-and-essay questions. Concepts of atomic model are examined on aspects of relativistic corrections, electron emission, photoelectric effects, Compton effect, quantum theories, electrolysis experiments, atomic number and mass,…
100th anniversary of Bohr's model of the atom.
Schwarz, W H Eugen
2013-11-18
In the fall of 1913 Niels Bohr formulated his atomic models at the age of 27. This Essay traces Bohr's fundamental reasoning regarding atomic structure and spectra, the periodic table of the elements, and chemical bonding. His enduring insights and superseded suppositions are also discussed. PMID:24123759
Modeling of atom-diatom scattering. Technical report
Sindoni, J.M.
1992-05-30
This report entails the work performed on modeling atom-diatom scattering processes utilizing the Impulse Approach (IA). Results of the model, obtained with a computer code, have proven to be in remarkable agreement with laboratory measurements for several atom-diatom scattering systems. Two scattering systems, in particular, that were successfully modeled and compared to measurements were Ar-KBr and Ar-CsF. The IA model provided an explanation for the rapid deactivation evident in the Ar-KBr system. Experimental results in the Ar-CsF experiment that could not be explained by conventional models were also successfully modeled using the IA. Results fit the experimental observations.
A liquid drop model for embedded atom method cluster energies
NASA Technical Reports Server (NTRS)
Finley, C. W.; Abel, P. B.; Ferrante, J.
1996-01-01
Minimum energy configurations for homonuclear clusters containing from two to twenty-two atoms of six metals, Ag, Au, Cu, Ni, Pd, and Pt have been calculated using the Embedded Atom Method (EAM). The average energy per atom as a function of cluster size has been fit to a liquid drop model, giving estimates of the surface and curvature energies. The liquid drop model gives a good representation of the relationship between average energy and cluster size. As a test the resulting surface energies are compared to EAM surface energy calculations for various low-index crystal faces with reasonable agreement.
Detailed atomic modeling of Sn plasmas for the EUV source
NASA Astrophysics Data System (ADS)
Sasaki, A.; Sunahara, A.; Nishihawra, K.; Nishikawa, T.; Koike, F.; Tanuma, H.
2008-05-01
An atomic model of Sn plasmas is developed to calculate coefficients of radiative transfer, based on the calculated atomic data using the Hullac code. We find that the emission spectrum and conversion efficiency depend critically on the wavelength and spectral structure of the 4d-4f transition arrays. Satellite lines, which have a significant contribution to the emission, are determined after iterative calculations by changing the number of levels in the atomic model. We also correct transition wavelengths through comparison with experiments. Using the present emissivity and opacity, the radiation hydrodynamics simulation will be carried out toward the optimization of the EUV source.
Alpha-cluster model of atomic nuclei
NASA Astrophysics Data System (ADS)
Sosin, Zbigniew; Błocki, Jan; Kallunkathariyil, Jinesh; Łukasik, Jerzy; Pawłowski, Piotr
2016-05-01
The description of a nuclear system in its ground state and at low excitations based on the equation of state (EoS) around normal density is presented. In the expansion of the EoS around the saturation point, additional spin polarization terms are taken into account. These terms, together with the standard symmetry term, are responsible for the appearance of the α-like clusters in the ground-state configurations of the N = Z even-even nuclei. At the nuclear surface these clusters can be identified as alpha particles. A correction for the surface effects is introduced for atomic nuclei. Taking into account an additional interaction between clusters the binding energies and sizes of the considered nuclei are very accurately described. The limits of the EoS parameters are established from the properties of the α, 3He and t particles.
Modeling sympathetic cooling of molecules by ultracold atoms
NASA Astrophysics Data System (ADS)
Lim, Jongseok; Frye, Matthew D.; Hutson, Jeremy M.; Tarbutt, M. R.
2015-11-01
We model sympathetic cooling of ground-state CaF molecules by ultracold Li and Rb atoms. The molecules are moving in a microwave trap, while the atoms are trapped magnetically. We calculate the differential elastic cross sections for CaF-Li and CaF-Rb collisions, using model Lennard-Jones potentials adjusted to give typical values for the s -wave scattering length. Together with trajectory calculations, these differential cross sections are used to simulate the cooling of the molecules, the heating of the atoms, and the loss of atoms from the trap. We show that a hard-sphere collision model based on an energy-dependent momentum transport cross section accurately predicts the molecule cooling rate but underestimates the rates of atom heating and loss. Our simulations suggest that Rb is a more effective coolant than Li for ground-state molecules, and that the cooling dynamics is less sensitive to the exact value of the s -wave scattering length when Rb is used. Using realistic experimental parameters, we find that molecules can be sympathetically cooled to 100 μ K in about 10 s. By applying evaporative cooling to the atoms, the cooling rate can be increased and the final temperature of the molecules can be reduced to 1 μ K within 30 s.
Surface Adsorption in Nonpolarizable Atomic Models.
Whitmer, Jonathan K; Joshi, Abhijeet A; Carlton, Rebecca J; Abbott, Nicholas L; de Pablo, Juan J
2014-12-01
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. PMID:26583244
Enhanced NLTE Atomic Kinetics Modeling Capabilities in HYDRA
NASA Astrophysics Data System (ADS)
Patel, Mehul V.; Scott, Howard A.; Marinak, Michael M.
2014-10-01
In radiation hydrodynamics modeling of ICF targets, an NLTE treatment of atomic kinetics is necessary for modeling high-Z hohlraum wall materials, high-Z dopants mixed in the central gas hotspot, and is potentially needed for accurate modeling of outer layers of the capsule ablator. Over the past several years, the NLTE DCA atomic physics capabilities in the 3D ICF radiation hydrodynamics code HYDRA have been significantly enhanced. The underlying atomic models have been improved, additional kinetics options including the ability to run DCA in cells with dynamic mixing of species has been added, and the computational costs have been significantly reduced using OpenMP threading. To illustrate the improved capabilities, we will show higher fidelity results from simulations of ICF hohlraum energetics, laser irradiated sphere experiments, and ICF capsule implosions. Prepared by LLNL under Contract DE-AC52-07NA27344.
Modelling spectral properties of non-equilibrium atomic hydrogen plasma
NASA Astrophysics Data System (ADS)
D'Ammando, G.; Pietanza, L. D.; Colonna, G.; Longo, S.; Capitelli, M.
2010-02-01
A model to predict the emissivity and absorption coefficient of atomic hydrogen plasma is presented in detail. Non-equilibrium plasma is studied through coupling of the model with a collisional-radiative code for the excited states population as well as with the Boltzmann equation for the electron energy distribution function.
Atomic-scale modeling of cellulose nanocrystals
NASA Astrophysics Data System (ADS)
Wu, Xiawa
Cellulose nanocrystals (CNCs), the most abundant nanomaterials in nature, are recognized as one of the most promising candidates to meet the growing demand of green, bio-degradable and sustainable nanomaterials for future applications. CNCs draw significant interest due to their high axial elasticity and low density-elasticity ratio, both of which are extensively researched over the years. In spite of the great potential of CNCs as functional nanoparticles for nanocomposite materials, a fundamental understanding of CNC properties and their role in composite property enhancement is not available. In this work, CNCs are studied using molecular dynamics simulation method to predict their material' behaviors in the nanoscale. (a) Mechanical properties include tensile deformation in the elastic and plastic regions using molecular mechanics, molecular dynamics and nanoindentation methods. This allows comparisons between the methods and closer connectivity to experimental measurement techniques. The elastic moduli in the axial and transverse directions are obtained and the results are found to be in good agreement with previous research. The ultimate properties in plastic deformation are reported for the first time and failure mechanism are analyzed in details. (b) The thermal expansion of CNC crystals and films are studied. It is proposed that CNC film thermal expansion is due primarily to single crystal expansion and CNC-CNC interfacial motion. The relative contributions of inter- and intra-crystal responses to heating are explored. (c) Friction at cellulose-CNCs and diamond-CNCs interfaces is studied. The effects of sliding velocity, normal load, and relative angle between sliding surfaces are predicted. The Cellulose-CNC model is analyzed in terms of hydrogen bonding effect, and the diamond-CNC model compliments some of the discussion of the previous model. In summary, CNC's material properties and molecular models are both studied in this research, contributing to
Physically representative atomistic modeling of atomic-scale friction
NASA Astrophysics Data System (ADS)
Dong, Yalin
Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the
The chaotic atom model via a fractal approximation of motion
NASA Astrophysics Data System (ADS)
Agop, M.; Nica, P.; Gurlui, S.; Focsa, C.; Magop, D.; Borsos, Z.
2011-10-01
A new model of the atom is built based on a complete and detailed nonlinear dynamics analysis (complete time series, Poincaré 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).
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. PMID:25933864
Model based control of dynamic atomic force microscope
Lee, Chibum; Salapaka, Srinivasa M.
2015-04-15
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{sub ∞} control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.
Atmospheric turbulence optical model (ATOM) based on fractal theory
NASA Astrophysics Data System (ADS)
Jaenisch, Holger M.; Handley, James W.; Scoggins, Jim; Carroll, Marvin P.
1994-06-01
An Atmospheric Turbulence Optical Model (ATOM) is presented that used cellular automata (CA) rules as the basis for modeling synthetic phase sheets. This method allows image fracture, scintillation and blur to be correctly models using the principle of convolution with a complex kernel derived from CA rules interaction. The model takes into account the changing distribution of turbules from micro-turbule domination at low altitudes to macro-domination at high altitudes. The wavelength of propagating images (such as a coherent laser beam) and the range are taken into account. The ATOM model is written in standard FORTRAN 77 and enables high-speed in-line calculation of atmospheric effects to be performed without resorting to computationally intensive solutions of Navier Stokes equations or Cn2 profiles.
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
Quan, Wei; Lv, Lin Liu, Baiqi
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.
A Nonlinear Model for Fuel Atomization in Spray Combustion
NASA Technical Reports Server (NTRS)
Liu, Nan-Suey (Technical Monitor); Ibrahim, Essam A.; Sree, Dave
2003-01-01
Most gas turbine combustion codes rely on ad-hoc statistical assumptions regarding the outcome of fuel atomization processes. The modeling effort proposed in this project is aimed at developing a realistic model to produce accurate predictions of fuel atomization parameters. The model involves application of the nonlinear stability theory to analyze the instability and subsequent disintegration of the liquid fuel sheet that is produced by fuel injection nozzles in gas turbine combustors. The fuel sheet is atomized into a multiplicity of small drops of large surface area to volume ratio to enhance the evaporation rate and combustion performance. The proposed model will effect predictions of fuel sheet atomization parameters such as drop size, velocity, and orientation as well as sheet penetration depth, breakup time and thickness. These parameters are essential for combustion simulation codes to perform a controlled and optimized design of gas turbine fuel injectors. Optimizing fuel injection processes is crucial to improving combustion efficiency and hence reducing fuel consumption and pollutants emissions.
ATOMIC DATA AND SPECTRAL MODEL FOR Fe III
Bautista, Manuel A.; Ballance, Connor P.; Quinet, Pascal
2010-08-01
We present new atomic data (radiative transitions rates and collision strengths) from large-scale calculations and a non-LTE spectral model for Fe III. This model is in very good agreement with observed astronomical emission spectra, in contrast with previous models that yield large discrepancies in observations. The present atomic computations employ a combination of atomic physics methods, e.g., relativistic Hartree-Fock, the Thomas-Fermi-Dirac potential, and Dirac-Fock computation of A-values and the R-matrix with intermediate coupling frame transformation and the Dirac R-matrix. We study advantages and shortcomings of each method. It is found that the Dirac R-matrix collision strengths yield excellent agreement with observations, much improved over previously available models. By contrast, the transformation of the LS-coupling R-matrix fails to yield accurate effective collision strengths at around 10{sup 4} K, despite using very large configuration expansions, due to the limited treatment of spin-orbit effects in the near-threshold resonances of the collision strengths. The present work demonstrates that accurate atomic data for low-ionization iron-peak species are now within reach.
A collisional-radiative average atom model for hot plasmas
Rozsnyai, B.F.
1996-10-17
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.
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. PMID:26575759
Modeling atomic hydrogen diffusion in GaAs
NASA Astrophysics Data System (ADS)
Kagadei, Valerii A.; Nefyodtsev, E.
2004-05-01
The hydrogen diffusion model in GaAs in conditions of an intense flow of penetrating atoms has been developed. It is shown that the formation undersurface diffusion barrier layer from immobile interstitial molecules of hydrogen reduce probability of atoms penetration into crystal and rate of their diffusion in GaAs, and influence on the process of shallow- and/or deep-centers passivation. It is exhibited that the influence of diffusion barrier should be taken into account at optimum mode selection of GaAs structure hydrogenation.
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. PMID:15323678
Atomic scale modeling of boron transient diffusion in silicon
Caturla, M. J.; Diaz de la Rubia, T.; Foad, M.; Giles, M.; Johnson, M. D.; Law, M.; Lilak, A.
1998-06-17
We presents results from a predictive atomic level simulation of Boron diffusion in Silicon under a wide variety of implant and annealing conditions. The parameters for this simulation have been extracted from first principle approximation models and molecular dynamics simulations. The results are compared with experiments showing good agreement in all cases. The parameters and reactions used have been implemented into a continuum-level model simulator.
Quantum Transport Modeling of Atomic Nanostructures on Silicon
NASA Astrophysics Data System (ADS)
Smeu, Manuel
Surface effects can adversely influence the performance of a nanoelectronic device, but may also lead to new functionality. The focus of this thesis is to theoretically study the role of surfaces in nanoelectronics. Our theoretical analysis is from atomic first principles achieved by combining density functional theory with the Keldysh nonequilibrium Green's function approach. This technique allows for all atoms in a system to be treated on an equal footing without any phenomenological parameters. The first part of the thesis considers conduction through a molecule with no substrate to illustrate the sort of system typically modeled in transport calculations. Two Au electrodes are bridged by a substituted benzenediamine molecule (R = CH3, NH2, OH) where an H atom is removed to form a radical that may behave as a spin filter, depending on the R group. Next is considered a π-stacked line of ethylbenzene molecules on the Si(100) surface, where the Si atoms are explicitly included in the calculation. Although the molecules conduct electrons at certain energies, a channel occurs through the substrate, which can dominate the conductance. The use of substituent groups to modulate the electron transport properties of such wires is also investigated, showing that the conductance of the molecular wire could be tuned to dominate over the substrate. Finally, the conductance of the Si(111)-7 × 7 metallic surface is studied. Inspired by experiments suggesting that atomic steps reduce the surface conductance, the atomic structure and transport properties of such steps are examined, revealing that dimer atom buckling along the step edges is the primary culprit since it leads to an opening of a local band gap at the step.
A constructive model potential method for atomic interactions
NASA Technical Reports Server (NTRS)
Bottcher, C.; Dalgarno, A.
1974-01-01
A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.
Modeling of Turbulence Effect on Liquid Jet Atomization
NASA Technical Reports Server (NTRS)
Trinh, H. P.
2007-01-01
Recent studies indicate that turbulence behaviors within a liquid jet have considerable effect on the atomization process. Such turbulent flow phenomena are encountered in most practical applications of common liquid spray devices. This research aims to model the effects of turbulence occurring inside a cylindrical liquid jet to its atomization process. The two widely used atomization models Kelvin-Helmholtz (KH) instability of Reitz and the Taylor analogy breakup (TAB) of O'Rourke and Amsden portraying primary liquid jet disintegration and secondary droplet breakup, respectively, are examined. Additional terms are formulated and appropriately implemented into these two models to account for the turbulence effect. Results for the flow conditions examined in this study indicate that the turbulence terms are significant in comparison with other terms in the models. In the primary breakup regime, the turbulent liquid jet tends to break up into large drops while its intact core is slightly shorter than those without turbulence. In contrast, the secondary droplet breakup with the inside liquid turbulence consideration produces smaller drops. Computational results indicate that the proposed models provide predictions that agree reasonably well with available measured data.
Atomic Data and the Modeling of Supernova Spectra
NASA Astrophysics Data System (ADS)
Fontes, Christopher
2012-06-01
The modeling of supernovae (SNe) incorporates a variety of disciplines, including hydrodynamics, radiation transport, nuclear physics and atomic physics. These efforts require numerical simulation of the final stages of a star's life, the supernova explosion phase, and the radiation that is subsequently emitted by the supernova remnant, which can occur over a time span of tens of thousands of years. While there are several different types of SNe, they all emit radiation in some form. The measurement and interpretation of these spectra provide important information about the structure of the exploding star and the supernova engine. In this talk, the role of atomic data is highlighted as it pertains to the modeling of supernova spectra. Recent applications [1,2] involve the Los Alamos OPLIB opacity database, which has been used to provide atomic opacities for modeling supernova plasmas under local thermodynamic equilibrium (LTE) conditions. Ongoing work includes the application of atomic data generated by the Los Alamos suite of atomic physics codes under more complicated, non-LTE conditions [3]. As a specific, recent example, a portion of the x-ray spectrum produced by Tycho's supernova remnant (SN 1572) will be discussed [4].[4pt] [1] C.L. Fryer et al., Astrophys. J. 707, 193 (2009).[0pt] [2] C.L. Fryer et al., Astrophys. J. 725, 296 (2009).[0pt] [3] C.J. Fontes et al., Conference Proceedings for ICPEAC XXVII (Belfast, Northern Ireland), in press, (2011).[0pt] [4] K.A. Eriksen et al., Presentation at the 2012 AAS Meeting (Austin, TX).
Extended Bose-Hubbard models with ultracold magnetic atoms.
Baier, S; Mark, M J; Petter, D; Aikawa, K; Chomaz, L; Cai, Z; Baranov, M; Zoller, P; Ferlaino, F
2016-04-01
The Hubbard model underlies our understanding of strongly correlated materials. Whereas its standard form only comprises interactions between particles at the same lattice site, extending it to encompass long-range interactions is predicted to profoundly alter the quantum behavior of the system. We realize the extended Bose-Hubbard model for an ultracold gas of strongly magnetic erbium atoms in a three-dimensional optical lattice. Controlling the orientation of the atomic dipoles, we reveal the anisotropic character of the onsite interaction and hopping dynamics and their influence on the superfluid-to-Mott insulator quantum phase transition. Moreover, we observe nearest-neighbor interactions, a genuine consequence of the long-range nature of dipolar interactions. Our results lay the groundwork for future studies of exotic many-body quantum phases. PMID:27124454
Semirelativistic model for ionization of atomic hydrogen by electron impact
Attaourti, Y.; Taj, S.; Manaut, B.
2005-06-15
We present a semirelativistic model for the description of the ionization process of atomic hydrogen by electron impact in the first Born approximation by using the Darwin wave function to describe the bound state of atomic hydrogen and the Sommerfeld-Maue wave function to describe the ejected electron. This model, accurate to first order in Z/c in the relativistic correction, shows that, even at low kinetic energies of the incident electron, spin effects are small but not negligible. These effects become noticeable with increasing incident electron energies. All analytical calculations are exact and our semirelativistic results are compared with the results obtained in the nonrelativistic Coulomb Born approximation both for the coplanar asymmetric and the binary coplanar geometries.
Empirical model of atomic nitrogen in the upper thermosphere
NASA Technical Reports Server (NTRS)
Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.
1977-01-01
Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.
Extended Bose-Hubbard models with ultracold magnetic atoms
NASA Astrophysics Data System (ADS)
Baier, S.; Mark, M. J.; Petter, D.; Aikawa, K.; Chomaz, L.; Cai, Z.; Baranov, M.; Zoller, P.; Ferlaino, F.
2016-04-01
The Hubbard model underlies our understanding of strongly correlated materials. Whereas its standard form only comprises interactions between particles at the same lattice site, extending it to encompass long-range interactions is predicted to profoundly alter the quantum behavior of the system. We realize the extended Bose-Hubbard model for an ultracold gas of strongly magnetic erbium atoms in a three-dimensional optical lattice. Controlling the orientation of the atomic dipoles, we reveal the anisotropic character of the onsite interaction and hopping dynamics and their influence on the superfluid-to-Mott insulator quantum phase transition. Moreover, we observe nearest-neighbor interactions, a genuine consequence of the long-range nature of dipolar interactions. Our results lay the groundwork for future studies of exotic many-body quantum phases.
Generalized Kronig-Penney model for ultracold atomic quantum systems
NASA Astrophysics Data System (ADS)
Negretti, A.; Gerritsma, R.; Idziaszek, Z.; Schmidt-Kaler, F.; Calarco, T.
2014-10-01
We study the properties of a quantum particle interacting with a one-dimensional structure of equidistant scattering centers. We derive an analytical expression for the dispersion relation and for the Bloch functions in the presence of both even and odd scattering waves within the pseudopotential approximation. This generalizes the well-known solid-state physics textbook result known as the Kronig-Penney model. Our generalized model can be used to describe systems such as degenerate Fermi gases interacting with ions or with another neutral atomic species confined in an optical lattice, thus enabling the investigation of polaron or Kondo physics within a simple formalism. We focus our attention on the specific atom-ion system and compare our findings with quantum defect theory. Excellent agreement is obtained within the regime of validity of the pseudopotential approximation. This enables us to derive a Bose-Hubbard Hamiltonian for a degenerate quantum Bose gas in a linear chain of ions.
Charged Neutrinos and Atoms in the Standard Model
NASA Astrophysics Data System (ADS)
Takasugi, E.; Tanaka, M.
1992-03-01
The possibility of the charge quantization in the standard model is examined in the absence of the ``generation as copies'' rule. It is shown that neutrinos and atoms can have mini-charges, while neutron is neutral. If a triplet Higgs boson is introduced, neutrinos have masses. Two neutrinos form a Konopinski-Mahmoud Dirac particle and the other becomes a Majorana particle due to the hidden local anomaly free U(1) symmetry.
AtomDB and PyAtomDB: Atomic Data and Modelling Tools for High Energy and Non-Maxwellian Plasmas
NASA Astrophysics Data System (ADS)
Foster, Adam; Smith, Randall K.; Brickhouse, Nancy S.; Cui, Xiaohong
2016-04-01
The release of AtomDB 3 included a large wealth of inner shell ionization and excitation data allowing accurate modeling of non-equilibrium plasmas. We describe the newly calculated data and compare it to published literature data. We apply the new models to existing supernova remnant data such as W49B and N132D. We further outline progress towards AtomDB 3.1, including a new energy-dependent charge exchange cross sections.We present newly developed models for the spectra of electron-electron bremsstrahlung and those due to non-Maxwellian electron distributions.Finally, we present our new atomic database access tools, released as PyAtomDB, allowing powerful use of the underlying fundamental atomic data as well as the spectral emissivities.
Modeling of Turbulence Effects on Liquid Jet Atomization and Breakup
NASA Technical Reports Server (NTRS)
Trinh, Huu P.; Chen, C. P.
2005-01-01
Recent experimental investigations and physical modeling studies have indicated that turbulence behaviors within a liquid jet have considerable effects on the atomization process. This study aims to model the turbulence effect in the atomization process of a cylindrical liquid jet. Two widely used models, the Kelvin-Helmholtz (KH) instability of Reitz (blob model) and the Taylor-Analogy-Breakup (TAB) secondary droplet breakup by O Rourke et al, are further extended to include turbulence effects. In the primary breakup model, the level of the turbulence effect on the liquid breakup depends on the characteristic scales and the initial flow conditions. For the secondary breakup, an additional turbulence force acted on parent drops is modeled and integrated into the TAB governing equation. The drop size formed from this breakup regime is estimated based on the energy balance before and after the breakup occurrence. This paper describes theoretical development of the current models, called "T-blob" and "T-TAB", for primary and secondary breakup respectivety. Several assessment studies are also presented in this paper.
A Comprehensive X-Ray Absorption Model for Atomic Oxygen
NASA Technical Reports Server (NTRS)
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.; de Vries, C. P.; Zatsarinny, O.
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.
ERIC Educational Resources Information Center
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…
Atomic collision processes for modelling cool star spectra
NASA Astrophysics Data System (ADS)
Barklem, Paul
2015-05-01
The abundances of chemical elements in cool stars are very important in many problems in modern astrophysics. They provide unique insight into the chemical and dynamical evolution of the Galaxy, stellar processes such as mixing and gravitational settling, the Sun and its place in the Galaxy, and planet formation, to name a just few examples. Modern telescopes and spectrographs measure stellar spectral lines with precision of order 1 per cent, and planned surveys will provide such spectra for millions of stars. However, systematic errors in the interpretation of observed spectral lines leads to abundances with uncertainties greater than 20 per cent. Greater precision in the interpreted abundances should reasonably be expected to lead to significant discoveries, and improvements in atomic data used in stellar atmosphere models play a key role in achieving such advances in precision. In particular, departures from the classical assumption of local thermodynamic equilibrium (LTE) represent a significant uncertainty in the modelling of stellar spectra and thus derived chemical abundances. Non-LTE modelling requires large amounts of radiative and collisional data for the atomic species of interest. I will focus on inelastic collision processes due to electron and hydrogen atom impacts, the important perturbers in cool stars, and the progress that has been made. I will discuss the impact on non-LTE modelling, and what the modelling tells us about the types of collision processes that are important and the accuracy required. More specifically, processes of fundamentally quantum mechanical nature such as spin-changing collisions and charge transfer have been found to be very important in the non-LTE modelling of spectral lines of lithium, oxygen, sodium and magnesium.
Atomic mechanism of internal friction in a model metallic glass
NASA Astrophysics Data System (ADS)
Yu, Hai-Bin; Samwer, Konrad
2014-10-01
Internal friction (IF) describes the ability of materials to damp out mechanical oscillations. It is a crucial engineering parameter and also conveys unique microscopic information about structural defects, transport phenomena, and phase transformations in solids. While IF predominately results from lattice defects in crystalline materials, the origin of IF remains unclear in disordered materials, like metallic glasses. In this paper, we study the atomic rearrangements that govern IF in a model metallic glass, via numerical simulations of dynamical mechanical spectroscopy together with structural analysis. We identify cooperative and avalanchelike thermal-driven excitations as an underlying mechanism and demonstrate a linearlike relation between the concentrations of these excitations and the values of IF. Structurally, these excitations can be hindered, and thus suppress IF, by slow atoms that usually associate with full icosahedral symmetry. Our results also provide practical guides in tuning IF in metallic glasses from atomistic perspectives.
Theoretical model for electrophilic oxygen atom insertion into hydrocarbons
Bach, R.D.; Su, M.D. ); Andres, J.L. Wayne State Univ., Detroit, MI ); McDouall, J.J.W. )
1993-06-30
A theoretical model suggesting the mechanistic pathway for the oxidation of saturated-alkanes to their corresponding alcohols and ketones is described. Water oxide (H[sub 2]O-O) is employed as a model singlet oxygen atom donor. Molecular orbital calculations with the 6-31G basis set at the MP2, QCISD, QCISD(T), CASSCF, and MRCI levels of theory suggest that oxygen insertion by water oxide occurs by the interaction of an electrophilic oxygen atom with a doubly occupied hydrocarbon fragment orbital. The electrophilic oxygen approaches the hydrocarbon along the axis of the atomic carbon p orbital comprising a [pi]-[sub CH(2)] or [pi]-[sub CHCH(3)] fragment orbital to form a carbon-oxygen [sigma] bond. A concerted hydrogen migration to an adjacent oxygen lone pair of electrons affords the alcohol insertion product in a stereoselective fashion with predictable stereochemistry. Subsequent oxidation of the alcohol to a ketone (or aldehyde) occurs in a similar fashion and has a lower activation barrier. The calculated (MP4/6-31G*//MP2/6-31G*) activation barriers for oxygen atom insertion into the C-H bonds of methane, ethane, propane, butane, isobutane, and methanol are 10.7, 8.2, 3.9, 4.8, 4.5, and 3.3 kcal/mol, respectively. We use ab initio molecular orbital calculations in support of a frontier MO theory that provides a unique rationale for both the stereospecificity and the stereoselectivity of insertion of electrophilic oxygen and related electrophiles into the carbon-hydrogen bond. 13 refs., 7 figs., 2 tabs.
Bohr model and dimensional scaling analysis of atoms and molecules
NASA Astrophysics Data System (ADS)
Urtekin, Kerim
It is generally believed that the old quantum theory, as presented by Niels Bohr in 1913, fails when applied to many-electron systems, such as molecules, and nonhydrogenic atoms. It is the central theme of this dissertation to display with examples and applications the implementation of a simple and successful extension of Bohr's planetary model of the hydrogenic atom, which has recently been developed by an atomic and molecular theory group from Texas A&M University. This "extended" Bohr model, which can be derived from quantum mechanics using the well-known dimentional scaling technique is used to yield potential energy curves of H2 and several more complicated molecules, such as LiH, Li2, BeH, He2 and H3, with accuracies strikingly comparable to those obtained from the more lengthy and rigorous "ab initio" computations, and the added advantage that it provides a rather insightful and pictorial description of how electrons behave to form chemical bonds, a theme not central to "ab initio" quantum chemistry. Further investigation directed to CH, and the four-atom system H4 (with both linear and square configurations), via the interpolated Bohr model, and the constrained Bohr model (with an effective potential), respectively, is reported. The extended model is also used to calculate correlation energies. The model is readily applicable to the study of molecular species in the presence of strong magnetic fields, as is the case in the vicinities of white dwarfs and neutron stars. We find that magnetic field increases the binding energy and decreases the bond length. Finally, an elaborative review of doubly coupled quantum dots for a derivation of the electron exchange energy, a straightforward application of Heitler-London method of quantum molecular chemistry, concludes the dissertation. The highlights of the research are (1) a bridging together of the pre- and post quantum mechanical descriptions of the chemical bond (Bohr-Sommerfeld vs. Heisenberg-Schrodinger), and
Bohr model and dimensional scaling analysis of atoms and molecules
NASA Astrophysics Data System (ADS)
Svidzinsky, Anatoly; Chen, Goong; Chin, Siu; Kim, Moochan; Ma, Dongxia; Murawski, Robert; Sergeev, Alexei; Scully, Marlan; Herschbach, Dudley
It is generally believed that the old quantum theory, as presented by Niels Bohr in 1913, fails when applied to few electron systems, such as the H2 molecule. Here we review recent developments of the Bohr model that connect it with dimensional scaling procedures adapted from quantum chromodynamics. This approach treats electrons as point particles whose positions are determined by optimizing an algebraic energy function derived from the large-dimension limit of the Schrödinger equation. The calculations required are simple yet yield useful accuracy for molecular potential curves and bring out appealing heuristic aspects. We first examine the ground electronic states of H2, HeH, He2, LiH, BeH and Li2. Even a rudimentary Bohr model, employing interpolation between large and small internuclear distances, gives good agreement with potential curves obtained from conventional quantum mechanics. An amended Bohr version, augmented by constraints derived from Heitler-London or Hund-Mulliken results, dispenses with interpolation and gives substantial improvement for H2 and H3. The relation to D-scaling is emphasized. A key factor is the angular dependence of the Jacobian volume element, which competes with interelectron repulsion. Another version, incorporating principal quantum numbers in the D-scaling transformation, extends the Bohr model to excited S states of multielectron atoms. We also discuss kindred Bohr-style applications of D-scaling to the H atom subjected to superstrong magnetic fields or to atomic anions subjected to high frequency, superintense laser fields. In conclusion, we note correspondences to the prequantum bonding models of Lewis and Langmuir and to the later resonance theory of Pauling, and discuss prospects for joining D-scaling with other methods to extend its utility and scope.
Minimal non-Abelian model of atomic dark matter
NASA Astrophysics Data System (ADS)
Choquette, Jeremie; Cline, James M.
2015-12-01
A dark sector resembling the Standard Model, where the abundance of matter is explained by baryon and lepton asymmetries and stable constituents bind to form atoms, is a theoretically appealing possibility. We show that a minimal model with a hidden SU(2) gauge symmetry broken to U(1), with a Dirac fermion doublet, suffices to realize this scenario. Supplemented with a dark Higgs doublet that gets no vacuum expectation value, we readily achieve the dark matter asymmetry through leptogenesis. The model can simultaneously have three portals to the Standard Model, through the Higgs, non-Abelian kinetic mixing, and the heavy neutrino, with interesting phenomenology for direct and collider searches, as well as cosmologically relevant dark matter self-interactions. Exotic bound states consisting of two fermions and a doubly charged vector boson can exist in one phase of the theory.
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. PMID:25683601
Assessment of Some Atomization Models Used in Spray Calculations
NASA Technical Reports Server (NTRS)
Raju, M. S.; Bulzin, Dan
2011-01-01
The paper presents the results from a validation study undertaken as a part of the NASA s fundamental aeronautics initiative on high altitude emissions in order to assess the accuracy of several atomization models used in both non-superheat and superheat spray calculations. As a part of this investigation we have undertaken the validation based on four different cases to investigate the spray characteristics of (1) a flashing jet generated by the sudden release of pressurized R134A from cylindrical nozzle, (2) a liquid jet atomizing in a subsonic cross flow, (3) a Parker-Hannifin pressure swirl atomizer, and (4) a single-element Lean Direct Injector (LDI) combustor experiment. These cases were chosen because of their importance in some aerospace applications. The validation is based on some 3D and axisymmetric calculations involving both reacting and non-reacting sprays. In general, the predicted results provide reasonable agreement for both mean droplet sizes (D32) and average droplet velocities but mostly underestimate the droplets sizes in the inner radial region of a cylindrical jet.
Using colloids to model atomic thin film growth
NASA Astrophysics Data System (ADS)
Ganapathy, Rajesh; Buckley, Mark; Cohen, Itai
2009-03-01
We epitaxially grow colloidal thin films by sedimenting micron sized colloidal particles on a microfabricated substrate. The attractive interaction between the colloids, induced by a depletant polymer, leads to the nucleation of islands that grow and coalesce with one another. We use confocal microscopy and particle tracking to study the dynamics of the colloidal particles as they diffuse, aggregate and rearrange configurations during deposition. The saturation island density is estimated as a function of the deposition rate and depletant concentration. We find that our results are in excellent agreement with those obtained from atomic deposition experiments suggesting that our system can be used to model various phenomena that occur in atomic thin film growth. Furthermore, we quantify the Ehrlich-Schwoebel step edge barrier by using holographic optical tweezers to create artificial islands and study the dynamics of colloidal monomers placed on the edge of these islands. Owing to the short-range of the attractive interaction in our system, the origin of the step edge barrier in colloids is strikingly different from atoms.
Modeling atomization processes in high-pressure vaporizing sprays
NASA Astrophysics Data System (ADS)
Reitz, Rolf D.
The theoretical basis and numerical implementation of KIVA, a multidimensional computer code for the simulation of atomization and vaporization processes in the injection of a liquid through a round hole into a compressed gas, are described. KIVA is based on the blob-injection model of Reitz and Diwakar (1987), taking into account the effects of liquid inertia, surface tension, and the aerodynamic forces on the jet, as well as drop collision and coalescence and the effect of drops on turbulence in the gas. The predictions of KIVA for different injection regimes are compared with published experimental data in extensive graphs, and good agreement is demonstrated.
Quantitative Modeling of Single Atom High Harmonic Generation
Gordon, Ariel; Kaertner, Franz X.
2005-11-25
It is shown by comparison with numerical solutions of the Schroedinger equation that the three step model (TSM) of high harmonic generation (HHG) can be improved to give a quantitatively reliable description of the process. Excellent agreement is demonstrated for the H atom and the H{sub 2}{sup +} molecular ion. It is shown that the standard TSM heavily distorts the HHG spectra, especially of H{sub 2}{sup +}, and an explanation is presented for this behavior. Key to the improvement is the use of the Ehrenfest theorem in the TSM.
A comprehensive X-ray absorption model for atomic oxygen
Gorczyca, T. W.; Bautista, M. A.; Mendoza, C.; Hasoglu, M. F.; García, J.; Gatuzz, E.; Kaastra, J. S.; Raassen, A. J. J.; De Vries, C. P.; Kallman, T. R.; Manson, S. T.; Zatsarinny, O.
2013-12-10
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, 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.
Low energy neutral atoms in the earth's magnetosphere: Modeling
Moore, K.R.; McComas, D.J.; Funsten, H.O.; Thomsen, M.F.
1992-01-01
Detection of low energy neutral atoms (LENAs) produced by the interaction of the Earth's geocorona with ambient space plasma has been proposed as a technique to obtain global information about the magnetosphere. Recent instrumentation advances reported previously and in these proceedings provide an opportunity for detecting LENAs in the energy range of <1 keV to {approximately}50 keV. In this paper, we present results from a numerical model which calculates line of sight LENA fluxes expected at a remote orbiting spacecraft for various magnetospheric plasma regimes. This model uses measured charge exchange cross sections, either of two neural hydrogen geocorona models, and various empirical modes of the ring current and plasma sheet to calculate the contribution to the integrated directional flux from each point along the line of sight of the instrument. We discuss implications for LENA imaging of the magnetosphere based on these simulations. 22 refs.
Numerical modeling for primary atomization of liquid jets
NASA Technical Reports Server (NTRS)
Przekwas, A. J.; Chuech, S. G.; Singhal, A. K.
1989-01-01
In the proposed numerical model for primary atomization, surface-wave dispersion equations are solved in conjunction with the jet-embedding technique of solving mean flow equations of a liquid jet. Linear and approximate nonlinear models have been considered. In each case, the dispersion equation is solved over the whole wavelength spectrum to predict drop sizes, frequency, and liquid-mass breakup rates without using any empirical constants. The present model has been applied to several low-speed and high-speed jets. For the high-speed case (the LOX/H2 coaxial injector of the Space Shuttle Main Engine Preburner), predicted drop sizes and liquid breakup rates are in good agreement with the results of the CICM code, which have been calibrated against measured data.
Chapman, Michael S.; Trzynka, Andrew; Chapman, Brynmor K.
2013-01-01
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. PMID:23376441
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. PMID:23376441
Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N
2009-05-01
Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035
A generalized model of atomic processes in dense plasmas
NASA Astrophysics Data System (ADS)
Chung, Hyun-Kyung; Chen, M.; Ciricosta, O.; Vinko, S.; Wark, J.; Lee, R. W.
2015-11-01
A generalized model of atomic processes in plasmas, FLYCHK, has been developed over a decade to provide experimentalists fast and simple but reasonable predictions of atomic properties of plasmas. For a given plasma condition, it provides charge state distributions and spectroscopic properties, which have been extensively used for experimental design and data analysis and currently available through NIST web site. In recent years, highly transient and non-equilibrium plasmas have been created with X-ray free electron lasers (XFEL). As high intensity x-rays interact with matter, the inner-shell electrons are ionized and Auger electrons and photo electrons are generated. With time, electrons participate in the ionization processes and collisional ionization by these electrons dominates photoionization as electron density increases. To study highly complex XFEL produced plasmas, SCFLY, an extended version of FLYCHK code has been used. The code accepts the time-dependent history of x-ray energy and intensity to compute population distribution and ionization distribution self-consistently with electron temperature and density assuming an instantaneous equilibration. The model and its applications to XFEL experiments will be presented as well as its limitations.
Model of spacecraft atomic oxygen and solar exposure microenvironments
NASA Technical Reports Server (NTRS)
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.
Four-component united-atom model of bitumen.
Hansen, J S; Lemarchand, Claire A; Nielsen, Erik; Dyre, Jeppe C; Schrøder, Thomas
2013-03-01
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 diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From 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, and resinous oil tend to form nano-aggregates. The characteristic dynamical relaxation time of these aggregates is larger than that of the homogeneously distributed parts of the system, leading to strong dynamical heterogeneity. PMID:23485314
Four-component united-atom model of bitumen
NASA Astrophysics Data System (ADS)
Hansen, J. S.; Lemarchand, Claire A.; Nielsen, Erik; Dyre, Jeppe C.; Schrøder, Thomas
2013-03-01
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 diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From 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, and resinous oil tend to form nano-aggregates. The characteristic dynamical relaxation time of these aggregates is larger than that of the homogeneously distributed parts of the system, leading to strong dynamical heterogeneity.
Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF
NASA Technical Reports Server (NTRS)
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.
Independent-particle models for light negative atomic ions
NASA Technical Reports Server (NTRS)
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.
Atomic scale modelling of hexagonal structured metallic fission product alloys
Middleburgh, S. C.; King, D. M.; Lumpkin, G. R.
2015-01-01
Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)—making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperatures. The variation of Mo content was modelled to understand the change in alloy structure and behaviour with fuel burnup (Mo molar content decreases in these alloys as burnup increases). The predicted structures compare extremely well with experimentally ascertained values. Vacancy formation energies and the behaviour of extrinsic defects (including iodine and xenon) in the epsilon phase were also investigated to further understand the impact that the metallic precipitates have on fuel performance. PMID:26064629
SLIMP: Strong laser interaction model package for atoms and molecules
NASA Astrophysics Data System (ADS)
Zhang, Bin; Zhao, Zengxiu
2015-07-01
We present the SLIMP package, which provides an efficient way for the calculation of strong-field ionization rate and high-order harmonic spectra based on the single active electron approximation. The initial states are taken as single-particle orbitals directly from output files of the general purpose quantum chemistry programs GAMESS, Firefly and Gaussian. For ionization, the molecular Ammosov-Delone-Krainov theory, and both the length gauge and velocity gauge Keldysh-Faisal-Reiss theories are implemented, while the Lewenstein model is used for harmonic spectra. Furthermore, it is also efficient for the evaluation of orbital coordinates wavefunction, momentum wavefunction, orbital dipole moment and calculation of orbital integrations. This package can be applied to quite large basis sets and complex molecules with many atoms, and is implemented to allow easy extensions for additional capabilities.
Simulating and Modeling Transport Through Atomically Thin Membranes
NASA Astrophysics Data System (ADS)
Ostrowski, Joseph; Eaves, Joel
2014-03-01
The world is running out of clean portable water. The efficacy of water desalination technologies using porous materials is a balance between membrane selectivity and solute throughput. These properties are just starting to be understood on the nanoscale, but in the limit of atomically thin membranes it is unclear whether one can apply typical continuous time random walk models. Depending on the size of the pore and thickness of the membrane, mass transport can range from single stochastic passage events to continuous flow describable by the usual hydrodynamic equations. We present a study of mass transport through membranes of various pore geometries using reverse nonequilibrium simulations, and analyze transport rates using stochastic master equations.
Atomic-level models of the bacterial carboxysome shell
Tanaka, S.; Kerfeld, C.A.; Sawaya, M.R.; Cai, F.; Heinhorst, S.; Cannon, G.C.; Yeates, T.O.
2008-06-03
The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.
Atomic-scale simulations of atomic and molecular mobility in models of interstellar ice
NASA Astrophysics Data System (ADS)
Andersson, Stefan
The mobility of atoms and molecular radicals at ice-covered dust particles controls the surprisingly rich chemistry of circumstellar and interstellar environments, where a large number of different organic molecules have been observed. Both thermal and non-thermal processes, for instance caused by UV radiation, have been inferred to play important roles in this chemistry. A growing number of experimental studies support previously suggested mechanisms and add to the understanding of possible astrochemical processes. Simulations, of both experiments and astrophysical environments, aid in interpreting experiments and suggesting important mechanisms. Still, the exact mechanisms behind the mobility of species in interstellar ice are far from fully understood. We have performed calculations at the molecular level on the mobility of H atoms and OH radicals at water ice surfaces of varying morphology. Calculations of binding energies and diffusion barriers of H atoms at crystalline and amorphous ice surfaces show that the experimentally observed slower diffusion at amorphous ice is due to considerably stronger binding energies and higher diffusion barriers than at crystalline ice. These results are in excellent agreement with recent experiments. It was also found that quantum tunneling is important for H atom mobility below 10 K. The binding energies and diffusion barriers of OH radicals at crystalline ice have been studied using the ONIOM(QM:AMOEBA) approach. Results indicate that OH diffusion over crystalline ice, contrary to the case of H atoms, might be slower at crystalline ice than at amorphous ice, due to a higher surface density of stronger binding sites at crystalline ice. We have also performed molecular dynamics simulations of the photoexcitation of vapor-deposited water at a range of surface temperatures. These results support that the experimentally observed desorption of H atoms following UV excitation is best explained by release of H atoms from
A computer model for liquid jet atomization in rocket thrust chambers
NASA Astrophysics Data System (ADS)
Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Yang, H. Q.; Ibrahim, E.; Chuech, S.; Przekwas, A. J.
1991-12-01
The process of atomization has been used as an efficient means of burning liquid fuels in rocket engines, gas turbine engines, internal combustion engines, and industrial furnaces. Despite its widespread application, this complex hydrodynamic phenomenon has not been well understood, and predictive models for this process are still in their infancy. The difficulty in simulating the atomization process arises from the relatively large number of parameters that influence it, including the details of the injector geometry, liquid and gas turbulence, and the operating conditions. In this study, numerical models are developed from first principles, to quantify factors influencing atomization. For example, the surface wave dynamics theory is used for modeling the primary atomization and the droplet energy conservation principle is applied for modeling the secondary atomization. The use of empirical correlations has been minimized by shifting the analyses to fundamental levels. During applications of these models, parametric studies are performed to understand and correlate the influence of relevant parameters on the atomization process. The predictions of these models are compared with existing experimental data. The main tasks of this study were the following: development of a primary atomization model; development of a secondary atomization model; development of a model for impinging jets; development of a model for swirling jets; and coupling of the primary atomization model with a CFD code.
Atomic Models of Strong Solids Interfaces Viewed as Composite Structures
NASA Astrophysics Data System (ADS)
Staffell, I.; Shang, J. L.; Kendall, K.
2014-02-01
This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture energy of a composite interface is needed. Using an interface model based on atomic interaction forces, it is shown that a single layer of contaminant atoms between the matrix and the reinforcement can reduce the interface fracture energy by an order of magnitude, giving a large delamination effect. The paper also looks to a future in which cars will be made largely from composite materials. Radical improvements in automobile design are necessary because the number of cars worldwide is predicted to double. This paper predicts gains in fuel economy by suggesting a new theory of automobile fuel consumption using an adaptation of Coulomb's friction law. It is demonstrated both by experiment and by theoretical argument that the energy dissipated in standard vehicle tests depends only on weight. Consequently, moving from metal to fibre construction can give a factor 2 improved fuel economy performance, roughly the same as moving from a petrol combustion drive to hydrogen fuel cell propulsion. Using both options together can give a factor 4 improvement, as demonstrated by testing a composite car using the ECE15 protocol.
Atomic-orbital expansion model for describing ion-atom collisions at intermediate and low energies
Lin, C.D.; Fritsch, W.
1983-01-01
In the description of inelastic processes in ion-atom collisions at moderate energies, the semiclassical close-coupling method is well established as the standard method. Ever since the pioneering work on H/sup +/ + H in the early 60's, the standard procedure is to expand the electronic wavefunction in terms of molecular orbitals (MO) or atomic orbitals (AO) for describing collisions at, respectively, low or intermediate velocities. It has been recognized since early days that traveling orbitals are needed in the expansions in order to represent the asymptotic states in the collisions correctly. While the adoption of such traveling orbitals presents no conceptual difficulties for expansions using atomic orbitals, the situation for molecular orbitals is less clear. In recent years, various forms of traveling MO's have been proposed, but conflicting results for several well-studied systems have been reported.
One-dimensional extended Hubbard model in the atomic limit
NASA Astrophysics Data System (ADS)
Mancini, F.; Mancini, F. P.
2008-06-01
We present the exact solution of the one-dimensional extended Hubbard model in the atomic limit within the Green’s function and equations of motion formalism. We provide a comprehensive and systematic analysis of the model by considering all the relevant response and correlation functions as well as thermodynamic quantities in the whole parameters space. At zero temperature we identify four phases in the plane (U,n) ( U is the on-site potential and n is the filling) and relative phase transitions as well as different types of charge ordering. These features are endorsed by investigating at T=0 the chemical potential and pertinent local correlators, the particle and double occupancy correlation functions, the entropy, and by studying the behavior in the limit T→0 of the charge and spin susceptibilities. A detailed study of the thermodynamic quantities is also presented at finite temperature. This study evidences that a finite-range order persists for a wide range of the temperature, as shown by the behavior of the correlation functions and by the two-peak structure exhibited by the charge susceptibility and by the entropy. Moreover, the equations of motion formalism, together with the use of composite operators, allows us to exactly determine the set of elementary excitations. As a result, the density of states can be determined and a detailed analysis of the specific heat allows for identifying the excitations and for ascribing its two-peak structure to a redistribution of the charge density.
Magnetic-sublevel atomic kinetics modeling for line polarization spectroscopy
Hakel, P.; Mancini, R. C.
2004-01-01
We discuss the mechanism of polarized X-ray line emission in plasmas, its connection to plasma anisotropy, and introduce an atomic kinetics model and code (POLAR) based on the population kinetics of magnetic sublevels. POLAR represents a multi-level, multi-process approach to the problem of polarized spectra in plasmas, and hence it is well suited for plasma applications where cascade effects and alignment transfer can become important. Polarization degrees of X-ray spectral lines computed with POLAR were successfully benchmarked against calculations done with other formalisms, and experimental results obtained at the EBIT facility of Lawrence Livermore National Laboratory. We also investigated the polarization of He-like Si X-ray satellite lines as spectral signatures of anisotropy in the electron distribution function. A comprehensive modeling study was performed taking into account hydrodynamics and electron kinetics. We find that two satellite lines connecting singlet states develop a noticeable polarization while the triplet lines remain unpolarized. These results suggest a scenario where triplet lines could be used as a reference while the singlets could be used as polarized markers of plasma anisotropy.
Secondary Students' Mental Models of Atoms and Molecules: Implications for Teaching Chemistry.
ERIC Educational Resources Information Center
Harrison, Allan G.; Treagust, David F.
1996-01-01
Examines the reasoning behind views of atoms and molecules held by students (n=48) and investigates how mental models may assist or hamper further instruction in chemistry. Reports that students prefer models of atoms and molecules that depict them as discrete, concrete structures. Recommends that teachers develop student modeling skills and…
Development of a phenomenological model for coal slurry atomization
Dooher, J.P.
1995-11-01
Highly concentrated suspensions of coal particles in water or alternate fluids appear to have a wide range of applications for energy production. For enhanced implementation of coal slurry fuel technology, an understanding of coal slurry atomization as a function coal and slurry properties for specific mechanical configurations of nozzle atomizers should be developed.
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
NASA Technical Reports Server (NTRS)
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.
Improving the Ni I atomic model for solar and stellar atmospheric models
Vieytes, M. C.; Fontenla, J. M. E-mail: johnf@digidyna.com
2013-06-01
Neutral nickel (Ni I) is abundant in the solar atmosphere and is one of the important elements that contribute to the emission and absorption of radiation in the spectral range between 1900 and 3900 Å. Previously, the Solar Radiation Physical Modeling (SRPM) models of the solar atmosphere only considered a few levels of this species. Here, we improve the Ni I atomic model by taking into account 61 levels and 490 spectral lines. We compute the populations of these levels in full NLTE using the SRPM code and compare the resulting emerging spectrum with observations. The present atomic model significantly improves the calculation of the solar spectral irradiance at near-UV wavelengths, which is important for Earth atmospheric studies, and particularly for ozone chemistry.
Operation of the computer model for direct atomic oxygen exposure of Earth satellites
NASA Technical Reports Server (NTRS)
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.
Coupling of an average-atom model with a collisional-radiative equilibrium model
Faussurier, G. Blancard, C.; Cossé, P.
2014-11-15
We present a method to combine a collisional-radiative equilibrium model and an average-atom model to calculate bound and free electron wavefunctions in hot dense plasmas by taking into account screening. This approach allows us to calculate electrical resistivity and thermal conductivity as well as pressure in non local thermodynamic equilibrium plasmas. Illustrations of the method are presented for dilute titanium plasma.
'Bubble chamber model' of fast atom bombardment induced processes.
Kosevich, Marina V; Shelkovsky, Vadim S; Boryak, Oleg A; Orlov, Vadim V
2003-01-01
A hypothesis concerning FAB mechanisms, referred to as a 'bubble chamber FAB model', is proposed. This model can provide an answer to the long-standing question as to how fragile biomolecules and weakly bound clusters can survive under high-energy particle impact on liquids. The basis of this model is a simple estimation of saturated vapour pressure over the surface of liquids, which shows that all liquids ever tested by fast atom bombardment (FAB) and liquid secondary ion mass spectrometry (SIMS) were in the superheated state under the experimental conditions applied. The result of the interaction of the energetic particles with superheated liquids is known to be qualitatively different from that with equilibrium liquids. It consists of initiation of local boiling, i.e., in formation of vapour bubbles along the track of the energetic particle. This phenomenon has been extensively studied in the framework of nuclear physics and provides the basis for construction of the well-known bubble chamber detectors. The possibility of occurrence of similar processes under FAB of superheated liquids substantiates a conceptual model of emission of secondary ions suggested by Vestal in 1983, which assumes formation of bubbles beneath the liquid surface, followed by their bursting accompanied by release of microdroplets and clusters as a necessary intermediate step for the creation of molecular ions. The main distinctive feature of the bubble chamber FAB model, proposed here, is that the bubbles are formed not in the space and time-restricted impact-excited zone, but in the nearby liquid as a 'normal' boiling event, which implies that the temperature both within the bubble and in the droplets emerging on its burst is practically the same as that of the bulk liquid sample. This concept can resolve the paradox of survival of intact biomolecules under FAB, since the part of the sample participating in the liquid-gas transition via the bubble mechanism has an ambient temperature
Fast and accurate modeling of molecular atomization energies with machine learning.
Rupp, Matthias; Tkatchenko, Alexandre; Müller, Klaus-Robert; von Lilienfeld, O Anatole
2012-02-01
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of ∼10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves. PMID:22400967
NASA Astrophysics Data System (ADS)
Jin, Lin; Auerbach, Scott M.; Monson, Peter A.
2011-04-01
We present an atomic lattice model for studying the polymerization of silicic acid in sol-gel and related processes for synthesizing silica materials. Our model is based on Si and O atoms occupying the sites of a body-centered-cubic lattice, with all atoms arranged in SiO4 tetrahedra. This is the simplest model that allows for variation in the Si-O-Si angle, which is largely responsible for the versatility in silica polymorphs. The model describes the assembly of polymerized silica structures starting from a solution of silicic acid in water at a given concentration and pH. This model can simulate related materials—chalcogenides and clays—by assigning energy penalties to particular ring geometries in the polymerized structures. The simplicity of this approach makes it possible to study the polymerization process to higher degrees of polymerization and larger system sizes than has been possible with previous atomistic models. We have performed Monte Carlo simulations of the model at two concentrations: a low density state similar to that used in the clear solution synthesis of silicalite-1, and a high density state relevant to experiments on silica gel synthesis. For the high concentration system where there are NMR data on the temporal evolution of the Qn distribution, we find that the model gives good agreement with the experimental data. The model captures the basic mechanism of silica polymerization and provides quantitative structural predictions on ring-size distributions in good agreement with x-ray and neutron diffraction data.
Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I.
NASA Technical Reports Server (NTRS)
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
Project Physics Reader 5, Models of the Atom.
ERIC Educational Resources Information Center
Harvard Univ., Cambridge, MA. Harvard Project Physics.
As a supplement to Project Physics Unit 5, a collection of articles is presented in this reader for student browsing. Nine excerpts are given under the following headings: failure and success, Einstein, Mr. Tompkins and simultaneity, parable of the surveyors, outside and inside the elevator, the teacher and the Bohr theory of atom, Dirac and Born,…
A simple model for optical capture of atoms in strong magnetic quadrupole fields
NASA Astrophysics Data System (ADS)
Haubrich, D.; Höpe, A.; Meschede, D.
1993-10-01
The radiative capture of cesium atoms from the gas phase in a magnetooptic trap with strong magnetic field gradients is studied. A simplified analytic model is used to derive an upper limit for capture velocities. The resulting scaling law agrees well with the observed number of atoms and with the density as a function of field gradient.
Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness
ERIC Educational Resources Information Center
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
NASA Technical Reports Server (NTRS)
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.
Plasma injection and atomic physics models for use in particle simulation codes
Procassini, R.J. California Univ., Berkeley, CA . Electronics Research Lab.)
1991-06-12
Models of plasma injection (creation) and charged/neutral atomic physics which are suitable for incorporation into particle simulation codes are described. Both planar and distributed source injection models are considered. Results obtained from planar injection into a collisionless plasma-sheath region are presented. The atomic physics package simulates the charge exchange and impact ionization interactions which occur between charged particles and neutral atoms in a partially-ionized plasma. These models are applicable to a wide range of problems, from plasma processing of materials to transport in the edge region of a tokamak plasma. 18 refs., 6 figs.
Atomic charges for modeling metal–organic frameworks: Why and how
Hamad, Said Balestra, Salvador R.G.; Bueno-Perez, Rocio; Calero, Sofia; Ruiz-Salvador, A. Rabdel
2015-03-15
Atomic partial charges are parameters of key importance in the simulation of Metal–Organic Frameworks (MOFs), since Coulombic interactions decrease with the distance more slowly than van der Waals interactions. But despite its relevance, there is no method to unambiguously assign charges to each atom, since atomic charges are not quantum observables. There are several methods that allow the calculation of atomic charges, most of them starting from the electronic wavefunction or the electronic density or the system, as obtained with quantum mechanics calculations. In this work, we describe the most common methods employed to calculate atomic charges in MOFs. In order to show the influence that even small variations of structure have on atomic charges, we present the results that we obtained for DMOF-1. We also discuss the effect that small variations of atomic charges have on the predicted structural properties of IRMOF-1. - Graphical abstract: We review the different method with which to calculate atomic partial charges that can be used in force field-based calculations. We also present two examples that illustrate the influence of the geometry on the calculated charges and the influence of the charges on structural properties. - Highlights: • The choice of atomic charges is crucial in modeling adsorption and diffusion in MOFs. • Methods for calculating atomic charges in MOFs are reviewed. • We discuss the influence of the framework geometry on the calculated charges. • We discuss the influence of the framework charges on structural the properties.
Modeling Linear and Cyclic PKS Intermediates through Atom Replacement
2015-01-01
The mechanistic details of many polyketide synthases (PKSs) remain elusive due to the instability of transient intermediates that are not accessible via conventional methods. Here we report an atom replacement strategy that enables the rapid preparation of polyketone surrogates by selective atom replacement, thereby providing key substrate mimetics for detailed mechanistic evaluations. Polyketone mimetics are positioned on the actinorhodin acyl carrier protein (actACP) to probe the underpinnings of substrate association upon nascent chain elongation and processivity. Protein NMR is used to visualize substrate interaction with the actACP, where a tetraketide substrate is shown not to bind within the protein, while heptaketide and octaketide substrates show strong association between helix II and IV. To examine the later cyclization stages, we extended this strategy to prepare stabilized cyclic intermediates and evaluate their binding by the actACP. Elongated monocyclic mimics show much longer residence time within actACP than shortened analogs. Taken together, these observations suggest ACP-substrate association occurs both before and after ketoreductase action upon the fully elongated polyketone, indicating a key role played by the ACP within PKS timing and processivity. These atom replacement mimetics offer new tools to study protein and substrate interactions and are applicable to a wide variety of PKSs. PMID:25406716
Metelkin, E. V.; Ryazanov, A. I. Semenov, E. V.
2008-09-15
A new theoretical model is developed for the investigation of atomic collision cascades and subcascades in irradiated solids consisting of atoms of a single type. The model is based on an analytical description of the elastic collisions between moving atoms knocked out of the crystal lattice sites and the immobile atoms of the lattice. The description is based on the linear kinetic Boltzmann equation describing the retardation of primary recoil atoms (PRAs) in irradiated solids. The laws of conservation for the total number and the kinetic energy of moving atoms, which follow from the kinetic Boltzmann equation, are analyzed using the proposed model. An analytical solution is obtained for the stationary kinetic Boltzmann equation, which describes the retardation of PRAs for a given source responsible for their production. A kinetic equation for the moving atoms and the corresponding laws of conservation are also analyzed with allowance for the binding energy of atoms at the crystal lattice sites. A criterion for determining the threshold energy of subcascade formation in irradiated solids is formulated. Based on this criterion, the threshold energy of subcascade formation is calculated using the Thomas-Fermi potential. Formulas are presented for determining the mean size and number of subcascades formed in a solid as functions of the PRA energy.
NASA Technical Reports Server (NTRS)
Banks, Bruce A.; Stueber, Thomas J.; Norris, Mary Jo
1998-01-01
A Monte Carlo computational model has been developed which simulates atomic oxygen attack of protected polymers at defect sites in the protective coatings. The parameters defining how atomic oxygen interacts with polymers and protective coatings as well as the scattering processes which occur have been optimized to replicate experimental results observed from protected polyimide Kapton on the Long Duration Exposure Facility (LDEF) mission. Computational prediction of atomic oxygen undercutting at defect sites in protective coatings for various arrival energies was investigated. The atomic oxygen undercutting energy dependence predictions enable one to predict mass loss that would occur in low Earth orbit, based on lower energy ground laboratory atomic oxygen beam systems. Results of computational model prediction of undercut cavity size as a function of energy and defect size will be presented to provide insight into expected in-space mass loss of protected polymers with protective coating defects based on lower energy ground laboratory testing.
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. PMID:27420398
Computational model for noncontact atomic force microscopy: energy dissipation of cantilever
NASA Astrophysics Data System (ADS)
Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M.
2016-09-01
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.
Modeling Atoms and Molecules: A New Lesson for Upper Elementary and Middle School Students.
ERIC Educational Resources Information Center
Schwaner, Terry D.; And Others
1994-01-01
Describes a study involving 86 fifth-grade science students to enhance their understandings of basic biological chemistry. Contains a lesson that allows students to build models of atoms and molecules. (ZWH)
Atomic bomb survivors and the sigmoidal response model
Kondo, S.
1994-12-31
Epidemiological data on health effects of low-level radiation based on 40-yr followup studies of 75000 atomic bomb survivors and 35000 control people show that there were no measurable risks from low-level radiation in regard to noncancer diseases, genetic, teratogenic, and carcinogenic effects. However, seemingly sigmoidal responses of bomb radiation-induced cancers, which must have been caused by tumorigenic mutations contradict experimental results that mutations linearly increase with increase in radiation dose. An explanation is proposed for this superficial contradiction.
NASA Astrophysics Data System (ADS)
Jung, Hyunseung; in, Chihun; Choi, Hyunyong; Lee, Hojin
2014-06-01
Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems.
Invited review article: The statistical modeling of atomic clocks and the design of time scales.
Levine, Judah; Ibarra-Manzano, O
2012-02-01
I will show how the statistical models that are used to describe the performance of atomic clocks are derived from their internal design. These statistical models form the basis for time scales, which are used to define international time scales such as International Atomic Time and Coordinated Universal Time. These international time scales are realized by ensembles of clocks at national laboratories such as the National Institute of Standards and Technology, and I will describe how ensembles of atomic clocks are characterized and managed. PMID:22380071
Invited Review Article: The statistical modeling of atomic clocks and the design of time scales
Levine, Judah
2012-02-15
I will show how the statistical models that are used to describe the performance of atomic clocks are derived from their internal design. These statistical models form the basis for time scales, which are used to define international time scales such as International Atomic Time and Coordinated Universal Time. These international time scales are realized by ensembles of clocks at national laboratories such as the National Institute of Standards and Technology, and I will describe how ensembles of atomic clocks are characterized and managed.
Jung, Hyunseung; In, Chihun; Choi, Hyunyong; Lee, Hojin
2014-01-01
Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems. PMID:24910144
Nonlinear Jaynes–Cummings model for two interacting two-level atoms
NASA Astrophysics Data System (ADS)
de los Santos-Sánchez, O.; González-Gutiérrez, C.; Récamier, J.
2016-08-01
In this work we examine a nonlinear version of the Jaynes–Cummings model for two identical two-level atoms allowing for Ising-like and dipole–dipole interplays between them. The model is said to be nonlinear in the sense that it can incorporate both a general intensity-dependent interaction between the atomic system and the cavity field and/or the presence of a nonlinear medium inside the cavity. As an example, we consider a particular type of atom-field coupling based upon the so-called Buck–Sukumar model and a lossless Kerr-like cavity. We describe the possible effects of such features on the evolution of some quantities of current interest, such as atomic excitation, purity, concurrence, the entropy of the field and the evolution of the latter in phase space.
A simple model of molecular imaging with noncontact atomic force microscopy
NASA Astrophysics Data System (ADS)
Moll, Nikolaj; Gross, Leo; Mohn, Fabian; Curioni, Alessandro; Meyer, Gerhard
2012-08-01
Using functionalized tips, the atomic resolution of a single organic molecule can be achieved by noncontact atomic force microscopy (nc-AFM) operating in the regime of short-ranged repulsive Pauli forces. To theoretically describe the atomic contrast in such AFM images, we propose a simple model in which the Pauli repulsion is assumed to follow a power law as a function of the probed charge density. As the exponent in this power law is found to be largely independent of the sample molecule, our model provides a general method for simulating atomically resolved AFM images of organic molecules. For a single perylene-tetracarboxylic-dianhydride (PTCDA) molecule imaged with a CO-terminated tip, we find excellent agreement with the experimental data. Our model eliminates the need to take into account the full tip and sample system and therefore reduces computational cost by three orders of magnitude.
Kinetic modeling of primary and secondary oxygen atom fluxes at 1 AU
NASA Astrophysics Data System (ADS)
Balyukin, Igor; Katushkina, Olga; Alexashov, Dmitry; Izmodenov, Vladislav
2016-07-01
The first quantitative measurements of the interstellar heavy (oxygen and neon) neutral atoms obtained on the IBEX spacecraft were presented in Park et al. (ApJS, 2015). Qualitative analysis of these data shows that the secondary component of the interstellar oxygen atoms was also measured along with the primary interstellar atoms. This component is formed near the heliopause due to process of charge exchange of interstellar oxygen ions with hydrogen atoms and its existence in the heliosphere was previously predicted theoretically (Izmodenov et al, 1997, 1999, 2001). Quantitative analysis of fluxes of interstellar heavy neutral atoms is only possible with the help of a model which takes into account both filtration of the primary and origin of the secondary interstellar oxygen in the region of interaction of the solar wind with the local interstellar medium as well as a detailed simulation of the motion of interstellar atoms inside the heliosphere. This simulation must take into account the temporal and heliolatitudinal dependences of ionization, the process of charge exchange with the protons of the solar wind and the effect of the solar gravitational attraction. This paper presents the results of modeling interstellar oxygen and neon atoms in the heliospheric shock layer and inside the heliosphere based on a new three-dimensional kinetic-MHD model of the solar wind interaction with the local interstellar medium (Izmodenov and Alexashov, ApJS, 2015) and the comparison of this results with the data obtained on the IBEX spacecraft.
NASA Astrophysics Data System (ADS)
Tsivilskiy, I. V.; Nagulin, K. Yu.; Gilmutdinov, A. Kh.
2016-02-01
A full three-dimensional nonstationary numerical model of graphite electrothermal atomizers of various types is developed. The model is based on solution of a heat equation within solid walls of the atomizer with a radiative heat transfer and numerical solution of a full set of Navier-Stokes equations with an energy equation for a gas. Governing equations for the behavior of a discrete phase, i.e., atomic particles suspended in a gas (including gas-phase processes of evaporation and condensation), are derived from the formal equations molecular kinetics by numerical solution of the Hertz-Langmuir equation. The following atomizers test the model: a Varian standard heated electrothermal vaporizer (ETV), a Perkin Elmer standard THGA transversely heated graphite tube with integrated platform (THGA), and the original double-stage tube-helix atomizer (DSTHA). The experimental verification of computer calculations is carried out by a method of shadow spectral visualization of the spatial distributions of atomic and molecular vapors in an analytical space of an atomizer.
NASA Astrophysics Data System (ADS)
Farrell, Kathryn; Oden, J. Tinsley
2014-07-01
Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and
YUP.SCX: Coaxing Atomic Models into Medium Resolution Electron Density Maps
Tan, Robert K.-Z.; Devkota, Batsal; Harvey, Stephen C.
2008-01-01
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 33 Å, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments. PMID:18572416
Models of atoms in plasmas based on common formalism for bound and free electrons
NASA Astrophysics Data System (ADS)
Blenski, T.; Piron, R.; Caizergues, C.; Cichocki, B.
2013-12-01
Atom-in-plasma models: Thomas-Fermi (TF) and INFERNO, AJCI and VAAQP, that use the same formalism for all electrons are briefly described and analyzed from the point of view of their thermodynamic consistence. While the TF and VAAQP models may be derived from variational principle and respect the virial theorem, it appears that two earlier quantum extensions of the quasi-classical TF model, INFERNO and AJCI, are not fully variational. The problems of the two latter approaches are analyzed from the point of view of the VAAQP model. However all quantum models seem to give unrealistic description of atoms in plasma at low temperature and high plasma densities. These difficulties are connected with the Wigner-Seitz cavity approach to non-central ions that is present in all considered models. Comparison of some equation-of-state data from TF, INFERNO and VAAQP models are shown on a chosen example. We report also on the status of our research on the frequency-dependent linear-response theory of atoms in plasma. A new Ehrenfest-type sum rule, originally proposed in the quantum VAAQP model, was proven in the case of the response of the TF atom with the Bloch hydrodynamics (TFB) and checked by numerical example. The TFB case allows one to have a direct insight into the rather involved mathematics of the self-consistent linear response calculations in situations when both the central atom and its plasma vicinity are perturbed by an electric field.
NASA Astrophysics Data System (ADS)
Wheeldon, Ruth
2012-06-01
Chemistry students' explanations of ionisation energy phenomena often involve a number of non-scientific or inappropriate ideas being used to form causality arguments. Research has attributed this to many science teachers using these ideas themselves (Tan and Taber, in J Chem Educ 86(5):623-629, 2009). This research extends this work by considering which atomic models are used in pre-service teachers' explanations and how that relates to the causality ideas expressed. Thirty-one pre-service teachers were interviewed. Each was asked to describe and explain four different atomic representations (Rutherford, Electron cloud micrograph, Bohr and Schrödinger types) in as much detail as they could. They also provided an explanation for the subsequent ionisation energy values for an oxygen atom and identified which representations were helpful in explaining the values. Significantly, when pre-service teachers only used Bohr type representations, they did not use repelling electron ideas in their explanations. However, arguments that were based on electron-electron repulsion used features from Schrödinger type atoms. These findings suggest that many pre-service teachers need to develop their atomic modelling skills so that they select and use models more expertly and that subsequent ionisation explanations offer a context in which to explore different atomic models' limitations and their deployment as explanatory resources.
NASA Astrophysics Data System (ADS)
O'Sullivan, Colm
2016-03-01
The role of "semi-classical" (Bohr-Sommerfeld) and "semi-quantum-mechanical" (atomic orbital) models in the context of the teaching of atomic theory is considered. It is suggested that an appropriate treatment of such models can serve as a useful adjunct to quantum mechanical study of atomic systems.
Efficient Nonlinear Atomization Model for Thin 3D Free Liquid Films
NASA Astrophysics Data System (ADS)
Mehring, Carsten
2007-03-01
Reviewed is a nonlinear reduced-dimension thin-film model developed by the author and aimed at the prediction of spray formation from thin films such as those found in gas-turbine engines (e.g., prefilming air-blast atomizers), heavy-fuel-oil burners (e.g., rotary-cup atomizers) and in the paint industry (e.g., flat-fan atomizers). Various implementations of the model focusing on different model-aspects, i.e., effect of film geometry, surface tension, liquid viscosity, coupling with surrounding gas-phase flow, influence of long-range intermolecular forces during film rupture are reviewed together with a validation of the nonlinear wave propagation characteristics predicted by the model for inviscid planar films using a two-dimensional vortex- method. An extension and generalization of the current nonlinear film model for implementation into a commercial flow- solver is outlined.
Influence of atomic modeling on integrated simulations of laser-produced Au plasmas.
Frank, Yechiel; Raicher, Erez; Ehrlich, Yosi; Hurvitz, Gilad; Shpilman, Zeev; Fraenkel, Moshe; Zigler, Arie; Henis, Zohar
2015-11-01
Time-integrated x-ray emission spectra of laser-irradiated Au disks were recorded using transmission grating spectrometry, at laser intensities of 10(13) to 10(14) W/cm(2). Radiation-hydrodynamics and atomic physics calculations were used to simulate the emitted spectra. Three major plasma regions can be recognized: the heat wave, the corona, and an intermediate region connecting them. An analysis of the spectral contribution of these three plasma regions to the integrated recorded spectrum is presented. The importance of accurate atomic modeling of the intermediate plasma region, between the corona and the heat wave, is highlighted. The influence of several aspects of the atomic modeling is demonstrated, in particular multiply-excited atomic configurations and departure from local thermal equilibrium. PMID:26651806
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.
2013-06-10
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data. We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of O III and Fe II and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe II].
Reasoning with Atomic-Scale Molecular Dynamic Models
ERIC Educational Resources Information Center
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Optical Pattern Formation in Spatially Bunched Atoms: A Self-Consistent Model and Experiment
NASA Astrophysics Data System (ADS)
Schmittberger, Bonnie L.; Gauthier, Daniel J.
2014-05-01
The nonlinear optics and optomechanical physics communities use different theoretical models to describe how optical fields interact with a sample of atoms. There does not yet exist a model that is valid for finite atomic temperatures but that also produces the zero temperature results that are generally assumed in optomechanical systems. We present a self-consistent model that is valid for all atomic temperatures and accounts for the back-action of the atoms on the optical fields. Our model provides new insights into the competing effects of the bunching-induced nonlinearity and the saturable nonlinearity. We show that it is crucial to keep the fifth and seventh-order nonlinearities that arise when there exists atomic bunching, even at very low optical field intensities. We go on to apply this model to the results of our experimental system where we observe spontaneous, multimode, transverse optical pattern formation at ultra-low light levels. We show that our model accurately predicts our experimentally observed threshold for optical pattern formation, which is the lowest threshold ever reported for pattern formation. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.
NASA Astrophysics Data System (ADS)
Park, Eun Jung
The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced
[Application of model 4650 type I compressor atomizer in bronchial challenge test].
Yuan, Y; Wang, Y; Zeng, J; He, T
2000-06-01
This study was directed to the feasibility of applying a simple atomizer-model 4650 type I (abbrev. M)-to bronchial challenge test. 92 cases of asthma were divided into 3 groups randomly. All of them were subjected to the bronchial challenge test by M atomizer, and by standard Dosimeter atomizer (abbrev. D) as a comparison. In the test by M atomizer, the times for inspiring challenging medicine were 1, 1.5 and 2 minutes for the 3 groups respectively, while the time for D atomizer was 1 minute for all. The results showed no significant differences (P > 0.2-0.5) between the two atomizers in the 3 groups, their values were linear correlated. When the inspiring time was 1 minute for both M and D, the test needed a higher concentration of challenging medicine for M than for D, their coefficient of correlation (r = 0.285) was relatively low. When inspiring time postponed to 1.5 minute for M, the difference in medicine concentration between M and D was smallest (-0.075 g/L), r = 0.665. However, a further postponed inspiring time to 2 minute for M reversely broadened their difference. These results indicated that the efficiency of M atomizer was a little lower than that of D, postponing the inspiring time for M could make up this weakness. A 1.5 minute inspiring time for M atomizer was the suggestion. Some modifications on M atomizer were done by us for a better efficiency, and the cheap and popular M atomizer could be a good replacement in bronchial challenge test. PMID:12515156
Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling
NASA Astrophysics Data System (ADS)
Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki
2015-12-01
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.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. Electronic supplementary information (ESI) available: Three TEM movies, additional TEM data corresponding to movies, calculated models, and lifetime results. See DOI: 10.1039/c5nr05913e
Fast Three-Dimensional Method of Modeling Atomic Oxygen Undercutting of Protected Polymers
NASA Technical Reports Server (NTRS)
Snyder, Aaron; Banks, Bruce A.
2002-01-01
A method is presented to model atomic oxygen erosion of protected polymers in low Earth orbit (LEO). Undercutting of protected polymers by atomic oxygen occurs in LEO due to the presence of scratch, crack or pin-window defects in the protective coatings. As a means of providing a better understanding of undercutting processes, a fast method of modeling atomic-oxygen undercutting of protected polymers has been developed. Current simulation methods often rely on computationally expensive ray-tracing procedures to track the surface-to-surface movement of individual "atoms." The method introduced in this paper replaces slow individual particle approaches by substituting a model that utilizes both a geometric configuration-factor technique, which governs the diffuse transport of atoms between surfaces, and an efficient telescoping series algorithm, which rapidly integrates the cumulative effects stemming from the numerous atomic oxygen events occurring at the surfaces of an undercut cavity. This new method facilitates the systematic study of three-dimensional undercutting by allowing rapid simulations to be made over a wide range of erosion parameters.
Theoretical modeling of laser-induced plasmas using the ATOMIC code
NASA Astrophysics Data System (ADS)
Colgan, James; Johns, Heather; Kilcrease, David; Judge, Elizabeth; Barefield, James, II; Clegg, Samuel; Hartig, Kyle
2014-10-01
We report on efforts to model the emission spectra generated from laser-induced breakdown spectroscopy (LIBS). LIBS is a popular and powerful method of quickly and accurately characterizing unknown samples in a remote manner. In particular, LIBS is utilized by the ChemCam instrument on the Mars Science Laboratory. We model the LIBS plasma using the Los Alamos suite of atomic physics codes. Since LIBS plasmas generally have temperatures of somewhere between 3000 K and 12000 K, the emission spectra typically result from the neutral and singly ionized stages of the target atoms. We use the Los Alamos atomic structure and collision codes to generate sets of atomic data and use the plasma kinetics code ATOMIC to perform LTE or non-LTE calculations that generate level populations and an emission spectrum for the element of interest. In this presentation we compare the emission spectrum from ATOMIC with an Fe LIBS laboratory-generated plasma as well as spectra from the ChemCam instrument. We also discuss various physics aspects of the modeling of LIBS plasmas that are necessary for accurate characterization of the plasma, such as multi-element target composition effects, radiation transport effects, and accurate line shape treatments. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.
Mathematical modelling of the liquid atomization process by cocurrent gas flow
NASA Astrophysics Data System (ADS)
Arkhipov, V. A.; Boiko, V. M.; Goldin, V. D.; Maslov, E. A.; Orlov, S. E.; Poplavskiy, S. V.; Usanina, A. S.; Zharova, I. K.
2016-04-01
This paper focuses on the physical-mathematical model of liquid atomization in the spray pattern of an ejection nozzle. A flow field of a gas phase behind the nozzle section is computed using the Ansys Fluent package. Dynamics of molten metal droplets in the gas phase within a trajectory approach is calculated. Using the presented model, numerical calculation results are given.
Re-examination of an early model of two-electron atoms
NASA Astrophysics Data System (ADS)
Wesenberg, G. E.; Noid, D. W.; Delos, J. B.
1985-07-01
A classical model for the helium atom, originally proposed in 1920 by Irving Langmuir, is re-examined. This model gives surprisingly good energies over a wide range of nuclear charges. In the limit of very large nuclear charge, agreement with the Wilson-Sommerfeld quantization rules is seen. A discussion of stable and unstable orbits is given.
Nano Goes to School: A Teaching Model of the Atomic Force Microscope
ERIC Educational Resources Information Center
Planinsic, Gorazd; Kovac, Janez
2008-01-01
The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…
ERIC Educational Resources Information Center
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…
Everyone Wants to Be a Model Teacher: Part III: Extensions to Atomic Structures and Bonding.
ERIC Educational Resources Information Center
Schrader, C. L.
1985-01-01
Describes activities in which students: (1) propose creative atomic models that account for observed properties and predict additional experimental data; (2) calculate empirical formulas for 27 binary compounds; (3) propose a model to explain why certain elements have certain valences; and (4) arrange hypothetical elements into a periodic chart.…
ERIC Educational Resources Information Center
Battino, Rubin
1983-01-01
Describes the design, construction, and use of oversize lecture-demonstration atomic/molecular models. These models appeal to both concrete and formal operational students. Also describes construction and use of an "spdf" sandwich board and an experiment using attribute blocks. (JN)
A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.
Genheden, Samuel; Essex, Jonathan W
2015-10-13
We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264
Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation
NASA Technical Reports Server (NTRS)
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.
Expansion of the USDA ARS Aerial Application spray atomization models
Technology Transfer Automated Retrieval System (TEKTRAN)
An effort is underway to update the USDA ARS aerial spray nozzle models using new droplet sizing instrumen-tation and measurement techniques. As part of this effort, the applicable maximum airspeed is being increased from 72 to 80 m/s to provide guidance to applicators when using new high speed air...
Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen
NASA Technical Reports Server (NTRS)
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
Collisional radiative average atom code based on a relativistic Screened Hydrogenic Model
NASA Astrophysics Data System (ADS)
Benita, A. J.; Mínguez, E.; Mendoza, M. A.; Rubiano, J. G.; Gil, J. M.; Rodríguez, R.; Martel, P.
2015-03-01
A steady-state and time-dependent collisional-radiative ''average-atom'' (AA) model (ATMED CR) is presented for the calculation of atomic and radiative properties of plasmas for a wide range of laboratory and theoretical conditions: coronal, local thermodynamic equilibrium or nonlocal thermodynamic equilibrium, optically thin or thick plasmas and photoionized plasmas. The radiative and collisional rates are a set of analytical approximations that compare well with more sophisticated quantum treatment of atomic rates that yield fast calculations. The atomic model is based on a new Relativistic Screened Hydrogenic Model (NRSHM) with a set of universal screening constants including nlj-splitting that has been obtained by fitting to a large database of ionization potentials and excitation energies compiled from the National Institute of Standards and Technology (NIST) database and the Flexible Atomic Code (FAC). The model NRSHM has been validated by comparing the results with ionization energies, transition energies and wave functions computed using sophisticated self-consistent codes and experimental data. All the calculations presented in this work were performed using ATMED CR code.
NASA Astrophysics Data System (ADS)
Gorokhov, A. V.; Sinaiski, I. E.
2006-03-01
The Jaynes-Cummings model (JCM) of two-level atom interacting with the photon mode in ideal cavity plays an essential role in modern quantum optics. In previous papers 1,2 an exact form of density matrix of the JCM with fixed atom position and photons dissipation was found. Here, taking into account the classical motion of the atom through the cavity, it is considered a case of nonideal cavity with zero temperature. We have obtained an exact expression for density matrix and calculated photon spectra and spectra of the mean number of photons in a cavity and and time dependencies of some values relevant for the one-atom maser theory.
Planar hydrogen-like atom in inhomogeneous magnetic fields: Exactly or quasi-exactly solvable models
NASA Astrophysics Data System (ADS)
Liu, Liyan; Hao, Qinghai
2015-05-01
We use a simple mathematical method to solve the problem of a two-dimensional hydrogen-like atom in the inhomogeneous magnetic fields B = ( k/ r)z and B = ( k/ r 3)z. We construct a Hamiltonian that takes the same form as the Hamiltonian of a hydrogen-like atom in the homogeneous magnetic fields and obtain the energy spectrum by comparing the Hamiltonians. The results show that the whole spectrum of the atom in the magnetic field B = ( k/ r)z can be obtained, and the problem is exactly solvable in this case. We find analytic solutions of the Schrödinger equation for the atom in the magnetic field B = ( k/ r 3)z for particular values of the magnetic strength k and thus present a quasi-exactly solvable model.
Numerical Modeling of Turbulence Effects within an Evaporating Droplet in Atomizing Sprays
NASA Technical Reports Server (NTRS)
Balasubramanyam, M. S.; Chen, C. P.; Trinh, H. P.
2006-01-01
A new approach to account for finite thermal conductivity and turbulence effects within atomizing liquid sprays is presented in this paper. The model is an extension of the T-blob and T-TAB atomization/spray model of Trinh and Chen (2005). This finite conductivity model is based on the two-temperature film theory, where the turbulence characteristics of the droplet are used to estimate the effective thermal diffhsivity within the droplet phase. Both one-way and two-way coupled calculations were performed to investigate the performance of this model. The current evaporation model is incorporated into the T-blob atomization model of Trinh and Chen (2005) and implemented in an existing CFD Eulerian-Lagrangian two-way coupling numerical scheme. Validation studies were carried out by comparing with available evaporating atomization spray experimental data in terms of jet penetration, temperature field, and droplet SMD distribution within the spray. Validation results indicate the superiority of the finite-conductivity model in low speed parallel flow evaporating spray.
NASA Astrophysics Data System (ADS)
Lüdde, Hans Jürgen; Achenbach, Alexander; Kalkbrenner, Thilo; Jankowiak, Hans-Christian; Kirchner, Tom
2016-04-01
A new model to account for geometric screening corrections in an independent-atom-model description of ion-molecule collisions is introduced. The ion-molecule cross sections for net capture and net ionization are represented as weighted sums of atomic cross sections with weight factors that are determined from a geometric model of overlapping cross section areas. Results are presented for proton collisions with targets ranging from diatomic to complex polyatomic molecules. Significant improvement compared to simple additivity rule results and in general good agreement with experimental data are found. The flexibility of the approach opens up the possibility to study more detailed observables such as orientation-dependent and charge-state-correlated cross sections for a large class of complex targets ranging from biomolecules to atomic clusters.
Masses of atomic nuclei in the infinite nuclear matter model
Satpathy, L.; Nayak, R.C.
1988-07-01
We present mass excesses of 3481 nuclei in the range 18less than or equal toAless than or equal to267 using the infinite nuclear matter model based on the Hugenholtz-Van Hove theorem. In this model the ground-state energy of a nucleus of asymmetry ..beta.. is considered equivalent to the energy of a perfect sphere made up of the infinite nuclear matter of the same asymmetry plus the residual energy due to shell effects, deformation, etc., called the local energy eta. In this model there are two kinds of parameters: global and local. The five global parameters characterizing the properties of the above sphere are determined by fitting the mass of all nuclei (756) in the recent mass table of Wapstra et al. having error bar less than 30 keV. The local parameters are determined for 25 regions each spanning 8 or 10 A values. The total number of parameters including the five global ones is 238. The root-mean-square deviation for the calculated masses from experiment is 397 keV for the 1572 nuclei used in the least-squares fit. copyright 1988 Academic Press, Inc.
An atomic model of brome mosaic virus using direct electron detection and real-space optimization
Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah
2014-01-01
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. PMID:25185801
An atomic model of brome mosaic virus using direct electron detection and real-space optimization
NASA Astrophysics Data System (ADS)
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
2014-01-01
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. PMID:25185801
NASA Astrophysics Data System (ADS)
Ling, Yue; Zaleski, Stéphane; Institut Jean Le Rond d'Alembert Team
2014-11-01
Numerical simulation is conducted to investigate the drop formation and evolution in gas-assisted atomization. The atomizer consists of two parallel planar jets: the fast gas jet and the slow liquid jet. Due to the shear between gas and liquid streams, the liquid-gas interface is unstable, and this eventually leads to full atomization. A fundamental challenge in atomization simulations is the existence of multiple length scales involved. In order to accurately capture both the gas-liquid interface instability and the drop dynamics, a multi-scale multiphase flow simulation strategy is proposed. In the present model, the gas-liquid interface is resolved by the Volume-of-Fluid (VOF) method, while the small drops are represented by Lagrangian point-particle (LPP) models. Particular attention is paid on validating the coupling and conversion between LPP and VOF. The present model is validated by comparing with direct numerical simulation (DNS) results and also experimental data. The simulation results show complex coupling between the interface instability and the turbulent gas jet, which in turn influence the formation and evolution of the drops formed in atomization. ANR-11-MONU-0011.
The LANL atomic kinetics modeling effort and its application to W plasmas
Colgan, James; Abdallah, Joseph; Fontes, Christopher; Zhang, Honglin
2010-12-10
This is the work of the LANL group on atomic kinetics modelling. There are various levels of detail in the LANL suite of atomic physics codes: (1) Non-relativistic configuration average kinetics (nl{sup w}) + UTA spectra, (2) Relativistic configuration average kinetics (nlj{sup w}) + UTA spectra, (3) Mixed UTA (MUTA) - configuration average kinetics and spectra composed of mixture of UTAs and fine-structure features and (4) Fine-structure levels. The LANL suite of atomic physics codes consists of 5 codes: (1) CATS/RATS atomic structure codes (semi-relativistic Cowan code or Dirac-Fock-Slater code), (2) ACE collisional excitation code (Plane-wave Born, Columb-Born and distorted-wave methods) and (3) GIPPER ionization code (scaled-hydrogenic and distorted-wave methods). An on-line version of the codes is available at http://aphysics2.lanl.gov/tempweb. ATOMIC kinetics modelling code uses the atomic data for LTE or NLTE population kinetics models and spectral modelling of a broad range of plasma applications. The mixed UTA (MUTA) approach was developed for the spectra of complex ions and the results are in very good agreement with the Sandia-Z Iron opacity experiments. The LANL configuration-average/MUTA calculations were applied to tungsten problems of the non-LTE kinetics code comparison workshops. The LANL group plans to perform much larger calculations to assess the accuracy of the older results and to investigate low-temperature tungsten processes relevant to the divertor modelling.
NASA Astrophysics Data System (ADS)
Brecht, A. S.; Bougher, S. W.; Gérard, J.-C.; Soret, L.
2012-02-01
Nightglow emissions provide insight into the global thermospheric circulation, specifically in the transition region (˜70-120 km). The O 2 IR nightglow statistical map created from Venus Express (VEx) Visible and InfraRed Thermal Imaging Spectrometer (VIRTIS) observations has been used to deduce a three-dimensional atomic oxygen density map. In this study, the National Center of Atmospheric Research (NCAR) Venus Thermospheric General Circulation Model (VTGCM) is utilized to provide a self-consistent global view of the atomic oxygen density distribution. More specifically, the VTGCM reproduces a 2D nightside atomic oxygen density map and vertical profiles across the nightside, which are compared to the VEx atomic oxygen density map. Both the simulated map and vertical profiles are in close agreement with VEx observations within a ˜30° contour of the anti-solar point. The quality of agreement decreases past ˜30°. This discrepancy implies the employment of Rayleigh friction within the VTGCM may be an over-simplification for representing wave drag effects on the local time variation of global winds. Nevertheless, the simulated atomic oxygen vertical profiles are comparable with the VEx profiles above 90 km, which is consistent with similar O 2 ( 1Δ) IR nightglow intensities. The VTGCM simulations demonstrate the importance of low altitude trace species as a loss for atomic oxygen below 95 km. The agreement between simulations and observations provides confidence in the validity of the simulated mean global thermospheric circulation pattern in the lower thermosphere.
Laser-induced photofragmentation of triethylaluminum: Modeling H-atom production
NASA Astrophysics Data System (ADS)
Brum, Jeffrey L.; Deshmukh, Subhash; Koplitz, Brent
1990-12-01
A rate-equation approach is presented that models H-atom formation during the pulsed laser photolysis of a triethyl metal compound, the specific case being triethylaluminum excited at 193 nm. An excimer laser initiates the chemistry under collisionless conditions, and H atoms are produced that are detected using two-photon (121.6+364.7 nm) ionization. Experimentally, the H-atom intensity is monitored as a function of photolysis laser power. Mechanistically, the primary photodissociation step is postulated to involve cleavage of the metal-carbon bond, thereby producing an ethyl radical. This species can then either: (1) form C2H4 and H directly; or (2) absorb an additional photon and produce an H-atom photofragment. The rate equations and their solutions allow one to calculate how H-atom production should vary as a function of photolysis laser power, and the interplay between the two H-atom production channels is calculated for various absorption cross sections and dissociation rates. A comparison with experimental power dependence data suggests that an overall one-photon dissociation process predominates under the experimental conditions actually used.
Modeling the Reaction of Fe Atoms with CCl4
Camaioni, Donald M.; Ginovska, Bojana; Dupuis, Michel
2009-01-05
The reaction of zero-valent iron with carbon tetrachloride (CCl4) in gas phase was studied using density functional theory. Temperature programmed desorption experiments over a range of Fe and CCl4 coverages on a FeO(111) surface, demonstrate a rich surface chemistry with several reaction products (C2Cl4, C2Cl6, OCCl2, CO, FeCl2, FeCl3) observed. The reactivity of Fe and CCl4 was studied under three stoichiometries, one Fe with one CCl4, one Fe with two CCl4 molecules and two Fe with one CCl4, modeling the environment of the experimental work. The electronic structure calculations give insight into the reactions leading to the experimentally observed products and suggest that novel Fe-C-Cl containing species are important intermediates in these reactions. The intermediate complexes are formed in highly exothermic reactions, in agreement with the experimentally observed reactivity with the surface at low temperature (30 K). This initial survey of the reactivity of Fe with CCl4 identifies some potential reaction pathways that are important in the effort to use Fe nano-particles to differentiate harmful pathways that lead to the formation of contaminants like chloroform (CHCl3) from harmless pathways that lead to products such as formate (HCO2-) or carbon oxides in water and soil. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.
NASA Astrophysics Data System (ADS)
Yin, Cong; Lin, Zheng-Zhe; Li, Min; Tang, Hao
2016-04-01
A condensing potential (CP) model was established for predicting the geometric structure of two-dimensional (2D) atomic islands on crystal surfaces. To further verify the CP model, statistical molecular dynamics simulations are performed to investigate the trapping adatom process of atomic island steps on Pt (111). According to the detailed analysis on the adatom trapping process, the CP model should be a universal theory to understand the shape of the 2D atomic islands on crystal surfaces.
Building a pseudo-atomic model of the anaphase-promoting complex
Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; Fonseca, Paula C. A. da; Barford, David
2013-11-01
This article describes an example of molecular replacement in which atomic models are used to interpret electron-density maps determined using single-particle electron-microscopy data. The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14–15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.
A model of optical trapping cold atoms using a metallic nano wire with surface plasmon effect
NASA Astrophysics Data System (ADS)
Thi Phuong Lan, Nguyen; Thi Nga, Do; Viet, Nguyen Ai
2016-06-01
In this work, we construct a new model of optical trapping cold atoms with a metallic nano wire by using surface plasmon effect generated by strong field of laser beams. Using the skin effect, we send a strong oscillated electromagnetic filed through the surface of a metallic nano wire. The local field generated by evanescent effect creates an effective attractive potential near the surface of metallic nano wires. The consideration of some possible boundary and frequency conditions might lead to non-trivial bound state solution for a cold atom. We discus also the case of the laser reflection optical trap with shell-core design, and compare our model with another recent schemes of cold atom optical traps using optical fibers and carbon nanotubes.
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. PMID:23014503
Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model
NASA Astrophysics Data System (ADS)
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
2012-10-01
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 over \\vec{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.
Transport-theoretic model for the electron-proton-hydrogen atom aurora. I. Theory
Basu, B.; Jasperse, J.R; Strickland, D.J.
1993-12-01
The first self-consistent transport-theoretic model for the combined electron-proton-hydrogen atom aurora is presented. This is needed for accurate modeling of the diffuse aurora, particularly in the midnight sector, for which a statistical study indicates that the proton contribution to the total auroral energy flux is (on the average) about 20 to 25% of that of the electrons. As a result, the ionization yield as well as the yields of many emission features will be underestimated (on the average) by about the same percentage if the proton-hydrogen atom contributions are neglected. The model presented here can also be used to study a pure electron aurora or a pure proton-hydrogen atom aurora by choosing the appropriate boundary conditions, namely, by setting the incident flux of one or the other particle population equal to zero. In the latter case, the new feature of the present model is the rigorous transport-theoretic treatment of the contributions to ionization rates and to emission rates and yields from the secondary electrons produced by protons and hydrogen atoms. A coupled set of three linear transport equations is presented. Protons and hydrogen atoms are coupled only to each other through charge-changing (charge exchange and stripping) collisions, while the electrons are coupled to both protons and hydrogen atoms through the secondary electrons that they produce. Source functions for the secondary electrons produced by the three primary particle populations are compared and contrasted, and the numerical methods for solving the coupled transport equations are described. Finally, formulas for calculating pertinent aurora-related quantities from the particle fluxes are given. 66 refs., 9 figs., 2 tabs.
UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions
Siebert, Xavier; Navaza, Jorge
2009-01-01
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/. PMID:19564685
Atomic Dipole Squeezing in the Correlated Two-Mode Two-Photon Jaynes-Cummings Model
NASA Technical Reports Server (NTRS)
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.
Elliott, Simon D; Dey, Gangotri; Maimaiti, Yasheng; Ablat, Hayrensa; Filatova, Ekaterina A; Fomengia, Glen N
2016-07-01
Recent progress in the simulation of the chemistry of atomic layer deposition (ALD) is presented for technologically important materials such as alumina, silica, and copper metal. Self-limiting chemisorption of precursors onto substrates is studied using density functional theory so as to determine reaction pathways and aid process development. The main challenges for the future of ALD modeling are outlined. PMID:26689290
NASA Astrophysics Data System (ADS)
El-Orany, Faisal A. A.
2006-11-01
In this paper, we study the evolution of two two-level atoms interacting with a single-mode quantized radiation field, namely, the two-atom multiphoton Jaynes-Cummings model (JCM). We assume that the field and the atoms are initially prepared in the superposition of displaced number states and excited atomic states, respectively. For this system, we investigate the atomic inversion, Wigner function, phase distribution and entanglement. We show that for symmetric (asymmetric) atoms, the system can generate asymmetric (symmetric) cat states at a quarter of the revival time. Furthermore, the degrees of entanglement for the field-atoms and the one-atom-remainder tangles depend on the rate of energy flow between the parties. The interference in phase space decreases the degree of entanglement in the bipartite.
NASA Astrophysics Data System (ADS)
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.
Berry phase in a two-atom Jaynes-Cummings model with Kerr medium
NASA Astrophysics Data System (ADS)
Bu, Shen-Ping; Zhang, Guo-Feng; Liu, Jia; Chen, Zi-Yu
2008-12-01
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-ɛ 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.
Mathematical Modeling of Ultracold Few-Body Processes in Atomic Traps
NASA Astrophysics Data System (ADS)
Melezhik, V. S.
2016-02-01
We discuss computational aspects of the developed mathematical models for ultracold few-body processes in atomic traps. The key element of the elaborated computational schemes is a nondirect product discrete variable representation (npDVR) we have suggested and applied to the time-dependent and stationary Schrödinger equations with a few spatial variables. It turned out that this approach is very effcient in quantitative analysis of low-dimensional ultracold few-body systems arising in confined geometry of atomic traps. The effciency of the method is demonstrated here on two examples. A brief review is also given of novel results obtained recently.
A robust all-atom model for LCAT generated by homology modeling[S
Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.
2015-01-01
LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A2 (PLA2) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15–20 Å relative to PLA2. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport. PMID:25589508
An attempt for modeling the atmospheric transport of 3H around Kakrapar Atomic Power Station.
Patra, A K; Nankar, D P; Joshi, C P; Venkataraman, S; Sundar, D; Hegde, A G
2008-01-01
Prediction of downwind tritium air concentrations in the environment around Kakrapar Atomic Power Station (KAPS) was studied on the basis of Gaussian plume dispersion model. The tritium air concentration by field measurement [measured tritium air concentrations in the areas adjacent to KAPS] were compared with the theoretically calculated values (predicted) to validate the model. This approach will be useful in evaluating environmental radiological impacts due to pressurised heavy water reactors. PMID:18664562
Estimation of the adequacy of the fractal model of the atomic structure of amorphous silicon
Golodenko, A. B.
2010-01-15
A method of constructing a fractal model of noncrystalline solid substance is considered using the example of amorphous silicon. In systems of iteration functions, the physical meaning of dihedral and valence angles of the elementary crystallographic cell is assigned to arguments. The model adequacy is estimated by the radial distribution function, the atomic structure density, the distribution of valence and dihedral angles, and the density of dangling interatomic bonds.
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
2015-02-01
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. PMID:25393218
Influence of the plasma environment on atomic structure using an ion-sphere model
NASA Astrophysics Data System (ADS)
Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel
2015-09-01
Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene
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.
Modeling the Formation of Tropical Rings of Atomic Bromine and Iodine
NASA Astrophysics Data System (ADS)
Saiz-Lopez, A.; Fernandez, R.; Salawitch, R. J.; Kinnison, D. E.; Lamarque, J. F.; Ordoñez, C.; Gomez Martin, J. C.; Tilmes, S.
2014-12-01
Very short-lived (VSL) bromo- and iodocarbons are produced at a prodigious rate by ocean biology and these source compounds (SGVSL), together with their degradation inorganic products (PGVSL), are lofted by vigorous convection to the tropical tropopause layer (TTL). Using a state-of-the-art photochemical mechanism within a global model, we investigate the partitioning and loading of reactive inorganic halogens within the TTL. The specific low ozone and low temperature conditions of this region of the atmosphere changes the steady-state between halogen atoms and oxides, making the atoms the dominant species. We suggest that this leads to the formation of two daytime "tropical rings" of both atomic bromine and iodine that circle the tropics with the sun. In addition to a description of this photochemical phenomenon, this communication the partitioning of inorganic halogen reservoirs within the TTL and assess its relevance for the injection of bromine to stratosphere.
Modeling the formation of tropical rings of atomic bromine and iodine
NASA Astrophysics Data System (ADS)
Saiz-Lopez, Alfonso; Fernandez, Rafael; Gomez Martin, Juan Carlos; Salawitch, Ross; Kinnison, Douglas; Lamarque, Jean-Francois; Tilmes, Simone
2015-04-01
Very short-lived (VSL) bromo- and iodocarbons are produced at a prodigious rate by ocean biology and these source compounds (SGVSL), together with their degradation inorganic products (PGVSL), are lofted by vigorous convection to the tropical tropopause layer (TTL). Using a state-of-the-art photochemical mechanism within a global model, we investigate the partitioning and loading of reactive inorganic halogens within the TTL. The specific low ozone and low temperature conditions of this region of the atmosphere changes the steady-state between halogen atoms and oxides, making the atoms the dominant species. We suggest that this leads to the formation of two daytime "tropical rings" of both atomic bromine and iodine that circle the tropics with the sun. In addition to a description of this photochemical phenomenon, this communication the partitioning of inorganic halogen reservoirs within the TTL and assess its relevance for the injection of bromine to stratosphere.
Adsorption and recombination of hydrogen atoms on a model graphite surface. [in interstellar space
NASA Technical Reports Server (NTRS)
Aronowitz, S.; Chang, S.
1985-01-01
The adsorption and recombination of atomic hydrogen on a model graphite grain have been examined in a series of calculations in which a modified, iterative, extended Hueckel program was used. The hydrogen atom is found to be chemisorbed at a site with a zero-point binding energy of 0.7 eV and at an equilibrium distance of 2.25 A above the site. Despite a barrier of about 0.4 eV between adjacent sites, calculations suggest that at temperatures as low as 10 K, an H atom will tunnel through to adjacent sites in less than one nanosecond. However, a potential barrier to the recombination of two hydrogen atoms has been found which displays high sensitivity to the mutual arrangement of the two hydrogen atoms with respect to the graphite surface. Results show that at very low temperatures, recombinations can occur only by tunneling. Consistent with experiment, the region in which H2 begins to form exhibits a repulsive potential with respect to possible chemisorption of the incipient H2 entity.
Collisional radiative model for heavy atoms in hot non-local-thermodynamical-equilibrium plasmas
NASA Astrophysics Data System (ADS)
Bar-Shalom, A.; Oreg, J.; Klapisch, M.
1997-07-01
A collisional radiative model for calculating non-local-thermodynamical-equilibrium (non-LTE) spectra of heavy atoms in hot plasmas has been developed, taking into account the numerous excited and autoionizing states. This model uses superconfigurations as effective levels with an iterative procedure which converges to the detailed configuration spectrum. The non-LTE opacities and emissivities may serve as a reliable benchmark for simpler on-line models in hydrodynamic code simulations. The model is tested against detailed configuration calculations of selenium and is applied to non-LTE optically thin plasma of lutetium.
Modeling the heating and atomic kinetics of a photoionized neon plasma experiment
NASA Astrophysics Data System (ADS)
Lockard, Tom E.
Motivated by gas cell photoionized plasma experiments performed by our group at the Z facility of Sandia National Laboratories, we discuss in this dissertation a modeling study of the heating and ionization of the plasma for conditions characteristic of these experiments. Photoionized plasmas are non-equilibrium systems driven by a broadband x-ray radiation flux. They are commonly found in astrophysics but rarely seen in the laboratory. Several modeling tools have been employed: (1) a view-factor computer code constrained with side x-ray power and gated monochromatic image measurements of the z-pinch radiation, to model the time-history of the photon-energy resolved x-ray flux driving the photoionized plasma, (2) a Boltzmann self-consistent electron and atomic kinetics model to simulate the electron distribution function and configuration-averaged atomic kinetics, (3) a radiation-hydrodynamics code with inline non-equilibrium atomic kinetics to perform a comprehensive numerical simulation of the experiment and plasma heating, and (4) steady-state and time-dependent collisional-radiative atomic kinetics calculations with fine-structure energy level description to assess transient effects in the ionization and charge state distribution of the plasma. The results indicate that the photon-energy resolved x-ray flux impinging on the front window of the gas cell is very well approximated by a linear combination of three geometrically-diluted Planckian distributions. Knowledge of the spectral details of the x-ray drive turned out to be important for the heating and ionization of the plasma. The free electrons in the plasma thermalize quickly relative to the timescales associated with the time-history of the x-ray drive and the plasma atomic kinetics. Hence, electrons are well described by a Maxwellian energy distribution of a single temperature. This finding is important to support the application of a radiation-hydrodynamic model to simulate the experiment. It is found
A Monte Carlo model for seeded atomic flows in the transition regime
Longo, S. Diomede, P.
2009-06-01
A simple model for the numerical determination of separation effects in seeded atomic gas flows is presented. The model is based on the known possibility to provide a statistically convergent estimate of the exact solution for a linear transport equation using the test particle Monte Carlo method. Accordingly, the flow field of the main gas is preliminary calculated and as a second step the linear transport equations obtained by fixing the target distribution in the collision term of the Boltzmann equation for both main and minority components are solved. Both solutions are based on appropriately devised test particle Monte Carlo methods. The second step, the critical one in evaluating the separation effects, is exact and thereby completely free of numerical diffusion. The model is described in details and illustrated by 2D test cases of atomic separation in shock fronts.
ERIC Educational Resources Information Center
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…
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. PMID:27335760
Influence of the plasma environment on atomic structure using an ion-sphere model
Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel
2015-09-03
Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less
Influence of the plasma environment on atomic structure using an ion-sphere model
Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel
2015-09-03
Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe^{22+}, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy
Klocke, Michael
2016-01-01
Summary 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. PMID:27335760
Tunable two-dimensional arrays of single Rydberg atoms for realizing quantum Ising models.
Labuhn, Henning; Barredo, Daniel; Ravets, Sylvain; de Léséleuc, Sylvain; Macrì, Tommaso; Lahaye, Thierry; Browaeys, Antoine
2016-06-30
Spin models are the prime example of simplified many-body Hamiltonians used to model complex, strongly correlated real-world materials. However, despite the simplified character of such models, their dynamics often cannot be simulated exactly on classical computers when the number of particles exceeds a few tens. For this reason, quantum simulation of spin Hamiltonians using the tools of atomic and molecular physics has become a very active field over the past years, using ultracold atoms or molecules in optical lattices, or trapped ions. All of these approaches have their own strengths and limitations. Here we report an alternative platform for the study of spin systems, using individual atoms trapped in tunable two-dimensional arrays of optical microtraps with arbitrary geometries, where filling fractions range from 60 to 100 per cent. When excited to high-energy Rydberg D states, the atoms undergo strong interactions whose anisotropic character opens the way to simulating exotic matter. We illustrate the versatility of our system by studying the dynamics of a quantum Ising-like spin-1/2 system in a transverse field with up to 30 spins, for a variety of geometries in one and two dimensions, and for a wide range of interaction strengths. For geometries where the anisotropy is expected to have small effects on the dynamics, we find excellent agreement with ab initio simulations of the spin-1/2 system, while for strongly anisotropic situations the multilevel structure of the D states has a measurable influence. Our findings establish arrays of single Rydberg atoms as a versatile platform for the study of quantum magnetism. PMID:27281203
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. PMID:24061142
Observation of antiferromagnetic correlations in the Hubbard model with ultracold atoms.
Hart, Russell A; Duarte, Pedro M; Yang, Tsung-Lin; Liu, Xinxing; Paiva, Thereza; Khatami, Ehsan; Scalettar, Richard T; Trivedi, Nandini; Huse, David A; Hulet, Randall G
2015-03-12
Ultracold atoms in optical lattices have great potential to contribute to a better understanding of some of the most important issues in many-body physics, such as high-temperature superconductivity. The Hubbard model--a simplified representation of fermions moving on a periodic lattice--is thought to describe the essential details of copper oxide superconductivity. This model describes many of the features shared by the copper oxides, including an interaction-driven Mott insulating state and an antiferromagnetic (AFM) state. Optical lattices filled with a two-spin-component Fermi gas of ultracold atoms can faithfully realize the Hubbard model with readily tunable parameters, and thus provide a platform for the systematic exploration of its phase diagram. Realization of strongly correlated phases, however, has been hindered by the need to cool the atoms to temperatures as low as the magnetic exchange energy, and also by the lack of reliable thermometry. Here we demonstrate spin-sensitive Bragg scattering of light to measure AFM spin correlations in a realization of the three-dimensional Hubbard model at temperatures down to 1.4 times that of the AFM phase transition. This temperature regime is beyond the range of validity of a simple high-temperature series expansion, which brings our experiment close to the limit of the capabilities of current numerical techniques, particularly at metallic densities. We reach these low temperatures using a compensated optical lattice technique, in which the confinement of each lattice beam is compensated by a blue-detuned laser beam. The temperature of the atoms in the lattice is deduced by comparing the light scattering to determinant quantum Monte Carlo simulations and numerical linked-cluster expansion calculations. Further refinement of the compensated lattice may produce even lower temperatures which, along with light scattering thermometry, would open avenues for producing and characterizing other novel quantum states of
Atomic density functional and diagram of structures in the phase field crystal model
NASA Astrophysics Data System (ADS)
Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.
2016-02-01
The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindrical tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.
Atom-field entanglement in the Jaynes-Cummings model without rotating wave approximation
NASA Astrophysics Data System (ADS)
Mirzaee, M.; Batavani, M.
2015-04-01
In this paper, we present a structure for obtaining the exact eigenfunctions and eigenvalues of the Jaynes-Cummings model (JCM) without the rotating wave approximation (RWA). We study the evolution of the system in the strong coupling region using the time evolution operator without RWA. The entanglement of the system without RWA is investigated using the Von Neumann entropy as an entanglement measure. It is interesting that in the weak coupling regime, the population of the atomic levels and Von Neumann entropy without RWA model shows a good agreement with the RWA whereas in strong coupling domain, the results of these two models are quite different.
Computational model for non-LTE atomic process in laser produced plasmas
NASA Astrophysics Data System (ADS)
Takabe, Hideaki; Nishikawa, Takeshi
1994-02-01
A computational model for simulating hydro-radiation phenomena has been studied relating to the partially ionized gold plasma produced by irradiation of intense laser light. The screened hydrogenic model with l-splitting effect and the average ion model are used to determine the atomic state of gold ions in the collisional radiative equilibrium. A statistical method is used to evaluate the spectral opacity and emissivity due to the clusters of line transitions. The x-ray conversion rate and spectrum calculated with the hydrodynamic code ILESTA coupled with opacity and emissivity are compared with those observed experimentally.
Spatial Distributions of Metal Atoms During Carbon SWNTs Formation: Measurements and Modelling
NASA Technical Reports Server (NTRS)
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).
Atomization modeling in a multiphase flow environment and comparison with experiments
NASA Technical Reports Server (NTRS)
Liang, P. Y.; Schuman, M. D.
1990-01-01
An atomization model based on Reitz's instability wave analysis has been implemented into the ARICC3D multiphase CFD combustion code. Preliminary test runs with cold non-evaporating liquid jet and coaxial gas-liquid atomization cases appeared to have verified basic performance of the model, generating realistic-looking sprays. Furthermore, the extended liquid jet is explicitly resolved, and predicted jet lengths agree well with classical correlations. Fair agreement with test data is obtained for predicted spray tip penetrations and liquid mass flux radial distributions, with obvious room for improvement. Some numerical problems also appear to have resulted with the current implementation when low gas Mach number and high liquid velocities are involved.
NASA Astrophysics Data System (ADS)
Wu, X.; Sha, W.
2008-12-01
In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.
NASA Astrophysics Data System (ADS)
Lüdde, H. J.; Achenbach, A.; Kalkbrenner, T.; Jankowiak, H. C.; Kirchner, T.
2016-05-01
A recently introduced model to account for geometric screening corrections in an independent-atom-model description of ion-molecule collisions is applied to proton collisions from amino acids and DNA and RNA nucleobases. The correction coefficients are obtained from using a pixel counting method (PCM) for the exact calculation of the effective cross sectional area that emerges when the molecular cross section is pictured as a structure of (overlapping) atomic cross sections. This structure varies with the relative orientation of the molecule with respect to the projectile beam direction and, accordingly, orientation-independent total cross sections are obtained from averaging the pixel count over many orientations. We present net capture and net ionization cross sections over wide ranges of impact energy and analyze the strength of the screening effect by comparing the PCM results with Bragg additivity rule cross sections and with experimental data where available. Work supported by NSERC, Canada.
Na, Hyuntae; Jernigan, Robert L.; Song, Guang
2015-01-01
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. PMID:26473491
Quantum phase transitions in an interacting atom-molecule boson model
Santos, G.; Foerster, A.; Mattei, E.; Dahmen, S. R.; Links, J.
2010-06-15
We study the quantum phase transitions of a model that describes the interconversion of interacting bosonic atoms and molecules. Using a classical analysis, we identify a threshold coupling line separating a molecular phase and a mixed phase. Through studies of the energy gap, von Neumann entanglement entropy, and fidelity, we give evidence that this line is associated with a boundary line in the ground-state phase diagram of the quantum system.
NASA Astrophysics Data System (ADS)
Di Rocco, Héctor O.; Lanzini, Fernando
2016-04-01
The correction to the Coulomb repulsion between two electrons due to the exchange of a transverse photon, referred to as the Breit interaction, as well as the main quantum electrodynamics contributions to the atomic energies (self-energy and vacuum polarization), are calculated using the recently formulated relativistic screened hydrogenic model. Comparison with the results of multiconfiguration Dirac-Hartree-Fock calculations and experimental X- ray energies is made.
NASA Astrophysics Data System (ADS)
Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina
2016-07-01
Atomic oxygen (AO) of the upper atmosphere is one of the most important space factors that can cause degradation of spacecraft surface. In our previous mathematical model the Monte Carlo method and the "large particles" approximation were used for simulating processes of polymer etching under the influence of AO [1]. The interaction of enlarged AO particles with the polymer was described in terms of probabilities of reactions such as etching of polymer and specular and diffuse scattering of the AO particles on polymer. The effects of atomic oxygen on protected polymers and microfiller containing composites were simulated. The simulation results were in quite good agreement with the results of laboratory experiments on magnetoplasmadynamic accelerator of the oxygen plasma of SINP MSU [2]. In this paper we present a new model that describes the reactions of AO interactions with polymeric materials in more detail. Reactions of formation and further emission of chemical compounds such as CO, CO _{2}, H _{2}O, etc. cause the modification of the chemical composition of the polymer and change the probabilities of its consequent interaction with the AO. The simulation results are compared with the results of previous simulation and with the results of laboratory experiments. The reasons for the differences between the results of natural experiments on spacecraft, laboratory experiments and simulations are discussed. N. Chirskaya, M. Samokhina, Computer modeling of polymer structures degradation under the atomic oxygen exposure, WDS'12 Proceedings of Contributed Papers: Part III - Physics, Matfyzpress Prague, 2012, pp. 30-35. E. Voronina, L. Novikov, V. Chernik, N. Chirskaya, K. Vernigorov, G. Bondarenko, and A. Gaidar, Mathematical and experimental simulation of impact of atomic oxygen of the earth's upper atmosphere on nanostructures and polymer composites, Inorganic Materials: Applied Research, 2012, vol. 3, no. 2, pp. 95-101.
McElfresh, Mike; Baesu, Eveline; Balhorn, Rod; Belak, James; Allen, Michael J.; Rudd, Robert E.
2002-01-01
The goal of this work is to study the properties of living cells and cell membranes by using atomic force microscopy. During atomic force microscopy (AFM) measurement, there is a strong mechanical coupling between the AFM tip and the cell. The purpose of this paper is to present a model of the overall mechanical response of the cell that allows us to separate out the mechanical response of the cell from the local surface interactions we wish to quantify. These local interactions include recognition (or binding) events between molecules bound to an AFM tip (e.g., an antibody) and molecules or receptors on the cell surface (e.g., the respective antigen). The computational model differs from traditional Hertzian contact models by explicitly taking into account the mechanics of the biomembrane and cytoskeleton. The model also accounts for the mechanical response of the living cell during arbitrary deformation. The indentation of a bovine sperm cell is used to test the validity of this model, and further experiments are proposed to fully parameterize the model. PMID:11983924
NASA Technical Reports Server (NTRS)
Kostelecky, V. Alan
1993-01-01
Atomic supersymmetry is a quantum-mechanical supersymmetry connecting the properties of different atoms and ions. A short description of some established results in the subject are provided and a few recent developments are discussed including the extension to parabolic coordinates and the calculation of Stark maps using supersymmetry-based models.
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
NASA Astrophysics Data System (ADS)
Yang, Yantao; Cui, Junzhi; Han, Tiansi
2016-04-01
Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.
Intrinsic chirp of attosecond pulses: Single-atom model versus experiment
Kazamias, S.; Balcou, Ph.
2004-06-01
We demonstrate and evaluate the importance of an intrinsic chirp inherent to attosecond pulse creation accompanying high-order harmonic generation in recently published experimental data by Dinu et al. [Phys. Rev. Lett. 91, 063901 (2003)]. We present an analytical model, from which the atomic origin of the harmonic chirp is clearly understood. Moreover, the behavior of the chirp as a function of experimental parameters such as laser intensity is inferred. The comparison between our model and the experimental data provides us with useful information about the conditions in which the high-order harmonics is generated.
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
NASA Astrophysics Data System (ADS)
Yang, Yantao; Cui, Junzhi; Han, Tiansi
2016-08-01
Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.
Atomic-scale modeling of particle size effects for the oxygen reduction reaction on Pt.
Tritsaris, G. A.; Greeley, J.; Rossmeisl, J.; Norskov, J. K.
2011-07-01
We estimate the activity of the oxygen reduction reaction on platinum nanoparticles of sizes of practical importance. The proposed model explicitly accounts for surface irregularities and their effect on the activity of neighboring sites. The model reproduces the experimentally observed trends in both the specific and mass activities for particle sizes in the range between 2 and 30 nm. The mass activity is calculated to be maximized for particles of a diameter between 2 and 4 nm. Our study demonstrates how an atomic-scale description of the surface microstructure is a key component in understanding particle size effects on the activity of catalytic nanoparticles.
NASA Astrophysics Data System (ADS)
Porter, R. L.; Bauman, R. P.; MacAdam, K. B.; Ferland, G. J.
2004-12-01
We have completed the development of a new model helium atom for the spectra simulation code Cloudy. All relevant astrophysically significant processes are included, and the spectrum is solved self-consistently with the thermal and ionization structure of the simulated system. We present here an overview of the differences that distinguish our model from those by previous authors. We also compare predicted case B emissivities with those from previous works. The differences will have significant consequences for the interpretation of spectra of a wide variety of systems. We also explore deviations from the case B approximation and present an estimate of the primordial helium abundance.
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. PMID:24076304
Yang-Baxter integrable models in experiments: from condensed matter to ultracold atoms
NASA Astrophysics Data System (ADS)
Batchelor, Murray T.; Foerster, Angela
2016-04-01
The Yang-Baxter equation has long been recognised as the masterkey to integrability, providing the basis for exactly solved models which capture the fundamental physics of a number of realistic classical and quantum systems. In this article we provide an introductory survey of the impact of Yang-Baxter integrable models on experiments in condensed matter physics and ultracold atoms. A number of prominent examples are covered, including the hard-hexagon model, the Heisenberg spin chain, the transverse quantum Ising chain, a spin ladder model, the Lieb-Liniger Bose gas, the Gaudin-Yang Fermi gas and the two-site Bose-Hubbard model. The review concludes by pointing to some other recent developments with promise for further progress.
NASA Astrophysics Data System (ADS)
Rozsnyai, Balazs F.
2012-03-01
We use a "self-consistent average atom" (SCAA) model to compute shock Hugoniots for aluminum, iron, molybdenum, strontium, barium and thulium. The pressures and energies include relativistic effects. We make comparisons with the Thomas-Fermi-Dirac (TFD) model and with the available experimental data including pressures, shock and particle speeds and energy deposition. The connection between the usage of the "average atom" (AA) model and "detailed configuration accounting" (DCA) is discussed in the Appendix.
NASA Astrophysics Data System (ADS)
Balzer, Karsten; Bauch, Sebastian; Bonitz, Michael
2010-04-01
In this contribution, we discuss the finite-element discrete variable representation (FE-DVR) of the nonequilibrium Green's function and its implications on the description of strongly inhomogeneous quantum systems. In detail, we show that the complementary features of FEs and the DVR allow for a notably more efficient solution of the two-time Schwinger/Keldysh/Kadanoff-Baym equations compared to a general basis approach. Particularly, the use of the FE-DVR leads to an essential speedup in computing the self-energies. As atomic and molecular examples we consider the He atom and the linear version of H+3 in one spatial dimension. For these closed-shell models we, in Hartree-Fock and second Born approximation, compute the ground-state properties and compare with the exact findings obtained from the solution of the few-particle time-dependent Schrödinger equation.
An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water
Stauffer, D.; Dragneva, N.; Floriano, W. B.; Rubel, O.; Mawhinney, R. C.; Fanchini, G.; French, S.
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.
Fullerene film on metal surface: Diffusion of metal atoms and interface model
Li, Wen-jie; Li, Hai-Yang; Li, Hong-Nian; Wang, Peng; Wang, Xiao-Xiong; Wang, Jia-Ou; Wu, Rui; Qian, Hai-Jie; Ibrahim, Kurash
2014-05-12
We try to understand the fact that fullerene film behaves as n-type semiconductor in electronic devices and establish a model describing the energy level alignment at fullerene/metal interfaces. The C{sub 60}/Ag(100) system was taken as a prototype and studied with photoemission measurements. The photoemission spectra revealed that the Ag atoms of the substrate diffused far into C{sub 60} film and donated electrons to the molecules. So the C{sub 60} film became n-type semiconductor with the Ag atoms acting as dopants. The C{sub 60}/Ag(100) interface should be understood as two sub-interfaces on both sides of the molecular layer directly contacting with the substrate. One sub-interface is Fermi level alignment, and the other is vacuum level alignment.
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
Tung, Chang-Shung; Joseph, Simpson; Sanbonmatsu, Kevin Y
2002-10-01
Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit. We find that the tertiary structure of the ribosome core, including the A-, P- and E-sites, is highly conserved. The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome. PMID:12244297
Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment
Joseph, Agnel Praveen; Malhotra, Sony; Burnley, Tom; Wood, Chris; Clare, Daniel K.; Winn, Martyn; Topf, Maya
2016-01-01
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 (2.5–4.5 Å) 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. PMID:26988127
Average-atom model combined with the hypernetted chain approximation applied to warm dense matter.
Hou, Yong; Bredow, Richard; Yuan, Jianmin; Redmer, Ronald
2015-03-01
We have combined the average-atom model with the hypernetted chain approximation (AAHNC) to describe the electronic and ionic structure in the warm dense matter regime. On the basis of the electronic and ionic structures, the x-ray Thomson scattering (XRTS) spectrum is calculated using the random-phase approximation. While the electronic structure is described within the average-atom model, the effects of other ions on the electronic structure are considered using an integral equation method of the theory of liquids, namely the hypernetted chain approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution. Finally, the electronic and ionic structures are determined self-consistently. The XRTS spectrum is calculated according to the Chihara formula, where the scattering contributions are divided into three components: elastic, bound-free, and free-free. Comparison of the present AAHNC results with other theoretical models and experimental data shows very good agreement. Thus the AAHNC model can give a reasonable description of the electronic and ionic structure in warm dense matter. PMID:25871231
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. PMID:26988127
Quantum model for double ionization of atoms in strong laser fields
NASA Astrophysics Data System (ADS)
Prauzner-Bechcicki, Jakub S.; Sacha, Krzysztof; Eckhardt, Bruno; Zakrzewski, Jakub
2008-07-01
We discuss double ionization of atoms in strong laser pulses using a reduced dimensionality model. Following the insight obtained from an analysis of the classical mechanics of the process, we confine each electron to move along the lines that point towards the two-particle Stark saddle in the presence of a field. The resulting effective two-dimensional model is similar to the aligned electron model, but it enables correlated escape of electrons with equal momenta, as observed experimentally. The time-dependent solution of the Schrödinger equation allows us to discuss in detail the time dynamics of the ionization process, the formation of electronic wave packets, and the development of the momentum distribution of the outgoing electrons. In particular, we are able to identify the rescattering process, simultaneous direct double ionization during the same field cycle, as well as other double ionization processes. We also use the model to study the phase dependence of the ionization process.
Charge-state-dependent energy loss of slow ions. II. Statistical atom model
NASA Astrophysics Data System (ADS)
Wilhelm, Richard A.; Möller, Wolfhard
2016-05-01
A model for charge-dependent energy loss of slow ions is developed based on the Thomas-Fermi statistical model of atoms. Using a modified electrostatic potential which takes the ionic charge into account, nuclear and electronic energy transfers are calculated, the latter by an extension of the Firsov model. To evaluate the importance of multiple collisions even in nanometer-thick target materials we use the charge-state-dependent potentials in a Monte Carlo simulation in the binary collision approximation and compare the results to experiment. The Monte Carlo results reproduce the incident charge-state dependence of measured data well [see R. A. Wilhelm et al., Phys. Rev. A 93, 052708 (2016), 10.1103/PhysRevA.93.052708], even though the experimentally observed charge exchange dependence is not included in the model.
Wang, Junmei; Cieplak, Piotr; Li, Jie; Hou, Tingjun; Luo, Ray; Duan, Yong
2011-01-01
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, i.e. whether the interactions of two atoms that form bond, bond angle and dihedral angle are turned off or scaled down. When 1-2 (bonded), 1-3 (separated by two bonds) interactions are turned off and/or 1-4 (separated by three bonds) interactions are scaled down, all the models including the Applequist model achieved similar performance: the average percentage errors (APE) ranges from 1.15% to 1.23%, and The average unsigned errors (AUE) ranges from 0.143 to 0.158 Å3. 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 Å3 for the three Thole models, compared to 0.446 Å3 for the Applequist model. Further assessement 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 more accurate 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. PMID:21391553
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. PMID:21391553
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.
2015-07-28
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 severalmore » 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.« less
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.
2015-07-28
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.
Mazzarella, G.; Giampaolo, S. M.; Illuminati, F.
2006-01-15
For systems of interacting, ultracold spin-zero neutral bosonic atoms, harmonically trapped and subject to an optical lattice potential, we derive an Extended Bose Hubbard (EBH) model by developing a systematic expansion for the Hamiltonian of the system in powers of the lattice parameters and of a scale parameter, the lattice attenuation factor. We identify the dominant terms that need to be retained in realistic experimental conditions, up to nearest-neighbor interactions and nearest-neighbor hoppings conditioned by the on-site occupation numbers. In the mean field approximation, we determine the free energy of the system and study the phase diagram both at zero and at finite temperature. At variance with the standard on site Bose Hubbard model, the zero-temperature phase diagram of the EBH model possesses a dual structure in the Mott insulating regime. Namely, for specific ranges of the lattice parameters, a density wave phase characterizes the system at integer fillings, with domains of alternating mean occupation numbers that are the atomic counterparts of the domains of staggered magnetizations in an antiferromagnetic phase. We show as well that in the EBH model, a zero-temperature quantum phase transition to pair superfluidity is, in principle, possible, but completely suppressed at the lowest order in the lattice attenuation factor. Finally, we determine the possible occurrence of the different phases as a function of the experimentally controllable lattice parameters.
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.
2015-07-28
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.
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. PMID:23848795
NASA Astrophysics Data System (ADS)
Chaney, Andrea; Espinosa, James; Espinosa, James
2006-10-01
At the turn of the twentieth century, physicists and chemists were developing atomic models. Some of the phenomena that they had to explain were the periodic table, the stability of the atom, and the emission spectra. Niels Bohr is known as making the first modern picture that accounted for these. Unknown to much of the physics community is the work of Walter Ritz. His model explained more emission spectra and predates Bohr's work. We will fit several spectra using Ritz's magnetic model for the atom. The problems of stability and chemical periodicity will be shown to be challenges that this model has difficulty solving, but we will present some potentially useful adaptations to the Ritzian atom that can account for them.
Why Do We Believe that an Atom Is Colourless? Reflections about the Teaching of the Particle Model.
ERIC Educational Resources Information Center
Albanese, Alessandro; Vicentini, Matilde
1997-01-01
Highlights students' ideas about the particle model of matter and its use. Discusses the atomic model in teaching and the rules of the particle modeling game. Demonstrates how a complete understanding of the rules of the model construction yields guidelines for didactic practice. Focuses on problems connected with visual communication through…
Quantum simulation of the Hubbard model with dopant atoms in silicon
Salfi, J.; Mol, J. A.; Rahman, R.; Klimeck, G.; Simmons, M. Y.; Hollenberg, L. C. L.; Rogge, S.
2016-01-01
In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose–Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model. PMID:27094205
Atomic spin-chain realization of a model for quantum criticality
NASA Astrophysics Data System (ADS)
Toskovic, R.; van den Berg, R.; Spinelli, A.; Eliens, I. S.; van den Toorn, B.; Bryant, B.; Caux, J.-S.; Otte, A. F.
2016-07-01
The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum computing and spintronic devices; on the other hand, they can be used as fundamental building blocks for the realization of textbook many-body quantum models, illustrating key concepts such as quantum phase transitions, topological order or frustration as a function of system size. Here, we use low-temperature scanning tunnelling microscopy to construct arrays of magnetic atoms on a surface, designed to behave like spin-1/2 XXZ Heisenberg chains in a transverse field, for which a quantum phase transition from an antiferromagnetic to a paramagnetic phase is predicted in the thermodynamic limit. Site-resolved measurements on these finite-size realizations reveal a number of sudden ground state changes when the field approaches the critical value, each corresponding to a new domain wall entering the chains. We observe that these state crossings become closer for longer chains, suggesting the onset of critical behaviour. Our results present opportunities for further studies on quantum behaviour of many-body systems, as a function of their size and structural complexity.
NASA Astrophysics Data System (ADS)
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. PMID:25730881