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…
A theorem concerning fermion interaction is postulated and applied to the problems of atomic (electronic) and nuclear physics. Model building based solely upon the postulate that adjacent like fermions must be singlet paired accounts for the closed shells of both nuclear and atomic structure. The implied antiferromagnetic FCC lattice of protons and neutrons in alternating layers has been found by previous workers to be the lowest-energy solid configuration of nuclear matter (N = P). The buildup of the FCC lattice from a central tetrahedron reproduces all of the shells and subshells of the isotropic harmonic oscillator, which is the basis for the shell model. In atomic structure, the singlet pairing of adjacent electrons implies closed-shell structures uniquely at the six noble gases and the three noble metals, Ni, Pd, and Pt. The basis for the postulate concerning fermions is found in terms of classical electrodynamics; it is a microscopic corollary of Biot-Savart's law that parallel currents attract whereas antiparallel currents repel. (author)
The author describes in this paper the atom-in-jellium calculations he has been doing over the last ten years. He tries to emphasize reasons for doing this sort of calculations and why he devised a model which is different in some respects from others
"Electronium": A Quantum Atomic Teaching Model.
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Outlines an alternative atomic model to the probability model, the descriptive quantum atomic model Electronium. Discusses the way in which it is intended to support students in learning quantum-mechanical concepts. (Author/MM)
Extensions to the two atom blocking model
This paper contains viewgraphs on the use of the blocking model to describe atom-atom collisions in solids. Experimental results on two particle emissions for attractive and repulsive coulomb potentials are given
The Completeness Criterion in Atomic Modeling
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
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
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
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.
Atomic model of liquid pure Fe
无
2001-01-01
Using a θ-θX-ray diffractometer, the liquid structure of pure Fewas investigated and the diffraction intensity, structure factor, pair distribution function as well as the coordination number and atomic distance were obtained. The experimental results showed that there was also a pre-peak on the curve of the structure factor of liquid pure Fe. The pre-peak is a mark of medium-range order in melts. According to the characteristics of pre-peak, an atomic model of liquid pure Fe is constructed, namely, the structure of liquid pure Fe is a combination of clusters consisting of bcc cells with shared vertexes and other atoms with random dense atom distribution.
Contemporary models of the atomic nucleus
Nemirovskii, P E
2013-01-01
Contemporary Models of the Atomic Nucleus discusses nuclear structure and properties, expounding contemporary theoretical concepts of the low-energy nuclear processes underlying in nuclear models. This book focuses on subjects such as the optical nuclear model, unified or collective model, and deuteron stripping reaction. Other topics discussed include the basic nuclear properties; shell model; theoretical analysis of the shell model; and radiative transitions and alpha-decay. The deuteron theory and the liquid drop nuclear model with its application to fission theory are also mentioned, but o
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
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
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.
Calculation of Al-Zn diagram from central atoms model
无
1999-01-01
A slightly modified central atoms model was proposed. The probabilities of various clusters with the central atoms and their nearest neighboring shells can be calculated neglecting the assumption of the param eter of energy in the central atoms model in proportion to the number of other atoms i (referred with the central atom). A parameter Pα is proposed in this model, which equals to reciprocal of activity coefficient of a component, therefore, the new model can be understood easily. By this model, the Al-Zn phase diagram and its thermodynamic properties were calculated, the results coincide with the experimental data.
Atomic data for integrated tokamak modelling
The Integrated Tokamak Modeling Task Force (ITM-TF) was set up in 2004. The main target is to coordinate the European fusion modeling effort and providing a complete European modeling structure for International Thermonuclear Experimental Reactor (ITER), with the highest degree of flexibility. For the accurate simulation of the processes in the active fusion reactor in the ITM-TF, numerous atomic, molecular, nuclear and surface related data are required. In this work we present total-, single- and multiple-ionization and charge exchange cross sections in close connection to the ITM-TF. Interpretation of these cross sections in multi-electron ion-atom collisions is a challenging task for theories. The main difficulty is caused by the many-body feature of the collision, involving the projectile, projectile electron(s), target nucleus, and target electron(s). The classical trajectory Monte Carlo (CTMC) method has been quite successful in dealing with the atomic processes in ion-atom collisions. One of the advantages of the CTMC method is that many-body interactions are exactly taken into account related CTMC simulations for a various collision systems are presented. To highlight the efficiency of the method we present electron emission cross sections in collision between dressed Alq+ ions with He target. The theory delivers separate spectra for electrons emitted from the target and the projectile. By summing these two components in the rest frame of the target we may make a comparison with available experimental data. For the collision system in question, a significant contribution from Fermi-shuttle ionization has to be expected in the spectra at energies higher than E=0.5 me (nV)2, where me is the mass of the electron, V the projectile velocity and n an integer greater than 1. We found enhanced electron yields compared to first order theory in this region of CTMC spectra, which can be directly attributed to the contribution of Fermi-shuttle type multiple scattering
Early Atomic Models - From Mechanical to Quantum (1904-1913)
Baily, Charles
2012-01-01
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 p...
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.
Atomic theory and tests of the Standard Model in atomic experiments
Measurements of the weak charge characterizing the strength of the electron-nucleon weak interaction provide tests of the Standard Model and a way of searching for new physics beyond the Standard Model. Atomic experiments give limits on the extra Z-boson, leptoquarks, composite fermions, and radiative corrections produced by particles that are predicted by new theories. To extract the accurate value of the weak charge from atomic experiments one has to perform high precision atomic calculations of the PNC effects
Harmonic oscillator model for the helium atom
Carlsen, Martin
2015-01-01
A harmonic oscillator model in four dimensions is presented for the helium atom to estimate the distance to the inner and outer electron from the nucleus, the angle between electrons and the energy levels. The method is algebraic and is not based on the choice of correct trial wave function. Three harmonic oscillators and thus three quantum numbers are sufficient to describe the two-electron system. We derive a simple formula for the energy in the general case and in the special case of the Wannier Ridge. For a set of quantum numbers the distance to the electrons and the angle between the electrons are uniquely determined as the intersection between three surfaces. We show that the excited states converge either towards ionization thresholds or towards extreme parallel or antiparallel states and provide an estimate of the ground state energy.
Operation of the computer model for microenvironment atomic oxygen exposure
Bourassa, R. J.; Gillis, J. R.; Gruenbaum, P. E.
1995-01-01
A computer model for microenvironment atomic oxygen exposure has been developed to extend atomic oxygen modeling capability to include shadowing and reflections. The model uses average exposure conditions established by the direct exposure model and extends the application of these conditions to treat surfaces of arbitrary shape and orientation.
An atomic model for neutral and singly ionized uranium
Maceda, E. L.; Miley, G. H.
1979-01-01
A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.
Proposed reference models for atomic oxygen in the terrestrial atmosphere
Llewellyn, E. J.; Mcdade, I. C.; Lockerbie, M. D.
1989-01-01
A provisional Atomic Oxygen Reference model was derived from average monthly ozone profiles and the MSIS-86 reference model atmosphere. The concentrations are presented in tabular form for the altitude range 40 to 130 km.
The Quantum Atomic Model "Electronium": A Successful Teaching Tool.
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Focuses on the quantum atomic model Electronium. Outlines the Bremen teaching approach in which this model is used, and analyzes the learning of two students as they progress through the teaching unit. (Author/MM)
Early atomic models - from mechanical to quantum (1904-1913)
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.
刘洪毓
2007-01-01
Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what
Atom diffusion in furnaces - models and measurements
Sadagoff, Y. M.; Dědina, Jiří
2002-01-01
Roč. 57, č. 3 (2002), s. 535-549. ISSN 0584-8547 R&D Projects: GA ČR GA203/01/0453 Institutional research plan: CEZ:AV0Z4031919 Keywords : diffusion coefficients * graphite furnace * atomic absorption spectrometry Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.695, year: 2002
Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)
Analytic Solutions of Three-Level Dressed-Atom Model
WANG Zheng-Ling; YIN Jian-Ping
2004-01-01
On the basis of the dressed-atom model, the general analytic expressions for the eigenenergies, eigenstates and their optical potentials of the A-configuration three-level atom system are derived and analysed. From the calculation of dipole matrix element of different dressed states, we obtain the spontaneous-emission rates in the dressed-atom picture. We find that our general expressions of optical potentials for the three-level dressed atom can be reduced to the same as ones in previous references under the approximation of a small saturation parameter. We also analyse the dependences of the optical potentials of a three-level 85Rb atom on the laser detuning and the dependences of spontaneous-emission rates on the radial position in the dark hollow beam, and discuss the probability (population) evolutions of dressed-atomic eigenstates in three levels in the hollow beam.
Atomic structure of grain boundaries in iron modeled using the atomic density function
Kapikranian, O.; Zapolsky, H; Domain, Ch.; Patte, R.; Pareige, C.; Radiguet, B.; Pareige, P.
2013-01-01
A model based on the continuous atomic density function (ADF) approach is applied to predict the atomic structure of grain boundaries (GBs) in iron. Symmetrical [100] and [110] tilt GBs in bcc iron are modeled with the ADF method and relaxed afterwards in molecular dynamics (MD) simulations. The shape of the GB energy curve obtained in the ADF model reproduces well the peculiarities of the angles of 70.53 deg. [$\\Sigma$ 3(112)] and 129.52 deg. [$\\Sigma$ 11(332)] for [110] tilt GBs. The result...
Detailed atomic modeling of Sn plasmas for the EUV source
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
Detailed atomic modeling of Sn plasmas for the EUV source
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.
Atomic spin chain realization of a model for quantum criticality
Toskovic, R.; Berg, R. van den; Spinelli, A.; Eliens, I. S.; Toorn, B. van den; Bryant, B.; Caux, J. -S.; Otte, A. F.
2016-01-01
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. Step-by-st...
The Bohr-Sommerfeld atom theory. Sommerfeld's extension of Bohr's atomic model 1915/16
In December 6th 1915 and January 8th 1916 Arnold Sommerfeld put the Bavarian Academy of Sciences two treatises in the amount of 75 printed pages before, by which he extended Bohr's atomic model from the year 1913 to the Bohr-Sommerfeld atom theory. In Sommerfeld's collected works only the publication submitted 1916 by Sommerfeld in the Annals of Physics about this is found.''My spectral lines are finally printed in the Academy to the impure. In the Annals they will appear in purer form'', so Sommerfeld has announced in this publication in February 10th 1916 to the editor of the Annals of Physics. From the science-historical view however for the extension of Bohr's atom theory just the Academy-treatises published before the purification process are of special interest. To the reproduction of these Academy-treatises an extensive physics-historical essay is prepended.
Modelling spectral properties of non-equilibrium atomic hydrogen plasma
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.
Modelling spectral properties of non-equilibrium atomic hydrogen plasma
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.
Guo, Y Q; Song, H S
2005-01-01
The method of perturbative expansion of master equation is employed to study the dissipative properties of system and of atom in the two-photon Jaynes-Cummings model (JCM) with degenerate atomic levels. The numerical results show that the degeneracy of atomic levels prolongs the period of entanglement between the atom and the field. The asymptotic value of atomic linear entropy is apparently increased by the degeneration. The amplitude of local entanglement and disentanglement is suppressed. The better the initial coherence property of the degenerate atom, the larger the coherence loss.
Modelling atomic scale manipulation with the non-contact atomic force microscope
We present the results of calculations performed to model the process of lateral manipulation of an oxygen vacancy in the MgO(001) surface using the non-contact atomic force microscope (NC-AFM). The potential energy surfaces for the manipulation as a function of tip position are determined from atomistic modelling of the MgO(001) surface interacting with a Mg terminated MgO tip. These energies are then used to model the dynamical evolution of the system as the tip oscillates and at a finite temperature using a kinetic Monte Carlo method. The manipulation process is strongly dependent on the lateral position of the tip and the system temperature. It is also found that the expectation value of the point at which the vacancy jumps depends on the trajectory of the oscillating cantilever as the surface is approached. The effect of the manipulation on the operation of the NC-AFM is modelled with a virtual dynamic AFM, which explicitly simulates the entire experimental instrumentation and control loops. We show how measurable experimental signals can result from a single controlled atomic scale event and suggest the most favourable conditions for achieving successful atomic scale manipulation experimentally
Model based control of dynamic atomic force microscope
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
Unitary model for atomic ionization by intense XUV laser pulses
Bustamante, M G
2016-01-01
A unitary model describing the electronic transitions in an atom subject to a strong high frequency laser pulse is proposed. The model fully accounts for the initial state coupling with the continuum spectrum. Continuum-continuum as well as discrete-discrete transitions are neglected. The model leads to a single integro-differential equation for the initial state amplitude. Exact numerical and approximate closed semi-analytical solutions of this equation are obtained. A comparison of present results with full time dependent Schr\\"odinger equation solution for Hydrogen atoms subject to a laser pulse is presented. The initial state time dependent population is rather well described by the model and two approximate solutions. The electron energy spectrum is also well reproduced by the model and by a new improved Weiskopf-Wigner related approximation.
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
Quan, Wei; Lv, Lin, E-mail: lvlinlch1990@163.com; Liu, Baiqi [School of Instrument Science and Opto-Electronics Engineering, Beihang University, Beijing 100191 (China)
2014-11-15
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Ab initio calculations and modelling of atomic cluster structure
Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.;
2004-01-01
framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...
Exactly solvable models for atom-molecule Hamiltonians
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
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
Four-component united-atom model of bitumen
Hansen, Jesper Schmidt; Lemarchand, Claire; Nielsen, Erik; Dyre, J. C.; Schrøder, Thomas
2013-01-01
We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based...... software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The...
A constructive model potential method for atomic interactions
Bottcher, C.; Dalgarno, A.
1974-01-01
A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.
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.
Empirical model of atomic nitrogen in the upper thermosphere
Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.
1977-01-01
Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.
Generalized photon and atomic statistics in Jaynes-Cummings models
The interaction between a single two-level and a single mode is studied in some Jaynes-Cummings models. The coupling is supposed to depend on a function of the photon number operator. The evolution operator is calculated; then the probability distribution is obtained. Different statistical quantities are computed for the two states of the atom and different initial distributions for the radiation mode. Three modes are taken, namely, thermal, coherent and squeezed coherent light. (author)
ADAS: Atomic data, modelling and analysis for fusion
The Atomic Data and Analysis Structure, ADAS, comprises extensive fundamental and derived atomic data collections, interactive codes for the manipulation and generation of collisional-radiative data and models, off-line codes for large scale fundamental atomic data production and codes for diagnostic analysis in the fusion and astrophysical environments. ADAS data are organized according to precise specifications, tuned to application and are assigned to numbered ADAS data formats. Some of these formats contain very large quantities of data and some have achieved wide-scale adoption in the fusion community.The paper focuses on recent extensions of ADAS designed to orient ADAS to the needs of ITER. The issue of heavy atomic species, expected to be present as ITER wall and divertor materials, dopants or control species, will be addressed with a view to the economized handling of the emission and ionisation state data needed for diagnostic spectral analysis. Charge exchange and beam emission spectroscopic capabilities and developments in ADAS will be reviewed from an ITER perspective and in the context of a shared analysis between fusion laboratories. Finally an overview and summary of current large scale fundamental data production in the framework of the ADAS project will be given and its intended availability in both fusion and astrophysics noted
A Comprehensive X-Ray Absorption Model for Atomic Oxygen
Gorczyca, T. W.; Bautista, M. A.; Hasoglu, M. F.; Garcia, J.; Gatuzz, E.; Kaastra, J. S.; Kallman, T. R.; Manson, S. T.; Mendoza, C.; Raassen, A. J. J.; 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.
Modeling DNA bubble formation at the atomic scale
We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequence dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.
Computational models of the single substitutional nitrogen atom in diamond
The single substitutional nitrogen atom in diamond is apparently a very simple defect in a very simple elemental solid. It has been modelled by a range of computational models, few of which either agree with each other, or with the experimental data on the defect. If the computational models of less well understood defects in this and more complex materials are to be reliable, we should understand why the discrepancies arise and how they can be avoided in future modelling. This paper presents an all-electron, augmented plane-wave (APW) density functional theory (DFT) calculation using the modern APW with local orbitals full potential periodic approximation. This is compared to DFT, finite cluster pseudopotential calculations and a semi-empirical Hartree-Fock model. Comparisons between the results of these and previous models allow us to discuss the reliability of computational methods of this and similar defects
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…
Lattice location of dopant atoms: An -body model calculation
N K Deepak
2010-03-01
The channelling and scattering yields of 1 MeV -particles in the $\\langle 1 0 0 \\rangle$, $\\langle 1 1 0 \\rangle and $\\langle 1 1 1 \\rangle$ directions of silicon implanted with bismuth and ytterbium have been simulated using -body model. The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and Fontenille method. All previous works reported in literature so far have been done with computer programmes using a statistical analytical expression or by a binary collision model or a continuum model. These results at the best gave only the transverse displacement of the lattice site from the concerned channelling direction. Here we applied the superior -body model to study the yield from bismuth in silicon. The finding that bismuth atom occupies a position close to the silicon substitutional site is new. The transverse displacement of the suggested lattice site from the channelling direction is consistent with the experimental results. The above model is also applied to determine the location of ytterbium in silicon. The present values show good agreement with the experimental results.
Whitford, Paul C.; Jeffrey K Noel; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.
2009-01-01
Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding...
Atomically crafted spin lattices as model systems for quantum magnetism
Low-dimensional quantum magnetism presents a seemingly unlimited source of rich, intriguing physics. Yet, because realistic experimental representations are difficult to come by, the field remains predominantly theoretical. In recent years, artificial spin structures built through manipulation of magnetic atoms in a scanning tunnelling microscope have developed into a promising testing ground for experimental verification of theoretical models. Here, we present an overview of available tools and discuss recent achievements as well as future avenues. Moreover, we show new observations on magnetic switching in a bistable bit that can be used to extrapolate information on the magnetisation of the microscope tip. (topical review)
Modeling atomization processes in high-pressure vaporizing sprays
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.
Terrestrial magnetospheric imaging: Numerical modeling of low energy neutral atoms
Imaging of the terrestrial magnetosphere can be performed by detection of low energy neutral atoms (LENAs) that are produced by charge exchange between magnetospheric plasma ions and cold neutral atoms of the Earth's geocorona. As a result of recent instrumentation advances it is now feasible to make energy-resolved measurements of LENAs from less than I key to greater than 30 key. To model expected LENA fluxes at a spacecraft, we initially used a simplistic, spherically symmetric magnetospheric plasma model.6 We now present improved calculations of both hydrogen and oxygen line-of-sight LENA fluxes expected on orbit for various plasma regimes as predicted by the Rice University Magnetospheric Specification Model. We also estimate expected image count rates based on realistic instrument geometric factors, energy passbands, and image accumulation intervals. The results indicate that presently proposed LENA instruments are capable of imaging of storm time ring current and potentially even quiet time ring current fluxes, and that phenomena such as ion injections from the tail and subsequent drifts toward the dayside magnetopause may also be deduced
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Peter C Lai
2012-05-01
Full Text Available Olfactory receptors (ORs are a type of GTP-binding protein-coupled receptor (GPCR. These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can validate experimental functional studies as well as generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level. Here we have shown the specific advantages of simulating the dynamic environment that is associated with OR-odorant interactions. We present a rigorous methodology that ranges from the creation of a computationally-derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.
A generalized model of atomic processes in dense plasmas
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.
Analysis and application of the scale effect of flood discharge atomization model
无
2011-01-01
The phenomenon of discharge atomization occurs as hydraulic structures discharging,which influences the safety of power station,electrical equipment and produces environmental pollution.A series of physical model tests and feedback analysis are adapted to preliminarily study the scale effect of discharge atomization model by use of the field observation data of discharge atomization.The effect of Re and We numbers of flow on the atomization intensity is analyzed.A conversion relationship of atomization intensity between prototype and model results and the similarity criteria of the atomization range are developed. The conclusion is that the surface tension of discharge atomization model could be ignored when the Weber number is larger than 500.Some case studies are given by use of the similitude criteria of the atomization model.
Chemisorption of ordered atomic layers on a model transition metal
The effect of chemisorption of ordered atomic layers with p(1x1), p(2x1), c(2x2), p(2x2), p(4x1), and c(4x2) structures on the (001) surface of a tight-binding (model transition) metal is investigated within the Newns-Anderson model using the Hartree-Fock Green's function formalism and the phase shift technique. The self-consistent adatom charge q, the heat of adsorption ΔE, and the change in the electronic density of states during chemisorption are calculated for the two binding sites (on-site and centered fourfold-site). Particular attention is paid to the H/W (001) system and the results are compared with the available experimental results. It is shown that the long-range order and adsorption geometry of the overlayers are of great importance for the electronic properties of the chemisorbed systems. (author)
Properties of light atomic nuclei in the potential cluster model
Dubovichenko, S B
2010-01-01
Monograph includes the results of the scientific work of the author for approximately 10 years and it is dedicated to theoretical studies of the structure of light atomic nuclei on the basis of potential cluster model with the forbidden states. Are examined questions of the single-valued construction of the intercluster potentials, which contain the forbidden states and simultaneously applied in the continuous and discrete spectra for the light nuclear systems with a mass of from 2 to 16. Is presented the mathematical apparatus and some calculation methods, utilized in the cluster model. Many questions, until now, considered here did not be reflected in the monographic literature. The book can represent interest for the students of elder courses, probationers, graduate students and scientific workers, who work in the field of theoretical nuclear physics. This Book is written in Russian, but will perhaps present certain interest.
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.
Model of spacecraft atomic oxygen and solar exposure microenvironments
Bourassa, R. J.; Pippin, H. G.
1993-01-01
Computer models of environmental conditions in Earth orbit are needed for the following reasons: (1) derivation of material performance parameters from orbital test data, (2) evaluation of spacecraft hardware designs, (3) prediction of material service life, and (4) scheduling spacecraft maintenance. To meet these needs, Boeing has developed programs for modeling atomic oxygen (AO) and solar radiation exposures. The model allows determination of AO and solar ultraviolet (UV) radiation exposures for spacecraft surfaces (1) in arbitrary orientations with respect to the direction of spacecraft motion, (2) overall ranges of solar conditions, and (3) for any mission duration. The models have been successfully applied to prediction of experiment environments on the Long Duration Exposure Facility (LDEF) and for analysis of selected hardware designs for deployment on other spacecraft. The work on these models has been reported at previous LDEF conferences. Since publication of these reports, a revision has been made to the AO calculation for LDEF, and further work has been done on the microenvironments model for solar exposure.
Graphical abstract: Self-consistent coupling between radiation, state-to-state kinetics, electron kinetics and fluid dynamics. Highlight: ► A CR model of shock-wave in hydrogen plasma has been presented. ► All equations have been coupled self-consistently. ► Non-equilibrium electron and level distributions are obtained. ► The results show non-local effects and non-equilibrium radiation. - Abstract: A collisional-radiative model for hydrogen atom, coupled self-consistently with the Boltzmann equation for free electrons, has been applied to model a shock tube. The kinetic model has been completed considering atom–atom collisions and the vibrational kinetics of the ground state of hydrogen molecules. The atomic level kinetics has been also coupled with a radiative transport equation to determine the effective adsorption and emission coefficients and non-local energy transfer.
Modeling a semiconductor laser with an intracavity atomic absorber
The dynamics of a semiconductor laser with an intracavity atomic absorber is studied numerically. The study is motivated by the experiments of Barbosa et al. [Opt. Lett. 32, 1869 (2007)], using a semiconductor junction as an active medium, with its output face being antireflection coated, and a cell containing cesium vapor placed in a cavity that was closed by a diffraction grating (DG). The DG allowed scanning the lasing frequency across the D2 line in the Cs spectrum, and different regimes such as frequency bistability or dynamic instability were observed depending on the operating conditions. Here we propose a rate-equation model that takes into account the dispersive losses and the dispersive refractive index change in the laser cavity caused by the presence of the Cs vapor cell. These effects are described through a modification of the complex susceptibility. The numerical results are found to be in qualitative good agreement with some of the observations; however, some discrepancies are also noticed, which can be attributed to multi-longitudinal-mode emission in the experiments. The simulations clearly show the relevant role of the Lamb dips and crossover resonances, which arise on top of the Doppler-broadened D2 line in the Cs spectrum, and are due to the forward and backward intracavity fields interacting resonantly with the Cs atoms. When the laser frequency is locked in a dip, a reduction in the frequency noise and of the intensity noise is demonstrated.
Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity
Gammelmark, S.; Molmer, K.; Alt, W.;
2014-01-01
We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian...... manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic...
Three L-subshells atomic model to compute counting efficiency of electron-capture nuclides
The present paper develops a three L-subshell a and K, M-a hells atomic model in order to obtain the counting efficiency in liquid scintillation counting. Mathematical expressions are given to calculate the probabilities of 264 different atomic rearrangement way so as the corresponding effective energies. This new model will permit to test the influence of the different atomic and nuclear parameters upon the counting efficiency nuclides of low and medium atomic number decaying by electron capture. (Author) 8 refs
Independent-particle models for light negative atomic ions
Ganas, P. S.; Talman, J. D.; Green, A. E. S.
1980-01-01
For the purposes of astrophysical, aeronomical, and laboratory application, a precise independent-particle model for electrons in negative atomic ions of the second and third period is discussed. The optimum-potential model (OPM) of Talman et al. (1979) is first used to generate numerical potentials for eight of these ions. Results for total energies and electron affinities are found to be very close to Hartree-Fock solutions. However, the OPM and HF electron affinities both depart significantly from experimental affinities. For this reason, two analytic potentials are developed whose inner energy levels are very close to the OPM and HF levels but whose last electron eigenvalues are adjusted precisely with the magnitudes of experimental affinities. These models are: (1) a four-parameter analytic characterization of the OPM potential and (2) a two-parameter potential model of the Green, Sellin, Zachor type. The system O(-) or e-O, which is important in upper atmospheric physics is examined in some detail.
Atomic-level models of the bacterial carboxysome shell
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.
Global atmospheric model for mercury including oxidation by bromine atoms
C. D. Holmes
2010-12-01
Full Text Available Global models of atmospheric mercury generally assume that gas-phase OH and ozone are the main oxidants converting Hg^{0} to Hg^{II} and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg^{0} oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming gas-phase Br to be the sole Hg^{0} oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O_{3} model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O_{3} models, we add an aqueous photochemical reduction of Hg^{II} in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O_{3} models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of Hg^{II} deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux to the Arctic of 60 Mg a^{−1}. Summertime events of depleted Hg^{0} at Antarctic sites due to subsidence are much better simulated by
Atomic Models of Strong Solids Interfaces Viewed as Composite Structures
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.
Organization of atomic bond tensions in model glasses
Kustanovich, T.; Rabin, Y.; Olami, Z.
2002-01-01
In order to understand whether internal stresses in glasses are correlated or randomly distributed, we study the organization of atomic bond tensions (normal forces between pairs of atoms). Measurements of the invariants of the atomic bond tension tensor in simulated 2D and 3D binary Lennard-Jones glasses, reveal new and unexpected correlations and provide support for Alexander's conjecture about the non-random character of internal stresses in amorphous solids.
Voitkiv, A. B.; Najjari, B.; Shevelko, S. P.
2010-01-01
At impact energies $ \\stackrel{>}{\\sim}1$ GeV/u the projectile-electron excitation and loss occurring in collisions between highly charged ions and neutral atoms is already strongly influenced by the presence of atomic electrons. In order to treat these processes in collisions with heavy atoms we generalize the symmetric eikonal model, used earlier for considerations of electron transitions in ion-atom collisions within the scope of a three-body Coulomb problem. We show that at asymptotically...
Magnetic-sublevel atomic kinetics modeling for line polarization spectroscopy
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) [1] 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. (author)
Y(sl(2)) Algebra Application in Extended Hydrogen Atom and Monopole Models
TIAN Li-Jun; ZHANG Hong-Biao; JIN Shuo; XUE Kang
2004-01-01
We present the extended hydrogen atom and monopole-hydrogen atom theory through generalizing the usual hydrogen atom model and with a monopole model respectively, in which Y (sl(2) ) algebras are realized. We derive the Hamiltonians of the two models based on the Y(sl(2) ) and the generalized Pauli equation. The energy spectra of the systems are also given in terms of Yangian algebra and quantum mechanics.
Netzell, Elisabeth
2015-01-01
This study is a systematic literature review on the role of models and representations in the teaching, learning and understanding of the atom and atomic concepts. The aim of the study is to investigate the role of different visual representations, what models and representations are used in the science classroom, how learners interpret different external representations of the atom, what mental models students construct, and how the representations can be used and designed for meaningful lea...
Khater, Antoine; Szczesniak, Dominik [Laboratoire de Physique de l' Etat Condense UMR 6087, Universite du Maine, 72085 Le Mans (France)
2011-04-01
An analytical model is presented for the electronic conductance in a one dimensional atomic chain across an isolated defect. The model system consists of two semi infinite lead atomic chains with the defect atom making the junction between the two leads. The calculation is based on a linear combination of atomic orbitals in the tight-binding approximation, with a single atomic one s-like orbital chosen in the present case. The matching method is used to derive analytical expressions for the scattering cross sections for the reflection and transmission processes across the defect, in the Landauer-Buttiker representation. These analytical results verify the known limits for an infinite atomic chain with no defects. The model can be applied numerically for one dimensional atomic systems supported by appropriate templates. It is also of interest since it would help establish efficient procedures for ensemble averages over a field of impurity configurations in real physical systems.
Weak Interactions in Atoms and Nuclei: The Standard Model and Beyond
Ramsey-Musolf, M. J.; Secrest, J.
2003-01-01
Studies in nuclear and atomic physics have played an important role in developing our understanding of the Standard Model of electroweak interactions. We review the basic ingredients of the Standard Model, and discuss some key nuclear and atomic physics experiments used in testing these ideas. We also summarize the conceptual issues of the Standard Model that motivate the search for new physics.
Development of a phenomenological model for coal slurry atomization
Dooher, J.P. [Adelphi Univ., Garden City, NY (United States)
1995-11-01
Highly concentrated suspensions of coal particles in water or alternate fluids appear to have a wide range of applications for energy production. For enhanced implementation of coal slurry fuel technology, an understanding of coal slurry atomization as a function coal and slurry properties for specific mechanical configurations of nozzle atomizers should be developed.
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.
1993-01-01
The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.
Improving the Ni I atomic model for solar and stellar atmospheric models
Vieytes, Mariela C
2013-01-01
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 A. Previously, the Solar Radiation Physical Modeling (SRPM) models of the solar atmosphere considered only 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 improves significantly the calculation of the solar spectral irradiance at near-UV wavelengths that are important for Earth atmo spheric studies, and particularly for ozone chemistry.
Operation of the computer model for direct atomic oxygen exposure of Earth satellites
Bourassa, R. J.; Gruenbaum, P. E.; Gillis, J. R.; Hargraves, C. R.
1995-01-01
One of the primary causes of material degradation in low Earth orbit (LEO) is exposure to atomic oxygen. When atomic oxygen molecules collide with an orbiting spacecraft, the relative velocity is 7 to 8 km/sec and the collision energy is 4 to 5 eV per atom. Under these conditions, atomic oxygen may initiate a number of chemical and physical reactions with exposed materials. These reactions contribute to material degradation, surface erosion, and contamination. Interpretation of these effects on materials and the design of space hardware to withstand on-orbit conditions requires quantitative knowledge of the atomic oxygen exposure environment. Atomic oxygen flux is a function of orbit altitude, the orientation of the orbit plan to the Sun, solar and geomagnetic activity, and the angle between exposed surfaces and the spacecraft heading. We have developed a computer model to predict the atomic oxygen exposure of spacecraft in low Earth orbit. The application of this computer model is discussed.
Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models
Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.
2010-01-01
In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the curr...
Four shells atomic model to computer the counting efficiency of electron-capture nuclides
The present paper develops a four-shells atomic model in order to obtain the efficiency of detection in liquid scintillation courting, Mathematical expressions are given to calculate the probabilities of the 229 different atomic rearrangements so as the corresponding effective energies. This new model will permit the study of the influence of the different parameters upon the counting efficiency for nuclides of high atomic number. (Author) 7 refs
Solving time-dependent Schroedinger equation numerically, we investigate the high-order harmonic generation and ionization probability of one dimensional, two dimensional and three dimensional hydrogen atom exposed to intense laser field. In the tunneling ionization regime, our results show that the HHG plateau features and cutoff positions of model hydrogen atoms are well agreement with those of real hydrogen atom, and the trend of changing of the ionization probabilities with time is similar, but the values of ionization probabilities for model atoms are different from ones for three dimensional hydrogen atom. We explain the reason for the difference of ionization probabilities between model atoms and real hydrogen atom according to the semiclassical three-step model. (author)
Photon statistical properties of the cavity field in the two-atom Jaynes-Cummings model
无
2001-01-01
The model that two two-level atoms interact with a singel-mode cavity is studied. The exact solution of the time evolution operator for the two-atom Jaynes-Cummings model is presented by the bare-states approach. Furthermore, we investigate the dynamical properties of the photon statistics of the cavity field, and obtain a number of novel features.
王忠纯; 王琪; 张永生; 郭光灿
2005-01-01
We study the properties of atoms and cavity field in the two-atom Tavis-Cummings model where the two atoms interact with each other and are also driven by an external classical field. We consider the special case that the cavity is initially in a coherent state. The atomic inversion, the average photons number and the Mandel parameter in the driven Tavis-Cummings model are given and analysed numerically. We pay special attention to the dynamical behaviour of the atoms and the cavity field modified by the external field.
Modeling molecular crystals formed by spin-active metal complexes by atom-atom potentials
Sinitskiy, Anton V; Tokmachev, Andrei M; Dronskowski, Richard
2009-01-01
We apply the atom-atom potentials to molecular crystals of iron (II) complexes with bulky organic ligands. The crystals under study are formed by low-spin or high-spin molecules of Fe(phen)$_{2}$(NCS)$_{2}$ (phen = 1,10-phenanthroline), Fe(btz)$_{2}$(NCS)$_{2}$ (btz = 5,5$^{\\prime }$,6,6$^{\\prime}$-tetrahydro-4\\textit{H},4$^{\\prime}$\\textit{H}-2,2$^{\\prime }$-bi-1,3-thiazine), and Fe(bpz)$_{2}$(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2$^{\\prime}$-bipyridine). All molecular geometries are taken from the X-ray experimental data and assumed to be frozen. The unit cell dimensions and angles, positions of the centers of masses of molecules, and the orientations of molecules corresponding to the minimum energy at 1 atm and 1 GPa are calculated. The optimized crystal structures are in a good agreement with the experimental data. Sources of the residual discrepancies between the calculated and experimental structures are discussed. The intermolecular contributions to the enthalpy of the spin transiti...
Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I.
Bautista, M. A.; Fivet, V.; Quinet, P.; Dunn, J.; Gull, T. R.; Kallman, T. R.; Mendoza, C.
2013-01-01
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data.We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of Oiii and Fe ii and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe ii]. Key words: atomic data - atomic processes - line: formation - methods: data analysis - molecular data - molecular processes - techniques: spectroscopic
Friesecke, G.; Goddard, B.D.
2009-01-01
Configuration-interaction (CI) models are approximations to the electronic Schrödinger equation which are widely used for numerical electronic structure calculations in quantum chemistry. Based on our recent closed-form asymptotic results for the full atomic Schrödinger equation in the limit of fixed electron number and large nuclear charge [SIAM J. Math. Anal., 41 (2009), pp. 631-664], we introduce a class of CI models for atoms which reproduce, at fixed finite model dimension, the correct S...
Electron structure of atoms in laser plasma: The Debye shielding model
The electronic structure and the energy spectra of multielectron atoms in laser plasmas are examined by the Debye shielding model. The effect of the plasma environment on the electrons bound in an atom is taken into account by introducing the screened Coulomb-type potentials into the electronic Hamiltonian of an atom in place of the standard nuclear attraction and electron repulsion potentials. The capabilities of this new Hamiltonian are demonstrated for He and Li in laser plasmas. (author)
Atom diffusion in furnaces-models and measurements
Sadagoff, Y. M.; Dědina, Jiří
Pretoria : South African Society and South African chemical Institute, 2001, s. FR4-4. [Colloquium Spectroscopicum Internationale /32./. Pretoria (ZA), 08.07.2001-13.07.2001] R&D Projects: GA ČR GA203/01/0453 Institutional research plan: CEZ:AV0Z4031919 Keywords : AAS * diffusion coefficient * graphite atomizer Subject RIV: CB - Analytical Chemistry, Separation
Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness
Park, Eun Jung; Light, Gregory
2009-01-01
Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…
Enhanced ion backscattering near 1800 scattering angles in the two-atom scattering model
An analytical two-atom scattering model has been developed to treat the recent discovery of the enhancement near 1800 of Rutherford backscattering yields from disordered solids. In contrast to conventional calculations of Rutherford backscattering that treat scattering from a single atom only (the backscattering atom), the present model includes the interaction of a second atom lying between the target surface and the backscattering atom. The projectile ion makes a glancing collision with this second atom both before and after it is backscattered. A weighted average is made over all possible positions of this second atom. The model predicts an enhancement effect whose physical origin arises from the tolerance of path for those ions whose ingoing and outgoing trajectories lie in the vicinity of the critical impact parameter. Results using Moliere scattering show how the yield enhancement depends on ion energy, backscattering depth, exit angle, scattering potential, atomic numbers of the projectile and target, and target density. In the model the critical impact parameter and critical angle play important roles. It is shown that these quantities depend on a single dimensionless parameter and formulas accurate to better than 1% are given for them
Atomic charges for modeling metal–organic frameworks: Why and how
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
Atomic charges for modeling metal–organic frameworks: Why and how
Hamad, Said, E-mail: said@upo.es; 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.
Mg I as a probe of the solar chromosphere - The atomic model
Mauas, Pablo J.; Avrett, Eugene H.; Loeser, Rudolf
1988-01-01
This paper presents a complete atomic model for Mg I line synthesis, where all the atomic parameters are based on recent experimental and theoretical data. It is shown how the computed profiles at 4571 A and 5173 A are influenced by the choice of these parameters and the number of levels included in the model atom. In addition, observed profiles of the 5173 A b2 line and theoretical profiles for comparison (based on a recent atmospheric model for the average quiet sun) are presented.
Collapse-revival dynamics and atom-field entanglement in the non-resonant Dicke model
Alvermann, A; Fehske, H; 10.1103/PhysRevA.85.043803
2012-01-01
We consider the dynamics of atomic and field coherent states in the non-resonant Dicke model. At weak coupling an initial product state evolves into a superposition of multiple field coherent states that are correlated with the atomic configuration. This process is accompanied by the buildup and decay of atom-field entanglement and leads to the periodic collapse and revival of Rabi oscillations. We provide a perturbative derivation of the underlying dynamical mechanism that complements the rotating wave approximation at resonance. The identification of two different time scales explains how the dynamical signatures depend on the sign of detuning between the atomic and field frequency, and predicts the generation of either atomic or field cat states in the two opposite cases. We finally discuss the restrictions that the buildup of atom-field entanglement during the collapse of Rabi oscillations imposes on the validity of semi-classical approximations that neglect entanglement.
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 temperature...
Embedded Atom model use for microstructural defects study
Pure metallic systems properties, as Ni, Al and Ni3 alloys, are studied in presence of a vacancy. Such systems were submitted to cohesion by an interatomic potential of the Embedded Atom type, as a substantial improvement regarding the pairs' traditional potentials. The vacancy in its equilibrium and saddle point configurations is specifically analyzed, thus evaluating the formation and migration energies of this defect, and vibrational entropies in defective nets subject to cohesion with these potentials. (Author)
Simple Theoretical Models for Resonant Cold Atom Interactions
Julienne, Paul S.; Gao, Bo
2006-01-01
Magnetically tunable scattering resonances have been used with great success for precise control of s-wave scattering lengths in ultracold atomic collisions. We describe relatively simple yet quite powerful analytic treatments of such resonances based on the analytic properties of the van der Waals long range potential. This theory can be used to characterize a number of properties of specific resonances that have been used successfully in various experiments with $^{87}$Rb, $^{85}$Rb, $^{40}...
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
Currents algebra for an atom-molecule Bose-Einstein condensate model
Filho, Gilberto N. Santos
2016-01-01
I present an interconversion currents algebra for an atom-molecule Bose-Einstein condensate model and use it to get the quantum dynamics of the currents. For different choices of the Hamiltonian parameters I get different currents dynamics.
Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling
Tawara, H. [ed.
1997-01-01
This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)
Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling
This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)
Simple Theoretical Models for Resonant Cold Atom Interactions
Julienne, P S; Julienne, Paul S.; Gao, Bo
2006-01-01
Magnetically tunable scattering resonances have been used with great success for precise control of s-wave scattering lengths in ultracold atomic collisions. We describe relatively simple yet quite powerful analytic treatments of such resonances based on the analytic properties of the van der Waals long range potential. This theory can be used to characterize a number of properties of specific resonances that have been used successfully in various experiments with $^{87}$Rb, $^{85}$Rb, $^{40}$K, and $^{6}$Li. Optical Feshbach resonances are also possible and may be practical with narrow intercombination line photoassociative transitions in species like Sr and Yb.
The structure of warm dense matter modeled with an average atom model with ion-ion correlations
Saumon, D.; Starrett, C. E.; Anta, J. A.; Daughton, W.; Chabrier, G.
2013-01-01
We present a new model of warm dense matter that represents an intermediate approach between the relative simplicity of ''one-ion'' average atom models and the more realistic but computationally expensive ab initio simulation methods. Physical realism is achieved primarily by including the correlations in the plasma that surrounds a central ion. The plasma is described with the Ornstein-Zernike integral equations theory of fluids, which is coupled to an average atom model for the central ion....
An Analytical Model for Adsorption and Diffusion of Atoms/Ions on Graphene Surface
Yan-Zi Yu
2015-01-01
Full Text Available Theoretical investigations are made on adsorption and diffusion of atoms/ions on graphene surface based on an analytical continuous model. An atom/ion interacts with every carbon atom of graphene through a pairwise potential which can be approximated by the Lennard-Jones (L-J potential. Using the Fourier expansion of the interaction potential, the total interaction energy between the adsorption atom/ion and a monolayer graphene is derived. The energy-distance relationships in the normal and lateral directions for varied atoms/ions, including gold atom (Au, platinum atom (Pt, manganese ion (Mn2+, sodium ion (Na1+, and lithium-ion (Li1+, on monolayer graphene surface are analyzed. The equilibrium position and binding energy of the atoms/ions at three particular adsorption sites (hollow, bridge, and top are calculated, and the adsorption stability is discussed. The results show that H-site is the most stable adsorption site, which is in agreement with the results of other literatures. What is more, the periodic interaction energy and interaction forces of lithium-ion diffusing along specific paths on graphene surface are also obtained and analyzed. The minimum energy barrier for diffusion is calculated. The possible applications of present study include drug delivery system (DDS, atomic scale friction, rechargeable lithium-ion graphene battery, and energy storage in carbon materials.
Fast procedure for reconstruction of full-atom protein models from reduced representations
Rotkiewicz, Piotr; Skolnick, Jeffrey
2008-01-01
We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on...
Invited Review Article: The statistical modeling of atomic clocks and the design of time scales
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.
A simple model of molecular imaging with noncontact atomic force microscopy
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.
Classical trajectory perspective of atomic ionization in strong laser fields semiclassical modeling
Liu, Jie
2014-01-01
The ionization of atoms and molecules in strong laser fields is an active field in modern physics and has versatile applications in such as attosecond physics, X-ray generation, inertial confined fusion (ICF), medical science and so on. Classical Trajectory Perspective of Atomic Ionization in Strong Laser Fields covers the basic concepts in this field and discusses many interesting topics using the semiclassical model of classical trajectory ensemble simulation, which is one of the most successful ionization models and has the advantages of a clear picture, feasible computing and accounting for many exquisite experiments quantitatively. The book also presents many applications of the model in such topics as the single ionization, double ionization, neutral atom acceleration and other timely issues in strong field physics, and delivers useful messages to readers with presenting the classical trajectory perspective on the strong field atomic ionization. The book is intended for graduate students and researchers...
A simple model of molecular imaging with noncontact atomic force microscopy
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. (paper)
Sound speed and oscillation frequencies for solar models evolved with Los Alamos ATOMIC opacities
Guzik, Joyce A; Walczak, P; Wood, S R; Mussack, K; Farag, E
2016-01-01
Los Alamos National Laboratory has calculated a new generation of radiative opacities (OPLIB data using the ATOMIC code) for elements with atomic number Z=1-30 with improved physics input, updated atomic data, and finer temperature grid to replace the Los Alamos LEDCOP opacities released in the year 2000. We calculate the evolution of standard solar models including these new opacities, and compare with models evolved using the Lawrence Livermore National Laboratory OPAL (Iglesias and Rogers 1996) opacities. We use the solar abundance mixture of Asplund et al. (2009). The new Los Alamos ATOMIC opacities have steeper opacity derivatives than those of OPAL for temperatures and densities of the solar interior radiative zone. We compare the calculated nonadiabatic solar oscillation frequencies and solar interior sound speed to observed frequencies and helioseismic inferences. The calculated sound-speed profiles are similar for models evolved using either the updated Iben evolution code (see \\cite{Guzik2010}), or ...
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.
Mathematical modeling of nanomachining with atomic force microscope cantilevers
This article theoretically analyzes the cutting depth and material removal rate of an atomic force microscope (AFM) cantilever during nanomachining. An analytical expression for the vibration frequency and displacement of the cantilever has been obtained by using the modified couple stress theory. The theory includes one additional material length scale parameter revealing the micro-scale effect. According to the analysis, the results show that the effect of size-dependent on the vibration behavior of the AFM cantilever is obvious. The maximum displacement of nanomachining with the AFM cantilever represents the cutting depth. The area under the displacement-time curve is related to the material removal rate. When the excitation frequency is closer to the nature frequency of the cantilever, a larger material removal rate is obtained
Classical trajectory perspective of atomic ionization in strong laser fields. Semiclassical modeling
Dealing with timely and interesting issues in strong laser physics. Illustrates complex strong field atomic ionization with the simple semiclassical model of classical trajectory perspective for the first time. Provides a theoretical model that can be used to account for recent experiments. The ionization of atoms and molecules in strong laser fields is an active field in modern physics and has versatile applications in such as attosecond physics, X-ray generation, inertial confined fusion (ICF), medical science and so on. Classical Trajectory Perspective of Atomic Ionization in Strong Laser Fields covers the basic concepts in this field and discusses many interesting topics using the semiclassical model of classical trajectory ensemble simulation, which is one of the most successful ionization models and has the advantages of a clear picture, feasible computing and accounting for many exquisite experiments quantitatively. The book also presents many applications of the model in such topics as the single ionization, double ionization, neutral atom acceleration and other timely issues in strong field physics, and delivers useful messages to readers with presenting the classical trajectory perspective on the strong field atomic ionization. The book is intended for graduate students and researchers in the field of laser physics, atom molecule physics and theoretical physics. Dr. Jie Liu is a professor of Institute of Applied Physics and Computational Mathematics, China and Peking University.
Models of atoms in plasmas based on common formalism for bound and free electrons
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. (authors)
Models of atoms in plasmas based on common formalism for bound and free electrons
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.
Ion-reversibility studies in amorphous solids using the two-atom scattering model
An analytical two-atom scattering model has been developed to treat the recent discovery of the enhancement near 1800 of Rutherford backscattering yields from disordered solids. In contrast to conventional calculations of Rutherford backscattering that treat scattering from a single atom only (the backscattering atom), the present model includes the interaction of a second atom lying between the target surface and the backscattering plane. The projectile ion makes a glancing collision with this second atom both before and after it is backscattered. The model predicts an enhancement effect whose physical origin arises from the tolerance of path for those ions whose inward and outward trajectories lie in the vicinity of the critical impact parameter. Results using Moliere scattering show how the yield enhancement depends on ion energy, backscattering depth, exit angle, scattering potential, atomic numbers of the projectile and target, and target density. In the model the critical impact parameter and critical angle play important roles. It is shown that these quantities depend on a single dimensionless parameter and analytical expressions for them are given which are accurate to better than 1%
Engineering the Dynamics of Effective Spin-Chain Models for Strongly Interacting Atomic Gases
Volosniev, A. G.; Petrosyan, D.; Valiente, M.; Fedorov, D. V.; Jensen, A. S.; Zinner, Nikolaj Thomas
2015-01-01
We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We...... find that bosonic atoms offer more flexibility for tuning independently the parameters of the spin Hamiltonian through interatomic (intra-species) interaction which is absent for fermions due to the Pauli exclusion principle. Our formalism can have important implications for control and manipulation of...
UNCERTAINTIES IN ATOMIC DATA AND THEIR PROPAGATION THROUGH SPECTRAL MODELS. I
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].
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, Manuel A; Quinet, Pascal; Dunn, Jay; Kallman, Theodore R Gull Timothy R; Mendoza, Claudio
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 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].
UNCERTAINTIES IN ATOMIC DATA AND THEIR PROPAGATION THROUGH SPECTRAL MODELS. I
Bautista, M. A.; Fivet, V. [Department of Physics, Western Michigan University, Kalamazoo, MI 49008 (United States); Quinet, P. [Astrophysique et Spectroscopie, Universite de Mons-UMONS, B-7000 Mons (Belgium); Dunn, J. [Physical Science Department, Georgia Perimeter College, Dunwoody, GA 30338 (United States); Gull, T. R. [Code 667, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Kallman, T. R. [Code 662, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Mendoza, C., E-mail: manuel.bautista@wmich.edu [Centro de Fisica, Instituto Venezolano de Investigaciones Cientificas (IVIC), P.O. Box 20632, Caracas 1020A (Venezuela, Bolivarian Republic of)
2013-06-10
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data. We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of O III and Fe II and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe II].
JANNUS: experimental validation at the scale of atomic modelling
Ion irradiation is well suited to simulate neutron irradiation because primary knock-on atoms (PKA) produced by neutron collisions are self ions of the target. As the main difference, the energy spectrum of ion-produced PKAs is somewhat broader than in the case of fast neutrons. Studies of the combined effects of target damaging, ion implantation effects, helium and hydrogen production, and the occurrence of nuclear reactions should be performed by co-irradiation experiments (dual or triple beam irradiation). The JANNUS project (Joint Accelerators for Nano-sciences and NUclear Simulation) was started in 2002. Two experimental sites are involved. At Saclay, three electrostatic accelerators are being coupled: a new 3 MV Pelletron machine equipped with an Ecr multi-charged ion source, a 2.5 MV single ended Van de Graaff and a 2.25 MV General Ionex tandem. At Orsay, the 2 MV tandem ARAMIS and the 190 kV ion implanter IRMA are being coupled with a 200 kV TECNAI transmission electron microscope to allow simultaneous co-irradiation and observation. This paper will first discuss both advantages and limitations of the use of ion beam irradiation to simulate neutron irradiation. A technical description of both set-ups is then presented, and some details will be given concerning multi-irradiation facilities running worldwide. The main application fields of JANNUS will be further detailed (authors)
Reasoning with Atomic-Scale Molecular Dynamic Models
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling
Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki
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
[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
Fast Three-Dimensional Method of Modeling Atomic Oxygen Undercutting of Protected Polymers
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.
Simulating Quantum Spin Models using Rydberg-Excited Atomic Ensembles in Magnetic Microtrap Arrays
Whitlock, Shannon; Hannaford, Peter
2016-01-01
We propose a scheme to simulate lattice spin models based on strong and long-range interacting Rydberg atoms stored in a large-spacing array of magnetic microtraps. Each spin is encoded in a collective spin state involving a single $nP$ Rydberg atom excited from an ensemble of ground-state alkali atoms prepared via Rydberg blockade. After the excitation laser is switched off the Rydberg spin states on neighbouring lattice sites interact via general isotropic or anisotropic spin-spin interactions. To read out the collective spin states we propose a single Rydberg atom triggered avalanche scheme in which the presence of a single Rydberg atom conditionally transfers a large number of ground-state atoms in the trap to an untrapped state which can be readily detected by site-resolved absorption imaging. Such a quantum simulator should allow the study of quantum spin systems in almost arbitrary two-dimensional configurations. This paves the way towards engineering exotic spin models, such as spin models based on tr...
Mapping the Two-Component Atomic Fermi Gas to the Nuclear Shell-Model
Özen, C.; Zinner, Nikolaj Thomas
2014-01-01
the external potential becomes important. A system of two-species fermionic cold atoms with an attractive zero-range interaction is analogous to a simple model of nucleus in which neutrons and protons interact only through a residual pairing interaction. In this article, we discuss how the problem of...... a two-component atomic fermi gas in a tight external trap can be mapped to the nuclear shell model so that readily available many-body techniques in nuclear physics, such as the Shell Model Monte Carlo (SMMC) method, can be directly applied to the study of these systems. We demonstrate an...
Simple statistical model for predicting thermal atom diffusion on crystal surfaces
A simple model based on the statistics of single atoms is developed to predict the diffusion rate of thermal atoms in (or on) bulk materials without empirical parameters. Compared with vast classical molecular-dynamics simulations for predicting the self-diffusion rate of Pt, Cu, and Ar adatoms on crystal surfaces, the model is proved to be much more accurate than the Arrhenius law and the transition state theory. Applying this model, the theoretical predictions agree well with the experimental values in the presented paper about the self-diffusion of Pt (Cu) adatoms on the surfaces
Empirical model for electron impact ionization cross sections of neutral atoms
A simple empirical formula is proposed for the rapid calculation of electron impact total ionization cross sections both for the open- and closed-shell neutral atoms considered in the range 1 ≤ Z ≤ 92 and the incident electron energies from threshold to about 104 eV. The results of the present analysis are compared with the available experimental and theoretical data. The proposed model provides a fast method for calculating fairly accurate electron impact total ionization cross sections of atoms. This model may be a prudent choice, for the practitioners in the field of applied sciences e.g. in plasma modeling, due to its simple inherent structure. (authors)
Four-component united-atom model of bitumen
Hansen, Jesper S; Nielsen, Erik; Dyre, Jeppe C; Schrøder, Thomas B
2013-01-01
We propose a four-component 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 being carried out using Graphic-Processor-Units based software in time spans in order of microseconds, and this enables the study of slow relaxation processes characterizing bitumen. This paper focuses on the high-temperature 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 as a result of the different constituents in the system. 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 ...
Nano Goes to School: A Teaching Model of the Atomic Force Microscope
Planinsic, Gorazd; Kovac, Janez
2008-01-01
The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…
Valentin, Jan B.; Andreetta, Christian; Boomsma, Wouter;
2014-01-01
We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length s...
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…
Mathematical modelling of the liquid atomization process by cocurrent gas flow
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.
Expansion of the USDA ARS Aerial Application spray atomization models
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
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
UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions
UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples. Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30–10 Å range and sometimes even beyond 10 Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
Jonikas, Magdalena A; RADMER, RANDALL J.; Altman, Russ B
2009-01-01
Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. Results: We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA ...
Many-Body Quantum Optics with Decaying Atomic Spin States: ($\\gamma$, $\\kappa$) Dicke model
Gelhausen, Jan; Strack, Philipp
2016-01-01
We provide a theory for quantum-optical realizations of the open Dicke model with internal, atomic spin states subject to uncorrelated, single-site spontaneous emission with rate $\\gamma$. This introduces a second decay channel for excitations to irreversibly dissipate into the environment, in addition to the photon loss with rate $\\kappa$. We compute the mean-field non-equilibrium steady states for spin and photon observables in the long-time limit, $t\\rightarrow \\infty$. Although $\\gamma$ does not conserve the total angular momentum of the spin array, we argue that our solution is exact in the thermodynamic limit, for the number of atoms $N\\rightarrow \\infty$. In light of recent and upcoming experiments realizing superradiant phase transitions using internal atomic states with pinned atoms in optical lattices, our work lays the foundation for the pursuit of a new class of open quantum magnets coupled to quantum light.
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.
Various applications of atomic physics and kinetics codes to plasma modeling
A collection of computer codes developed at Los Alamos have been applied to a variety of plasma modeling problems. The CATS, RATS, ACE, and GIPPER codes are used to calculate a consistent set of atomic physics data for a given problem. The calculated data include atomic energy levels, oscillator strengths, electron impact excitation and ionization cross sections, photoionization cross sections, and autoionization rates. The FINE and LINES codes access these data sets directly to perform plasma modeling calculations. Preliminary results of some of the current applications are presented, including, the calculation of holmium opacity, the modeling of plasma flat panel display devices, the analysis of some new results from the LANL TRIDENT laser and prediction of the radiative properties of the plasma wakefield light source for extreme ultraviolet lithography (EUVL). For the latter project, the simultaneous solution of atomic kinetics for the level populations and the Boltzmann equation for the electron energy distribution is currently being implemented. copyright 1996 American Institute of Physics
Model studies on pump sump for Tarapur Atomic Power Plant
In a typical pump intake composite model of Tarapur Project the flow conditions were improved and not only visible swirls and vortices were eliminated, but also prerotation observed at location of pump impeller in the rising pipe was reduced and swirls angles were kept below the 5 degree limit, assuring stable performance of the pump with respect to the sump geometry. (author). 9 refs., 3 figs., 4 tabs
周玲; 宋鹤山; 李崇; 郭彦青
2003-01-01
The dissipation of the field in the two-photon Jaynes-Cummings model (JCM) with degenerate atomic levels was studied. The initial degenerate atomic state affects the field coherence loss. When the degenerate atom is initially in an equal probability superposition state, the field coherence loss is smallest. It is found that the degeneracy of the atomic level increases the period of entanglement between the atom and the field. When the degeneracy was considered, the coherence properties of the field could be affected by the reservoir qualitatively, if a nonlinear two-photon process is involved. This is different from the dissipation of one-photon JCM with degenerate atomic levels.
The contribution of atom accessibility to site of metabolism models for cytochromes P450
Rydberg, Patrik; Rostkowski, M.; Gloriam, D.E.; Olsen, L.
2013-01-01
Three different types of atom accessibility descriptors are investigated in relation to site of metabolism predictions. To enable the integration of local accessibility we have constructed 2DSASA, a method for the calculation of the atomic solvent accessible surface area that is independent of 3D...... coordinates. The method was implemented in the SMARTCyp site of metabolism prediction models and improved the results by up to 4 percentage points for nine cytochrome P450 isoforms. The final models are made available at http://www.farma.ku.dk/smartcyp....
Popa, Alexandru
2013-01-01
Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamic Systems is intended for scientists and graduate students interested in the foundations of quantum mechanics and applied scientists interested in accurate atomic and molecular models. This is a reference to those working in the new field of relativistic optics, in topics related to relativistic interactions between very intense laser beams and particles, and is based on 30 years of research. The novelty of this work consists of accurate connections between the properties of quantum equations and correspon
Exact semi-relativistic model for ionization of atomic hydrogen by electron impact
Attaourti, Y.; Taj, S.; Manaut, B.
2004-01-01
We present a semi-relativistic 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. Thes...
Atomic Data and Spectral Models for FeII
Bautista, Manuel A; Ballance, Connor; Quinet, Pascal; Ferland, Gary; Mendoza, Claudio; Kallman, Timothy R
2015-01-01
We present extensive calculations of radiative transition rates and electron impact collision strengths for Fe II. The data sets involve 52 levels from the $3d\\,^7$, $3d\\,^64s$, and $3d\\,^54s^2$ configurations. Computations of $A$-values are carried out with a combination of state-of-the-art multiconfiguration approaches, namely the relativistic Hartree--Fock, Thomas--Fermi--Dirac potential, and Dirac--Fock methods; while the $R$-matrix plus intermediate coupling frame transformation, Breit--Pauli $R$-matrix and Dirac $R$-matrix packages are used to obtain collision strengths. We examine the advantages and shortcomings of each of these methods, and estimate rate uncertainties from the resulting data dispersion. We proceed to construct excitation balance spectral models, and compare the predictions from each data set with observed spectra from various astronomical objects. We are thus able to establish benchmarks in the spectral modeling of [Fe II] emission in the IR and optical regions as well as in the UV Fe...
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.
Exact theory and numeric results for short pulse ionization of simple model atom in one dimension
Rokhlenko, Alexander
2015-01-01
Our exact theory for continuous harmonic perturbation of a one dimensional model atom by parametric variations of its potential is generalized for the cases when a) the atom is exposed to short pulses of an external harmonic electric field and b) the forcing is represented by short bursts of different shape changing the strength of the binding potential. This work is motivated not only by the wide use of laser pulses for atomic ionization, but also by our earlier study of the same model which successfully described the ionization dynamics in all orders, i.e. the multi-photon processes, though being treated by the non-relativistic Schr\\"odinger equation. In particular, it was shown that the bound atom cannot survive the excitation of its potential caused by any non-zero frequency and amplitude of the continuous harmonic forcing. Our present analysis found important laws of the atomic ionization by short pulses, in particular the efficiency of ionizing this model system and presumably real ones as well.
Laser-induced photofragmentation of triethylaluminum: Modeling H-atom production
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.
Predicting Transcription Factor Specificity with All-Atom Models
Rahi, Sahand Jamal; Mirny, Leonid A; Kardar, Mehran
2008-01-01
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rather start with the structure of a protein-DNA complex. We study the PurR E. coli TF, and explore to which extent atomistic models of protein-DNA complexes can be used to distinguish between cognate and non-cognate DNA sites. Particular emphasis is placed on systematic evaluation of this approach by comparing its performance with bioinformatic methods, by testing it against random decoys and sites of homologous TFs. We also examine a set of experimental mutations in both DNA and the protein. Using our explicit estimates of energy, we show that the specificity for PurR is dominated by direct protein-DNA interactions, and w...
Atomic Model and Micelle Dynamics of QS-21 Saponin
Conrado Pedebos
2014-03-01
Full Text Available QS-21 is a saponin extracted from Quillaja saponaria, widely investigated as a vaccine immunoadjuvant. However, QS-21 use is mainly limited by its chemical instability, significant variety in molecular composition and low tolerance dose in mammals. Also, this compound tends to form micelles in a concentration-dependent manner. Here, we aimed to characterize its conformation and the process of micelle formation, both experimentally and computationally. Therefore, molecular dynamics (MD simulations were performed in systems containing different numbers of QS-21 molecules in aqueous solution, in order to evaluate the spontaneous micelle formation. The applied methodology allowed the generation of micelles whose sizes were shown to be in high agreement with small-angle X-ray scattering (SAXS. Furthermore, the ester linkage between fucose and acyl chain was less solvated in the micellar form, suggesting a reduction in hydrolysis. This is the first atomistic interpretation of previous experimental data, the first micellar characterization of saponin micelles by SAXS and first tridimensional model of a micelle constituted of saponins, contributing to the understanding of the molecular basis of these compounds.
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
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
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.
Modeling and understanding of effects of randomness in arrays of resonant meta-atoms
Tretyakov, Sergei A.; Albooyeh, Mohammad; Alitalo, Pekka;
2013-01-01
In this review presentation we will discuss approaches to modeling and understanding electromagnetic properties of 2D and 3D lattices of small resonant particles (meta-atoms) in transition from regular (periodic) to random (amorphous) states. Nanostructured metasurfaces (2D) and metamaterials (3D......) are arrangements of optically small but resonant particles (meta-atoms). We will present our results on analytical modeling of metasurfaces with periodical and random arrangements of electrically and magnetically resonant meta-atoms with identical or random sizes, both for the normal and oblique......-angle excitations. We show how the electromagnetic response of metasurfaces is related to the statistical parameters of the structure. Furthermore, we will discuss the phenomenon of anti-resonance in extracted effective parameters of metamaterials and clarify its relation to the periodicity (or amorphous nature) of...
Non local thermodynamic equilibrium self-consistent average atom model for plasma physics
A time-dependent collisional-radiative average-atom model is presented to study statistical properties of highly-charged ion plasmas in off-equilibrium conditions. Atomic structure is described either with a screened-hydrogenic model including l-splitting, or by calculating one electron states in a self-consistent average-atom potential. Collisional and radiative excitation/deexcitation and ionization/recombination rats, as well as auto-ionization and dielectronic recombination rates, are formulated within the average-configuration framework. A good agreement with experiment is found for the charge-state distribution of a gold plasma at electron and density temperature equal to 6 x 1020 cm-3 and 2200 eV. (author)
Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model
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 k-vector 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.
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
2012-10-01
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.
Liu, Yi-Mou; Yan, Dong; Tian, Xue-Dong; Cui, Cui-Li; Wu, Jin-Hui
2014-03-01
We present an improved superatom model for examining nonlinear optical responses of cold Rydberg atoms in the regime of electromagnetically induced transparency (EIT). By going beyond the weak-probe approximation, we find that several higher-order collective states should be included to correctly describe the coherent Rydberg excitation of superatoms. Otherwise, numerical results based on the simple ladder system of superatoms will contribute wrong predictions on light intensity and photon correlation of the transmitted probe field. In particular, a great photon-bunching effect will be improperly expected somewhere out of the EIT window in one dilute atomic sample. The essence of this improved superatom model lies in that it can provide reliable predictions on the nonlinear Rydberg-EIT phenomena even in dense atomic samples and may be extended to realize lossless conditional light interactions in appropriate multilevel systems exhibiting dipole blockade.
Explicit all-atom modeling of realistically sized ligand-capped nanocrystals
Kaushik, Ananth P.
2012-01-01
We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.
Derouich, Moncef
2016-01-01
Simulations of the generation of the atomic polarization is necessary for interpreting the second solar spectrum. For this purpose, it is important to rigorously determine the effects of the isotropic collisions with neutral hydrogen on the atomic polarization of the neutral atoms, ionized atoms and molecules. Our aim is to treat in generality the problem of depolarizing isotropic collisions between singly ionized atoms and neutral hydrogen in its ground state. Using our numerical code, we computed the collisional depolarization rates of the $p$-levels of ions for large number of values of the effective principal quantum number $n^{*}$ and the Uns\\"old energy $E_p$. Then, genetic programming has been utilized to fit the available depolarization rates. As a result, strongly non-linear relationships between the collisional depolarization rates, $n^{*}$ and $E_p$ are obtained, and are shown to reproduce the original data with accuracy clearly better than 10\\%. These relationships allow quick calculations of the ...
Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former
The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes–Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude. (paper)
Atomic Dipole Squeezing in the Correlated Two-Mode Two-Photon Jaynes-Cummings Model
Dong, Zhengchao; Zhao, Yonglin
1996-01-01
In this paper, we study the atomic dipole squeezing in the correlated two-mode two-photon JC model with the field initially in the correlated two-mode SU(1,1) coherent state. The effects of detuning, field intensity and number difference between the two field modes are investigated through numerical calculation.
A simple model for atomic layer doped field-effect transistor (ALD-FET) electronic states
Mora R, M.E. [Centro de Investigaciones en Optica, Unidad Aguascalientes. Juan de Montoro 207, Zona Centro, 20000 Aguascalientes (Mexico); Gaggero S, L.M. [Escuela de Fisica, Universidad Autonoma de Zacatecas, Av. Preparatoria 301, 98060 Zacatecas (Mexico)
1998-12-31
We propose a simple potential model based on the Thomas-Fermi approximation to reproduce the main properties of the electronic structure of an atomic layer doped field effect transistor. Preliminary numerical results for a Si-based ALD-FET justify why bound electronic states are not observed in the experiment. (Author)
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.
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.
The chemisorption of atomic hydrogen and oxygen on a cobalt surface has been studied on a five-atom cluster model using one-electron effective core potential (le- ECP) and all-electron calculations at the ab initio SCF and MCPF levels. Also, density functional calculations have been carried out. The different approaches are evaluated. The le- ECP has been compared to similar ECPS for nickel and copper. Our results indicate that this approach is valid also for cobalt. Different contributions to the cluster-adsorbate bonding energy are discussed. 31 refs., 1 fig., 1 tab
Mathematical Modeling of Ultracold Few-Body Processes in Atomic Traps
Melezhik V.S.
2016-01-01
Full Text Available 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 kinetic neutral atom model for tokamak scrape-off layer tubulence simulations
Wersal, Christoph; Ricci, Paolo; Halpern, Federico David; Riva, Fabio
2014-01-01
The first-principle understanding of the processes in the Scrape-Off-Layer (SOL) of a tokamak is crucial for the developement of a thermonuclear re- actor. Since the plasma temperature in the SOL is rather low, the plasma is typically not fully ionized, and the neutral atoms play an important role in determining the SOL regimes. The description of a simple kinetic model for neutral atoms in the SOL is presented and first results of self-consistent non-linear turbulence simulations with the GB...
Popa, Alexandru
2013-01-01
Applications of Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamical Systems is a reference on the new field of relativistic optics, examining topics related to relativistic interactions between very intense laser beams and particles. Based on 30 years of research, this unique book connects the properties of quantum equations to corresponding classical equations used to calculate the energetic values and the symmetry properties of atomic, molecular and electrodynamical systems. In addition, it examines applications for these methods, and for the calculation of
Model for Interaction Between Photon and Cold Atom in QED Cavity
ZHANG Li; WANG Cheng; LI Yan-Min; RUAN Sheng-Ping; XUAN Li
2004-01-01
A model has been established for the interaction between a single-mode optical field and a 2-energy-level cold atom with exact analytic solutions given. The processes of momentum and energy exchanges between the optical field and the cold atom due to the interaction between them are discussed in detail, and a formula has been given for the variation of momentum and energy exchange volumes with time t in dress state while both the effects of photon recoil and Doppler effect are taken into consideration.
Kozlov, Alex; Quiney, Harry
2016-01-01
We describe a method for the calculation of photoionization cross-sections using square-integrable amplitudes obtained from the diagonalization of finite-basis set representations of the electronic Hamiltonian. Three examples are considered: a model example in which the final state is a free particle, the hydrogen atom and neutral atomic sodium. The method exploits the Whittaker-Shannon-Kotel'nikov sampling theorem, which is widely used in digital signal sampling and reconstruction. The approach reproduces known data with very good accuracy and converges to the exact solution with increase of the basis set size.
Berry phase in a two-atom Jaynes-Cummings model with Kerr medium
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.
Multiple-cascade model for the filling of hollow Ne atoms moving below an Al surface
Analytic expressions for a multiple-cascade model were derived to study the filling of L and K vacancies of hollow Ne atoms moving in shallow layers of an Al surface. The model requires cross sections for charge transfer into the L shell of the projectile that were determined from molecular-orbital calculations including screening effects of hollow atoms and asymptotic solid-state energies. The analysis accounts for mechanisms of Landau-Zener curve crossing and Fano-Lichten promotion. To describe the transport of the electrons within the solid, absorption and buildup effects were taken into account. The results from the cascade model show good agreement with angular distributions of Ne K Auger electrons recently measured. Attenuation effects were found to produce shifts in the K Auger spectra at varying observation angles. The significant difference previously observed for the mean L-shell occupation numbers during L and K Auger emission is explained by the present model
An extended empirical model for L- and M-shell ionizations of atoms
Talukder, M R
2011-01-01
An extension of the analytical model of Talukder et al (Int. J. Mass Spectrom. 269 (2008) 118) is proposed to estimate electron impact single L- and M-shell ionization cross sections of atoms with incident energy from threshold to ultra-relativistic range. Comparisons are made with other theoretical calculations. It is found that this model agrees well with the experimental data and quantum calculations.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Andrzej Koliński; Maksim Kouza; Dominik Gront; Sebastian Kmiecik; Jacek Wabik
2013-01-01
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combi...
Dynamic Modeling for the Design and Cyclic Operation of an Atomic Layer Deposition (ALD) Reactor
Curtisha D. Travis; Raymond A. Adomaitis
2013-01-01
A laboratory-scale atomic layer deposition (ALD) reactor system model is derived for alumina deposition using trimethylaluminum and water as precursors. Model components describing the precursor thermophysical properties, reactor-scale gas-phase dynamics and surface reaction kinetics derived from absolute reaction rate theory are integrated to simulate the complete reactor system. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm ...
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
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Jackson, Bret [Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom); Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main (Germany); Martinazzo, Rocco, E-mail: rocco.martinazzo@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Richerche, v. Golgi 19, 20133 Milano (Italy)
2015-09-28
An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.
Using monte Carlo simulation have been carried out an atomistic description of the structure and ordering processes in the system Cu-Au in a two-dimensional model. The ABV model of the alloy is a system of N atoms A and B, located in rigid lattice with some vacant sites. In the model we assume pair wise interactions between nearest neighbors with constant ordering energy J = 0,03 eV. The dynamics was introduced by means of a vacancy that exchanges of place with any atom of its neighbors. The simulations were carried out in a square lattice with 1024 and 4096 particles, using periodic boundary conditions to avoid border effects. We calculate the first two parameters of short range order of Warren-Cowley as function of the concentration and temperature. It was also studied the probabilities of formation of different atomic clusters that consist of 9 atoms as function of the concentration of the alloy and temperatures in a wide range of values. In some regions of temperature and concentration it was observed compositional and thermal polymorphism
We propose a scheme for approximately and conditionally teleporting an unknown atomic-entangled state in dissipative cavity QED. It is the further development of the scheme of [Phys. Rev. A 69 (2004) 064302], where the cavity mode decay has not been considered and the state teleportated is an unknown atomic state. In this paper, we investigate the influence of the decay on the approximate and conditional teleportation of the unknown atomic-entangled state, which is different from that teleportated in [Phys. Rev. A 69 (2004) 064302] and then give the fidelity of the teleportation, which depends on the cavity mode decay. The scheme may be generalized to not only the teleportation of the cavity-mode-entangled-state by means of a single atom but also the teleportation of the unknown trapped-ion-entangled-state in a linear ion trap
LIU Zong-Liang; LI Shao-Hua; CHEN Chang-Yong
2008-01-01
We propose a scheme for approximately and conditionally teleporting an unknown atomic-entangled state in dissipative cavity QED.It is the further development of the scheme of [Phys.Rev.A 69 (2004) 064302],where the cavity mode decay has not been considered and the state teleportated is an unknown atomic state.In this paper,we investigate the influence of the decay on the approximate and conditional teleportation of the unknown atomic-entangled state,which is different from that teleportated in [Phys.Rev.A 69 (2004) 064302] and then give the fidelity of the teleportation,which depends on the cavity mode decay.The scheme may be generalized to not only the teleportation of the cavity-mode-entangled-state by means of a single atom but also the teleportation of the unknown trapped-ion-entangled-state in a linear ion trap.
Anisotropic character of atoms in a two-dimensional Frenkel-Kontorova model
Wang Cang-Long; Duan Wen-Shan; Chen Jian-Min; Shi Yu-Ren
2011-01-01
The dynamics of a certain density of interacting atoms arranged on a two-dimensional square lattice, which is made to slide over a two-dimensional periodic substrate potential with also the quare lattice symmetry, in the presence of dissipation, by an externally applied driving force, is studied. By rotating the misfit angle θ, the dynamical behaviour displays two different tribological regimes: one is smooth, the other becomes intermittent. We comment both on the nature of the atomic dynamics in the locked-to-sliding transition, and on the dynamical states displayed during the atom motion at different values of the driving force. In tribological applications, we also investigate how the main model parameters such as the stiffness strength and the magnitude of the adhesive force affect the static friction of the system.In particular, our simulation indicates that the superlubricity will appear.
Effect of atomic spontaneous decay on entanglement in the generalized Jaynes-Cummings model
Some aspects of the irreversible dynamics of a generalized Jaynes-Cummings model are addressed. By working in the dressed-state representation, it is possible to split the dynamics of the entanglement and coherence. The exact solution of the master equation in the case of a high-Q cavity with atomic decay is found. Effects of the atomic spontaneous decay on the temporal evolution of partial entropies of the atom or the field and the total entropy as a quantitative measure entanglement are elucidated. The degree of entanglement, through the sum of the negative eigenvalues of the partially transposed density matrix and the negative mutual information has been studied and compared with other measures.
Adsorption and recombination of hydrogen atoms on a model graphite surface. [in interstellar space
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.
Atomic distributions in model Cu-Al alloys: a Monte Carlo simulation
In this paper we report the results of Monte Carlo simulation of the atomic distributions in the Cu - Al solid solutions. We use the ABV model of the alloy where it is assumed the pair interaction approach between nearest neighbors atoms and constant ordering energy. The dynamic was introduced by the movement of a vacancy that exchanges of place with the nearest neighbors atoms. The simulation was made on a fcc lattice with 256 and 2048 sites, using periodic boundary conditions to avoid edge effects. It was determined the probability of formation of different atomic clusters A13-mBm (m 0, 1, 2, ... 13) consisting of 13 atoms, as a function of temperature, as well as the first short-range parameters of Warren-Cowley . It was found that in the alloy Cu + 14at% Al is observed thermal polymorphism in the formation of clusters of C1 and C2, while in the alloy Cu +12.5 at.% Al is not such an exchange between the clusters C1 and C2. (author)
The entanglement between two isolated atoms in the double mode–mode competition model
Extending the double Jaynes–Cummings model to a more complicated case where the mode–mode competition is considered, we investigate the entanglement character of two isolated atoms by means of concurrence, and discuss the dependence of atom–atom entanglement on the different initial state and the relative coupling strength between the atom and the corresponding cavity field. The results show that the amplitude and the period of the atom–atom entanglement evolution can be controlled by the choice of initial state and relative coupling strength, respectively. We find that the phenomenon of entanglement sudden death (ESD) is sensitive to the initial conditions. The length of the time interval for zero entanglement depends not only on the initial degree of entanglement between two atoms but also on the relative coupling strength of atom–field interaction. The ESD effect can be weakened by enhancing the mode–mode competition between the three- and single-photon processes. (classical areas of phenomenology)
A phenomenological model of the growth of two-species atomic Bose-Einstein condensates
We introduce a phenomenological mean-field model to describe the growth of immiscible two-species atomic Bose-Einstein condensates towards some equilibrium. Our model is based on the coupled Gross-Pitaevskii equations with the addition of dissipative terms to account for growth. While our model may be applied generally, we take a recent Rb-Cs experiment [McCarron et al., Phys. Rev. A 84 011603(R) (2011)] as a case study. As the condensates grow, they can pass through ranging transient density structures which can be distinct from the equilibrium states, although such a model always predicts the predominance of one condensate species over longer evolution times.
Collisional radiative model for heavy atoms in hot non-local-thermodynamical-equilibrium plasmas
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
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
Quantitative tungsten study with reliable atomic modeling is important for successful achievement of ITER and fusion reactors. We have developed tungsten atomic modeling for understanding the tungsten behavior in fusion plasmas. The modeling is applied to the analysis of tungsten spectra observed from currentless plasmas of the Large Helical Device (LHD) with tungsten pellet injection. We found that extreme ultraviolet (EUV) lines of W24+ to W33+ ions are very sensitive to electron temperature (Te) and useful to examine the tungsten behavior in edge plasmas. Based on the first quantitative analysis of measured spatial profile of W44+ ion, the tungsten concentration is determined to be n(W44+)/ne= 1.4x10-4 and the total radiation loss is estimated as ∼4 MW, of which the value is roughly half the total NBI power. (author)
A Monte Carlo model for seeded atomic flows in the transition regime
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.
Quantum model for double ionization of atoms in strong laser fields
Prauzner-Bechcicki, Jakub S; Eckhardt, Bruno; Zakrzewski, Jakub
2007-01-01
Double ionization of atoms in strong laser pulses is discussed by use of a simplified atomic model. Each electron is allowed to move along the lines indicated by the positions of the Stark saddles when the phase of the field changes. The effective two dimensional model resembles to a large extend the known 1+1 dimensional aligned electrons model, but enables correlated escape of electrons with equal momenta -- the phenomenon observed experimentally. The time-dependent solution of the Schrodinger equation allows us to discuss in detail the time dynamics of the ionization process, formation of electronic wavepackets and the development of the final momenta distribution. In particular, we are able to distinguish between sequential double ionization, where electrons escape during different half-cycles of the pulse, and non-sequential one, where they escape during the same half-cycle. We consider the dependence of the measurable quantities on the absolute phase of the light pulse.
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…
We study modeling of laser-assisted discharge pumped plasma (LA-DPP) EUV sources, based on coupled hydrodynamics and atomic process simulations. Conditions to obtain intense EUV emission are discussed, by pumping uniform preformed plasma. Development of an accurate atomic model of Sn is also discussed, to calculate temperature and density dependence of the coefficients of radiative transfer of Sn plasmas. (author)
Protein Nano-Object Integrator (ProNOI for generating atomic style objects for molecular modeling
Smith Nicholas
2012-12-01
Full Text Available Abstract Background With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results Here we report the Protein Nano-Object Integrator (ProNOI which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions The Protein Nano-Object Integrator (ProNOI is a convenient tool for
Influence of the plasma environment on atomic structure using an ion-sphere model
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 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
Atomic hydration potentials using a Monte Carlo Reference State (MCRS for protein solvation modeling
Makeev Vsevolod J
2007-03-01
Full Text Available Abstract Background Accurate description of protein interaction with aqueous solvent is crucial for modeling of protein folding, protein-protein interaction, and drug design. Efforts to build a working description of solvation, both by continuous models and by molecular dynamics, yield controversial results. Specifically constructed knowledge-based potentials appear to be promising for accounting for the solvation at the molecular level, yet have not been used for this purpose. Results We developed original knowledge-based potentials to study protein hydration at the level of atom contacts. The potentials were obtained using a new Monte Carlo reference state (MCRS, which simulates the expected probability density of atom-atom contacts via exhaustive sampling of structure space with random probes. Using the MCRS allowed us to calculate the expected atom contact densities with high resolution over a broad distance range including very short distances. Knowledge-based potentials for hydration of protein atoms of different types were obtained based on frequencies of their contacts at different distances with protein-bound water molecules, in a non-redundant training data base of 1776 proteins with known 3D structures. Protein hydration sites were predicted in a test set of 12 proteins with experimentally determined water locations. The MCRS greatly improves prediction of water locations over existing methods. In addition, the contribution of the energy of macromolecular solvation into total folding free energy was estimated, and tested in fold recognition experiments. The correct folds were preferred over all the misfolded decoys for the majority of proteins from the improved Rosetta decoy set based on the structure hydration energy alone. Conclusion MCRS atomic hydration potentials provide a detailed distance-dependent description of hydropathies of individual protein atoms. This allows placement of water molecules on the surface of proteins and in
Features of an electrodynamical interpretation suggested by Schroedinger for the wave function are discribed. According to this conception electron charges are continuously distributed all over the volume of an atomic system. The proof is given that classical electrodynamics keeps its action inside atom. Schroedinger's atom has been shown to be the only model in which electrones do not lose their energy for emission when they move around nucleus. A significance of the distributed electron charge self-field is estimated. Practical applications of this conception have been noted including the new trend in quantum electrodynamics. Experimental and theoretical corroborations of the atom model with a continuous electron charge are adduced
COUPLED ATOMIZATION AND SPRAY MODELLING IN THE SPRAY FORMING PROCESS USING OPENFOAM
Gjesing, Rasmus; Hattel, Jesper Henri; Fritsching, Udo
2009-01-01
The paper presents a numerical model capable of simulating the atomization, break-up and in-flight spray phenomena in the spray forming process. The model is developed and implemented in the freeware code openFOAM. The focus is on studying the coupling effect of the melt break-up phenomena with t...... describing the thermal state of the particles in the spray. Therefore, the model includes a full thermal solver for the droplets, which also takes the rapid solidification of different drop sizes into account.......The paper presents a numerical model capable of simulating the atomization, break-up and in-flight spray phenomena in the spray forming process. The model is developed and implemented in the freeware code openFOAM. The focus is on studying the coupling effect of the melt break-up phenomena with the...... model for droplet cooling and solidification. The model is tested and validated against results from literature and experiments. Subsequently, the model is used to simulate the complex flow fields in the spray forming process and the results are discussed. The presented model of the spray forming...
王忠纯
2004-01-01
@@ We study the properties of the atoms and cavity field in the Tavis-Cummings Model where the two atoms interact each other and also are driven by an external classical field.We consider the special case that the cavity is initially in a coherent state.After work out the atomic inversion, the average photons number and the Mandel parameter in the driven Tavis-Cummings Model, we do numerical analysis of them, and pay special attention to the dynamical behavior of the atoms and the cavity field modified by the external field.
Atomic density functional and diagram of structures in the phase field crystal model
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.
A quasi-stationary numerical model of atomized metal droplets, II: Prediction and assessment
Pryds, Nini H.; Hattel, Jesper Henri; Thorborg, Jesper
1999-01-01
A new model which extends previous studies and includes the interaction between enveloping gas and an array of droplets has been developed and presented in a previous paper. The model incorporates the probability density function of atomized metallic droplets into the heat transfer equations. The...... main thrust of the model is that the gas temperature was not predetermined and calculated empirically but calculated numerically based on heat balance consideration. In this paper, the accuracy of the numerical model and the applicability of the model as a predictive tool have been investigated by...... been illustrated.A comparison between the numerical model and the experimental results shows an excellent agreement and demonstrates the validity of the present model, e.g. the calculated gas temperature which has an important influence on the droplet solidification behaviour as well as the calculated...
COUPLED ATOMIZATION AND SPRAY MODELLING IN THE SPRAY FORMING PROCESS USING OPENFOAM
Gjesing, Rasmus; Hattel, Jesper Henri; Fritsching, Udo
2009-01-01
The paper presents a numerical model capable of simulating the atomization, break-up and in-flight spray phenomena in the spray forming process. The model is developed and implemented in the freeware code openFOAM. The focus is on studying the coupling effect of the melt break-up phenomena with the...... model for droplet cooling and solidification. The model is tested and validated against results from literature and experiments. Subsequently, the model is used to simulate the complex flow fields in the spray forming process and the results are discussed. The presented model of the spray forming...... process is able to predict the droplet size distribution of the spray from the process conditions, by introducing submodels for the melt fragmentation and successive secondary break-up processes as part of the spray model. Furthermore, the competition of drop break-up and solidification is derived by...
Computational model for non-LTE atomic process in laser produced plasmas
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.
Atom-field entanglement in the Jaynes-Cummings model without rotating wave approximation
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.
Argon 4s and 4p Excited States Atomic Data Applied in ARC-JET Modeling
K. Katsonis
2011-01-01
Full Text Available Evaluated atomic data concerning the 4s and 4p configurations of Ar I are averaged in order to simplify their use in various cases of Ar plasma modeling and diagnostics. These data are used here to model a low-power arcjet, running with Argon at low pressure. In so doing, they are explicitly introduced in the chemical processes included in a fluid Navier-Stokes type code, allowing for evaluation of the spectroscopically measurable level populations and of the electronic temperatures. The characteristics of the model are described and the main processes are discussed in view of the results of the calculations.
王金照; 陈民; 过增元
2002-01-01
Pair distribution functions and constant-volume heat capacities of liquid copper, silver and nickel have been calculated by molecular dynamics simulations with four different versions of the embedded-atom method (EAM) model, namely, the versions of Johnson, Mei, Cai and Pohlong. The simulated structural properties with the four potential models show reasonable agreement with experiments and have little difference with each other, while the calculated heat capacities with the different EAM versions show remarkable discrepancies. Detailed analyses of the energy of the liquid metallic system show that, to predict successfully the heat capacity, an EAM model should match the state equation first proposed by Rose.
Characterization of atom clusters in irradiated pressure vessel steels and model alloys
In order to characterize the microstructural evolution of the iron solid solution under irradiation, two pressure vessel steels irradiated in service conditions and, for comparison, low copper model alloys irradiated with neutrons and electrons have been studied. The characterization has been carried out mainly thanks to small angle neutron scattering and atom probe experiments. Both techniques lead to the conclusion that clusters develop with irradiations. In Fe-Cu model alloys, copper clusters are formed containing uncertain proportions of iron. In the low copper industrial steels, the feature is more complex. Solute atoms like Ni, Mn and Si, sometimes associated with Cu, segregate as ''clouds'' more or less condensed in the iron solid solution. These silicides, or at least Si, Ni, Mn association, may facilitate the copper segregation although the initial iron matrix contains a low copper concentration. (authors). 24 refs., 3 figs., 2 tabs
Monte Carlo simulation of atomic aggregates formation in model bcc binary alloys. Preliminary report
By means of the Monte Carlo simulation an atomistic description of the structure of model bcc binary alloys was made. We used ABV model of the alloy where the approach of pair interaction to first neighbours with constant ordering energy is assumed. The dynamics was introduced by means of a vacancy that interchanges of place with nearest neighbouring atoms. The simulations were made in a bcc lattice with 128, 1024, 8192 and 16000 sites, applying periodic boundary conditions to avoid edge effects. We calculate the formation probabilities of different atomic aggregate A9-m Bm (m = 0, 1, 2,... 9) as function of concentration of the components and the temperature. In some regions of temperature and concentration, compositional and thermal polymorphism of aggregates is observed. (author)
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
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.
Atomization modeling in a multiphase flow environment and comparison with experiments
Liang, P. Y.; Schuman, M. D.
1990-01-01
An atomization model based on Reitz's instability wave analysis has been implemented into the ARICC3D multiphase CFD combustion code. Preliminary test runs with cold non-evaporating liquid jet and coaxial gas-liquid atomization cases appeared to have verified basic performance of the model, generating realistic-looking sprays. Furthermore, the extended liquid jet is explicitly resolved, and predicted jet lengths agree well with classical correlations. Fair agreement with test data is obtained for predicted spray tip penetrations and liquid mass flux radial distributions, with obvious room for improvement. Some numerical problems also appear to have resulted with the current implementation when low gas Mach number and high liquid velocities are involved.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Andrzej Koliński
2013-05-01
Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej
2013-01-01
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Average-Atom Model for X-ray Scattering from Warm Dense Matter
Johnson, W R; Cheng, K T
2012-01-01
A scheme for analyzing Thomson scattering of x-rays by warm dense matter, based on the average-atom model, is developed. Emphasis is given to x-ray scattering by bound electrons. Contributions to the scattered x-ray spectrum from elastic scattering by electrons moving with the ions and from inelastic scattering by free and bound electrons are evaluated using parameters (chemical potential, average ionic charge, free electron density, bound and continuum wave functions, and occupation numbers) taken from the average-atom model. The resulting scheme provides a relatively simple diagnostic for use in connection with x-ray scattering measurements. Applications are given to dense hydrogen, beryllium, aluminum, titanium, and tin plasmas. At high momentum transfer, contributions from inelastic scattering by bound electrons are dominant features of the scattered x-ray spectrum for aluminum, titanium, and tin.
Balleza D, E
2004-07-01
In the first chapter of this work we will show a detailed analysis of the one cooling Doppler phenomenon that appears when a laser induces a dipolar moment to the atoms in such a way that these may interact with him to transfer moment to the field with the subsequent decrease of kinetic energy that macroscopically it is translated in cooling of the atomic cloud. When the experiments of atomic cooling were carried out it was observed that the temperature was smaller to the one than it predicted the cooling Doppler, this originates the creation of a theory but it dies in which the over simplification is eliminated that the alone atom consists of two energy levels and levels are introduced of it structures fine that are able to explain the extra cooling. To this phenomenon it is called Sisifo effect and it is studied detailedly in the chapter two. The first two chapters talk each other about the atomic cooling, but it stops that the atomic cloud can be manipulated, before being confined, problem that we will expose in the chapter three with experimental solutions that at the moment they are implemented in the laboratories around the world. In particular we will concentrate on the traps FORT (Far Off Resonance Trap, trap very outside of resonance) that confine to the atoms in optic nets. The lasers gaussianos originate a potential sinusoidal along the propagation address and gaussiano in the perpendicular plane to this. In the I surrender four he/she intends a three-dimensional model that substitutes To the variation sinusoidal for a function crenel and he/she makes an approach To first order in the radial dependence to obtain an oscillator potential Harmonic instead of the gaussiano that you taenia. The pattern is solved in a similar way To the pattern unidimensional of bands: they are the functions of wave solution For every period and they are coupled among if so that they satisfy conditions of rhythm, When making this you arrives to a womb that couples the
Error sources in atomic force microscopy for dimensional measurements: Taxonomy and modeling
Marinello, F.; Voltan, A.; Savio, E.; Carmignato, S.; De Chiffre, Leonardo
2010-01-01
This paper aimed at identifying the error sources that occur in dimensional measurements performed using atomic force microscopy. In particular, a set of characterization techniques for errors quantification is presented. The discussion on error sources is organized in four main categories......: scanning system, tip-surface interaction, environment, and data processing. The discussed errors include scaling effects, squareness errors, hysteresis, creep, tip convolution, and thermal drift. A mathematical model of the measurement system is eventually described, as a reference basis for errors...
On model materials designed by atomic layer deposition for catalysis purposes
2011-01-01
The aim of this work was to investigate the potential of model materials designed by atomic layer deposition toward applications in catalysis research. Molybdenum based catalysts promoted with cobalt were selected as target materials, considering their important roles in various industrial processes. Particular attention was paid to understand the growth dynamics of the ALD processes involved and further to characterize the obtained materials carefully. It was of main concern to verify the fe...
Thomas, M.S. (Royal Military Coll. of Canada, Kingston, Ontario); Gruber, B. (Technische Univ. Clausthal, Clausthal-Zellerfeld (Germany, F.R.). Inst. fuer Theoretische Physik)
1982-01-01
In this article symmetry chains for the atomic shell model are investigated which lead from the group SO(8l+-5) to the subgroup SOsub(L)(3). The tail group SOsub(L)(3) corresponds to total orbital angular momentum. Along these chains total orbital angular momentum L is a good quantum number, but not total spin S. Total orbital angular momentum can be considered as being made up of four quasi angular momenta.
A mathematical model for the atomic clock error in case of jumps
We extend the mathematical model based on stochastic differential equations describing the error gained by an atomic clock to the cases of anomalous behavior including jumps and an increase of instability. We prove an exact iterative solution that can be useful for clock simulation, prediction, and interpretation, as well as for the understanding of the impact of clock error in the overall system in which clocks may be inserted as, for example, the Global Satellite Navigation Systems. (authors)
Sha, Wei
2008-01-01
In this seminar, I will talk about 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 microscopy (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 simulations were then carried out to investigate the ...
Modeling inelastic phonon scattering in atomic- and molecular-wire junctions
Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads
2005-01-01
Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between...... the full nonequilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including nonequilibrium heating and provide...
HU ZHENG-FA; ZHOU SHI-KANG; GONG SHUN-SHENG; ZHAN MING-SHENG
2000-01-01
The potential model method for computation of Stark structure of Cs Rydberg states atoms and oscillator strength is described,for external electric fields varying from 0 to 600V/cm.Anticrossing,l-mixing and n-mixing phenomena are observed clearly from the map of Stark.Corresponding experiment is performed under the same condition,and the two results are in good agreement with each other within the experimental uncertainty.
Study of a Model Humic Acid-type Polymer by Fluorescence Spectroscopy and Atomic Force Microscopy
Marcos Antonio Piza; Nelson Consolin-Filho; Sérgio da Costa Saab; Daiana Kotra Deda; Fábio de Lima Leite; Marcilene Ferrari Barriquello; Ladislau Martin-Neto
2012-01-01
A model HA-type polymer of para-benzoquinone synthetic humic acid (SHA) and its complexes with copper, iron and manganese metal ions were studied using atomic force microscopy (AFM). Natural humic acids (HA) and synthetic humic acids (SHA) were examined by fluorescence spectroscopy, which indicated similarity of SHA and HA spectra. The AFM images of SHA and its complexes revealed variable morphologies, such as small spheres, aggregates and a sponge-like structure. The SHA complexes displayed ...
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.
A distributed atomic physics database and modeling system for plasma spectroscopy
We are undertaking to develop a set of computational capabilities which will facilitate the access, manipulation, and understanding of atomic data in calculations of x-ray spectral modeling. In this present limited description we will emphasize the objectives for this work, the design philosophy, and aspects of the atomic database, as a more complete description of this work is available. The project is referred to as the Plasma Spectroscopy Initiative; the computing environment is called PSI, or the ''PSI shell'' since the primary interface resembles a UNIX shell window. The working group consists of researchers in the fields of x-ray plasma spectroscopy, atomic physics, plasma diagnostics, line shape theory, astrophysics, and computer science. To date, our focus has been to develop the software foundations, including the atomic physics database, and to apply the existing capabilities to a range of working problems. These problems have been chosen in part to exercise the overall design and implementation of the shell. For successful implementation the final design must have great flexibility since our goal is not simply to satisfy our interests but to vide a tool of general use to the community
Model for Atomic Oxygen Visible Line Emissions in Comet C/1995 O1 Hale-Bopp
Raghuram, Susarla
2012-01-01
We have recently developed a coupled chemistry-emission model for the green and red-doublet emissions of atomic oxygen on comet Hyakutake. In the present work we applied our model to comet Hale-Bopp, which had an order of magnitude higher H2O production rate than comet Hyakutake, to evaluate the photochemistry associated with the production and loss of O(1S) and O(1D) atoms and emission processes of green and red-doublet lines. We present the wavelength-dependent photo-attenuation rates for different photodissociation processes forming O(1S) and O(1D). The calculated radiative efficiency profiles of O(1S) and O(1D) atoms show that in comet Hale-Bopp the green and red-doublet emissions are emitted mostly above radial distances of 10^3 and 10^4 km, respectively. The model calculated [OI] 6300 A emission surface brightness and average intensity over the Fabry-P{\\'e}rot spectrometer field of view are consistent with the observation of Morgenthaler et al. (2001), while the intensity ratio of green to red-doublet e...
In this work the influence of Li atoms in solid solution on plastic deformation, recrystallization and texture development in model Al-0.8%Li alloy was investigated. It was stated that Li atoms lead to shear band formation during cold rolling. Moreover, in compare with traditional aluminium alloys, the interactions between grain boundaries and Li atoms causes a continuous recrystallization and the formation of a different texture. (author)
Lewandowska, M.; Mizera, J.; Wawrzykowski, J.W. [Faculty of Materials Science and Engineering, Warsaw University of Technology, Warsaw (Poland)
1995-12-31
In this work the influence of Li atoms in solid solution on plastic deformation, recrystallization and texture development in model Al-0.8%Li alloy was investigated. It was stated that Li atoms lead to shear band formation during cold rolling. Moreover, in compare with traditional aluminium alloys, the interactions between grain boundaries and Li atoms causes a continuous recrystallization and the formation of a different texture. (author). 6 refs, 6 figs.
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.
The final Research Coordination Meeting on 'Atom and Molecular Data for Plasma Modelling' of the Coordinated Research Project (CRP) was held on 17-19 November 2008, at IAEA Headquarters in Vienna. Participants summarized the results obtained in the course of the CRP, and the impact of the data on modelling, especially for the plasma edge and divertor regions. Data needs still exist, and the specialists hoped that further research on these processes will be supported in the future. The discussions, conclusions and recommendations of the RCM are described in this report. (author)
Atomically thin spherical shell-shaped superscatterers based on Bohr model
Li, Rujiang; Lin, Shisheng; Liu, Xu; Chen, Hongsheng
2015-01-01
Graphene monolayers can be used for atomically thin three-dimensional shell-shaped superscatterer designs. Due to the excitation of the first-order resonance of transverse magnetic (TM) graphene plasmons, the scattering cross section of the bare subwavelength dielectric particle is enhanced significantly by five orders of magnitude. The superscattering phenomenon can be intuitively understood and interpreted with Bohr model. Besides, based on the analysis of Bohr model, it is shown that contrary to the TM case, superscattering is hard to occur by exciting the resonance of transverse electric (TE) graphene plasmons due to their poor field confinements.
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
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.
Atomic-Scale Modeling of Particle Size Effects for the Oxygen Reduction Reaction of Pt
Tritsaris, Georgios; Greeley, Jeffrey Philip; Rossmeisl, Jan;
2011-01-01
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.......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...
A quasi-stationary numerical model of atomized metal droplets, II: Prediction and assessment
Pryds, Nini H.; Hattel, Jesper Henri; Thorborg, Jesper
1999-01-01
A new model which extends previous studies and includes the interaction between enveloping gas and an array of droplets has been developed and presented in a previous paper. The model incorporates the probability density function of atomized metallic droplets into the heat transfer equations. The...... main thrust of the model is that the gas temperature was not predetermined and calculated empirically but calculated numerically based on heat balance consideration. In this paper, the accuracy of the numerical model and the applicability of the model as a predictive tool have been investigated by...... comparing experimental and calculated results for the powder particles of 12Cr-Mo-V steel. The study is also focusing on some aspects of the process which are not available experimentally, e.g. the effect of undercooling and gas/metal ratio on the solidification. The important effect of these parameters has...
Yang–Baxter integrable models in experiments: from condensed matter to ultracold atoms
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. (review)
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.