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…
Constructing many atomic models in $\\aleph_1$
Baldwin, John T.; Laskowski, Michael C.; Shelah, Saharon
2015-01-01
We introduce the notion of pseudo-algebraicity to study atomic models of first order theories (equivalently models of a complete sentence of $L_{\\omega_1,\\omega}$. Theorem: Let $T$ be any complete first-order theory in a countable language with an atomic model. If the pseudo-minimal types are not dense, then there are $2^{\\aleph_1}$ pairwise non-isomorphic atomic models of $T$, each of size $\\aleph_1$.
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.
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.
Students' Mental Models of Atomic Spectra
Körhasan, Nilüfer Didis; Wang, Lu
2016-01-01
Mental modeling, which is a theory about knowledge organization, has been recently studied by science educators to examine students' understanding of scientific concepts. This qualitative study investigates undergraduate students' mental models of atomic spectra. Nine second-year physics students, who have already taken the basic chemistry and…
Atomic model of liquid pure Fe
Institute of Scientific and Technical Information of China (English)
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
Standard Model tests with trapped radioactive atoms
Behr, J A; 10.1088/0954-3899/36/3/033101
2009-01-01
We review the use of laser cooling and trapping for Standard Model tests, focusing on trapping of radioactive isotopes. Experiments with neutral atoms trapped with modern laser cooling techniques are testing several basic predictions of electroweak unification. For nuclear $\\beta$ decay, demonstrated trap techniques include neutrino momentum measurements from beta-recoil coincidences, along with methods to produce highly polarized samples. These techniques have set the best general constraints on non-Standard Model scalar interactions in the first generation of particles. They also have the promise to test whether parity symmetry is maximally violated, to search for tensor interactions, and to search for new sources of time reversal violation. There are also possibilites for exotic particle searches. Measurements of the strength of the weak neutral current can be assisted by precision atomic experiments using traps of small numbers of radioactive atoms, and sensitivity to possible time-reversal violating elec...
Atom-Role-Based Access Control Model
Cai, Weihong; Huang, Richeng; Hou, Xiaoli; Wei, Gang; Xiao, Shui; Chen, Yindong
Role-based access control (RBAC) model has been widely recognized as an efficient access control model and becomes a hot research topic of information security at present. However, in the large-scale enterprise application environments, the traditional RBAC model based on the role hierarchy has the following deficiencies: Firstly, it is unable to reflect the role relationships in complicated cases effectively, which does not accord with practical applications. Secondly, the senior role unconditionally inherits all permissions of the junior role, thus if a user is under the supervisor role, he may accumulate all permissions, and this easily causes the abuse of permission and violates the least privilege principle, which is one of the main security principles. To deal with these problems, we, after analyzing permission types and role relationships, proposed the concept of atom role and built an atom-role-based access control model, called ATRBAC, by dividing the permission set of each regular role based on inheritance path relationships. Through the application-specific analysis, this model can well meet the access control requirements.
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…
Cipolla, Laura; Ferrari, Lia A.
2016-01-01
A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).
Calculation of Al-Zn diagram from central atoms model
Institute of Scientific and Technical Information of China (English)
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.
The two-atom Jaynes-Cummings model's dynamic properties
Institute of Scientific and Technical Information of China (English)
无
2003-01-01
The model of two two-level atoms interact with a single-mode cavity was investigated. The formulation of the time evolution operator for the two-atom Jaynes-Cummings model is pressented by the bare-states approach. Besides, the time evolution of the two-atom common population probabilities is studied, and some novel features are obtained.
Atomic data for integrated tokamak modelling
International Nuclear Information System (INIS)
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
Atomic Models for Motional Stark Effects Diagnostics
Energy Technology Data Exchange (ETDEWEB)
Gu, M F; Holcomb, C; Jayakuma, J; Allen, S; Pablant, N A; Burrell, K
2007-07-26
We present detailed atomic physics models for motional Stark effects (MSE) diagnostic on magnetic fusion devices. Excitation and ionization cross sections of the hydrogen or deuterium beam traveling in a magnetic field in collisions with electrons, ions, and neutral gas are calculated in the first Born approximation. The density matrices and polarization states of individual Stark-Zeeman components of the Balmer {alpha} line are obtained for both beam into plasma and beam into gas models. A detailed comparison of the model calculations and the MSE polarimetry and spectral intensity measurements obtained at the DIII-D tokamak is carried out. Although our beam into gas models provide a qualitative explanation for the larger {pi}/{sigma} intensity ratios and represent significant improvements over the statistical population models, empirical adjustment factors ranging from 1.0-2.0 must still be applied to individual line intensities to bring the calculations into full agreement with the observations. Nevertheless, we demonstrate that beam into gas measurements can be used successfully as calibration procedures for measuring the magnetic pitch angle through {pi}/{sigma} intensity ratios. The analyses of the filter-scan polarization spectra from the DIII-D MSE polarimetry system indicate unknown channel and time dependent light contaminations in the beam into gas measurements. Such contaminations may be the main reason for the failure of beam into gas calibration on MSE polarimetry systems.
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.
Institute of Scientific and Technical Information of China (English)
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
Analytic Solutions of Three-Level Dressed-Atom Model
Institute of Scientific and Technical Information of China (English)
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
International Nuclear Information System (INIS)
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.
Alpha-cluster model of atomic nuclei
Energy Technology Data Exchange (ETDEWEB)
Sosin, Zbigniew; Kallunkathariyil, Jinesh [Jagiellonian University, M. Smoluchowski Institute of Physics, Krakow (Poland); Blocki, Jan [NCBJ, Theoretical Physics Division (BP2), Swierk (Poland); Lukasik, Jerzy; Pawlowski, Piotr [IFJ PAN, Krakow (Poland)
2016-05-15
The description of a nuclear system in its ground state and at low excitations based on the equation of state (EoS) around normal density is presented. In the expansion of the EoS around the saturation point, additional spin polarization terms are taken into account. These terms, together with the standard symmetry term, are responsible for the appearance of the α-like clusters in the ground-state configurations of the N=Z even-even nuclei. At the nuclear surface these clusters can be identified as alpha particles. A correction for the surface effects is introduced for atomic nuclei. Taking into account an additional interaction between clusters the binding energies and sizes of the considered nuclei are very accurately described. The limits of the EoS parameters are established from the properties of the α, {sup 3}He and t particles. (orig.)
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
International Nuclear Information System (INIS)
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.
Hirshfeld atom refinement for modelling strong hydrogen bonds.
Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon
2014-09-01
High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.
Modelling atomic scale manipulation with the non-contact atomic force microscope
International Nuclear Information System (INIS)
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
Gas Atomization of Aluminium Melts: Comparison of Analytical Models
Directory of Open Access Journals (Sweden)
Georgios Antipas
2012-06-01
Full Text Available A number of analytical models predicting the size distribution of particles during atomization of Al-based alloys by N2, He and Ar gases were compared. Simulations of liquid break up in a close coupled atomizer revealed that the finer particles are located near the center of the spray cone. Increasing gas injection pressures led to an overall reduction of particle diameters and caused a migration of the larger powder particles towards the outer boundary of the flow. At sufficiently high gas pressures the spray became monodisperse. The models also indicated that there is a minimum achievable mean diameter for any melt/gas system.
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
Energy Technology Data Exchange (ETDEWEB)
Quan, Wei; Lv, Lin, E-mail: lvlinlch1990@163.com; Liu, Baiqi [School of Instrument Science and Opto-Electronics Engineering, Beihang University, Beijing 100191 (China)
2014-11-15
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Quan, Wei; Lv, Lin; Liu, Baiqi
2014-11-01
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
Quan, Wei; Lv, Lin; Liu, Baiqi
2014-11-01
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.;
2004-01-01
The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...... framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....
Exactly solvable models for atom-molecule Hamiltonians
International Nuclear Information System (INIS)
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
Modeling of Turbulence Effect on Liquid Jet Atomization
Trinh, H. P.
2007-01-01
Recent studies indicate that turbulence behaviors within a liquid jet have considerable effect on the atomization process. Such turbulent flow phenomena are encountered in most practical applications of common liquid spray devices. This research aims to model the effects of turbulence occurring inside a cylindrical liquid jet to its atomization process. The two widely used atomization models Kelvin-Helmholtz (KH) instability of Reitz and the Taylor analogy breakup (TAB) of O'Rourke and Amsden portraying primary liquid jet disintegration and secondary droplet breakup, respectively, are examined. Additional terms are formulated and appropriately implemented into these two models to account for the turbulence effect. Results for the flow conditions examined in this study indicate that the turbulence terms are significant in comparison with other terms in the models. In the primary breakup regime, the turbulent liquid jet tends to break up into large drops while its intact core is slightly shorter than those without turbulence. In contrast, the secondary droplet breakup with the inside liquid turbulence consideration produces smaller drops. Computational results indicate that the proposed models provide predictions that agree reasonably well with available measured data.
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
Indian Academy of Sciences (India)
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.
Model study in chemisorption: atomic hydrogen on beryllium clusters
Energy Technology Data Exchange (ETDEWEB)
Bauschlicher, C.W. Jr.
1976-08-01
The interaction between atomic hydrogen and the (0001) surface of Be metal has been studied by ab initio electronic structure theory. Self-consistent-field (SCF) calculations have been performed using minimum, optimized minimum, double zeta and mixed basis sets for clusters as large as 22 Be atoms. The binding energy and equilibrium geometry (the distance to the surface) were determined for 4 sites. Both spatially restricted (the wavefunction was constrained to transform as one of the irreducible representations of the molecular point group) and unrestricted SCF calculations were performed. Using only the optimized minimum basis set, clusters containing as many as 22 beryllium atoms have been investigated. From a variety of considerations, this cluster is seen to be nearly converged within the model used, providing the most reliable results for chemisorption. The site dependence of the frequency is shown to be a geometrical effect depending on the number and angle of the bonds. The diffusion of atomic hydrogen through a perfect beryllium crystal is predicted to be energetically unfavorable. The cohesive energy, the ionization energy and the singlet-triplet separation were computed for the clusters without hydrogen. These quantities can be seen as a measure of the total amount of edge effects. The chemisorptive properties are not related to the total amount of edge effects, but rather the edge effects felt by the adsorbate bonding berylliums. This lack of correlation with the total edge effects illustrates the local nature of the bonding, further strengthening the cluster model for chemisorption. A detailed discussion of the bonding and electronic structure is included. The remaining edge effects for the Be/sub 22/ cluster are discussed.
Atomically crafted spin lattices as model systems for quantum magnetism
International Nuclear Information System (INIS)
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.
Analysis and application of the scale effect of flood discharge atomization model
Institute of Scientific and Technical Information of China (English)
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.
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.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Directory of Open Access Journals (Sweden)
Peter C Lai
2012-05-01
Full Text Available Olfactory receptors (ORs are a type of GTP-binding protein-coupled receptor (GPCR. These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can validate experimental functional studies as well as generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level. Here we have shown the specific advantages of simulating the dynamic environment that is associated with OR-odorant interactions. We present a rigorous methodology that ranges from the creation of a computationally-derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.
Three L-subshells atomic model to compute counting efficiency of electron-capture nuclides
International Nuclear Information System (INIS)
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
Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity
DEFF Research Database (Denmark)
Gammelmark, S.; Molmer, K.; Alt, W.;
2014-01-01
We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian...... manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory...
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...
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.
Global atmospheric model for mercury including oxidation by bromine atoms
Directory of Open Access Journals (Sweden)
C. D. Holmes
2010-12-01
Full Text Available Global models of atmospheric mercury generally assume that gas-phase OH and ozone are the main oxidants converting Hg^{0} to Hg^{II} and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg^{0} oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming gas-phase Br to be the sole Hg^{0} oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O_{3} model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O_{3} models, we add an aqueous photochemical reduction of Hg^{II} in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O_{3} models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of Hg^{II} deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux to the Arctic of 60 Mg a^{−1}. Summertime events of depleted Hg^{0} at Antarctic sites due to subsidence are much better simulated by
Y(sl(2)) Algebra Application in Extended Hydrogen Atom and Monopole Models
Institute of Scientific and Technical Information of China (English)
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...
Global atmospheric model for mercury including oxidation by bromine atoms
Directory of Open Access Journals (Sweden)
C. D. Holmes
2010-08-01
Full Text Available Global models of atmospheric mercury generally assume that 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 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 of 60 Mg a^{−1}. Summertime events of depleted Hg^{0} at Antarctic sites due to subsidence are much better simulated by the Hg + Br model. Model
Development of a phenomenological model for coal slurry atomization
Energy Technology Data Exchange (ETDEWEB)
Dooher, J.P. [Adelphi Univ., Garden City, NY (United States)
1995-11-01
Highly concentrated suspensions of coal particles in water or alternate fluids appear to have a wide range of applications for energy production. For enhanced implementation of coal slurry fuel technology, an understanding of coal slurry atomization as a function coal and slurry properties for specific mechanical configurations of nozzle atomizers should be developed.
Operation of the computer model for direct atomic oxygen exposure of Earth satellites
Bourassa, R. J.; Gruenbaum, P. E.; Gillis, J. R.; Hargraves, C. R.
1995-01-01
One of the primary causes of material degradation in low Earth orbit (LEO) is exposure to atomic oxygen. When atomic oxygen molecules collide with an orbiting spacecraft, the relative velocity is 7 to 8 km/sec and the collision energy is 4 to 5 eV per atom. Under these conditions, atomic oxygen may initiate a number of chemical and physical reactions with exposed materials. These reactions contribute to material degradation, surface erosion, and contamination. Interpretation of these effects on materials and the design of space hardware to withstand on-orbit conditions requires quantitative knowledge of the atomic oxygen exposure environment. Atomic oxygen flux is a function of orbit altitude, the orientation of the orbit plan to the Sun, solar and geomagnetic activity, and the angle between exposed surfaces and the spacecraft heading. We have developed a computer model to predict the atomic oxygen exposure of spacecraft in low Earth orbit. The application of this computer model is discussed.
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
International Nuclear Information System (INIS)
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
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.
International Nuclear Information System (INIS)
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
Institute of Scientific and Technical Information of China (English)
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.
Institute of Scientific and Technical Information of China (English)
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.
'Bubble chamber model' of fast atom bombardment induced processes.
Kosevich, Marina V; Shelkovsky, Vadim S; Boryak, Oleg A; Orlov, Vadim V
2003-01-01
A hypothesis concerning FAB mechanisms, referred to as a 'bubble chamber FAB model', is proposed. This model can provide an answer to the long-standing question as to how fragile biomolecules and weakly bound clusters can survive under high-energy particle impact on liquids. The basis of this model is a simple estimation of saturated vapour pressure over the surface of liquids, which shows that all liquids ever tested by fast atom bombardment (FAB) and liquid secondary ion mass spectrometry (SIMS) were in the superheated state under the experimental conditions applied. The result of the interaction of the energetic particles with superheated liquids is known to be qualitatively different from that with equilibrium liquids. It consists of initiation of local boiling, i.e., in formation of vapour bubbles along the track of the energetic particle. This phenomenon has been extensively studied in the framework of nuclear physics and provides the basis for construction of the well-known bubble chamber detectors. The possibility of occurrence of similar processes under FAB of superheated liquids substantiates a conceptual model of emission of secondary ions suggested by Vestal in 1983, which assumes formation of bubbles beneath the liquid surface, followed by their bursting accompanied by release of microdroplets and clusters as a necessary intermediate step for the creation of molecular ions. The main distinctive feature of the bubble chamber FAB model, proposed here, is that the bubbles are formed not in the space and time-restricted impact-excited zone, but in the nearby liquid as a 'normal' boiling event, which implies that the temperature both within the bubble and in the droplets emerging on its burst is practically the same as that of the bulk liquid sample. This concept can resolve the paradox of survival of intact biomolecules under FAB, since the part of the sample participating in the liquid-gas transition via the bubble mechanism has an ambient temperature
Modeling and understanding of effects of randomness in arrays of resonant meta-atoms
DEFF Research Database (Denmark)
Tretyakov, Sergei A.; Albooyeh, Mohammad; Alitalo, Pekka;
2013-01-01
In this review presentation we will discuss approaches to modeling and understanding electromagnetic properties of 2D and 3D lattices of small resonant particles (meta-atoms) in transition from regular (periodic) to random (amorphous) states. Nanostructured metasurfaces (2D) and metamaterials (3D......) are arrangements of optically small but resonant particles (meta-atoms). We will present our results on analytical modeling of metasurfaces with periodical and random arrangements of electrically and magnetically resonant meta-atoms with identical or random sizes, both for the normal and oblique-angle excitations......) of the arrangements of meta-atoms....
Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning
Rupp, Matthias; Müller, Klaus-Robert; von Lilienfeld, O Anatole
2011-01-01
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\\"odinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross-validation over more than seven thousand small organic molecules yields a mean absolute error of ~10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.
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...
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...
Study on the Mathematical Model of Hydraulic Jump Atomization
Institute of Scientific and Technical Information of China (English)
张华; 练继建; 刘昉
2004-01-01
An equation of atomization quantity from energy dissipation by hydraulic jump was derived from the dimensional analysis. By applying Gauss diffusion equation, the spray diffusion rule in valley was studied under the condition of continuous linear source and random wind direction.By considering the spray-rain switching process, coagulation, condensation and evaporation of droplets, the air temperature, air relative humidity, spray density and the rainfall intensity in the lower reaches of the linear source were calculated. The 3-D numerical simulation fitted well with prototype monitoring. Finally, the prediction of atomization influence on environments for Xiangjiaba Hydropower Station was conducted.
Seldam, C.A. ten; Groot, S.R. de
1952-01-01
From Jensen's and Gombás' modification of the statistical Thomas-Fermi atom model, a theory for compressed atoms is developed by changing the boundary conditions. Internal kinetic energy and polarizability of argon are calculated as functions of pressure. At 1000 atm. an internal kinetic energy of a
Analytical model for relativistic corrections to the nuclear magnetic shielding constant in atoms
Energy Technology Data Exchange (ETDEWEB)
Romero, Rodolfo H. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)]. E-mail: rhromero@exa.unne.edu.ar; Gomez, Sergio S. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)
2006-04-24
We present a simple analytical model for calculating and rationalizing the main relativistic corrections to the nuclear magnetic shielding constant in atoms. It provides good estimates for those corrections and their trends, in reasonable agreement with accurate four-component calculations and perturbation methods. The origin of the effects in deep core atomic orbitals is manifestly shown.
Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness
Park, Eun Jung; Light, Gregory
2009-01-01
Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…
Atomic charges for modeling metal–organic frameworks: Why and how
Energy Technology Data Exchange (ETDEWEB)
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.
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}...
UNIFIED MODEL FOR SPLASH DROPLETS AND SUSPENDED MIST OF ATOMIZED FLOW
Institute of Scientific and Technical Information of China (English)
LIU Shi-he; SUN Xiao-fei; LUO Jing
2008-01-01
In this article, the unified mathematical model for splash droplets and suspended mist of atomized flow was established, which classifies the atomized sources into the splash source and the suspended source. For the splash source, the Lagrangian method was used to simulate the random motion of splash water droplets, and for the suspended source the theory of air-water two-phase flow was used to simulate the mist flow moving in particle clouds. The rainfall intensity of the atomized flow was obtained by summarizing the rainfall intensities relative to the above two types of atomized sources. Both experimental data and prototype observation data were used for the verification of the mathematical model. For both the distribution of rainfall intensity, and the outer edge of the atomized flow, the simulation results are in agreement with the experimental data or prototype observation data.
Computational model for noncontact atomic force microscopy: energy dissipation of cantilever
Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M.
2016-09-01
We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.
Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling
Energy Technology Data Exchange (ETDEWEB)
Tawara, H. [ed.
1997-01-01
This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)
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.
An Analytical Model for Adsorption and Diffusion of Atoms/Ions on Graphene Surface
Directory of Open Access Journals (Sweden)
Yan-Zi Yu
2015-01-01
Full Text Available Theoretical investigations are made on adsorption and diffusion of atoms/ions on graphene surface based on an analytical continuous model. An atom/ion interacts with every carbon atom of graphene through a pairwise potential which can be approximated by the Lennard-Jones (L-J potential. Using the Fourier expansion of the interaction potential, the total interaction energy between the adsorption atom/ion and a monolayer graphene is derived. The energy-distance relationships in the normal and lateral directions for varied atoms/ions, including gold atom (Au, platinum atom (Pt, manganese ion (Mn2+, sodium ion (Na1+, and lithium-ion (Li1+, on monolayer graphene surface are analyzed. The equilibrium position and binding energy of the atoms/ions at three particular adsorption sites (hollow, bridge, and top are calculated, and the adsorption stability is discussed. The results show that H-site is the most stable adsorption site, which is in agreement with the results of other literatures. What is more, the periodic interaction energy and interaction forces of lithium-ion diffusing along specific paths on graphene surface are also obtained and analyzed. The minimum energy barrier for diffusion is calculated. The possible applications of present study include drug delivery system (DDS, atomic scale friction, rechargeable lithium-ion graphene battery, and energy storage in carbon materials.
Jung, Hyunseung; In, Chihun; Choi, Hyunyong; Lee, Hojin
2014-06-09
Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems.
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.
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
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.
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.
Does God Play Dice with Universe The Hydrogen Atomic Model of Bohr and de Broglie
Kamenov, P S
1999-01-01
In this paper it is shown that if one accept assumption of de Broglie that "unitary wave-particle" exists simultaneously and this coexistence is real, then one can find the mean life time of the hydrogen atom of Bohr (intensities). Something more, the acceptance of de Broglie's ideas show that a single excited hydrogen atom decays at exactly predictable moment (after excitation). The natural width of excited hydrogen atoms are found using the Bohr's model of this atom and de Broglie's ideas. The mean life time of the excited states is a characteristic only of a statistical ensemble of many atoms and coincide exactly with experimental data and can be used for analytical applications. It is shown also that resonant Mossbauer absorption in time domain provides a qualitative evidence of the existence of "own lifetime" for first excited states of the nuclei.
Classical trajectory perspective of atomic ionization in strong laser fields. Semiclassical modeling
International Nuclear Information System (INIS)
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
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.
Mathematical modeling of nanomachining with atomic force microscope cantilevers
International Nuclear Information System (INIS)
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
Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom
Lorente, M
2001-01-01
The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.
Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom
Lorente, M
2004-01-01
The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.
Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom
Lorente, Miguel
2001-07-01
The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.
O'Sullivan, Colm
2016-03-01
The role of "semi-classical" (Bohr-Sommerfeld) and "semi-quantum-mechanical" (atomic orbital) models in the context of the teaching of atomic theory is considered. It is suggested that an appropriate treatment of such models can serve as a useful adjunct to quantum mechanical study of atomic systems.
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
International Nuclear Information System (INIS)
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
Energy Technology Data Exchange (ETDEWEB)
Bautista, M. A.; Fivet, V. [Department of Physics, Western Michigan University, Kalamazoo, MI 49008 (United States); Quinet, P. [Astrophysique et Spectroscopie, Universite de Mons-UMONS, B-7000 Mons (Belgium); Dunn, J. [Physical Science Department, Georgia Perimeter College, Dunwoody, GA 30338 (United States); Gull, T. R. [Code 667, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Kallman, T. R. [Code 662, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Mendoza, C., E-mail: manuel.bautista@wmich.edu [Centro de Fisica, Instituto Venezolano de Investigaciones Cientificas (IVIC), P.O. Box 20632, Caracas 1020A (Venezuela, Bolivarian Republic of)
2013-06-10
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data. We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of O III and Fe II and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe II].
Atomic and field dynamics in the time-dependent Jaynes-Cummings model with arbitrary detuning
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
We propose a general numerical method for solving the time -dependent Jaynes-Cummings model with arbitrary detuning by integrating relate d groups of coupled equations using Runge-Kutta numerical technique. The atomic and field dynamics such as evolution of atomic population inversion and second -order correlation function of photons are studied in case of different detunin g. The results show that the field tends to exhibit bunching effect due to the I ncreasing of detuning.
Finite Bias Calculations to Model Interface Dipoles in Electrochemical Cells at the Atomic Scale
DEFF Research Database (Denmark)
Hansen, Martin Hangaard; Jin, Chengjun; Thygesen, Kristian Sommer;
2016-01-01
The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure...... to satisfy the thermodynamic constraints imposed by the environment. This is captured by the generalized computational hydrogen electrode model, which enables us to make efficient first-principles calculations of atomic scale properties of the electrochemical interface....
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
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...
Relativistic Corrections to the Bohr Model of the Atom
Kraft, David W.
1974-01-01
Presents a simple means for extending the Bohr model to include relativistic corrections using a derivation similar to that for the non-relativistic case, except that the relativistic expressions for mass and kinetic energy are employed. (Author/GS)
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.
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…
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…
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 ...
UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions
International Nuclear Information System (INIS)
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/
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 ...
Cold-atom quantum simulation of U(1) lattice gauge-Higgs model
Kasamatsu, Kenichi; Kuno, Yoshihito; Takahashi, Yoshiro; Ichinose, Ikuo; Matsui, Tetsuo
2015-03-01
We discuss the possible methods to construct a quantum simulator of the U(1) lattice gauge-Higgs model using cold atoms in an optical lattice. These methods require no severe fine tunings of parameters of atomic-interactions in contrast with the other previous literature. We propose some realistic experimental setups to realize the atomic quantum simulator of the U(1) lattice gauge-Higgs model in a two-dimensional optical lattice. Our target gauge-Higgs model has a nontrivial phase structure, i.e., existence of the phase boundary between confinement and Higgs phases, and this phase boundary is to be observed by cold-atom experiments. As a reference to such experiments, we make numerical simulations of the time-dependent Gross-Pitaevskii equation and observe the real-time dynamics of the atomic simulators. Clarification of the dynamics of this gauge-Higgs model sheds some lights upon various unsolved problems including the inflation process of the early universe.
Institute of Scientific and Technical Information of China (English)
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.
Two-channel emission model for collective quantum jumps in Rydberg atoms
Cayayan, Lyndon; Clemens, James
2016-05-01
We consider a system of driven, damped Rydberg atoms with dipole-dipole energy shifts which can give rise to a Rydberg blockade when the atoms are driven on resonance and collective quantum jumps when the atoms are driven off resonance. For the damping we consider a two-channel emission model with competition between fully independent and fully collective spontaneous emission. For independent emission a quasiclassical model predicts a bistable steady state and quantum fluctuations drive collective jumps between the two bistable branches. We show that the collective emission is enhanced, relative to the independent emission, which shifts the total effective spontaneous emission rate and impacts the presence or absence of bistability predicted by the quasiclassical model.
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...
Model studies on pump sump for Tarapur Atomic Power Plant
International Nuclear Information System (INIS)
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
The contribution of atom accessibility to site of metabolism models for cytochromes P450
DEFF Research Database (Denmark)
Rydberg, Patrik; Rostkowski, M.; Gloriam, D.E.;
2013-01-01
Three different types of atom accessibility descriptors are investigated in relation to site of metabolism predictions. To enable the integration of local accessibility we have constructed 2DSASA, a method for the calculation of the atomic solvent accessible surface area that is independent of 3D...... coordinates. The method was implemented in the SMARTCyp site of metabolism prediction models and improved the results by up to 4 percentage points for nine cytochrome P450 isoforms. The final models are made available at http://www.farma.ku.dk/smartcyp....
The contribution of atom accessibility to site of metabolism models for cytochromes P450.
Rydberg, Patrik; Rostkowski, Michal; Gloriam, David E; Olsen, Lars
2013-04-01
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...
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.
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...
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.
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 ...
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
Directory of Open Access Journals (Sweden)
Conrado Pedebos
2014-03-01
Full Text Available QS-21 is a saponin extracted from Quillaja saponaria, widely investigated as a vaccine immunoadjuvant. However, QS-21 use is mainly limited by its chemical instability, significant variety in molecular composition and low tolerance dose in mammals. Also, this compound tends to form micelles in a concentration-dependent manner. Here, we aimed to characterize its conformation and the process of micelle formation, both experimentally and computationally. Therefore, molecular dynamics (MD simulations were performed in systems containing different numbers of QS-21 molecules in aqueous solution, in order to evaluate the spontaneous micelle formation. The applied methodology allowed the generation of micelles whose sizes were shown to be in high agreement with small-angle X-ray scattering (SAXS. Furthermore, the ester linkage between fucose and acyl chain was less solvated in the micellar form, suggesting a reduction in hydrolysis. This is the first atomistic interpretation of previous experimental data, the first micellar characterization of saponin micelles by SAXS and first tridimensional model of a micelle constituted of saponins, contributing to the understanding of the molecular basis of these compounds.
Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former
Kim, Jeongmin; Sung, Bong June
2015-06-01
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.
Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former
International Nuclear Information System (INIS)
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)
Modelling of liquid flow after a hydraulic jump on a rotating disk prior to centrifugal atomization
Zhao, Y. Y.; Dowson, A. L.; Jacobs, M. H.
2000-01-01
This paper describes a simplified numerical model which is used to calculate the height distribution, and the radial and tangential velocities of a liquid on a rotating disk after a hydraulic jump and prior to centrifugal atomization. The results obtained from this numerical model are compared with predictions made using previously derived `hydraulic jump' and `analytical' models. Calculations, in conjunction with experimental measurements relating to the trajectory of liquid flow on the atomizing disk, have shown that the numerical model can not only give a reasonable prediction of the hydraulic jump location, but also yields more accurate information regarding the variations in liquid height, and radial and tangential velocities. The model is ideally suited for engineering applications.
A simple model for atomic layer doped field-effect transistor (ALD-FET) electronic states
Energy Technology Data Exchange (ETDEWEB)
Mora R, M.E. [Centro de Investigaciones en Optica, Unidad Aguascalientes. Juan de Montoro 207, Zona Centro, 20000 Aguascalientes (Mexico); Gaggero S, L.M. [Escuela de Fisica, Universidad Autonoma de Zacatecas, Av. Preparatoria 301, 98060 Zacatecas (Mexico)
1998-12-31
We propose a simple potential model based on the Thomas-Fermi approximation to reproduce the main properties of the electronic structure of an atomic layer doped field effect transistor. Preliminary numerical results for a Si-based ALD-FET justify why bound electronic states are not observed in the experiment. (Author)
NEW PHASES IN AN EXTENDED HUBBARD-MODEL EXPLICITLY INCLUDING ATOMIC POLARIZABILITIES
van den Brink, J.; Meinders, M.B J; Lorenzana, J.; Eder, R; Sawatzky, G.A
1995-01-01
We consider the influence of a nearest-neighbor Coulomb interaction in an extended Hubbard model and introduce a new interaction term which simulates atomic polarizabilities. This has the effect of screening the on-site Coulomb interaction for charged excitations, unlike a neighbor Coulomb interacti
Elliott, Simon D; Dey, Gangotri; Maimaiti, Yasheng; Ablat, Hayrensa; Filatova, Ekaterina A; Fomengia, Glen N
2016-07-01
Recent progress in the simulation of the chemistry of atomic layer deposition (ALD) is presented for technologically important materials such as alumina, silica, and copper metal. Self-limiting chemisorption of precursors onto substrates is studied using density functional theory so as to determine reaction pathways and aid process development. The main challenges for the future of ALD modeling are outlined.
Engineering the Dynamics of Effective Spin-Chain Models for Strongly Interacting Atomic Gases
DEFF Research Database (Denmark)
Volosniev, A. G.; Petrosyan, D.; Valiente, M.;
2015-01-01
We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We ...... of the dynamics of few- and many-body quantum systems; as an illustrative example relevant to quantum computation and communication, we consider state transfer in the simplest non-trivial system of four particles representing exchange-coupled qubits....
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.
International Nuclear Information System (INIS)
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
Model for Interaction Between Photon and Cold Atom in QED Cavity
Institute of Scientific and Technical Information of China (English)
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.
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
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
Multiple-cascade model for the filling of hollow Ne atoms moving below an Al surface
International Nuclear Information System (INIS)
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
International Nuclear Information System (INIS)
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
Institute of Scientific and Technical Information of China (English)
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
Institute of Scientific and Technical Information of China (English)
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.
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.
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 ...
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
International Nuclear Information System (INIS)
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
Energy Technology Data Exchange (ETDEWEB)
Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Jackson, Bret [Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom); Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main (Germany); Martinazzo, Rocco, E-mail: rocco.martinazzo@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Richerche, v. Golgi 19, 20133 Milano (Italy)
2015-09-28
An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.
A phenomenological model of the growth of two-species atomic Bose-Einstein condensates
International Nuclear Information System (INIS)
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.
DEFF Research Database (Denmark)
Valentin, Jan B.; Andreetta, Christian; Boomsma, Wouter;
2014-01-01
We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length...... scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy...
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
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…
International Nuclear Information System (INIS)
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)
Mapping the Two-Component Atomic Fermi Gas to the Nuclear Shell-Model
DEFF Research Database (Denmark)
Özen, C.; Zinner, Nikolaj Thomas
2014-01-01
The physics of a two-component cold fermi gas is now frequently addressed in laboratories. Usually this is done for large samples of tens to hundreds of thousands of particles. However, it is now possible to produce few-body systems (1-100 particles) in very tight traps where the shell structure...... of the external potential becomes important. A system of two-species fermionic cold atoms with an attractive zero-range interaction is analogous to a simple model of nucleus in which neutrons and protons interact only through a residual pairing interaction. In this article, we discuss how the problem of a two......-component atomic fermi gas in a tight external trap can be mapped to the nuclear shell model so that readily available many-body techniques in nuclear physics, such as the Shell Model Monte Carlo (SMMC) method, can be directly applied to the study of these systems. We demonstrate an application of the SMMC method...
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.
Protein Nano-Object Integrator (ProNOI for generating atomic style objects for molecular modeling
Directory of Open Access Journals (Sweden)
Smith Nicholas
2012-12-01
Full Text Available Abstract Background With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results Here we report the Protein Nano-Object Integrator (ProNOI which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions The Protein Nano-Object Integrator (ProNOI is a convenient tool for
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.
Klocke, Michael; Wolf, Dietrich E
2016-01-01
A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively. PMID:27335760
Institute of Scientific and Technical Information of China (English)
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.
Why has the bohr-sommerfeld model of the atom been ignoredby general chemistry textbooks?
Niaz, Mansoor; Cardellini, Liberato
2011-12-01
Bohr's model of the atom is considered to be important by general chemistry textbooks. A major shortcoming of this model was that it could not explain the spectra of atoms containing more than one electron. In order to increase the explanatory power of the model, Sommerfeld hypothesized the existence of elliptical orbits. This study has the following objectives: 1) Formulation of criteria based on a history and philosophy of science framework; and 2) Evaluation of university-level general chemistry textbooks based on the criteria, published in Italy and U.S.A. Presentation of a textbook was considered to be "satisfactory" if it included a description of the Bohr-Sommerfeld model along with diagrams of the elliptical orbits. Of the 28 textbooks published in Italy that were analyzed, only five were classified as "satisfactory". Of the 46 textbooks published in U.S.A., only three were classified as "satisfactory". This study has the following educational implications: a) Sommerfeld's innovation (auxiliary hypothesis) by introducing elliptical orbits, helped to restore the viability of Bohr's model; b) Bohr-Sommerfeld's model went no further than the alkali metals, which led scientists to look for other models; c) This clearly shows that scientific models are tentative in nature; d) Textbook authors and chemistry teachers do not consider the tentative nature of scientific knowledge to be important; e) Inclusion of the Bohr-Sommerfeld model in textbooks can help our students to understand how science progresses.
Argon 4s and 4p Excited States Atomic Data Applied in ARC-JET Modeling
Directory of Open Access Journals (Sweden)
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.
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.
Institute of Scientific and Technical Information of China (English)
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.
Energy Technology Data Exchange (ETDEWEB)
Balleza D, E
2004-07-01
In the first chapter of this work we will show a detailed analysis of the one cooling Doppler phenomenon that appears when a laser induces a dipolar moment to the atoms in such a way that these may interact with him to transfer moment to the field with the subsequent decrease of kinetic energy that macroscopically it is translated in cooling of the atomic cloud. When the experiments of atomic cooling were carried out it was observed that the temperature was smaller to the one than it predicted the cooling Doppler, this originates the creation of a theory but it dies in which the over simplification is eliminated that the alone atom consists of two energy levels and levels are introduced of it structures fine that are able to explain the extra cooling. To this phenomenon it is called Sisifo effect and it is studied detailedly in the chapter two. The first two chapters talk each other about the atomic cooling, but it stops that the atomic cloud can be manipulated, before being confined, problem that we will expose in the chapter three with experimental solutions that at the moment they are implemented in the laboratories around the world. In particular we will concentrate on the traps FORT (Far Off Resonance Trap, trap very outside of resonance) that confine to the atoms in optic nets. The lasers gaussianos originate a potential sinusoidal along the propagation address and gaussiano in the perpendicular plane to this. In the I surrender four he/she intends a three-dimensional model that substitutes To the variation sinusoidal for a function crenel and he/she makes an approach To first order in the radial dependence to obtain an oscillator potential Harmonic instead of the gaussiano that you taenia. The pattern is solved in a similar way To the pattern unidimensional of bands: they are the functions of wave solution For every period and they are coupled among if so that they satisfy conditions of rhythm, When making this you arrives to a womb that couples the
COUPLED ATOMIZATION AND SPRAY MODELLING IN THE SPRAY FORMING PROCESS USING OPENFOAM
DEFF Research Database (Denmark)
Gjesing, Rasmus; Hattel, Jesper Henri; Fritsching, Udo
2009-01-01
The paper presents a numerical model capable of simulating the atomization, break-up and in-flight spray phenomena in the spray forming process. The model is developed and implemented in the freeware code openFOAM. The focus is on studying the coupling effect of the melt break-up phenomena with the...... 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...
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.
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.
Modeling of inelastic transport in one-dimensional metallic atomic wires
DEFF Research Database (Denmark)
Frederiksen, Thomas; Brandbyge, Mads; Lorente, N;
2004-01-01
devices. A full description of the transport properties of atomic-size conductors therefore requires a quantum mechanical treatment of both the electronic and mechanical degrees of freedom. In this paper, we study a one-dimensional tight-binding model of the conducting electrons combined with a balls......-and-springs model for the mechanical motion of the nuclei comprising the wire. We determine the vibrational modes and frequencies for the wires. The electronic Hamiltonian is expanded to lowest order in these normal modes.......Atomic-size conductors represent the ultimate limit of miniaturization, and understanding their properties is an important problem in the fields of nanoelectronics and molecular electronics. Quantum effects become important which leads to a physical behavior fundamentally different from macroscopic...
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.
Characterization of atom clusters in irradiated pressure vessel steels and model alloys
International Nuclear Information System (INIS)
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
International Nuclear Information System (INIS)
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)
Energy Technology Data Exchange (ETDEWEB)
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.
Institute of Scientific and Technical Information of China (English)
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.
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...
Modeling inelastic phonon scattering in atomic- and molecular-wire junctions
DEFF Research Database (Denmark)
Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads
2005-01-01
Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between...... the full nonequilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including nonequilibrium heating and provide...
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...
Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina
2016-07-01
Atomic oxygen (AO) of the upper atmosphere is one of the most important space factors that can cause degradation of spacecraft surface. In our previous mathematical model the Monte Carlo method and the "large particles" approximation were used for simulating processes of polymer etching under the influence of AO [1]. The interaction of enlarged AO particles with the polymer was described in terms of probabilities of reactions such as etching of polymer and specular and diffuse scattering of the AO particles on polymer. The effects of atomic oxygen on protected polymers and microfiller containing composites were simulated. The simulation results were in quite good agreement with the results of laboratory experiments on magnetoplasmadynamic accelerator of the oxygen plasma of SINP MSU [2]. In this paper we present a new model that describes the reactions of AO interactions with polymeric materials in more detail. Reactions of formation and further emission of chemical compounds such as CO, CO _{2}, H _{2}O, etc. cause the modification of the chemical composition of the polymer and change the probabilities of its consequent interaction with the AO. The simulation results are compared with the results of previous simulation and with the results of laboratory experiments. The reasons for the differences between the results of natural experiments on spacecraft, laboratory experiments and simulations are discussed. N. Chirskaya, M. Samokhina, Computer modeling of polymer structures degradation under the atomic oxygen exposure, WDS'12 Proceedings of Contributed Papers: Part III - Physics, Matfyzpress Prague, 2012, pp. 30-35. E. Voronina, L. Novikov, V. Chernik, N. Chirskaya, K. Vernigorov, G. Bondarenko, and A. Gaidar, Mathematical and experimental simulation of impact of atomic oxygen of the earth's upper atmosphere on nanostructures and polymer composites, Inorganic Materials: Applied Research, 2012, vol. 3, no. 2, pp. 95-101.
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.
Atomic-Scale Modeling of Particle Size Effects for the Oxygen Reduction Reaction of Pt
DEFF Research Database (Denmark)
Tritsaris, Georgios; Greeley, Jeffrey Philip; Rossmeisl, Jan;
2011-01-01
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...
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
Yang, Yantao; Cui, Junzhi; Han, Tiansi
2016-08-01
Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.
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.
Atomically thin spherical shell-shaped superscatterers based on a Bohr model.
Li, Rujiang; Lin, Xiao; Lin, Shisheng; Liu, Xu; Chen, Hongsheng
2015-12-18
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 a Bohr model. In addition, based on the analysis of the Bohr model, it is shown that contrary to the TM case, superscattering is hard to achieve by exciting the resonance of transverse electric (TE) graphene plasmons due to their poor field confinements.
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.
A quasi-stationary numerical model of atomized metal droplets, II: Prediction and assessment
DEFF Research Database (Denmark)
Pryds, Nini H.; Hattel, Jesper Henri; Thorborg, Jesper
1999-01-01
A new model which extends previous studies and includes the interaction between enveloping gas and an array of droplets has been developed and presented in a previous paper. The model incorporates the probability density function of atomized metallic droplets into the heat transfer equations. The...... main thrust of the model is that the gas temperature was not predetermined and calculated empirically but calculated numerically based on heat balance consideration. In this paper, the accuracy of the numerical model and the applicability of the model as a predictive tool have been investigated 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...
An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water
Energy Technology Data Exchange (ETDEWEB)
Stauffer, D.; Dragneva, N.; Floriano, W. B.; Rubel, O. [Thunder Bay Regional Research Institute, 290 Munro St, Thunder Bay, Ontario P7B 6V4 (Canada); Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7A 7T1 (Canada); Mawhinney, R. C. [Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7A 7T1 (Canada); Fanchini, G. [Physics and Astronomy, University of Western Ontario, 1151 Richmond St, London, Ontario N6A 3K7 (Canada); French, S. [University of Calgary, South Health Campus, 4448 Front St. SE, Calgary, Alberta T3M 1M4 (Canada)
2014-07-28
Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.
A computer code for calculations in the algebraic collective model of the atomic nucleus
Welsh, T A
2016-01-01
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1,1) x SO(5) dynamical group. This, in particular, obviates the use of coefficients of fractional parentage. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [pi x q x pi]_0 and [pi x pi]_{LM}, where q_M are the model's quadrupole moments, and pi_N are corresponding conjugate momenta (-2>=M,N<=2). The code also provides ready access to SO(3)-reduced SO(5) Clebsch-Gordan coefficients through data files provided with the code.
Pairwise energies for polypeptide coarse-grained models derived from atomic force fields
Betancourt, Marcos R.; Omovie, Sheyore J.
2009-05-01
The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.
International Nuclear Information System (INIS)
Spatial atomic layer deposition (SALD) is a promising technology with the aim of combining the advantages of excellent uniformity and conformity of temporal atomic layer deposition (ALD), and an industrial scalable and continuous process. In this manuscript, an experimental and numerical combined model of atmospheric SALD system is presented. To establish the connection between the process parameters and the growth efficiency, a quantitative model on reactant isolation, throughput, and precursor utilization is performed based on the separation gas flow rate, carrier gas flow rate, and precursor mass fraction. The simulation results based on this model show an inverse relation between the precursor usage and the carrier gas flow rate. With the constant carrier gas flow, the relationship of precursor usage and precursor mass fraction follows monotonic function. The precursor concentration, regardless of gas velocity, is the determinant factor of the minimal residual time. The narrow gap between precursor injecting heads and the substrate surface in general SALD system leads to a low Péclet number. In this situation, the gas diffusion act as a leading role in the precursor transport in the small gap rather than the convection. Fluid kinetics from the numerical model is independent of the specific structure, which is instructive for the SALD geometry design as well as its process optimization
Mg line formation in late-type stellar atmospheres: I. The model atom
Osorio, Y; Lind, K; Belyaev, A K; Spielfiedel, A; Guitou, M; Feautrier, N
2015-01-01
Mg is often traced in late-type stars using lines of neutral magnesium, which is expected to be subject to departures from LTE. The astrophysical importance of Mg as well as its relative simplicity from an atomic physics point of view, makes it a prime target and test bed for detailed ab initio non-LTE modelling in stellar atmospheres. For the low-lying states of Mg i, electron collision data were calculated using the R-matrix method. Calculations for collisional broadening by neutral hydrogen were also performed where data were missing. These calculations, together with data from the literature, were used to build a model atom. First, the modelling was tested by comparisons with observed spectra of benchmark stars with well-known parameters. Second, the spectral line behaviour and uncertainties were explored by extensive experiments in which sets of collisional data were changed or removed. The modelled spectra agree well with observed spectra. The line-to-line scatter in the derived abundances shows improve...
International Nuclear Information System (INIS)
For systems of interacting, ultracold spin-zero neutral bosonic atoms, harmonically trapped and subject to an optical lattice potential, we derive an Extended Bose Hubbard (EBH) model by developing a systematic expansion for the Hamiltonian of the system in powers of the lattice parameters and of a scale parameter, the lattice attenuation factor. We identify the dominant terms that need to be retained in realistic experimental conditions, up to nearest-neighbor interactions and nearest-neighbor hoppings conditioned by the on-site occupation numbers. In the mean field approximation, we determine the free energy of the system and study the phase diagram both at zero and at finite temperature. At variance with the standard on site Bose Hubbard model, the zero-temperature phase diagram of the EBH model possesses a dual structure in the Mott insulating regime. Namely, for specific ranges of the lattice parameters, a density wave phase characterizes the system at integer fillings, with domains of alternating mean occupation numbers that are the atomic counterparts of the domains of staggered magnetizations in an antiferromagnetic phase. We show as well that in the EBH model, a zero-temperature quantum phase transition to pair superfluidity is, in principle, possible, but completely suppressed at the lowest order in the lattice attenuation factor. Finally, we determine the possible occurrence of the different phases as a function of the experimentally controllable lattice parameters
From deep TLS validation to ensembles of atomic models built from elemental motions
Energy Technology Data Exchange (ETDEWEB)
Urzhumtsev, Alexandre, E-mail: sacha@igbmc.fr [Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Université de Lorraine, BP 239, 54506 Vandoeuvre-les-Nancy (France); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); Van Benschoten, Andrew H.; Fraser, James S. [University of California, San Francisco, San Francisco, CA 94158 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); University of California Berkeley, Berkeley, CA 94720 (United States); Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France)
2015-07-28
Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
Energy Technology Data Exchange (ETDEWEB)
Deng, Zhang; He, Wenjie; Duan, Chenlong [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Chen, Rong, E-mail: rongchen@mail.hust.edu.cn [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Shan, Bin [State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)
2016-01-15
Spatial atomic layer deposition (SALD) is a promising technology with the aim of combining the advantages of excellent uniformity and conformity of temporal atomic layer deposition (ALD), and an industrial scalable and continuous process. In this manuscript, an experimental and numerical combined model of atmospheric SALD system is presented. To establish the connection between the process parameters and the growth efficiency, a quantitative model on reactant isolation, throughput, and precursor utilization is performed based on the separation gas flow rate, carrier gas flow rate, and precursor mass fraction. The simulation results based on this model show an inverse relation between the precursor usage and the carrier gas flow rate. With the constant carrier gas flow, the relationship of precursor usage and precursor mass fraction follows monotonic function. The precursor concentration, regardless of gas velocity, is the determinant factor of the minimal residual time. The narrow gap between precursor injecting heads and the substrate surface in general SALD system leads to a low Péclet number. In this situation, the gas diffusion act as a leading role in the precursor transport in the small gap rather than the convection. Fluid kinetics from the numerical model is independent of the specific structure, which is instructive for the SALD geometry design as well as its process optimization.
Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.
Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi
2015-03-17
Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.
Coqblin-Schrieffer model for an ultracold gas of ytterbium atoms with metastable state
Kuzmenko, Igor; Kuzmenko, Tetyana; Avishai, Yshai; Jo, Gyu-Boong
2016-03-01
Motivated by the impressive recent advance in manipulating cold ytterbium atoms, we explore and substantiate the feasibility of realizing the Coqblin-Schrieffer model in a gas of cold fermionic 173Yb atoms. Making use of different AC polarizabillity of the electronic ground state (electronic configuration S10) and the long lived metastable state (electronic configuration P30), it is substantiated that the latter can be localized and serve as a magnetic impurity while the former remains itinerant. The exchange mechanism between the itinerant S10 and the localized P30 atoms is analyzed and shown to be antiferromagnetic. The ensuing SU(6) symmetric Coqblin-Schrieffer Hamiltonian is constructed, and, using the calculated exchange constant J , perturbative renormalization group (RG) analysis yields the Kondo temperature TK that is experimentally accessible. A number of thermodynamic measurable observables are calculated in the weak-coupling regime T >TK (using perturbative RG analysis) and in the strong-coupling regime T
Baldus, Sabrina; Schröder, Daniel; Bibinov, Nikita; Schulz-von der Gathen, Volker; Awakowicz, Peter
2015-06-01
Cold atmospheric pressure plasmas are a promising alternative therapy for treatment of chronic wounds, as they have already shown in clinical trials. In this study an air dielectric barrier discharge (DBD) developed for therapeutic use in dermatology is characterized with respect to the plasma produced reactive oxygen species, namely atomic oxygen and ozone, which are known to be of great importance to wound healing. To understand the plasma chemistry of the applied DBD, xenon-calibrated two-photon laser-induced fluorescence spectroscopy and optical absorption spectroscopy are applied. The measured spatial distributions are shown and compared to each other. A model of the afterglow chemistry based on optical emission spectroscopy is developed to cross-check the measurement results and obtain insight into the dynamics of the considered reactive oxygen species. The atomic oxygen density is found to be located mostly between the electrodes with a maximum density of {{n}\\text{O}}=6× {{10}16} cm-3 . Time resolved measurements reveal a constant atomic oxygen density between two high voltage pulses. The ozone is measured up to 3 mm outside the active plasma volume, reaching a maximum value of {{n}{{\\text{O}3}}}=3× {{10}16} cm-3 between the electrodes.
Quantum simulation of the Hubbard model with dopant atoms in silicon
Salfi, J.; Mol, J. A.; Rahman, R.; Klimeck, G.; Simmons, M. Y.; Hollenberg, L. C. L.; Rogge, S.
2016-04-01
In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose-Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model.
Atomic spin-chain realization of a model for quantum criticality
Toskovic, R.; van den Berg, R.; Spinelli, A.; Eliens, I. S.; van den Toorn, B.; Bryant, B.; Caux, J.-S.; Otte, A. F.
2016-07-01
The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum computing and spintronic devices; on the other hand, they can be used as fundamental building blocks for the realization of textbook many-body quantum models, illustrating key concepts such as quantum phase transitions, topological order or frustration as a function of system size. Here, we use low-temperature scanning tunnelling microscopy to construct arrays of magnetic atoms on a surface, designed to behave like spin-1/2 XXZ Heisenberg chains in a transverse field, for which a quantum phase transition from an antiferromagnetic to a paramagnetic phase is predicted in the thermodynamic limit. Site-resolved measurements on these finite-size realizations reveal a number of sudden ground state changes when the field approaches the critical value, each corresponding to a new domain wall entering the chains. We observe that these state crossings become closer for longer chains, suggesting the onset of critical behaviour. Our results present opportunities for further studies on quantum behaviour of many-body systems, as a function of their size and structural complexity.
Vinícius Catão de Assis Souza; Rosária da Silva Justi; Poliana Flávia Maia Ferreira
2006-01-01
Assuming (i) the importance of using analogies in science teaching, (ii) the learning difficulties related to the atomic models both discussed in the literature and observed in our previous research, and (iii) the gap found in the literature concerning studies that probe how students really understand analogies presented to them in science teaching, we investigate, in this study, how students from the Medium Level understand the atomic models from analogies used to present and explain them. I...
Misquitta, Alston J; Stone, Anthony J
2016-09-13
Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models.
Misquitta, Alston J; Stone, Anthony J
2016-09-13
Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models. PMID:27467814
A Strongly-Coupled Average Atom Model for Warm Dense Mixtures
Stanton, Liam; Murillo, Michael; Cimarron Project Collaboration
2013-10-01
We present a new average atom model to determine the properties of dense, multi-component plasmas. Strong ion correlations are taken into account through the quantum Ornstein-Zernike relations and hypernetted-chain closures, while an orbital-free density functional theory is employed to calculate electronic structure. The formalism is derived without reference to a mean ionization state of the system which allows for a more consistent generalization to mixtures. Applications to EOS and XRTS are discussed, and numerical simulations are compared with other methods and experimental data. Prepared by LLNL under Contract DE-AC52-07NA27344.
Relativistic model for nuclear matter and atomic nuclei with momentum-dependent self-energies
Typel, S
2005-01-01
The Lagrangian density of standard relativistic mean-field (RMF) models with density-dependent meson-nucleon coupling vertices is modified by introducing couplings of the meson fields to derivative nucleon densities. As a consequence, the nucleon self energies, that describe the effective in-medium interaction, become momentum dependent. In this approach it is possible to increase the effective (Landau) mass of the nucleons, that is related to the density of states at the Fermi energy, as compared to conventional relativistic models. At the same time the relativistic effective (Dirac) mass is kept small in order to obtain a realistic strength of the spin-orbit interaction. Additionally, the empirical Schroedinger-equivalent central optical potential from Dirac phenomenology is reasonably well described. A parametrization of the model is obtained by a fit to properties of doubly magic atomic nuclei. Results for symmetric nuclear matter, neutron matter and finite nuclei are discussed.
Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains
Glaessgen, E. H.; Saether, E.; Yamakov, V.
2008-01-01
Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.
Transport and dielectric properties of dense ionized matter from the average-atom RESEOS model
Ovechkin, A. A.; Loboda, P. A.; Falkov, A. L.
2016-09-01
Electron transport properties of warm and hot dense matter are calculated using two versions of the average-atom approach: Liberman's model and the neutral Wigner-Seitz-sphere model. Electrical conductivity calculations employed the extended Ziman formula, the relaxation-time approximation, the Zubarev method, and the Kubo-Greenwood formula. Thermal conductivities were evaluated in the relaxation-time approximation. The results obtained are in good agreement with experimental data and ab initio calculations. The origin of nonphysical features appearing in the DC electrical and thermal conductivities calculated with the relaxation-time approximation and the Zubarev method is analyzed. AC conductivity and dielectric properties of dense ionized matter are obtained from the radiative opacity data calculated using the RESEOS model.
Models for L-shell filling of slow hollow atoms moving below a surface
International Nuclear Information System (INIS)
A multiple cascade model is used to analyze the filling of L- and K-vacancies of hollow Ne atoms moving in shallow layers of an Al (111) surface. The model requires cross sections for charge transfer into the L-shell of the projectile which were determined from molecular-orbital calculations based on solid-state energies and screening effects. The analysis includes mechanisms of Landau-Zener curve-crossing and Fano-Lichten promotion. Absorption and build-up effects within the solid were taken into account. The results from the cascade model show good agreement with the ratio of L- to K-Auger emission recently measured for Ne9+ incident on Al. (orig.)
Nuclear magnetic resonance parameters of atomic xenon dissolved in Gay-Berne model liquid crystal.
Lintuvuori, Juho; Straka, Michal; Vaara, Juha
2007-03-01
We present constant-pressure Monte Carlo simulations of nuclear magnetic resonance (NMR) spectral parameters, nuclear magnetic shielding relative to the free atom as well as nuclear quadrupole coupling, for atomic xenon dissolved in a model thermotropic liquid crystal. The solvent is described by Gay-Berne (GB) molecules with parametrization kappa=4.4, kappa{'}=20.0 , and mu=nu=1 . The reduced pressure of P{*}=2.0 is used. Previous simulations of a pure GB system with this parametrization have shown that upon lowering the temperature, the model exhibits isotropic, nematic, smectic- A , and smectic- B /molecular crystal phases. We introduce spherical xenon solutes and adjust the energy and length scales of the GB-Xe interaction to those of the GB-GB interaction. This is done through first principles quantum chemical calculations carried out for a dimer of model mesogens as well as the mesogen-xenon complex. We preparametrize quantum chemically the Xe nuclear shielding and quadrupole coupling tensors when interacting with the model mesogen, and use the parametrization in a pairwise additive fashion in the analysis of the simulation. We present the temperature evolution of {129/131}Xe shielding and 131Xe quadrupole coupling in the different phases of the GB model. From the simulations, separate isotropic and anisotropic contributions to the experimentally available total shielding can be obtained. At the experimentally relevant concentration, the presence of the xenon atoms does not significantly affect the phase behavior as compared to the pure GB model. The simulations reproduce many of the characteristic experimental features of Xe NMR in real thermotropic LCs: Discontinuity in the value or trends of the shielding and quadrupole coupling at the nematic-isotropic and smectic-A-nematic phase transitions, nonlinear shift evolution in the nematic phase reflecting the behavior of the orientational order parameter, and decreasing shift in the smectic-A phase. The last
Institute of Scientific and Technical Information of China (English)
LI Shichun
2004-01-01
Based on the Thomas-Fermi-Dirac-Cheng model, atomic phase diagram or electron density versus atomic radius diagram describing the interaction properties of atoms of different kinds in equilibrium state is developed. Atomic phase diagram is established based on the two-atoms model. Besides atomic radius, electron density and continuity condition for electron density on interfaces between atoms, the lever law of atomic phase diagram involving other physical parameters is taken into account, such as the binding energy, for the sake of simplicity.
Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model
Kuno, Yoshihito; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2016-01-01
In this paper, we study atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice. We start from an extended 3D Bose-Hubbard model with nearest-neighbor repulsions and show that it can simulate a U(1) gauge-Higgs model with next nearest-neighbor Higgs couplings. Here the phase of the boson variable on each site of the optical lattice describes the vector potential on each link of the gauge-model lattice. To determine the phase diagram of the gauge-Higgs model at a zero temperature, we perform Monte-Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the three phases, i.e., the confinement, Coulomb and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time-evolution of an electric flux initially put on a straight line connecting two external point charges. We also calculate the potential energy between this pair ...
A cluster expansion model for predicting activation barrier of atomic processes
Energy Technology Data Exchange (ETDEWEB)
Rehman, Tafizur; Jaipal, M. [Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208 016 (India); Chatterjee, Abhijit, E-mail: achatter@iitk.ac.in [Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208 016 (India); Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400 076 (India)
2013-06-15
We introduce a procedure based on cluster expansion models for predicting the activation barrier of atomic processes encountered while studying the dynamics of a material system using the kinetic Monte Carlo (KMC) method. Starting with an interatomic potential description, a mathematical derivation is presented to show that the local environment dependence of the activation barrier can be captured using cluster interaction models. Next, we develop a systematic procedure for training the cluster interaction model on-the-fly, which involves: (i) obtaining activation barriers for handful local environments using nudged elastic band (NEB) calculations, (ii) identifying the local environment by analyzing the NEB results, and (iii) estimating the cluster interaction model parameters from the activation barrier data. Once a cluster expansion model has been trained, it is used to predict activation barriers without requiring any additional NEB calculations. Numerical studies are performed to validate the cluster expansion model by studying hop processes in Ag/Ag(100). We show that the use of cluster expansion model with KMC enables efficient generation of an accurate process rate catalog.
Growth rate model and doping metrology by atom probe tomography in silicon nanowire
Energy Technology Data Exchange (ETDEWEB)
Chen, W.H.; Larde, R.; Cadel, E.; Pareige, P. [Groupe de Physique des Materiaux, Universite et INSA de Rouen, UMR CNRS 6634, Av. de l' Universite, BP 12, 76801 Saint Etienne du Rouvray (France); Xu, T.; Grandidier, B.; Nys, J.P.; Stievenard, D. [Institut d' Electronique, de Microelectronique et de Nanotechnologie, UMR CNRS 8520, Departement ISEN, 41 bd Vauban, 59046 Lille Cedex (France)
2011-03-15
Silicon nanowires (SiNWs) with different surface number density are fabricated using Chemical Vapor Deposition (CVD) method by controlling the catalyst droplet number density with in-situ evaporation. For comparison, another type of SiNWs is fabricated by Molecular Beam Epitaxy (MBE) method. To study these two types of SiNWs a general growth rate model is presented. The fit curves from this model are consistent with our experimental data. In both growing conditions the SiNW growth rate as a function of their diameter are compared and discussed. The p-type SiNWs have also been prepared by adding diborane into precursor. The doping metrology in an individual SiNW is realized by laser assisted Atom Probe Tomography (APT). We have shown that the doping atoms (e.g. B) can incorporate into SiNW and an accurate quantification can be given (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Benchmarking atomic physics models for magnetically confined fusion plasma physics experiments
International Nuclear Information System (INIS)
In present magnetically confined fusion devices, high and intermediate Z impurities are either puffed into the plasma for divertor radiative cooling experiments or are sputtered from the high Z plasma facing armor. The beneficial cooling of the edge as well as the detrimental radiative losses from the core of these impurities can be properly understood only if the atomic physics used in the modeling of the cooling curves is very accurate. To this end, a comprehensive experimental and theoretical analysis of some relevant impurities is undertaken. Gases (Ne, Ar, Kr, and Xe) are puffed and nongases are introduced through laser ablation into the FTU tokamak plasma. The charge state distributions and total density of these impurities are determined from spatial scans of several photometrically calibrated vacuum ultraviolet and x-ray spectrographs (3 - 1600 Angstrom), the multiple ionization state transport code transport code (MIST) and a collisional radiative model. The radiative power losses are measured with bolometery, and the emissivity profiles were measured by a visible bremsstrahlung array. The ionization balance, excitation physics, and the radiative cooling curves are computed from the Hebrew University Lawrence Livermore atomic code (HULLAC) and are benchmarked by these experiments. (Supported by U.S. DOE Grant No. DE-FG02-86ER53214 at JHU and Contract No. W-7405-ENG-48 at LLNL.) copyright 1999 American Institute of Physics
Benchmarking atomic physics models for magnetically confined fusion plasma physics experiments
May, M. J.; Finkenthal, M.; Soukhanovskii, V.; Stutman, D.; Moos, H. W.; Pacella, D.; Mazzitelli, G.; Fournier, K.; Goldstein, W.; Gregory, B.
1999-01-01
In present magnetically confined fusion devices, high and intermediate Z impurities are either puffed into the plasma for divertor radiative cooling experiments or are sputtered from the high Z plasma facing armor. The beneficial cooling of the edge as well as the detrimental radiative losses from the core of these impurities can be properly understood only if the atomic physics used in the modeling of the cooling curves is very accurate. To this end, a comprehensive experimental and theoretical analysis of some relevant impurities is undertaken. Gases (Ne, Ar, Kr, and Xe) are puffed and nongases are introduced through laser ablation into the FTU tokamak plasma. The charge state distributions and total density of these impurities are determined from spatial scans of several photometrically calibrated vacuum ultraviolet and x-ray spectrographs (3-1600 Å), the multiple ionization state transport code transport code (MIST) and a collisional radiative model. The radiative power losses are measured with bolometery, and the emissivity profiles were measured by a visible bremsstrahlung array. The ionization balance, excitation physics, and the radiative cooling curves are computed from the Hebrew University Lawrence Livermore atomic code (HULLAC) and are benchmarked by these experiments. (Supported by U.S. DOE Grant No. DE-FG02-86ER53214 at JHU and Contract No. W-7405-ENG-48 at LLNL.)
Non-equilibrium dynamical phases of the two-atom Dicke model
Energy Technology Data Exchange (ETDEWEB)
Bhattacherjee, Aranya B.
2014-09-12
In this paper, we investigate the non-equilibrium dynamical phases of the two-atom Dicke model, which can be realized in a two species Bose–Einstein condensate interacting with a single light mode in an optical cavity. Apart from the usual non-equilibrium normal and inverted phases, a non-equilibrium mixed phase is possible which is a combination of normal and inverted phase. A new kind of dynamical phase transition is predicted from non-superradiant mixed phase to the superradiant phase which can be achieved by tuning the two different atom–photon couplings. We also show that a dynamical phase transition from the non-superradiant mixed phase to the superradiant phase is forbidden for certain values of the two atom–photon coupling strengths. - Highlights: • We investigate the non-equilibrium dynamical phases of the two-atom Dicke model. • The dynamical phase diagram reveals a new kind of non-equilibrium mixed phase. • A new kind of dynamical phase transition is predicted from mixed phase to the superradiant phase. • In the dynamical phase diagram of the mixed phase, there are regions where the superradiant phase cannot exist.
Energy Technology Data Exchange (ETDEWEB)
Bertolus, Marjorie, E-mail: marjorie.bertolus@cea.fr [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Freyss, Michel; Dorado, Boris; Martin, Guillaume; Hoang, Kiet; Maillard, Serge; Skorek, Richard; Garcia, Philippe; Valot, Carole [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Chartier, Alain; Van Brutzel, Laurent; Fossati, Paul [CEA, DEN, DPC/SCCME, 91191 Gif-sur-Yvette (France); Grimes, Robin W.; Parfitt, David C.; Bishop, Clare L.; Murphy, Samuel T.; Rushton, Michael J.D. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Staicu, Dragos; Yakub, Eugen; Nichenko, Sergii [European Commission, Joint Research Centre, Institute for Transuranium Elements, 76125 Karlsruhe (Germany); and others
2015-07-15
This article presents a synthesis of the investigations at the atomic scale of the transport properties of defects and fission gases in uranium dioxide, as well as of the transfer of results from the atomic scale to models at the mesoscopic scale, performed during the F-BRIDGE European project (2008–2012). We first present the mesoscale models used to investigate uranium oxide fuel under irradiation, and in particular the cluster dynamics and kinetic Monte Carlo methods employed to model the behaviour of defects and fission gases in UO{sub 2}, as well as the parameters of these models. Second, we describe briefly the atomic scale methods employed, i.e. electronic structure calculations and empirical potential methods. Then, we show the results of the calculation of the data necessary for the mesoscale models using these atomic scale methods. Finally, we summarise the links built between the atomic and mesoscopic scale by listing the data calculated at the atomic scale which are to be used as input in mesoscale modelling. Despite specific difficulties in the description of fuel materials, the results obtained in F-BRIDGE show that atomic scale modelling methods are now mature enough to obtain precise data to feed higher scale models and help interpret experiments on nuclear fuels. These methods bring valuable insight, in particular the formation, binding and migration energies of point and extended defects, fission product localization, incorporation energies and migration pathways, elementary mechanisms of irradiation induced processes. These studies open the way for the investigation of other significant phenomena involved in fuel behaviour, in particular the thermochemical and thermomechanical properties and their evolution in-pile, complex microstructures, as well as of more complex fuels.
Johns, H. M.; Lanier, N. E.; Kline, J. L.; Fontes, C. J.; Perry, T. S.; Fryer, C. L.; Brown, C. R. D.; Morton, J. W.; Hager, J. D.; Sherrill, M. E.
2016-11-01
We present synthetic transmission spectra generated with PrismSPECT utilizing both the ATBASE model and the Los Alamos opacity library (OPLIB) to evaluate whether an alternative choice in atomic data will impact modeling of experimental data from radiation transport experiments using Sc-doped aerogel foams (ScSi6O12 at 75 mg/cm3 density). We have determined that in the 50-200 eV Te range there is a significant difference in the 1s-3p spectra, especially below 100 eV, and for Te = 200 eV above 5000 eV in photon energy. Examining synthetic spectra generated using OPLIB with 300 resolving power reveals spectral sensitivity to Te changes of ˜3 eV.
Directory of Open Access Journals (Sweden)
Nuri Yazdani
2014-03-01
Full Text Available Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD. Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.
Dynamic Modeling for the Design and Cyclic Operation of an Atomic Layer Deposition (ALD Reactor
Directory of Open Access Journals (Sweden)
Curtisha D. Travis
2013-08-01
Full Text Available 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 based on collocation discretization in time, resulting in an unambiguous definition of film growth-per-cycle (gpc. A key finding of this study is that unintended chemical vapor deposition conditions can mask regions of operation that would otherwise correspond to ideal saturating ALD operation. The use of the simulator for assisting in process design decisions is presented.
Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa; Park, Hyung Gyu; Utke, Ivo
2014-01-01
Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT) arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD). Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.
Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei
2015-12-28
Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.
Lasukov, V. V.; Rozhkova, S. V.; Abdrashitova, M. O.; Il'kin, E. E.; Novoselov, V. V.
2016-01-01
The nonlinear dynamics of the regular growth of the population of an aggregation of the Lemaitre-Friedmann primordial atoms has been investigated. It is analytically shown that there exists an asymptotic limit to the growth of the population of an aggregation of primordial atoms / galaxies. The nonlinear model, developed in this paper, of the information factor of the evolution of these primordial atoms can find wide application in biology, biological electronics, synthetic biology, in the mathematical history of the driving force of the noosphere, in cosmology, and in other areas of science and technology.
Mohammadi, M; Soltanolkotabi, M
2006-01-01
We present a theoretical scheme based on su(2) algebra to investigate the influence of homogeneous gravitational field on the quantum nondemolition measurement of atomic momentum in dispersive Jaynes-Cummings model. In the dispersive Jaynes-Cummings model, when detuning is large and the atomic motion is in a propagating light wave, we consider a two-level atom with quantized cavity-field in the presence of a homogeneous gravitational field. We derive an effective Hamiltonian describing the dispersive atom-field interaction in the presence of gravitational field. We can see gravitational influence both on the momentum filter and momentum distribution. Moreover, gravitational field decreases both tooth spacing of momentum and the width of teeth of momentum.
Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2016-01-01
In this paper, we study atomic quantum simulations of $(1+1)$-dimensional($(1+1)$D) U(1) gauge-Higgs models (GHMs) defined on a lattice. We explain how U(1) lattice GHMs appear from an extended Bose-Hubbard model (EBHM) describing ultra-cold atoms with a nearest neighbor repulsion in a 1D optical lattice. We first study a phase diagram of the 1D EBHM at low fillings by means of a quantum Monte-Carlo(MC) simulation. Next, we study the EBHM at large fillings and also GHMs by the MC simulations in the path-integral formalism and show that there are four phases, i.e., the Higgs phase(superfluid), the confinement phase (Mott insulator), and phases corresponding to the density wave and the supersolid. With the obtained phase diagrams, we investigate the relationship between the two models. Finally, we study real-time dynamic of an electric flux in the GHMs by the Gross-Pitaevskii equations and the truncated Wigner approximation.
Malinska, Maura; Dauter, Zbigniew
2016-06-01
In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F
2007-02-19
Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.
A computer code for calculations in the algebraic collective model of the atomic nucleus
Welsh, T. A.; Rowe, D. J.
2016-03-01
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1 , 1) × SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functions of the model's quadrupole moments qˆM and are at most quadratic in the corresponding conjugate momenta πˆN (- 2 ≤ M , N ≤ 2). The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [ π ˆ ⊗ q ˆ ⊗ π ˆ ] 0 and [ π ˆ ⊗ π ˆ ] LM. The code is made efficient by use of an analytical expression for the needed SO(5)-reduced matrix elements, and use of SO(5) ⊃ SO(3) Clebsch-Gordan coefficients obtained from precomputed data files provided with the code.
How Sommerfeld extended Bohr's model of the atom (1913-1916)
Eckert, Michael
2014-04-01
Sommerfeld's extension of Bohr's atomic model was motivated by the quest for a theory of the Zeeman and Stark effects. The crucial idea was that a spectral line is made up of coinciding frequencies which are decomposed in an applied field. In October 1914 Johannes Stark had published the results of his experimental investigation on the splitting of spectral lines in hydrogen (Balmer lines) in electric fields, which showed that the frequency of each Balmer line becomes decomposed into a multiplet of frequencies. The number of lines in such a decomposition grows with the index of the line in the Balmer series. Sommerfeld concluded from this observation that the quantization in Bohr's model had to be altered in order to allow for such decompositions. He outlined this idea in a lecture in winter 1914/15, but did not publish it. The First World War further delayed its elaboration. When Bohr published new results in autumn 1915, Sommerfeld finally developed his theory in a provisional form in two memoirs which he presented in December 1915 and January 1916 to the Bavarian Academy of Science. In July 1916 he published the refined version in the Annalen der Physik. The focus here is on the preliminary Academy memoirs whose rudimentary form is better suited for a historical approach to Sommerfeld's atomic theory than the finished Annalen-paper. This introductory essay reconstructs the historical context (mainly based on Sommerfeld's correspondence). It will become clear that the extension of Bohr's model did not emerge in a singular stroke of genius but resulted from an evolving process.
DiMaio, F; Chiu, W
2016-01-01
Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. PMID:27572730
The Pre-Service Science Teachers' Mental Models for Concept of Atoms and Learning Difficulties
Kiray, Seyit Ahmet
2016-01-01
The purpose of this study is to reveal the pre-service science teachers' difficulties about the concept of atoms. The data was collected from two different sources: The Draw an Atom Test (DAAT) and face-to-face interviews. Draw an atom test (DAAT) were administered to the 142 science teacher candidates. To elaborate the results, the researcher…
International Nuclear Information System (INIS)
The Joint ICTP-IAEA Workshop on Fusion Plasma Modelling using Atomic and Molecular Data was held from 23-27 January 2012 at Abdus Salam International Centre for Theoretical Physics in Trieste, Italy. Ten lecturers presented tutorials and reviews on topics in fusion plasma modelling and atomic, molecular and plasma-material interaction processes. There were 20 participants, generally early-career researchers in the area of A+M+PMI processes and also plasma modellers. The participants presented their work in short talks and a poster session. The proceedings of the workshop are summarized here. (author)
International Nuclear Information System (INIS)
The application of the Knudsen effusion method combined with mass spectrometry for the measurement of atomization energies of inorganic molecules is described. Recent results with emphasis on molecular metals, intermetallic molecules and metal carbides are presented. The use and limitations of various empirica models of bonding are illustrated by comparing experimental values with those calculated by the various models
Fast low-rank approximations of multidimensional integrals in ion-atomic collisions modelling
Litsarev, M S
2015-01-01
An efficient technique based on low-rank separated approximations is proposed for computation of three-dimensional integrals arising in the energy deposition model that describes ion-atomic collisions. Direct tensor-product quadrature requires grids of size $4000^3$ which is unacceptable. Moreover, several of such integrals have to be computed simultaneously for different values of parameters. To reduce the complexity, we use the structure of the integrand and apply numerical linear algebra techniques for the construction of low-rank approximation. The resulting algorithm is $10^3$ faster than spectral quadratures in spherical coordinates used in the original DEPOSIT code. The approach can be generalized to other multidimensional problems in physics.
The Challenge of Teaching Blind Students Atomic Models and the Process of Teacher Education
Directory of Open Access Journals (Sweden)
Renata Cardoso de Sá Ribeiro Razuck
2014-04-01
Full Text Available Based on the National Special Education in the Perspective of Inclusive Education (2008, students with special educational needs have to be included in the regular schools. Specifically blind students, because of their specific characteristics, they need necessary resources and suitable materials that can provide overcoming the lack of visualization. In this context, chemistry has a great visual appeal and provides a huge challenge for the acquisition of its concepts by the blinds. In order to try to fill some gaps in Chemistry contents with great visual appeal, this paper proposes a discussion on the importance of applying alternative pedagogical resources that enable visually impaired to understand and construct this imaginary science, working to this with prototypes of atomic models. This work is intended not only to contribute to the teaching-learning process, but also for the training of undergraduate courses to work towards inclusion.
Double ionization of a two-electron model atom in a single-cycle laser pulse
International Nuclear Information System (INIS)
We present theoretical results from the solution of a widely used model atom containing two interacting electrons in one dimension bound to a soft-Coulomb potential and ionized by an intense, short laser pulse. A half-cycle pulse leads to strong single but no double ionization (down to a probability density of 10-12). A full-cycle laser pulse at low frequency leads to double ionization which begins precisely at the classical return time for the first ejected electron. At weak field, double ionization occurs at the time of maximum return kinetic energy. When the excursion range for the first electron is truncated, the double ionization at later times, corresponding to longer excursions, disappears. When the field near the nucleus is turned off during the return of the first electron, double ionization persists
Kubo-Greenwood approach to conductivity in dense plasmas with average atom models
Starrett, C E
2016-01-01
A new formulation of the Kubo-Greenwood conductivity for average atom models is given. The new formulation improves upon previous by explicitly including the ionic-structure factor. Calculations based on this new expression lead to much improved agreement with ab initio results for DC conductivity of warm dense hydrogen and beryllium, and for thermal conductivity of hydrogen. We also give and test a slightly modified Ziman-Evans formula for the resistivity that includes a non-free electron density of states, thus removing an ambiguity in the original Ziman-Evans formula. Again results based on this expression are in good agreement with ab initio simulations for warm dense beryllium and hydrogen. However, for both these expressions, calculations of the electrical conductivity of warm dense aluminum lead to poor agreement at low temperatures compared to ab initio simulations.
Atomic Force Microscopy Based Nanorobotics Modelling, Simulation, Setup Building and Experiments
Xie, Hui; Régnier, Stéphane; Sitti, Metin
2012-01-01
The atomic force microscope (AFM) has been successfully used to perform nanorobotic manipulation operations on nanoscale entities such as particles, nanotubes, nanowires, nanocrystals, and DNA since 1990s. There have been many progress on modeling, imaging, teleoperated or automated control, human-machine interfacing, instrumentation, and applications of AFM based nanorobotic manipulation systems in literature. This book aims to include all of such state-of-the-art progress in an organized, structured, and detailed manner as a reference book and also potentially a textbook in nanorobotics and any other nanoscale dynamics, systems and controls related research and education. Clearly written and well-organized, this text introduces designs and prototypes of the nanorobotic systems in detail with innovative principles of three-dimensional manipulation force microscopy and parallel imaging/manipulation force microscopy.
An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.
Schur, Florian K M; Obr, Martin; Hagen, Wim J H; Wan, William; Jakobi, Arjen J; Kirkpatrick, Joanna M; Sachse, Carsten; Kräusslich, Hans-Georg; Briggs, John A G
2016-07-29
Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1. PMID:27417497
Distributed force probe bending model of critical dimension atomic force microscopy bias
Ukraintsev, Vladimir A.; Orji, Ndubuisi G.; Vorburger, Theodore V.; Dixson, Ronald G.; Fu, Joseph; Silver, Rick M.
2013-04-01
Critical dimension atomic force microscopy (CD-AFM) is a widely used reference metrology technique. To characterize modern semiconductor devices, small and flexible probes, often 15 to 20 nm in diameter, are used. Recent studies have reported uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements. To understand the source of these variations, tip-sample interactions between high aspect ratio features and small flexible probes, and their influence on measurement bias, should be carefully studied. Using theoretical and experimental procedures, one-dimensional (1-D) and two-dimensional (2-D) models of cylindrical probe bending relevant to carbon nanotube (CNT) AFM probes were developed and tested. An earlier 1-D bending model was refined, and a new 2-D distributed force (DF) model was developed. Contributions from several factors were considered, including: probe misalignment, CNT tip apex diameter variation, probe bending before snapping, and distributed van der Waals-London force. A method for extracting Hamaker probe-surface interaction energy from experimental probe-bending data was developed. Comparison of the new 2-D model with 1-D single point force (SPF) model revealed a difference of about 28% in probe bending. A simple linear relation between biases predicted by the 1-D SPF and 2-D DF models was found. The results suggest that probe bending can be on the order of several nanometers and can partially explain the observed CD-AFM probe-to-probe variation. New 2-D and three-dimensional CD-AFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.
Levashov, Valentin A
2015-01-01
It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a model 3D binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. Thus correlations relevant to the Green-Kubo expression for viscosity are interpreted in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonst...
Caffau, Elisabetta; Steffen, Matthias; Ayres, Thomas R; Bonifacio, Piercarlo; Cayrel, Roger; Freytag, Bernd; Plez, Bertrand
2008-01-01
The solar oxygen abundance has undergone a major downward revision in the last decade, the most noticeable one being the update including 3D hydrodynamical simulations to model the solar photosphere. Up to now, such an analysis has been carried out only by one group using one radiation-hydrodynamics code. We investigate the photospheric oxygen abundance considering lines from atomic transitions. We also consider the relationship between the solar model used and the resulting solar oxygen abundance, to understand whether the downward abundance revision is specifically related to 3D hydrodynamical effects. We perform a new determination of the solar photospheric oxygen abundance by analysing different high-resolution high signal-to-noise ratio atlases of the solar flux and disc-centre intensity making use of the latest generation of CO5BOLD 3D solar model atmospheres. We find 8.73 < logNoxygen/Nhydrogen +12 < 8.79. The lower and upper value represent extreme assumptions on the role of collisional excitati...
AxBAxB… pulsed atomic layer deposition: Numerical growth model and experiments
Muneshwar, Triratna; Cadien, Ken
2016-02-01
Atomic layer deposition (ALD) is widely used for the fabrication of advanced semiconductor devices and related nanoscale structures. During ALD, large precursor doses (>1000 L per pulse) are often required to achieve surface saturation, of which only a small fraction is utilized in film growth while the rest is pumped from the system. Since the metal precursor constitutes a significant cost of ALD, strategies to enhance precursor utilization are essential for the scaling of ALD processes. In the precursor reaction step, precursor physisorption is restricted by steric hindrance (mA1) from ligands on the precursor molecules. On reaction, some of these ligands are removed as by-products resulting in chemisorbed species with reduced steric hindrance (mA1 → mA2, where mA2 1, x ∈ I) short-pulses rather than a single pulse. A numerical first-order surface reaction kinetics growth model is presented and applied to study the effect of AxBAxB… pulsed ALD on the growth per cycle (GPC). The model calculations predict higher GPC for AxBAxB… pulsing than with ABAB… deposition. In agreement with the model predictions, with AxBAxB… pulsed deposition, the GPC was found to increase by ˜46% for ZrN plasma enhanced ALD (PEALD), ˜49% for HfO2 PEALD, and ˜8% for thermal Al2O3 ALD with respect to conventional ABAB… pulsed growth.
Rovibrationally Inelastic Atom-Molecule Collision Cross Sections from a Hard Sphere Model
Lashner, Jacob; Stewart, Brian
2016-05-01
Hard-shell models have long been used to elucidate the principal features of molecular energy transfer and exchange reaction in the A + BC system. Nevertheless, no three-dimensional hard-shell calculation of inelastic collision cross sections has been reported. This work aims to fill that void. A particular motivation comes from our experimental results, which show the importance of equatorial impacts in the vibrational excitation process. Working with the simple hard-sphere model, we incorporated secondary impacts, defined as those in which A strikes C after striking B. Such collisions are important in systems such as Li2 - X, in which vibrational energy transfer occurs principally through side impacts. We discuss the complexity this adds to the model and present fully three-dimensional cross sections for rovibrational excitation of an initially stationary molecule in the homonuclear A + B2 system, examining the cross section as a function of the masses and radii of the atoms. We show how the features in the cross section evolve as these parameters are varied and calculate the contribution of secondary (near-equatorial) impacts to the dynamics. We compare with recent measurements in our laboratory and with the results of quasiclassical trajectories.
Directory of Open Access Journals (Sweden)
Gront Dominik
2007-06-01
Full Text Available Abstract Background Although experimental methods for determining protein structure are providing high resolution structures, they cannot keep the pace at which amino acid sequences are resolved on the scale of entire genomes. For a considerable fraction of proteins whose structures will not be determined experimentally, computational methods can provide valuable information. The value of structural models in biological research depends critically on their quality. Development of high-accuracy computational methods that reliably generate near-experimental quality structural models is an important, unsolved problem in the protein structure modeling. Results Large sets of structural decoys have been generated using reduced conformational space protein modeling tool CABS. Subsequently, the reduced models were subject to all-atom reconstruction. Then, the resulting detailed models were energy-minimized using state-of-the-art all-atom force field, assuming fixed positions of the alpha carbons. It has been shown that a very short minimization leads to the proper ranking of the quality of the models (distance from the native structure, when the all-atom energy is used as the ranking criterion. Additionally, we performed test on medium and low accuracy decoys built via classical methods of comparative modeling. The test placed our model evaluation procedure among the state-of-the-art protein model assessment methods. Conclusion These test computations show that a large scale high resolution protein structure prediction is possible, not only for small but also for large protein domains, and that it should be based on a hierarchical approach to the modeling protocol. We employed Molecular Mechanics with fixed alpha carbons to rank-order the all-atom models built on the scaffolds of the reduced models. Our tests show that a physic-based approach, usually considered computationally too demanding for large-scale applications, can be effectively used in such
Aerosol cluster impact and break-up : II. Atomic and Cluster Scale Models.
Energy Technology Data Exchange (ETDEWEB)
Lechman, Jeremy B.; Takato, Yoichi (State University of New York at Buffalo, Buffalo, NY)
2010-09-01
Understanding the interaction of aerosol particle clusters/flocs with surfaces is an area of interest for a number of processes in chemical, pharmaceutical, and powder manufacturing as well as in steam-tube rupture in nuclear power plants. Developing predictive capabilities for these applications involves coupled phenomena on multiple length and timescales from the process macroscopic scale ({approx}1m) to the multi-cluster interaction scale (1mm-0.1m) to the single cluster scale ({approx}1000 - 10000 particles) to the particle scale (10nm-10{micro}m) interactions, and on down to the sub-particle, atomic scale interactions. The focus of this report is on the single cluster scale; although work directed toward developing better models of particle-particle interactions by considering sub-particle scale interactions and phenomena is also described. In particular, results of mesoscale (i.e., particle to single cluster scale) discrete element method (DEM) simulations for aerosol cluster impact with rigid walls are presented. The particle-particle interaction model is based on JKR adhesion theory and is implemented as an enhancement to the granular package in the LAMMPS code. The theory behind the model is outlined and preliminary results are shown. Additionally, as mentioned, results from atomistic classical molecular dynamics simulations are also described as a means of developing higher fidelity models of particle-particle interactions. Ultimately, the results from these and other studies at various scales must be collated to provide systems level models with accurate 'sub-grid' information for design, analysis and control of the underlying systems processes.
Modeling of adhesion in tablet compression - I. atomic force microscopy and molecular simulation.
Energy Technology Data Exchange (ETDEWEB)
Wang, J. J.; Li, T.; Bateman, S. D.; Erck, R.; Morris, K. R.; Energy Technology; Purdue Univ.; Novartis Pharmaceutical Corp.
2003-04-01
Adhesion problems during tablet manufacturing have been observed to be dependent on many formulation and process factors including the run time on the tablet press. Consequently, problems due to sticking may only become apparent towards the end of the development process when a prolonged run on the tablet press is attempted for the first time. It would be beneficial to predict in a relative sense if a formulation or new chemical entity has the potential for adhesion problems early in the development process. It was hypothesized that favorable intermolecular interaction between the drug molecules and the punch face is the first step or criterion in the adhesion process. Therefore, the rank order of adhesion during tablet compression should follow the rank order of these energies of interaction. The adhesion phenomenon was investigated using molecular simulations and contact mode atomic force microscopy (AFM). Three model compounds were chosen from a family of profen compounds. Silicon nitride AFM tips were modified by coating a 20-nm iron layer on the surfaces by sputter coating. Profen flat surfaces were made by melting and recrystallization. The modified AFM probe and each profen surface were immersed in the corresponding profen saturated water during force measurements using AFM. The work of adhesion between iron and ibuprofen, ketoprofen, and flurbiprofen in vacuum were determined to be -184.1, -2469.3, -17.3 mJ {center_dot} m-2, respectively. The rank order of the work of adhesion between iron and profen compounds decreased in the order: ketoprofen > ibuprofen > flurbiprofen. The rank order of interaction between the drug molecules and the iron superlattice as predicted by molecular simulation using Cerius2 is in agreement with the AFM measurements. It has been demonstrated that Atomic Force Microscopy is a powerful tool in studying the adhesion phenomena between organic drug compounds and metal surface. The study has provided insight into the adhesion problems
Modeling non local thermodynamic equilibrium plasma using the Flexible Atomic Code data
Han, Bo; Salzmann, David; Zhao, Gang
2015-01-01
We present a new code, RCF("Radiative-Collisional code based on FAC"), which is used to simulate steady-state plasmas under non local thermodynamic equilibrium condition, especially photoinization dominated plasmas. RCF takes almost all of the radiative and collisional atomic processes into rate equation to interpret the plasmas systematically. The Flexible Atomic Code (FAC) supplies all the atomic data RCF needed, which insures calculating completeness and consistency of atomic data. With four input parameters relating to the radiation source and target plasma, RCF calculates the population of levels and charge states, as well as potentially emission spectrum. In preliminary application, RCF successfully reproduces the results of a photoionization experiment with reliable atomic data. The effects of the most important atomic processes on the charge state distribution are also discussed.
Van der Waals interactions and the limits of isolated atom models at interfaces
Kawai, Shigeki; Foster, Adam S.; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H.; Jung, Thomas A.; Meyer, Ernst
2016-05-01
Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar-Xe, Kr-Xe and Xe-Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal-organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems.
HYBRID ORBITALS OF CARBON ATOMS IN THE D6hC36 MOLECULE UNDER THE ROTATING ELLIPSOID MODEL
Institute of Scientific and Technical Information of China (English)
Tong Guo-ping
2000-01-01
The hybrid orbitals of carbon atoms in the D6h C36 molecule arestudied using two rotating ellipsoid models. The model 1 is 1.66R for theshort semi-axis and 2.34R for the long semi-axis, and the model 2 is 1.78R and 2.26R respectively, where R is the C-C bond length. By comparison,we think the model 2 to be more proper in revealing the electronic properties of the D6h C36 molecule. The component of s orbitals in the states hybridized for each of the atoms is much larger than C60, in which the sorbit component is 0.0380 and the porbit is 0.9620. The most component is 0.2098and the least is 0.0482 for model 1; the most is 0.1764 and the least is0.0656 for model 2.
MULTIPHOTON IONIZATION OF ATOMS
Mainfray, G.
1985-01-01
Multiphoton ionization of one-electron atoms, such as atomic hydrogen and alkaline atoms, is well understood and correctly described by rigorous theoretical models. The present paper will be devoted to collisionless multiphoton ionization of many-electron atoms as rare gases. It induces removal of several electrons and the production of multiply charged ions. Up to Xe5+ ions are produced in Xe atoms. Doubly charged ions can be produced, either by simultaneous excitation of two electrons, or b...
Mathematical model of isotope-selective laser excitation of long-lived levels of atoms
International Nuclear Information System (INIS)
Method of laser isotope separation base on monophoton selective excitation of long-lived states of atoms could be classified as a new one. Taking zinc and rubidium as an example it is shown that long-lived excited states of atoms could effectively chemically react with a number of molecules, whereas basic states of atoms react weakly. In contrast to AVLIS the method is based on the use of one wavelength. This method does not require collimation of flow of atoms and electric extraction. The method uses Doppler contour property. This property resides in that frequency tuning increasing simultaneously from all the isotopes excitation selectivity rises
Cantrell, John H., Jr.; Cantrell, Sean A.
2008-01-01
A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.
Adsorption of metal atoms at a buckled graphene grain boundary using model potentials
Energy Technology Data Exchange (ETDEWEB)
Helgee, Edit E.; Isacsson, Andreas [Department of Applied Physics, Chalmers University of Technology, SE-412 96, Göteborg (Sweden)
2016-01-15
Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable.
Generalized boson model and α-cluster states of 44Ti atomic nucleus
International Nuclear Information System (INIS)
At present some rotational bands for the 44Ti atomic nucleus with a sequence of spins and parities are discovered. For an analysis of these bands the generalized boson model U(6) direct X U(4) including the collective (quadrupole) degree of freedom and cluster (dipole) variable as well as an inter-relation of quadrupole and dipole degrees of freedom is used. Different collective bands of U(6) direct X SU(3) model reduction are considered as well. Parameter of SU(3) symmetrical Hamiltonian are equal to k=0.0016 MeV. (3/4k-k')=0.085 MeV. The U(4)contains U(3)-symmetry, caused by dipole clusterization of nucleons, describes bands of α-cluster states kπ=04+,02-, with theoretical parameters E0=-11 MeV, εp=0.1 MeV, β=0.15 MeV. An interaction of the cluster (dipole) degree with he quadrupole one allows to explain the band of parity, kπ=01-, beginning with E=6.22 MeV by values of parameters of kp=0, γ=6.2 MeV
Xia, Ke; Shen, Guang-Bin; Zhu, Xiao-Qing
2015-06-14
32 F420 coenzyme models with alkylation of the three different N atoms (N1, N3 and N10) in the core structure (XFH(-)) were designed and synthesized and the thermodynamic driving forces (defined in terms of the molar enthalpy changes or the standard redox potentials in this work) of the 32 XFH(-) releasing hydride ions, hydrogen atoms and electrons, the thermodynamic driving forces of the 32 XFH˙ releasing protons and hydrogen atoms and the thermodynamic driving forces of XF(-)˙ releasing electrons in acetonitrile were determined using titration calorimetry and electrochemical methods. The effects of the methyl group at N1, N3 and N10 and a negative charge on N1 and N10 atoms on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were examined; the results show that seating arrangements of the methyl group and the negative charge have remarkably different effects on the thermodynamic properties of the F420 coenzyme models and their related reaction intermediates. The effects of the substituents at C7 and C8 on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were also examined; the results show that the substituents at C7 and C8 have good Hammett linear free energy relationships with the six thermodynamic parameters. Meanwhile, a reasonable determination of possible reactions between members of the F420 family and NADH family in vivo was given according to a thermodynamic analysis platform constructed using the elementary step thermodynamic parameter of F420 coenzyme model 2FH(-) and NADH model MNAH releasing hydride ions in acetonitrile. The information disclosed in this work can not only fill a gap in the chemical thermodynamics of F420 coenzyme models as a class of very important organic sources of electrons, hydride ions, hydrogen atoms and protons, but also strongly promote the fast development of the chemistry and applications of F420 coenzyme.
The atom-surface interaction potential for He-NaCl: A model based on pairwise additivity
Hutson, Jeremy M.; Fowler, P. W.
1986-08-01
The recently developed semi-empirical model of Fowler and Hutson is applied to the He-NaCl atom-surface interaction potential. Ab initio self-consistent field calculations of the repulsive interactions between He atoms and in-crystal Cl - and Na + ions are performed. Dispersion coefficients involving in-crystal ions are also calculated. The atom-surface potential is constructed using a model based on pairwise additivity of atom-ion forces. With a small adjustment of the repulsive part, this potential gives good agreement with the experimental bound state energies obtained from selective adsorption resonances in low-energy atom scattering experiments. Close-coupling calculations of the resonant scattering are performed, and good agreement with the experimental peak positions and intensity patterns is obtained. It is concluded that there are no bound states deeper than those observed in the selective adsorption experiments, and that the well depth of the He-NaCl potential is 6.0 ± 0.2 meV.
Savall-Alemany, Francisco; Domènech-Blanco, Josep Lluís; Guisasola, Jenaro; Martínez-Torregrosa, Joaquín
2016-06-01
Our study sets out to identify the difficulties that high school students, teachers, and university students encounter when trying to explain atomic spectra. To do so, we identify the key concepts that any quantum model for the emission and absorption of electromagnetic radiation must include to account for the gas spectra and we then design two questionnaires, one for teachers and the other for students. By analyzing the responses, we conclude that (i) teachers lack a quantum model for the emission and absorption of electromagnetic radiation capable of explaining the spectra, (ii) teachers and students share the same difficulties, and (iii) these difficulties concern the model of the atom, the model of radiation, and the model of the interaction between them.
Surface structure of polymers and their model compounds observed by atomic force microscopy
Stocker, W.; Bickmann, B.; Magonov, S.N.; Cantow, H.-J.; Lotz, B.; Wittmann, J.-C.; Möller, M.
1992-01-01
Results of atomic force microscopy (AFM) of normal alkanes, polyethylene, isotactic polypropylene and of a diblock copolymer are presented. Various types of surfaces - naturally and epitaxially grown on different substrates - have been examined from hundreds of nanometers down to the atomic scale. S
Modeling and simulation of the atomization process in the ceramic tile industry
International Nuclear Information System (INIS)
The aim of the present work is to numerically simulate the behaviour of the drying system for several sets of operating conditions in order to improve and optimize this process. However, the mathematical modeling adopted here can be employed to simulate other systems such as the processes that occur in liquid-fueled engines with direct spray injection and ceramic spraying for hard surfacing. Then, mathematical and physical models were established to simulate the interaction of continuous and disperse phases in drying processes of ceramic slurries. Solving the set of governing coupled partial differential equations, it is possible to study the influence of drying air on the atomized droplets of alumina slurry, and vice-versa. The materials used as continuous and disperse phase, air and alumina slurry respectively, are representative since any kind of gas and slurry can be used if its thermodynamic and transport properties are known. Several experimental tests were carried out in a spray dryer in the 'Laboratorio de Insumos', at IPEN - Instituto de Pesquisas Energeticas e Nucleares for different sets of operating conditions: initial temperature of the drying air, the gas flow rate, the slurry feed rate and atomiser configuration among others. Measurements of the wet and the dry bulb temperatures were made in some experimental tests to allow the calculations of the air humidity. The dynamic pressure were also measured in order to determine the gas flow rate. Some samples of the material used in the tile industry and of the one produced at IPEN were analysed to determine: the morphology of the atomized material and the range of granules diameter through scanning electron microscopy; the amount of pores and the bulk density through porosimetry; the residual moisture of the material through thermogravimetry; and the granulometric distribution of granules and particles through laser diffraction. Important information about the process and the final material are given by
Savall-Alemany, Francisco; Domènech-Blanco, Josep Lluís; Guisasola, Jenaro; Martínez-Torregrosa, Joaquín
2016-01-01
Our study sets out to identify the difficulties that high school students, teachers, and university students encounter when trying to explain atomic spectra. To do so, we identify the key concepts that any quantum model for the emission and absorption of electromagnetic radiation must include to account for the gas spectra and we then design two…
Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom
Clark, Ted M.; Chamberlain, Julia M.
2014-01-01
An activity supporting the PhET interactive simulation, Models of the Hydrogen Atom, has been designed and used in the laboratory portion of a general chemistry course. This article describes the framework used to successfully accomplish implementation on a large scale. The activity guides students through a comparison and analysis of the six…
Aguiar, Joana G.; Correia, Paulo R. M.
2016-01-01
In this paper, we explore the use of concept maps (Cmaps) as instructional materials prepared by teachers, to foster the understanding of chemistry. We choose fireworks as a macroscopic event to teach basic chemical principles related to the Bohr atomic model and matter-energy interaction. During teachers' Cmap navigation, students can experience…
Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling.
Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki
2016-01-01
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. PMID:26645468
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
International Nuclear Information System (INIS)
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
Energy Technology Data Exchange (ETDEWEB)
Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl; Kolinski, Andrzej [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw (Poland); Co, Nguyen Truong [Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City (Viet Nam); Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City (Viet Nam); Nguyen, Phuong H. [Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan, E-mail: masli@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)
2015-04-14
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in
Gillen, D R; Goelich,
2002-01-01
Non-resonant multiphoton ionisation combined with quadrupole and time-of-flight analysis has been used to measure energy distributions of sputtered copper atoms. The sputtering of a polycrystalline copper target by 3.6 keV Ar sup + , N sup + and CF sub 2 sup + and 1.8 keV N sup + and CF sub 2 sup + ion bombardment at 45 deg. has been investigated. The linear collision model in the isotropic limit fails to describe the high energy tail of the energy distributions. However the TRIM.SP computer simulation has been shown to provide a good description. The results indicate that an accurate description of sputtering by low energy, molecular ions requires the use of computer simulation rather than analytical approaches. This is particularly important when considering plasma-surface interactions in plasma etching and deposition systems.
Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A
2016-06-24
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.
Near-atomic resolution structural model of the yeast 26S proteasome.
Beck, Florian; Unverdorben, Pia; Bohn, Stefan; Schweitzer, Andreas; Pfeifer, Günter; Sakata, Eri; Nickell, Stephan; Plitzko, Jürgen M; Villa, Elizabeth; Baumeister, Wolfgang; Förster, Friedrich
2012-09-11
The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.
Modeling of an atomizer for two fluids; Modelacion de un atomizador de dos fluidos
Energy Technology Data Exchange (ETDEWEB)
Tapia Ramirez, Zoili [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)
1998-09-01
The work reported in this article presents the results of the effort to improve the basic understanding of the flow structure that is formed in a two fluid sprayer before and after the interaction between the sprayed fluid and the spraying fluid. The images in the interior of the mixing chamber of the atomizer are shown, which were taken with a high velocity video camera. Also the results of the numerical simulation of the internal flow obtained by means of a package of commercial modeling are shown. [Espanol] El trabajo reportado en este articulo presenta los resultados del esfuerzo por mejorar el entendimiento basico de la estructura del flujo que se forma en un atomizador de dos fluidos antes y despues de la interaccion entre el fluido atomizado y el fluido atomizante. Se muestran imagenes del flujo en el interior de la camara de mezclado del atomizador, las cuales fueron tomadas con una camara de video de alta velocidad. Tambien se incluyen los resultados de la simulacion numerica del flujo interno obtenidas por medio de un paquete de modelacion comercial.
Offner, Stella S R; Viti, Serena; Bell, Thomas A
2013-01-01
We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C+, C, H2 and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric probl...
Energy Technology Data Exchange (ETDEWEB)
Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: stella.offner@yale.edu [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)
2013-06-10
We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.
Kinkhabwala, A; Sako, M; Gu, M F; Kahn, S M; Paerels, F B S
2003-01-01
We present a detailed model of the discrete X-ray spectroscopic features expected from steady-state, low-density photoionized plasmas. We apply the Flexible Atomic Code (FAC) to calculate all of the necessary atomic data for the full range of ions relevant for the X-ray regime. These calculations have been incorporated into a simple model of a cone of ions irradiated by a point source located at its tip (now available as the XSPEC model PHOTOION). For each ionic species in the cone, photoionization is balanced by recombination and ensuing radiative cascades, and photoexcitation of resonance transitions is balanced by radiative decay. This simple model is useful for diagnosing X-ray emission mechanisms, determining photoionization/photoexcitation/recombination rates, fitting temperatures and ionic emission measures, and probing geometrical properties (covering factor/column densities/radial filling factor/velocity distributions) of absorbing/reemitting regions in photoionized plasmas. Such plasmas have already...
Mossman, Maren; Engels, Peter; D'Incao, Jose; Jin, Deborah; Cornell, Eric
2016-05-01
Ultracold atomic gases at or near quantum degeneracy provide a powerful tool for the investigation of few-body physics. A particularly intriguing few-body phenomenon is the existence of Efimov trimer states at large interatomic scattering lengths. These trimers are predicted to exhibit universal geometric scaling relations, but in practice the situation is complicated e.g. by finite-range and finite-temperature effects. While some Efimov trimers have already been experimentally observed by several groups in ground-based experiments, NASA's Cold Atom Laboratory (CAL) onboard the ISS will greatly enhance the experimentally accessible regimes by providing ultracold clouds of 39 K atoms with temperatures at or below 1 nK, low densities, and long observation times. We present results of numerical modelling and simulations that lay out Efimov experiments capitalizing on the particular strengths of CAL.
Schöllnberger, H.; Kaiser, J. C.; Jacob, P.; Walsh, L
2012-01-01
The non-cancer mortality data for cerebrovascular disease (CVD) and cardiovascular diseases from Report 13 on the atomic bomb survivors published by the Radiation Effects Research Foundation were analysed to investigate the dose–response for the influence of radiation on these detrimental health effects. Various parametric and categorical models (such as linear-no-threshold (LNT) and a number of threshold and step models) were analysed with a statistical selection protocol that rated the mode...
Simulation of Ionic Populations in Hot Dense Plasmas via a New Method beyond the Average Atom Model
Institute of Scientific and Technical Information of China (English)
WANG Min-Sheng; LIU Ling-Tao; LI Jia-Ming
2005-01-01
@@ In theoretical simulations and analysis of diagnostic measurements for hot dense plasmas in the inertial confinementfusion researches, it is usually necessary to consider thousands of transition arrays between a huge number of ionic energy states. Average atom models are adopted for practical purposes. In order to calculate ionic populations of hot dense plasmas more accurately either in local thermodynamic equilibrium or in non-local thermodynamic equilibrium conditions, a simple method beyond the AA model is proposed.
Institute of Scientific and Technical Information of China (English)
Jiuzhou ZHAO; Dongming LIU; Hengqiang YE
2003-01-01
In order to understand the solidification process of an atomized droplet and predict the fraction solidification ofdroplets with flight distance during spray forming, a numerical model based on the population dynamics approach isdeveloped to describe the microstructure evolution under the common action of the nucleation and growth of grains.The model is coupled with droplets heat transfer controlling equations and solved for Al-4.5 wt pct Cu alloy. It isdemonstrated that the numerical results describe the solidification process well.
International Nuclear Information System (INIS)
We present a family of exactly-solvable models involving the interaction of an ensemble of coupled SU(2) or SU(1,1) systems with a single bosonic field. They arise from the trigonometric Richardson-Gaudin models by replacing one SU(2) or SU(1,1) degree of freedom by an ideal boson. A first application to a system of bosonic atoms and a molecule dimer is reported. (Author) 14 refs., 3 figs
Energy Technology Data Exchange (ETDEWEB)
Pittel, S. [Bartol Research Institute, University of Delaware, Newark, Delaware 19716 (United States); Dukelsky, J. [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas, Serrano 123, 28006 Madrid (Spain); Dussel, G.G. [Departamento de Fisica Juan Jose Giambiagi, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina)
2004-12-01
We present a family of exactly-solvable models involving the interaction of an ensemble of coupled SU(2) or SU(1,1) systems with a single bosonic field. They arise from the trigonometric Richardson-Gaudin models by replacing one SU(2) or SU(1,1) degree of freedom by an ideal boson. A first application to a system of bosonic atoms and a molecule dimer is reported. (Author) 14 refs., 3 figs.
Beswick, Benjamin T; Gardiner, Simon A; Hughes, Ifan G; Andersen, Mikkel F; Daszuta, Boris
2016-01-01
Atom interferometers are a useful tool for precision measurements of fundamental physical phenomena, ranging from local gravitational field strength to the atomic fine structure constant. In such experiments, it is desirable to implement a high momentum transfer "beam-splitter," which may be achieved by inducing quantum resonance in a finite-temperature laser-driven atomic gas. We use Monte Carlo simulations to investigate these quantum resonances in the regime where the gas receives laser pulses of finite duration, and demonstrate that an $\\epsilon$-classical model for the dynamics of the gas atoms is capable of reproducing quantum resonant behavior for both zero-temperature and finite-temperature non-interacting gases. We show that this model agrees well with the fully quantum treatment of the system over a time-scale set by the choice of experimental parameters. We also show that this model is capable of correctly treating the time-reversal mechanism necessary for implementing an interferometer with this p...
Churkin, Yu V; Klimchitskaya, G L; Yurova, V A
2010-01-01
The van der Waals and Casimir-Polder interaction of different atoms with graphene is investigated using the Dirac model which assumes that the energy of quasiparticles is linear with respect to the momentum. The obtained results for the van der Waals coefficients of hydrogen atoms and molecules and atoms of metastable He${}^{\\ast}$ and Na as a function of separation are compared with respective results found using the hydrodynamic model of graphene. It is shown that, regardless of the value of the gap parameter, the Dirac model leads to much smaller values of the van der Waals coefficients than the hydrodynamic model. The experiment on quantum reflection of metastable He${}^{\\ast}$ and Na atoms on graphene is proposed which is capable to discriminate between the two models of the electronic structure of graphene. In this respect the parameters of the phenomenological potential for both these atoms interacting with graphene described by different models are determined.
Model of a realistic InP surface quantum dot extrapolated from atomic force microscopy results.
Barettin, Daniele; De Angelis, Roberta; Prosposito, Paolo; Auf der Maur, Matthias; Casalboni, Mauro; Pecchia, Alessandro
2014-05-16
We report on numerical simulations of a zincblende InP surface quantum dot (QD) on In₀.₄₈Ga₀.₅₂ buffer. Our model is strictly based on experimental structures, since we extrapolated a three-dimensional dot directly by atomic force microscopy results. Continuum electromechanical, [Formula: see text] bandstructure and optical calculations are presented for this realistic structure, together with benchmark calculations for a lens-shape QD with the same radius and height of the extrapolated dot. Interesting similarities and differences are shown by comparing the results obtained with the two different structures, leading to the conclusion that the use of a more realistic structure can provide significant improvements in the modeling of QDs fact, the remarkable splitting for the electron p-like levels of the extrapolated dot seems to prove that a realistic experimental structure can reproduce the right symmetry and a correct splitting usually given by atomistic calculations even within the multiband [Formula: see text] approach. Moreover, the energy levels and the symmetry of the holes are strongly dependent on the shape of the dot. In particular, as far as we know, their wave function symmetries do not seem to resemble to any results previously obtained with simulations of zincblende ideal structures, such as lenses or truncated pyramids. The magnitude of the oscillator strengths is also strongly dependent on the shape of the dot, showing a lower intensity for the extrapolated dot, especially for the transition between the electrons and holes ground state, as a result of a relevant reduction of the wave functions overlap. We also compare an experimental photoluminescence spectrum measured on an homogeneous sample containing about 60 dots with a numerical ensemble average derived from single dot calculations. The broader energy range of the numerical spectrum motivated us to perform further verifications, which have clarified some aspects of the experimental
Model of a realistic InP surface quantum dot extrapolated from atomic force microscopy results
International Nuclear Information System (INIS)
We report on numerical simulations of a zincblende InP surface quantum dot (QD) on In0.48Ga0.52P buffer. Our model is strictly based on experimental structures, since we extrapolated a three-dimensional dot directly by atomic force microscopy results. Continuum electromechanical, k-vector ⋅ p-vector bandstructure and optical calculations are presented for this realistic structure, together with benchmark calculations for a lens-shape QD with the same radius and height of the extrapolated dot. Interesting similarities and differences are shown by comparing the results obtained with the two different structures, leading to the conclusion that the use of a more realistic structure can provide significant improvements in the modeling of QDs fact, the remarkable splitting for the electron p-like levels of the extrapolated dot seems to prove that a realistic experimental structure can reproduce the right symmetry and a correct splitting usually given by atomistic calculations even within the multiband k-vector ⋅ p-vector approach. Moreover, the energy levels and the symmetry of the holes are strongly dependent on the shape of the dot. In particular, as far as we know, their wave function symmetries do not seem to resemble to any results previously obtained with simulations of zincblende ideal structures, such as lenses or truncated pyramids. The magnitude of the oscillator strengths is also strongly dependent on the shape of the dot, showing a lower intensity for the extrapolated dot, especially for the transition between the electrons and holes ground state, as a result of a relevant reduction of the wave functions overlap. We also compare an experimental photoluminescence spectrum measured on an homogeneous sample containing about 60 dots with a numerical ensemble average derived from single dot calculations. The broader energy range of the numerical spectrum motivated us to perform further verifications, which have clarified some aspects of the experimental
3D modeling of magnetic atom traps on type-II superconductor chips
International Nuclear Information System (INIS)
Magnetic traps for cold atoms have become a powerful tool in cold atom physics and condensed matter research. The traps on superconducting chips allow one to increase the trapped atom lifetime and coherence time by decreasing the thermal noise by several orders of magnitude compared to that of the typical normal-metal conductors. A thin superconducting film in the mixed state is, usually, the main element of such a chip. Using a finite element method to analyze thin film magnetization and transport current in type-II superconductivity, we study magnetic traps recently employed in experiments. The proposed approach allows us to predict important characteristics of the magnetic traps (their depth, shape, distance from the chip surface, etc) that are necessary when designing magnetic traps in cold atom experiments. (paper)
Directory of Open Access Journals (Sweden)
Qing-Sheng Yang
2014-01-01
Full Text Available This investigation focuses on the design of functionalization configuration at the atomic level to determine the influence of atomic structure on the mechanical properties of functionalized carbon nanotubes (F-CNTs and their composites. Tension and compressive buckling behaviors of different configurations of CNTs functionalized by H atoms are studied by a molecular dynamics (MD method. It is shown that H-atom functionalization reduces Young’s modulus of CNTs, but Young’s modulus is not sensitive to the functionalization configuration. The configuration does, however, affect the tensile strength and critical buckling stress of CNTs. Further, the stress-strain relations of composites reinforced by nonfunctionalized and various functionalized CNTs are analyzed.
International Nuclear Information System (INIS)
The use of an atomic force microscope for studying molecular dynamics through dielectric spectroscopy with spatial resolution in the nanometer scale is a recently developed approach. However, difficulties in the quantitative connection of the obtained data and the material dielectric properties, namely, frequency dependent dielectric permittivity, have limited its application. In this work, we develop a simple electrical model based on physically meaningful parameters to connect the atomic force microscopy (AFM) based dielectric spectroscopy experimental results with the material dielectric properties. We have tested the accuracy of the model and analyzed the relevance of the forces arising from the electrical interaction with the AFM probe cantilever. In this way, by using this model, it is now possible to obtain quantitative information of the local dielectric material properties in a broad frequency range. Furthermore, it is also possible to determine the experimental setup providing the best sensitivity in the detected signal
An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.
Förster, Friedrich; Lasker, Keren; Beck, Florian; Nickell, Stephan; Sali, Andrej; Baumeister, Wolfgang
2009-10-16
The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) is in excellent agreement with the recently identified base-precursor complexes formed during the assembly of the RP. Furthermore, the atomic CP-AAA-ATPase model suggests that the assembly chaperone Nas6 facilitates CP-RP association by enhancing the shape complementarity between Rpt3 and its binding CP alpha subunits partners.
An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome
Energy Technology Data Exchange (ETDEWEB)
Foerster, Friedrich [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany); Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Lasker, Keren [Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv (Israel); Beck, Florian; Nickell, Stephan [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany); Sali, Andrej [Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Baumeister, Wolfgang, E-mail: baumeist@biochem.mpg.de [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany)
2009-10-16
The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) is in excellent agreement with the recently identified base-precursor complexes formed during the assembly of the RP. Furthermore, the atomic CP-AAA-ATPase model suggests that the assembly chaperone Nas6 facilitates CP-RP association by enhancing the shape complementarity between Rpt3 and its binding CP alpha subunits partners.
Energy Technology Data Exchange (ETDEWEB)
Roy, Kunal, E-mail: kunalroy_in@yahoo.com [Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700 032 (India); Das, Rudra Narayan [Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700 032 (India)
2010-11-15
Aldehydes are a toxic class of chemicals causing severe health hazards. In this background, quantitative structure-toxicity relationship (QSTR) models have been developed in the present study using Extended Topochemical Atom (ETA) indices for a large group of 77 aromatic aldehydes for their acute toxicity against the protozoan ciliate Tetrahymena pyriformis. The ETA models have been compared with those developed using various non-ETA topological indices. Attempt was also made to include the n-octanol/water partition coefficient (log K{sub o/w}) as an additional descriptor considering the importance of hydrophobicity in toxicity prediction. Thirty different models were developed using different chemometric tools. All the models have been validated using internal validation and external validation techniques. The statistical quality of the ETA models was found to be comparable to that of the non-ETA models. The ETA models have shown the important effects of steric bulk, lipophilicity, presence of electronegative atom containing substituents and functionality of the aldehydic oxygen to the toxicity of the aldehydes. The best ETA model (without using log K{sub o/w}) shows encouraging statistical quality (Q{sub int}{sup 2}=0.709,Q{sub ext}{sup 2}=0.744). It is interesting to note that some of the topological models reported here are better in statistical quality than previously reported models using quantum chemical descriptors.
Pan, Jianjun; Khadka, Nawal K
2016-05-26
Quantitative characterization of membrane defects (pores) is important for elucidating the molecular basis of many membrane-active peptides. We study kinetic defects induced by melittin in vesicular and planar lipid bilayers. Fluorescence spectroscopy measurements indicate that melittin induces time-dependent calcein leakage. Solution atomic force microscopy (AFM) is used to visualize melittin-induced membrane defects. After initial equilibration, the most probable defect radius is ∼3.8 nm in 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) bilayers. Unexpectedly, defects become larger with longer incubation, accompanied by substantial shape transformation. The initial defect radius is ∼4.7 nm in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. Addition of 30 mol % cholesterol to DOPC bilayers suppresses defect kinetics, although the inhibitory impact is negated by longer incubation. Overall, the kinetic rate of defect development follows DLPC > DOPC > DOPC/cholesterol. Kinetic defects are also observed when anionic lipids are present. Based on the observation that defects can occupy as large as 40% of the bilayer surface, we propose a kinetic defect growth model. We also study the effect of melittin on the phase behavior of DOPC/egg-sphingomyelin/cholesterol bilayers. We find that melittin initially suppresses or eliminates liquid-ordered (Lo) domains; Lo domains gradually emerge and become the dominant species with longer incubation; and defects in phase-coexisting bilayers have a most probable radius of ∼5 nm and are exclusively localized in the liquid-disordered (Ld) phase. Our experimental data highlight that melittin-induced membrane defects are not static; conversely, spontaneous defect growth is intrinsically associated with membrane permeabilization exerted by melittin. PMID:27167473
Arafat, A Syed Yasir; Arun, A; Ilamathi, M; Asha, J; Sivashankari, P R; D'Souza, Cletus J M; Sivaramakrishnan, V; Dhananjaya, B L
2014-03-01
5' Nucleotidase (5' NUC) is a ubiquitously distributed enzyme known to be present in snake venoms (SV) that is responsible primarily for causing dysregulation of physiological homeostasis in humans by inducing anticoagulant effects and by inhibiting platelet aggregation. It is also known to act synergistically with other toxins to exert a more pronounced anti-coagulant effect during envenomation. Its structural and functional role is not yet ascertained clearly. The 3D structure of snake venom 5' nucleotidase (SV-5' NUC) is not yet known and was predicted by us for the first time using a comparative homology modeling approach using Demansia vestigiata protein sequence. The accuracy and stability of the predicted SV-5' NUC structure were validated using several computational approaches. Key interactions of SV-5' NUC were studied using experimental studies/molecular docking analysis of the inhibitors vanillin, vanillic acid and maltol. All these inhibitors were found to dock favorably following pharmacologically relevant absorption, distribution, metabolism and excretion (ADME) profiles. Further, atomic level docking interaction studies using inhibitors of the SV-5' NUC active site revealed amino acid residues Y65 and T72 as important for inhibitor-(SV-5' NUC) interactions. Our in silico analysis is in good agreement with experimental inhibition results of SV-5' NUC with vanillin, vanillic acid and maltol. The present study should therefore play a guiding role in the experimental design of new SV-5' NUC inhibitors for snake bite management. We also identified a few pharmacophoric features essential for SV-5' NUC inhibitory activity that can be utilized further for the discovery of putative anti-venom agents of therapeutic value for snake bite management.
Habchi, Chawki; Bohbot, Julien; Schmid, Andreas; Herrmann, Kai
2015-12-01
In this paper, a comprehensive two-fluid model is suggested in order to compute the in-nozzle cavitating flow and the primary atomization of liquid jets, simultaneously. This model has been applied to the computation of a typical large marine Diesel injector. The numerical results have shown a strong correlation between the in-nozzle cavitating flow and the ensuing spray orientation and atomization. Indeed, the results have confirmed the existence of an off-axis liquid core. This asymmetry is likely to be at the origin of the spray deviation observed experimentally. In addition, the primary atomization begins very close to the orifice exit as in the experiments, and the smallest droplets are generated due to cavitation pocket shape oscillations located at the same side, inside the orifice.
Hasan, Hashima (Technical Monitor); Kirby, K.; Babb, J.; Yoshino, K.
2005-01-01
We report on progress made in a joint program of theoretical and experimental research to study the line-broadening of alkali atom resonance lines due to collisions with species such as helium and molecular hydrogen. Accurate knowledge of the line profiles of Na and K as a function of temperature and pressure will allow such lines to serve as valuable diagnostics of the atmospheres of brown dwarfs and extra-solar giant planets. A new experimental apparatus has been designed, built and tested over the past year, and we are poised to begin collecting data on the first system of interest, the potassium resonance lines perturbed by collisions with helium. On the theoretical front, calculations of line-broadening due to sodium collisions with helium are nearly complete, using accurate molecular potential energy curves and transition moments just recently computed for this system. In addition we have completed calculations of the three relevant potential energy curves and associated transition moments for K - He, using the MOLPRO quantum chemistry codes. Currently, calculations of the potential surfaces describing K-H2 are in progress.
Modeling and Estimation of Stationary and Non-stationary Noises of Rubidium Atomic Clock
Directory of Open Access Journals (Sweden)
Deepak Mishra,
2014-07-01
Full Text Available Noise estimation of atomic clock is one of the important research areas in the field of atomic clock development and application. Most of the atomic clocks are having random-stochastic noises and periodic noises due to temperature variation. Random-stochastic noises have a well identified signature in time domain but periodic noises are difficult to analyze in time domain. However, in this paper, an effort is made to identify and analyze the deterministic trends of both random-stochastic noises and periodic noises due to variation in temperature using an alternate approach of least-squares normalized-error (LSNE regression algorithm. A MATLAB based application with graphical user interface (GUI is developed to estimate and analyze random-stochastic noises and periodic noises and re-estimate the stability of rubidium atomic clock after removing these noises from the raw phase data. The estimation of stationary noises are done using Allan variance from time domain data and noise profile is calculated using curve fit method. The estimation of periodic noises due to temperature variation is carried in frequency domain through spurious analysis of the frequency data of atomic clock.
International Nuclear Information System (INIS)
Describing the quantum dynamics in strong time-dependent external fields is challenging for at least two reasons. Firstly, the external driver has to be treated in a non-perturbative way. Secondly, correlations, responsible for phenomena such as single-photon double ionization, nonsequential double ionization, autoionization, Auger decay etc., have to be taken into account. The ab initio solution of the time-dependent Schroedinger equation for a many-body system is feasible for only a few constituents. Density functional theory (DFT) has been successful in overcoming the exponentially increasing complexity of solving the stationary Schroedinger equation in electronic structure applications. Its time-dependent extension (TDDFT) is widely applied within the linear response domain. However, its success when it comes to highly correlated electron dynamics in, for instance, strong laser fields, is very limited, reasons being the lack of a sufficiently accurate exchange-correlation potential in the Kohn-Sham equation and functionals for the relevant observables. Numerically exactly solvable model systems are hence very useful to proceed with the further development of TDDFT. In this thesis, the exact exchange-correlation potential for the highly correlated process of autoionization in a model Helium atom is constructed. Besides applying a suitable many-body technique one may try to employ the time-periodicity of external drivers such as laser fields. The Floquet theorem allows to rewrite partial differential equations with timeperiodic coefficients as sets of time-independent algebraic equations. If the Floquet theorem could also be applied to the time-dependent Kohn-Sham equation of TDDFT the time-dependent many-body problem could be reduced to a time-independent one. In this thesis, it is investigated under which circumstances this is possible. To that end a method is introduced to extract the information about light-induced states (Floquet states) and their
Quantum-Shell Corrections to the Finite-Temperature Thomas-Fermi-Dirac Statistical Model of the Atom
Energy Technology Data Exchange (ETDEWEB)
Ritchie, A B
2003-07-22
Quantum-shell corrections are made directly to the finite-temperature Thomas-Fermi-Dirac statistical model of the atom by a partition of the electronic density into bound and free components. The bound component is calculated using analytic basis functions whose parameters are chosen to minimize the energy. Poisson's equation is solved for the modified density, thereby avoiding the need to solve Schroedinger's equation for a self-consistent field. The shock Hugoniot is calculated for aluminum: shell effects characteristic of quantum self-consistent field models are fully captures by the present model.
Energy Technology Data Exchange (ETDEWEB)
Margulis, Vl.A. [Department of Physics, N.P. Ogarev Mordovian State University, Saransk 430000 (Russian Federation)]. E-mail: 612033@inbox.ru; Muryumin, E.E. [Department of Chemistry, N.P. Ogarev Mordovian State University, Saransk 430000 (Russian Federation)
2007-03-01
We report a model calculation of the chemisorption energies {delta}E{sub ads} of single fluorine atoms on the outer surface of zigzag single-walled carbon nanotubes (Z-SWCNTs) (p,0) with p ranging from 11 to 21. A simplified model based on an effective-mass theory is adopted to describe the electronic structure of the nanotubes. Chemisorption is treated within the Anderson-Newns approach, which takes account of Coulomb interaction between adsorbate electrons. Considering adsorption of an adatom directly on top of a surface carbon atom, we find that in the case of a fluorine atom bonded to the sidewall of the nanotubes, the absolute values of {delta}E{sub ads} are in the range 4.3-5.5eV for Z-SWCNTs with typical diameters of 0.86-1.66nm, larger {delta}E{sub ads} values being associated with semiconducting tubes. For the latter ones, {delta}E{sub ads} decreases rather significantly as the radius R of the tubes increases, tending towards the ''infinite'' radius graphene case, whereas for metallic tubes {delta}E{sub ads} slightly increases with increasing R. The localized acceptor states induced by a fluorine atom in the band gap of the semiconducting tubes are found to be responsible for such difference in the behaviour of {delta}E{sub ads} for the two above-mentioned types of tubes. The results obtained shed light on the possible mechanism of the atomic fluorine adsorption-induced hole-doping of the semiconducting tubes, which might significantly affect the transport properties of these tubes.
The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies
Hawelek, L.; Brodka, A.; Dore, J. C.; Honkimaki, V.; Burian, A.
2013-11-01
The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp3 defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.
Institute of Scientific and Technical Information of China (English)
2007-01-01
Using the numerical solution of the time-dependent Schr(o)dinger equation of a one-dimensional model atom in a two-colour laser field, we have investigated the effects of the potential models on coherent control of atomic multiphoton ionization. It is found that the photoelectron spectra are obviously different for the long-range (Coulomb-like) and short-range (with no excited bound states) potential model atoms, which are produced by two-colour coherent control of atomic multiphoton ionization in a few laser cycles. Our results indicate that two-colour coherent control of atomic multiphoton ionization can be observed in simulations, depending on the choice of the model potentials.
The Holographic Nature of Bohr Atomic Model%波尔原子模型及其全息性
Institute of Scientific and Technical Information of China (English)
赵丽特; 王喜建; 周党培
2016-01-01
This paper shows the holographic nature of the micro world and the macro world in physics by comparing the Bohr atomic model and the movement of the planets in the solar system.%文章通过波尔原子模型和太阳系中行星运动的对比，展现物理学中微观世界和宏观世界的全息性。
Paul, Saurabh; Johnson, P. R.; Tiesinga, Eite
2016-04-01
We show that, for ultracold neutral bosonic atoms held in a three-dimensional periodic potential or optical lattice, a Hubbard model with dominant, attractive three-body interactions can be generated. In fact, we derive that the effect of pairwise interactions can be made small or zero starting from the realization that collisions occur at the zero-point energy of an optical lattice site and the strength of the interactions is energy dependent from effective-range contributions. We determine the strength of the two- and three-body interactions for scattering from van der Waals potentials and near Fano-Feshbach resonances. For van der Waals potentials, which for example describe scattering of alkaline-earth atoms, we find that the pairwise interaction can only be turned off for species with a small negative scattering length, leaving the 88Sr isotope a possible candidate. Interestingly, for collisional magnetic Feshbach resonances this restriction does not apply and there often exist magnetic fields where the two-body interaction is small. We illustrate this result for several known narrow resonances between alkali-metal atoms as well as chromium atoms. Finally, we compare the size of the three-body interaction with hopping rates and describe limits due to three-body recombination.
The atomic parameter model for the fifth and sixth transition metal quasicrystal alloys (Mc=0.5)
Institute of Scientific and Technical Information of China (English)
LIAO ShuZhi; GUI XuChun; ZHANG Chun; PENG HaoJun; XIE HaoWen; OUYANG YiFang; ZHANG BangWei
2009-01-01
The forming ability of quasicrystal phase has a relationship with the atomic bond factors based on differences in atom size and electron factors.Usually,those factors or their combination are used to describe the forming ability,stability of alloys,etc.In this paper,the quasicrystal alloy forming abilities for the fifth and sixth transition metals (Y,Zr,Nb,Mo,Ru,Rh,Pd and La,Hf,Ta,W,Re,Os,Ir,Pt) based alloys have been studied by the size factor and the atomic parametric function.It has been found that an ellipse curve can be used to separate the quasicrystal formed area from the informed area in the size factor and atomic parameters functional graph.The ellipse curve can be defined by an equation(x-m)2/c2+(y-n)2/d2=1.The overall reliabilities for the model are up to 97.4% and 95.5% for the fifth and the sixth transition metals based quasicrystal alloys,respectively.Also,the ellipse parameters m,n,c and d can be paraphrased by some appropriate parameters for each host metal.
The atomic parameter model for the fifth and sixth transition metal quasicrystal alloys(Mc=0.5)
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
The forming ability of quasicrystal phase has a relationship with the atomic bond factors based on differences in atom size and electron factors.Usually,those factors or their combination are used to describe the forming ability,stability of alloys,etc.In this paper,the quasicrystal alloy forming abilities for the fifth and sixth transition metals(Y,Zr,Nb,Mo,Ru,Rh,Pd and La,Hf,Ta,W,Re,Os,Ir,Pt) based alloys have been studied by the size factor and the atomic parametric function.It has been found that an ellipse curve can be used to separate the quasicrystal formed area from the informed area in the size factor and atomic parameters functional graph.The ellipse curve can be defined by an equation(x-m)2/c2+(y?n)2/d2=1.The overall reliabilities for the model are up to 97.4% and 95.5% for the fifth and the sixth transition metals based quasicrystal alloys,respectively.Also,the ellipse parameters m,n,c and d can be paraphrased by some appropriate parameters for each host metal.
Sattonnay, G; Tétot, R
2014-02-01
Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd2Ti2O7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd2Zr2O7. Therefore, the defect stability in A2B2O7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd2Ti2O7 amorphization induced by irradiation.
Fredrickson, Kurt D.; McDaniel, Martin D.; Slepko, Alex; Ekerdt, John G.; Demkov, Alexander A.
2016-08-01
First-principle calculations are used to model the adsorption and hydration of strontium bis(cyclopentadienyl) [Sr(Cp)2] on TiO2-terminated strontium titanate, SrTiO3 (STO), for the deposition of strontium oxide, SrO, by atomic layer deposition (ALD). The Sr(Cp)2 precursor is shown to adsorb on the TiO2-terminated surface, with the Sr atom assuming essentially the bulk position in STO. The C-Sr bonds are weaker than in the free molecule, with a Ti atom at the surface bonding to one of the C atoms in the cyclopentadienyl rings. The surface does not need to be hydrogenated for precursor adsorption. The calculations are compared with experimental observations for a related Sr cyclopentadienyl precursor, strontium bis(triisopropylcyclopentadienyl) [Sr(iPr3Cp)2], adsorbed on TiO2-terminated STO. High-resolution x-ray photoelectron spectroscopy and low-energy ion scattering spectroscopy show adsorption of the Sr precursor on the TiO2-terminated STO after a single precursor dose. This study suggests that ALD growth from the strontium precursors featuring cyclopentadienyl ligands, such as Sr(Cp)2, may initiate film growth on non-hydroxylated surfaces.
Atomic model of anti-phase boundaries in a face-centred icosahedral Zn-Mg-Dy quasicrystal
Wang Jian Bo; Wang Ren Hui
2003-01-01
An atomic model in the physical space for an anti-phase boundary (APB) in the ordered face-centred icosahedral Zn-Mg-Dy quasicrystal phase is presented, based on a six-dimensional model suggested by Ishimasa and Shimizu (2000 Mater. Sci. Eng. A 294-296 232, Ishimasa 2001 private communication). The physical space atomic positions of the defected structure were used for the calculation of the corresponding exit-plane wavefunction and high-resolution transmission electron microscopy images. The analysis of the defect by inverse Fourier transformation reveals that when superstructure reflection spots are used for back-transformation, then at the APB, bright lattice fringes are found to turn into dark ones, and vice versa. When fundamental reflections are used, the APB is not visible. This phenomenon is the same as the corresponding experimental study recently published by Heggen et al(2001a Phys. Rev. B 64 014202). Based on this atomic model it is found that the APB perpendicular to a fivefold axis A5 (APB-A5) i...
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
A scheme is proposed to simulate the Ising model and preserve the maximum entangled states (Bell states) in cavity quantum electrodynamics (QED) driven by a classical field with large detuning. In the strong driving and large-detuning regime, the effective Hamiltonian of the system is the same as the standard Ising model, and the scheme can also make the initial four Bell states of two atoms at the maximum entanglement all the time. So it is a simple memory for the maximal entangled states. The system is insensitive to the cavity decay and the thermal field and more immune to decoherence. These advantages can warrant the experimental feasibility of the current scheme. Furthermore, the genuine four-atom entanglement may be acquired via two Bell states through one-step implementation on four two-level atoms in the strong-driven model, and when two Greenberger-Horne-Zeilinger (GHZ) states are prepared in our scheme, the entangled cluster state may be acquired easily. The success probability for the scheme is 1.
ATOM-PROBE RESULTS SUPPORT THE SKELETON MODEL FOR WC-Co
Henjered, A.; Hellsing, M.; Andrén, H.; Nordén, H.
1984-01-01
WC/WC boundaries in WC-Co type cemented carbides have been analysed with the atom-probe instrument. The boundaries contained about half a monolayer of cobalt (or Co + Cr) and can therefore be described as grain boundaries with cobalt segregation. The results support the "continuous skeleton" mode1 of WC-Co.
A Computer-Controlled Classroom Model of an Atomic Force Microscope
Engstrom, Tyler A.; Johnson, Matthew M.; Eklund, Peter C.; Russin, Timothy J.
2015-01-01
The concept of "seeing by feeling" as a way to circumvent limitations on sight is universal on the macroscopic scale--reading Braille, feeling one's way around a dark room, etc. The development of the atomic force microscope (AFM) in 1986 extended this concept to imaging in the nanoscale. While there are classroom demonstrations that use…
Characterization and modeling of atomic layer deposited high-density trench capacitors in silicon
Matters-Kammerer, M.K.; Jinesh, K.B.; Rijks, T.G.S.M.; Roozeboom, F.; Klootwijk, J.H.
2012-01-01
A detailed electrical analysis of multiple layer trench capacitors fabricated in silicon with atomic-layer-deposited Al 2O 3 and TiN is presented. It is shown that in situ ozone annealing of the Al 2O 3 layers prior to the TiN electrode deposition significantly improves the electric properties of th
A data base in atomic physics: ficato-ficspi, used in the collisional - radiative model Lasix
International Nuclear Information System (INIS)
This report describes the atomic structure of ions that are studied in the kinetic code LASIX, and the various processes that act in and between them, and then compares the various formulations with special attention to neon-like ions, selenium in particular
Entanglement and the Jaynes-Cummings model with Rydberg-dressed atoms
Biedermann, Grant
2016-05-01
Controlling quantum entanglement between parts of a many-body system is the key to unlocking the power of quantum information processing for applications such as quantum computation, high-precision sensing, and simulation of many-body physics. Spin degrees of freedom of ultracold neutral atoms in their ground electronic state provide a natural platform given their long coherence times and our ability to control them with magneto-optical fields, but creating strong coherent coupling between spins has been challenging. We demonstrate for the first time a strong and tunable Rydberg-dressed interaction between spins of individually trapped cesium atoms with energy shifts of order 1 MHz in units of Planck's constant. We spectroscopically demonstrate that this system is isomorphic to a Jaynes-Cummings Hamiltonian, and observe the √{ N} nonlinearity of the Jaynes-Cummings ladder with a single symmetric Rydberg excitation. This interaction enables a ground-state spin-flip blockade, whereby simultaneous hyperfine spin flips of two atoms are blockaded due to their mutual interaction. We employ this spin-flip blockade to rapidly produce single-step Bell-state entanglement between atoms. This work was supported by the Laboratory Directed Research and Development program at Sandia National Laboratories and through the National Science Foundation's Center for Quantum Information and Control NSF-1212445.
Collective electronic pulsation of compressed atoms in Thomas-Fermi model
Ludwig, Hendrik; Xue, She-Sheng
2014-01-01
Based on the Thomas-Fermi solution for compressed atoms, we study electric pulsations of electron number-density, pressure and electric fields, which can be caused by an external perturbations acting on the atom. We numerically obtain the eigen-frequencies and eigen-functions for stationary pulsation modes that fulfill the boundary-value problem established by electron-number and energy-momentum conservation, equation of state, laws of thermodynamics, and Maxwell's equations, as well as physical boundary conditions. The lowest-lying eigen-frequency is about a few $\\rm{keV}$ depending on the atomic number $Z$ and the radius of the compressed atoms. In addition, assuming all electrons compressed to the nuclear core, which can be of either microscopic or macroscopic dimension, we obtain an analytical solution. For large Z the lowest-lying eigen-frequency of this solution $\\omega_1\\approx2\\alpha^{1/2} \\langle {\\bar n}_e\\rangle^{1/3}\\approx 2.1\\, {\\rm MeV}$, when the average electron-density $\\langle {\\bar n}_e\\ra...
Bencs, László; Laczai, Nikoletta; Ajtony, Zsolt
2015-07-01
A combination of former convective-diffusive vapor-transport models is described to extend the calculation scheme for sensitivity (characteristic mass - m0) in graphite furnace atomic absorption spectrometry (GFAAS). This approach encompasses the influence of forced convection of the internal furnace gas (mini-flow) combined with concentration diffusion of the analyte atoms on the residence time in a spatially isothermal furnace, i.e., the standard design of the transversely heated graphite atomizer (THGA). A couple of relationships for the diffusional and convectional residence times were studied and compared, including in factors accounting for the effects of the sample/platform dimension and the dosing hole. These model approaches were subsequently applied for the particular cases of Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sn, V and Zn analytes. For the verification of the accuracy of the calculations, the experimental m0 values were determined with the application of a standard THGA furnace, operating either under stopped, or mini-flow (50 cm3 min- 1) of the internal sheath gas during atomization. The theoretical and experimental ratios of m0(mini-flow)-to-m0(stop-flow) were closely similar for each study analyte. Likewise, the calculated m0 data gave a fairly good agreement with the corresponding experimental m0 values for stopped and mini-flow conditions, i.e., it ranged between 0.62 and 1.8 with an average of 1.05 ± 0.27. This indicates the usability of the current model calculations for checking the operation of a given GFAAS instrument and the applied methodology.
Pollak, Eli
2016-07-21
This year we celebrate the 80th anniversary of the Landau-Teller model for energy exchange in a collinear collision of an atom with a harmonic diatomic molecule. Even after 80 years though, the analytic theory to date has not included in it the back-influence of the oscillator's motion on the energy transfer between the approaching particle and the molecule. This is the topic of the present paper. The back-influence can be obtained by employing classical second-order perturbation theory. The second-order theory is used in both a classical and semiclassical context. Classically, analytic expressions are derived for the final phase and action of the diatom, after the collision. The energy loss of the atom is shown to decrease linearly with the increasing energy of the oscillator. The magnitude of this decrease is a direct consequence of the back-reaction of the oscillator on the translational motion. The qualitative result is universal, in the sense that it is not dependent on the details of the interaction of the atom with the oscillator. A numerical application to a model collision of an Ar atom with a Br2 diatom demonstrates the importance and accuracy of the second-order perturbation theory. The same results are then used to derive a second-order perturbation theory semiclassical expression for the quantum transition probability from initial vibrational state ni to final vibrational state nf of the oscillator. A comparison of the theory with exact quantum data is presented for a model collision of Br2 with a hydrogen molecule, where the hydrogen molecule is considered as a single approaching particle.
Pollak, Eli
2016-07-21
This year we celebrate the 80th anniversary of the Landau-Teller model for energy exchange in a collinear collision of an atom with a harmonic diatomic molecule. Even after 80 years though, the analytic theory to date has not included in it the back-influence of the oscillator's motion on the energy transfer between the approaching particle and the molecule. This is the topic of the present paper. The back-influence can be obtained by employing classical second-order perturbation theory. The second-order theory is used in both a classical and semiclassical context. Classically, analytic expressions are derived for the final phase and action of the diatom, after the collision. The energy loss of the atom is shown to decrease linearly with the increasing energy of the oscillator. The magnitude of this decrease is a direct consequence of the back-reaction of the oscillator on the translational motion. The qualitative result is universal, in the sense that it is not dependent on the details of the interaction of the atom with the oscillator. A numerical application to a model collision of an Ar atom with a Br2 diatom demonstrates the importance and accuracy of the second-order perturbation theory. The same results are then used to derive a second-order perturbation theory semiclassical expression for the quantum transition probability from initial vibrational state ni to final vibrational state nf of the oscillator. A comparison of the theory with exact quantum data is presented for a model collision of Br2 with a hydrogen molecule, where the hydrogen molecule is considered as a single approaching particle. PMID:27309793
Institute of Scientific and Technical Information of China (English)
ChenLi; Shao Xiao-Qiang; Zhang Shou
2009-01-01
The influences of dipole-dipole interaction and detuning on the entanglement between two atoms with different initial tripartite entangled W-like states in the Tavis-Cummings model have been investigated by means of Wootters' concurrence, respectively. The results show that the entanglement between the two atoms can be enhanced via apprco-priately tuning the strength of dipole-dipole interaction of two atoms or the detunings between atom and cavity, and the so-called sudden death effect can be weakened simultaneously.
Johnson, T. H.; Yuan, Y.; Bao, W.; Clark, S. R.; Foot, C.; Jaksch, D.
2016-06-01
We investigate cold bosonic impurity atoms trapped in a vortex lattice formed by condensed bosons of another species. We describe the dynamics of the impurities by a bosonic Hubbard model containing occupation-dependent parameters to capture the effects of strong impurity-impurity interactions. These include both a repulsive direct interaction and an attractive effective interaction mediated by the Bose-Einstein condensate. The occupation dependence of these two competing interactions drastically affects the Hubbard model phase diagram, including causing the disappearance of some Mott lobes.
Institute of Scientific and Technical Information of China (English)
吴金辉; 王登攀; 张惠芳; 肖志宏; 高锦岳
2003-01-01
We propose a new four-level atomic model for achieving light amplification at a short wavelength, where direct incoherent pumping into the top level is avoided by the advantage of coherent pumping. In this model, the lower level of the probe transition is an excited state but not the usual ground state. By analytical as well as numerical calculations, we find that the probe gain, either with or without population inversion, which depends on the relation between spontaneous decay rates γ42 and γ21, can be achieved with proper parameters. We note that the Raman scattering gain always plays an important role in achieving the probe amplification.
Johnson, T H; Yuan, Y; Bao, W; Clark, S R; Foot, C; Jaksch, D
2016-06-17
We investigate cold bosonic impurity atoms trapped in a vortex lattice formed by condensed bosons of another species. We describe the dynamics of the impurities by a bosonic Hubbard model containing occupation-dependent parameters to capture the effects of strong impurity-impurity interactions. These include both a repulsive direct interaction and an attractive effective interaction mediated by the Bose-Einstein condensate. The occupation dependence of these two competing interactions drastically affects the Hubbard model phase diagram, including causing the disappearance of some Mott lobes.
Paziresh, M.; Kingston, A. M.; Latham, S. J.; Fullagar, W. K.; Myers, G. M.
2016-06-01
Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073-2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127-135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260-1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and
Levashov, V. A.
2016-03-01
It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.
Ab initio and atomic kinetic Monte Carlo modelling of segregation in concentrated FeCrNi alloys
International Nuclear Information System (INIS)
Internal structure of pressurised water reactors are made of austenitic materials. Under irradiation, the microstructure of these concentrated alloys evolves and solute segregation on grain boundaries or irradiation defects such as dislocation loops are observed to take place. In order to model and predict the microstructure evolution, a multi-scale modelling approach needs to be developed, which starts at the atomic scale. Atomic Kinetic Monte Carlo (AKMC) modelling is the method we chose to provide an insight on defect mediated diffusion under irradiation. In that approach, we model the concentrated commercial steel as a FeCrNi alloy (γ-Fe70Cr20Ni10). As no reliable empirical potential exists at the moment to reproduce faithfully the phase diagram and the interactions of the elements and point defects, we have adjusted a pair interaction model on large amount of DFT (Density Functional Theory) calculations. The point defect properties in the Fe70Cr20Ni10, and more precisely, how their formation energy depends on the local environment will be presented and some AKMC results on thermal non equilibrium segregation (TNES) and radiation induce segregation will be presented. The effect of Si on the segregation will also be discussed. Preliminary results show that it is the solute- grain boundaries interactions which drive TNES
Raju, Subramanian; Saibaba, Saroja
2016-09-01
The enthalpy of formation Δo H f is an important thermodynamic quantity, which sheds significant light on fundamental cohesive and structural characteristics of an alloy. However, being a difficult one to determine accurately through experiments, simple estimation procedures are often desirable. In the present study, a modified prescription for estimating Δo H f L of liquid transition metal alloys is outlined, based on the Macroscopic Atom Model of cohesion. This prescription relies on self-consistent estimation of liquid-specific model parameters, namely electronegativity ( ϕ L) and bonding electron density ( n b L ). Such unique identification is made through the use of well-established relationships connecting surface tension, compressibility, and molar volume of a metallic liquid with bonding charge density. The electronegativity is obtained through a consistent linear scaling procedure. The preliminary set of values for ϕ L and n b L , together with other auxiliary model parameters, is subsequently optimized to obtain a good numerical agreement between calculated and experimental values of Δo H f L for sixty liquid transition metal alloys. It is found that, with few exceptions, the use of liquid-specific model parameters in Macroscopic Atom Model yields a physically consistent methodology for reliable estimation of mixing enthalpies of liquid alloys.
Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*
Palmeri, P.; Quinet, P.; Mendoza, C.; Bautista, M. A.; Garcia, J.; Witthoeft, M. C.; Kallman, T. R.
2012-01-01
Complete data sets of level energies, transition wavelengths, A-values, radiative and Auger widths and fluorescence yields for K-vacancy levels of the F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn isonuclear sequences have been computed by a Hartree-Fock method that includes relativistic corrections as implemented in Cowan's atomic structure computer suite. The atomic parameters for more than 3 million fine-structure K lines have been determined. Ions with electron number N greater than 9 are treated for the first time, and detailed comparisons with available measurements and theoretical data for ions with N less than or equal to 9 are carried out in order to estimate reliable accuracy ratings.
Fast and accurate conversion of atomic models into electron density maps
Directory of Open Access Journals (Sweden)
Carlos O.S. Sorzano
2015-03-01
Full Text Available New image processing methodologies and algorithms have greatly contributed to the signi cant progress in three-dimensional electron microscopy (3DEM of biological complexes we have seen over the last decades. Naturally, the availability of accurate procedures for the objective testing of new algorithms is a crucial requirement for the further advancement of the eld. A good and accepted testing work ow involves the generation of realistic 3DEM-like maps of biological macromolecules from which some measure of ground truth can be derived, ideally because their 3D atomic structure is already known. In this work we propose a very accurate generation of maps using atomic form factors for electron scattering. We thoroughly review current approaches in the eld, quantitatively demonstrating the bene ts of the new methodology. Additionally, we study a concrete example of the use of this approach for hypothesis testing in 3D Electron Microscopy.
Derouich, M; Barklem, P S
2015-01-01
Interpretation of solar polarization spectra accounting for partial or complete frequency redistribution requires data on various collisional processes. Data for depolarization and polarization transfer are needed but often missing, while data for collisional broadening are usually more readily available. Recent work by Sahal-Br\\'echot and Bommier concluded that despite underlying similarities in the physics of collisional broadening and depolarization processes, relationships between them are not possible to derive purely analytically. We aim to derive accurate numerical relationships between the collisional broadening rates and the collisional depolarization and polarization transfer rates due to hydrogen atom collisions. Such relationships would enable accurate and efficient estimation of collisional data for solar applications. Using earlier results for broadening and depolarization processes based on general (i.e. not specific to a given atom), semi-classical calculations employing interaction potentials...
Institute of Scientific and Technical Information of China (English)
JIN Feng-Tao; YUAN Jian-Min
2005-01-01
@@ The open M-shell opacity of a hot bromine plasma has been calculated by using a detailed level accounting (DLA )model. One-electron orbitals obtained by solving the fully relativistic Dirac-Fock equations are used to obtain the atomic levels and the radiative transition oscillator strengths. Only the level mixing within the same electron configuration is considered to reduce the complexity of the calculations. Detailed comparisons have been made between the results of the DLA and average atom (AA) models. Good agreements are found for both the M-shell transition arrays and the Planck mean opacity but there are differences for the line positions in the 2p → 3d absorption region due to the statistical treatment for the one-electron orbitals in the AA model.
International Nuclear Information System (INIS)
Witten's generalization to arbitrary dimension has afforded new insight into the correlated motion of quantum particles [Phys. Today 33, (7), 38 (1980)]. We have used a classically based method to understand the resultant dimensionality dependence of the ground-state energy of the helium atom in the approximation which regards the quantum fluctuations of the system as being harmonic oscillations about a classical, correlated state of minimum effective potential energy. Making an analogy with thermal systems, this provides a ''phase diagram'' of a single helium atom that features a first-order melting transition, with inverse dimensionality playing the role of temperature. Our approximation gives an understanding of the high-dimensionality behavior of the quantum solution found with a perturbation theory expansion in inverse dimensionality by Goodson and Herschbach [Phys. Rev. Lett. 58, 1628 (1987)]. From comparison with variational quantum ground-state solutions by Loeser and Herschbach [J. Chem. Phys. 84, 3882 (1986)] for atomic numbers 2, 3, and 6 we find that the harmonic description improves with decreasing nuclear charge
Folman, R; Cassettari, D; Hessmo, B; Maier, T; Schmiedmayer, J; Folman, Ron; Krüger, Peter; Cassettari, Donatella; Hessmo, Björn; Maier, Thomas
1999-01-01
Atoms can be trapped and guided using nano-fabricated wires on surfaces, achieving the scales required by quantum information proposals. These Atom Chips form the basis for robust and widespread applications of cold atoms ranging from atom optics to fundamental questions in mesoscopic physics, and possibly quantum information systems.
Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang
2015-04-01
The phase behavior of multicomponent metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamical aspects of a model ternary metallic liquid Cu40Zr51Al9 using molecular dynamics simulations with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (self diffusion coefficient, self relaxation time, and shear viscosity) bordered at Tx˜1300 K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs well above the melting point of the system (Tm˜900 K) in the equilibrium liquid state; and the crossover temperature Tx is roughly twice of the glass-transition temperature of the system (Tg). Below Tx, we found the elemental dynamics decoupled and the Stokes-Einstein relation broke down, indicating the onset of heterogeneous spatially correlated dynamics in the system mediated by dynamic communications among local configurational excitations. To directly characterize and visualize the correlated dynamics, we employed a nonparametric, unsupervised machine learning technique and identified dynamical clusters of atoms with similar atomic mobility. The revealed average dynamical cluster size shows an accelerated increase below Tx and mimics the trend observed in other ensemble averaged quantities that are commonly used to quantify the spatially heterogeneous dynamics such as the non-Gaussian parameter α2 and the four-point correlation function χ4.
Atomic model of anti-phase boundaries in a face-centred icosahedral Zn-Mg-Dy quasicrystal
Energy Technology Data Exchange (ETDEWEB)
Wang Jianbo [Department of Physics, Wuhan University, Wuhan 430072 (China); Yang Wenge [Solid State Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831 (United States); Wang Renhui [Department of Physics, Wuhan University, Wuhan 430072 (China)
2003-03-19
An atomic model in the physical space for an anti-phase boundary (APB) in the ordered face-centred icosahedral Zn-Mg-Dy quasicrystal phase is presented, based on a six-dimensional model suggested by Ishimasa and Shimizu (2000 Mater. Sci. Eng. A 294-296 232, Ishimasa 2001 private communication). The physical space atomic positions of the defected structure were used for the calculation of the corresponding exit-plane wavefunction and high-resolution transmission electron microscopy images. The analysis of the defect by inverse Fourier transformation reveals that when superstructure reflection spots are used for back-transformation, then at the APB, bright lattice fringes are found to turn into dark ones, and vice versa. When fundamental reflections are used, the APB is not visible. This phenomenon is the same as the corresponding experimental study recently published by Heggen et al(2001a Phys. Rev. B 64 014202). Based on this atomic model it is found that the APB perpendicular to a fivefold axis A5 (APB-A5) is a non-conservative boundary, while the APB perpendicular to a pseudo-twofold axis A2P (APB-A2P) is a conservative one. This fact is consistent with the experimental observation (Heggen et al2002 J. Alloys Compounds 342 330) that the frequency of occurrence of APB-A5 is 90% in the heat-treated samples compared with that in the deformed samples (45%), while the frequency of occurrence of APB-A2P is 34% in the deformed samples compared with that in the heat-treated samples.
Directory of Open Access Journals (Sweden)
Osvaldo N. Oliveira
2012-10-01
Full Text Available The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS, it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of afs, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution.
Munoz Burgos, Jorge Manuel
Accurate knowledge of atomic processes plays a key role in modeling the emission in laboratory as well as in astrophysical plasmas. These processes are included in a collisional-radiative model and the results are compared with experimental measurements for Ar and Ne ions from the ASTRAL (Auburn Steady sTate Research fAciLity) experiment. The accuracy of our model depends upon the quality of the atomic data we use. Atomic data for near neutral systems present a challenge due to the low accuracy of perturbative methods for these systems. In order to improve our model we rely on non-perturbative methods such as R - Matrix and RMPS ( R -Matrix with Pseudo-States) to include correlation in the collision cross-sections. In the case of Ar + we compared R -Matrix electron-impact excitation data against the results from a new RMPS calculation. The aim was to assess the effects of continuum-coupling effects on the atomic data and the resulting spectrum. We do our spectral modeling using the ADAS suite of codes. Our collisional-radiative formalism assumes that the excited levels are in quasi- static equilibrium with the ground and metastable populations. In our model we allow for N e and T e variation along the line of sight by fitting our densities and temperature profiles with those measured within the experiment. The best results so far have been obtained by the fitting of the experimental temperature and density profiles with Gaussian and polynomial distribution functions. The line of sight effects were found to have a significant effect on the emission modeling. The relative emission rates were measured in the ASTRAL helicon plasma source. A spectrometer which features a 0.33 m Criss-Cross Scanning monochromator and a CCD camera is used for this study. ASTRAL produces bright intense Ar and Ne plasmas with n e = 10 11 to 10 13 cm -3 and T e = 2 to 10 eV. A series of 7 large coils produce an axial magnetic field up to 1.3 kGauss. A fractional helix antenna is used to
Modelling three-dimensional-quench cooling for alkaline-earth atoms
Mehlstaeubler, T E; Douillet, A; Rehbein, N; Rasel, E M; Ertmer, W
2003-01-01
Quench cooling is a promising technique to reach ultra-cold temperatures in alkaline-earth atoms by Doppler cooling on ultra-narrow transitions. The principles of quench cooling are derived from an effective two-level system with a linewidth adjustable by the quenching laser. A tunable linewidth reconciles the contradictory requirements of a fast cooling rate and a high velocity selectivity at high and low temperatures, respectively. In this paper, we investigate the efficiency of quench cooling in alkaline-earth systems. We present a one-dimensional analytical description of the quenching process. Cooling and trapping in three dimensions is studied with semi-classical Monte Carlo simulations. Our results for magnesium indicate a loading efficiency of up to 40% of pre-cooled atoms at 2 mK into a QuenchMOT. Final temperatures of 9 mu K and an increase in phase-space density by almost five orders of magnitude are observed in the simulations.
Schöllnberger, H; Kaiser, J C; Jacob, P; Walsh, L
2012-05-01
The non-cancer mortality data for cerebrovascular disease (CVD) and cardiovascular diseases from Report 13 on the atomic bomb survivors published by the Radiation Effects Research Foundation were analysed to investigate the dose-response for the influence of radiation on these detrimental health effects. Various parametric and categorical models (such as linear-no-threshold (LNT) and a number of threshold and step models) were analysed with a statistical selection protocol that rated the model description of the data. Instead of applying the usual approach of identifying one preferred model for each data set, a set of plausible models was applied, and a sub-set of non-nested models was identified that all fitted the data about equally well. Subsequently, this sub-set of non-nested models was used to perform multi-model inference (MMI), an innovative method of mathematically combining different models to allow risk estimates to be based on several plausible dose-response models rather than just relying on a single model of choice. This procedure thereby produces more reliable risk estimates based on a more comprehensive appraisal of model uncertainties. For CVD, MMI yielded a weak dose-response (with a risk estimate of about one-third of the LNT model) below a step at 0.6 Gy and a stronger dose-response at higher doses. The calculated risk estimates are consistent with zero risk below this threshold-dose. For mortalities related to cardiovascular diseases, an LNT-type dose-response was found with risk estimates consistent with zero risk below 2.2 Gy based on 90% confidence intervals. The MMI approach described here resolves a dilemma in practical radiation protection when one is forced to select between models with profoundly different dose-responses for risk estimates. PMID:22437350
Yannouleas, Constantine; Brandt, Benedikt B.; Landman, Uzi
2016-07-01
Advances with trapped ultracold atoms intensified interest in simulating complex physical phenomena, including quantum magnetism and transitions from itinerant to non-itinerant behavior. Here we show formation of antiferromagnetic ground states of few ultracold fermionic atoms in single and double well (DW) traps, through microscopic Hamiltonian exact diagonalization for two DW arrangements: (i) two linearly oriented one-dimensional, 1D, wells, and (ii) two coupled parallel wells, forming a trap of two-dimensional, 2D, nature. The spectra and spin-resolved conditional probabilities reveal for both cases, under strong repulsion, atomic spatial localization at extemporaneously created sites, forming quantum molecular magnetic structures with non-itinerant character. These findings usher future theoretical and experimental explorations into the highly correlated behavior of ultracold strongly repelling fermionic atoms in higher dimensions, beyond the fermionization physics that is strictly applicable only in the 1D case. The results for four atoms are well described with finite Heisenberg spin-chain and cluster models. The numerical simulations of three fermionic atoms in symmetric DWs reveal the emergent appearance of coupled resonating 2D Heisenberg clusters, whose emulation requires the use of a t-J-like model, akin to that used in investigations of high T c superconductivity. The highly entangled states discovered in the microscopic and model calculations of controllably detuned, asymmetric, DWs suggest three-cold-atom DW quantum computing qubits.
Universal bosonic tetramers of dimer-atom-atom structure
Deltuva, A
2012-01-01
Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.
Scientific models red atoms, white lies and black boxes in a yellow book
Gerlee, Philip
2016-01-01
A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches a...
International Nuclear Information System (INIS)
A combination of former convective–diffusive vapor-transport models is described to extend the calculation scheme for sensitivity (characteristic mass — m0) in graphite furnace atomic absorption spectrometry (GFAAS). This approach encompasses the influence of forced convection of the internal furnace gas (mini-flow) combined with concentration diffusion of the analyte atoms on the residence time in a spatially isothermal furnace, i.e., the standard design of the transversely heated graphite atomizer (THGA). A couple of relationships for the diffusional and convectional residence times were studied and compared, including in factors accounting for the effects of the sample/platform dimension and the dosing hole. These model approaches were subsequently applied for the particular cases of Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sn, V and Zn analytes. For the verification of the accuracy of the calculations, the experimental m0 values were determined with the application of a standard THGA furnace, operating either under stopped, or mini-flow (50 cm3 min−1) of the internal sheath gas during atomization. The theoretical and experimental ratios of m0(mini-flow)-to-m0(stop-flow) were closely similar for each study analyte. Likewise, the calculated m0 data gave a fairly good agreement with the corresponding experimental m0 values for stopped and mini-flow conditions, i.e., it ranged between 0.62 and 1.8 with an average of 1.05 ± 0.27. This indicates the usability of the current model calculations for checking the operation of a given GFAAS instrument and the applied methodology. - Highlights: • A calculation scheme for convective–diffusive vapor loss in GFAAS is described. • Residence time (τ) formulas were compared for sensitivity (m0) in a THGA furnace. • Effects of the sample/platform dimension and dosing hole on τ were assessed. • Theoretical m0 of 18 analytes were calculated for stopped & mini furnace gas flows. • Experimental
Energy Technology Data Exchange (ETDEWEB)
Bencs, László, E-mail: bencs.laszlo@wigner.mta.hu [Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Laczai, Nikoletta [Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Ajtony, Zsolt [Institute of Food Science, University of West Hungary, H-9200 Mosonmagyaróvár, Lucsony utca 15–17 (Hungary)
2015-07-01
A combination of former convective–diffusive vapor-transport models is described to extend the calculation scheme for sensitivity (characteristic mass — m{sub 0}) in graphite furnace atomic absorption spectrometry (GFAAS). This approach encompasses the influence of forced convection of the internal furnace gas (mini-flow) combined with concentration diffusion of the analyte atoms on the residence time in a spatially isothermal furnace, i.e., the standard design of the transversely heated graphite atomizer (THGA). A couple of relationships for the diffusional and convectional residence times were studied and compared, including in factors accounting for the effects of the sample/platform dimension and the dosing hole. These model approaches were subsequently applied for the particular cases of Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sn, V and Zn analytes. For the verification of the accuracy of the calculations, the experimental m{sub 0} values were determined with the application of a standard THGA furnace, operating either under stopped, or mini-flow (50 cm{sup 3} min{sup −1}) of the internal sheath gas during atomization. The theoretical and experimental ratios of m{sub 0}(mini-flow)-to-m{sub 0}(stop-flow) were closely similar for each study analyte. Likewise, the calculated m{sub 0} data gave a fairly good agreement with the corresponding experimental m{sub 0} values for stopped and mini-flow conditions, i.e., it ranged between 0.62 and 1.8 with an average of 1.05 ± 0.27. This indicates the usability of the current model calculations for checking the operation of a given GFAAS instrument and the applied methodology. - Highlights: • A calculation scheme for convective–diffusive vapor loss in GFAAS is described. • Residence time (τ) formulas were compared for sensitivity (m{sub 0}) in a THGA furnace. • Effects of the sample/platform dimension and dosing hole on τ were assessed. • Theoretical m{sub 0} of 18 analytes were
Shen, Lin; Yang, Weitao
2016-04-12
We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.
Energetic Neutral Atom Emissions From Venus: VEX Observations and Theoretical Modeling
Fok, M.-C.; Galli, A.; Tanaka, T.; Moore, T. E.; Wurz, P.; Holmstrom, M.
2007-01-01
Venus has almost no intrinsic magnetic field to shield itself from its surrounding environment. The solar wind thus directly interacts with the planetary ionosphere and atmosphere. One of the by-products of this close encounter is the production of energetic neutral atom (ENA) emissions. Theoretical studies have shown that significant amount of ENAs are emanated from the planet. The launch of the Venus Express (VEX) in 2005 provided the first light ever of the Venus ENA emissions. The observed ENA flux level and structure are in pretty good agreement with the theoretical studies. In this paper, we present VEX ENA data and the comparison with numerical simulations. We seek to understand the solar wind interaction with the planet and the impacts on its atmospheres.
A simple nonbinary scattering model applicable to atomic collisions is crystals at 1ow energies
DEFF Research Database (Denmark)
Andersen, Hans Henrik; Sigmund, Peter
1966-01-01
the projectile and each ring atom is described by a Born-Mayer potential, and the scattering is assumed to be elastic and governed by the classical equations of motion. Because of symmetry, the problem can be reduced to plane motion of a particle in a potential of elliptic symmetry. The elliptic force field...... is approximated by a spherical one, which is dependent on the initial conditions of the individual scattering problem. For the spherical symmetrical potential, scattering angles and related quantities have been tabulated, but simple analytical approximations can be used too. As a result, one obtains...... the elliptic to the spherical potential are investigated. Special attention is paid to proper definitions of collision time and collision length which are important in collisions in crystals. Limitations to classical scattering arising from the uncertainty principle prove to be more serious than assumed...
Directory of Open Access Journals (Sweden)
Y. M. Ji
2013-07-01
Full Text Available The atmospheric reactions of halogenated formaldehydes with halogen atoms were investigated by high-accuracy molecular orbital calculation. Studies showed that halogen atoms could easily abstract hydrogen atom from halogenated formaldehydes to form halogenated formyl radical and hydrogen halide (HX. In specific areas with high concentration of halogen atoms, such as the marine boundary layer (MBL, halogenated formyl radical was easily to react with halogen atoms and finally transformed into HX and CO2 in the presence of water; otherwise, this radical was degraded to CO2, halogen gas, and halogenated oxide. By using the canonical variational transition state theory, the kinetics calculations were performed within a wide atmospheric temperature range of 200–368 K, and theoretical values agreed well with the available experimental data. Under atmospheric conditions, the rate constants decreased as altitude increased, and especially the rate constants of halogen atoms reaction with FCHO quickly reduced. Although the reactions of halogenated formaldehydes with F atoms were more easily occurred than did those with Cl and Br atoms, the two latter reactions were still important atmospheric degradation process, especially in the MBL. The modified Arrhenius formulas of rate constants within the atmospheric temperature range were fitted, which helped to understand the established atmospheric model and estimate the contribution of title reactions to atmospheric chemistry pollution.
Enhancement of Squeezing in Two-Photon Jaynes-Cummings Model with Atomic Measurement
Institute of Scientific and Technical Information of China (English)
YE Sai-Yun
2006-01-01
We investigate the squeezing properties of the cavity field in the degenerate two-photon Jaynes-Cummings model. Compared with the one-photon Jaynes-Cummings model, the squeezing is more pronounced in the case of two-photon Jaynes-Cummings model under certain conditions.
Zemskova, Varvara; Deal, Morgan; Vauclair, Sylvie
2014-01-01
Iron-rich layers are known to form in the stellar subsurface through a combination of gravitational settling and radiative levitation. Their presence, nature and detailed structure can affect the excitation process of various stellar pulsation modes, and must therefore be modeled carefully in order to better interpret Kepler asteroseismic data. In this paper, we study the interplay between atomic diffusion and fingering convection in A-type stars, and its role in the establishment and evolution of iron accumulation layers. To do so, we use a combination of three-dimensional idealized numerical simulations of fingering convection, and one-dimensional realistic stellar models. Using the three-dimensional simulations, we first validate the mixing prescription for fingering convection recently proposed by Brown et al. (2013), and identify what system parameters (total mass of iron, iron diffusivity, thermal diffusivity, etc.) play a role in the overall evolution of the layer. We then implement the Brown et al. (2...
International Nuclear Information System (INIS)
A complete formulation of the post-version of the continuum distorted wave-eikonal initial state (CDW-EIS) model is used to investigate single ionization of multishell atoms by fast bare proton beams. The influence of the non-ionized electrons on the dynamic evolution is studied for each of the different shells of the targets. Its inclusion was made by means of the parametric Green–Sellin–Zachor potential. In this way, it is shown that discrepancies between the prior- and post-versions of the CDW-EIS model are avoided for any nl states of the systems studied here. The present analysis is supported by comparisons with existing experimental electron emission spectra. (paper)
Gleadall, Andrew; Pan, Jingzhe; Kruft, Marc-Anton
2015-11-01
Atomic simulations were undertaken to analyse the effect of polymer chain scission on amorphous poly(lactide) during degradation. Many experimental studies have analysed mechanical properties degradation but relatively few computation studies have been conducted. Such studies are valuable for supporting the design of bioresorbable medical devices. Hence in this paper, an Effective Cavity Theory for the degradation of Young's modulus was developed. Atomic simulations indicated that a volume of reduced-stiffness polymer may exist around chain scissions. In the Effective Cavity Theory, each chain scission is considered to instantiate an effective cavity. Finite Element Analysis simulations were conducted to model the effect of the cavities on Young's modulus. Since polymer crystallinity affects mechanical properties, the effect of increases in crystallinity during degradation on Young's modulus is also considered. To demonstrate the ability of the Effective Cavity Theory, it was fitted to several sets of experimental data for Young's modulus in the literature.
Reichel, Jakob
2010-01-01
This book provides a stimulating and multifaceted picture of a rapidly developing field. The first part reviews fundamentals of atom chip research in tutorial style, while subsequent parts focus on the topics of atom-surface interaction, coherence on atom chips, and possible future directions of atom chip research. The articles are written by leading researchers in the field in their characteristic and individual styles.
Improving Atomic Force Microscopy Imaging by a Direct Inverse Asymmetric PI Hysteresis Model
Directory of Open Access Journals (Sweden)
Dong Wang
2015-02-01
Full Text Available A modified Prandtl–Ishlinskii (PI model, referred to as a direct inverse asymmetric PI (DIAPI model in this paper, was implemented to reduce the displacement error between a predicted model and the actual trajectory of a piezoelectric actuator which is commonly found in AFM systems. Due to the nonlinearity of the piezoelectric actuator, the standard symmetric PI model cannot precisely describe the asymmetric motion of the actuator. In order to improve the accuracy of AFM scans, two series of slope parameters were introduced in the PI model to describe both the voltage-increase-loop (trace and voltage-decrease-loop (retrace. A feedforward controller based on the DIAPI model was implemented to compensate hysteresis. Performance of the DIAPI model and the feedforward controller were validated by scanning micro-lenses and standard silicon grating using a custom-built AFM.
Mohammadiarani, Hossein; Vashisth, Harish
2016-01-01
The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID
Energy Technology Data Exchange (ETDEWEB)
Mohammadi, M [Physics Department, Science and Research Campus Azad University of Tehran, Tehran (Iran, Islamic Republic of); Naderi, M H [Quantum Optics Group, University of Isfahan, Isfahan (Iran, Islamic Republic of); Soltanolkotabi, M [Quantum Optics Group, University of Isfahan, Isfahan (Iran, Islamic Republic of)
2006-09-01
We present a theoretical scheme based on an su(2) dynamical algebraic structure to investigate the influence of a homogeneous gravitational field on the quantum-nondemolition measurement of atomic momentum in the dispersive Jaynes-Cummings model. In the dispersive Jaynes-Cummings model, when detuning is large and the atomic motion is in a propagating light wave, we consider a two-level atom interacting with the quantized cavity field in the presence of a homogeneous gravitational field. We derive an effective Hamiltonian describing the dispersive atom-field interaction in the presence of the gravitational field. We investigate the influence of the gravitational field on both the momentum filter and momentum distribution. Particularly, we find that the gravitational field decreases both the tooth spacing of momentum and the tooth width of momentum.
Cohen, Brian W; Polyansky, Dmitry E; Achord, Patrick; Cabelli, Diane; Muckerman, James T; Tanaka, Koji; Thummel, Randolph P; Zong, Ruifa; Fujita, Etsuko
2012-01-01
Two isomers, [Ru(1)]2+ (Ru = Ru(bpy)2, bpy = 2,2'-bipyridine, 1 = 2-(pyrid-2'-yl)-1-azaacridine) and [Ru(2)]2+ (2 = 3-(pyrid-2'-yl)-4-azaacridine), are bioinspired model compounds containing the nicotinamide functionality and can serve as precursors for the photogeneration of C-H hydrides for studying reactions pertinent to the photochemical reduction of metal-C1 complexes and/or carbon dioxide. While it has been shown that the structural differences between the azaacridine ligands of [Ru(1)]2+ and [Ru(2)]2+ have a significant effect on the mechanism of formation of the hydride donors, [Ru(1HH)]2+ and [Ru(2HH)]2+, in aqueous solution, we describe the steric implications for proton, net-hydrogen-atom and net-hydride transfer reactions in this work. Protonation of [Ru(2*-)] in aprotic and even protic media is slow compared to that of [Ru(1*-)]+. The net hydrogen-atom transfer between *[Ru(1)]2+ and hydroquinone (H2Q) proceeds by one-step EPT, rather than stepwise electron-proton transfer. Such a reaction was not observed for *[Ru(2)]2+ because the non-coordinated N atom is not easily available for an interaction with H2Q. Finally, the rate of the net hydride ion transfer from [Ru(1HH)]2+ to [Ph3C]+ is significantly slower than that of [Ru (2HH)]2+ owing to steric congestion at the donor site. PMID:22470971
Edge-to-edge interfaces in Ti-Al modeled with the embedded atom method
Reynolds, W. T.; Farkas, D.
2006-03-01
The atomistic structure and energies of high-index interphase boundaries are explored using a combination of molecular statics and dynamics simulations with embedded atom potentials. We investigate planar boundaries between the α2 and γ phases in the Ti-Al system. The class of boundaries considered has a high-index boundary orientation; the orientation relationship between the α2 and γ phases also is high index, and a set of planes from each phase meet edge to edge at the boundary plane. For the particular case of a boundary that is commensurate in one direction and coincides with a moiré plane given by the so-called “Δ g” diffraction condition, the boundary is not structurally singular, but it is energetically stable and does not appear to dissociate into other low-energy configurations. Misfit compensating defects are not observed; misfit in directions other than the commensurate one appears to be distributed uniformly. The boundary energy is evaluated as a function of the orientation of the boundary plane, and the edge-to-edge (moiré) boundary is found to lie in an energy cusp.
Modeling of XFEL induced ionization and atomic displacement in protein nanocrystals
Caleman, Carl; Tîmneanu, Nicusor; Martin, Andrew V.; White, Thomas A.; Scott, Howard A.; Barty, Anton; Aquila, Andrew; Chapman, Henry N.
2012-10-01
X-ray free-electron lasers enable high-resolution imaging of biological materials by using short enough pulses to outrun many of the effects of radiation damage. Experiments conducted at the LCLS have obtained diffraction data from single particles and protein nanocrystals at doses to the sample over 3 GGy. The details of the interaction of the X-ray FEL pulse with the sample determine the limits of this new paradigm for imaging. Recent studies suggest that in the case of crystalline samples, such as protein nanocrystals, the atomic displacements and loss of bound electrons in the crystal (due to the high X- ray intensity) has the effect of gating the diffraction signal, and hence making the experiment less radiation sensitive. Only the incident photon intensity in the first part of the pulse, before the Bragg diffraction has died out, is relevant to acquiring signal and the rest of the pulse will mainly contribute to a diffuse background. In this work we use a plasma based non-local thermodynamic equilibrium code to explore the displacement and the ionization of a protein nanocrystal at various X-ray wavelengths and intensities.
Preparation of Inoculants Used in Superalloy and Analysis of the Atomic Matching Models
Institute of Scientific and Technical Information of China (English)
Fu Wang; Jun Zhang; Taiwen Huang; Lin Liu; Hengzhi Fu
2013-01-01
The mechanisms of grain refinement were investigated on two kinds of grain refiners used in Ni-Fe based superalloys and complete atomic matching modes were constructed in this study.It is found that there are at least three matching crystal planes having the small lattice disregistry between the refiner and the nucleated phase,which can lead to grain refinement of γ matrix.The results indicate that the (0001),(01-10) planes of CrFeNb have a fine crystallographic matching relationship with the (111),(110) planes of γ matrix.The disregistry of (0001)CrFeNb//(111)γ' (01-10)CrFeNb//(111)γ and (01-10)CrFeNb//(110)γ is 3.34％,6.60％ and 5.90％,respectively.The (0001),(01-10) planes of Co3FeNb2 and (111),(110) planes of γ matrix also have this relationship.The disregistry of (0001)Co3FeNb2//(111)γ' (0001)Co3FeNb2//(110)γ' (01-10)Co3FeNb2//(111)γ and (01-10)Co3FeNb2//(110)γ is 4.45％,9.35％,8.38％ and 6.12％,respectively.
Three-body scattering hypervolume for ultracold atoms with a model two-body potential
Zhu, Shangguo; Tan, Shina
2015-05-01
It has been known that the three-boson low energy effective interaction influences the dynamic and the static properties of many bosons, including the ground state energies of dilute Bose-Einstein condensates. The three-body scattering hypervolume, which is a three-body analogue of the two-body scattering length, characterizes this effective interaction. Surprisingly, knowledge of this fundamental quantity has still been lacking, except for hard sphere bosons and bosons with large scattering length. For bosons with a soft-ball potential--the repulsive Gaussian potential, we determine the scattering hypervolume by solving the three-body Schrödinger equation numerically, and matching the solution with the asymptotic expansions for the wave function at large hyperradii. Our analyses of the three-body scattering hypervolume can be extended to the long-range Van der Waals potential. They will be necessary in the precise understanding of the energetics and dynamics of three, more, or many ultracold bosonic atoms.
Foot, Christopher J
2007-01-01
This text will thoroughly update the existing literature on atomic physics. Intended to accompany an advanced undergraduate course in atomic physics, the book will lead the students up to the latest advances and the applications to Bose-Einstein Condensation of atoms, matter-wave inter-ferometry and quantum computing with trapped ions. The elementary atomic physics covered in the early chapters should be accessible to undergraduates when they are first introduced to the subject. To complement. the usual quantum mechanical treatment of atomic structure the book strongly emphasizes the experimen
Xiao, Ke; Malvankar, Nikhil S; Shu, Chuanjun; Martz, Eric; Lovley, Derek R; Sun, Xiao
2016-03-22
The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.
Xiao, Ke; Malvankar, Nikhil S; Shu, Chuanjun; Martz, Eric; Lovley, Derek R; Sun, Xiao
2016-01-01
The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics. PMID:27001169
HERschel Observations of Edge-on Spirals (HEROES). II: Tilted-ring modelling of the atomic gas disks
Allaert, F; Baes, M; De Geyter, G; Hughes, T M; Lewis, F; Bianchi, S; De Looze, I; Fritz, J; Holwerda, B W; Verstappen, J; Viaene, S
2015-01-01
Context. Edge-on galaxies can offer important insights in galaxy evolution as they are the only systems where the distribution of the different components can be studied both radially and vertically. The HEROES project was designed to investigate the interplay between the gas, dust, stars and dark matter (DM) in a sample of 7 massive edge-on spiral galaxies. Aims. In this second HEROES paper we present an analysis of the atomic gas content of 6 out of 7 galaxies in our sample. The remaining galaxy was recently analysed according to the same strategy. The primary aim of this work is to constrain the surface density distribution, the rotation curve and the geometry of the gas disks in a homogeneous way. In addition we identify peculiar features and signs of recent interactions. Methods. We construct detailed tilted-ring models of the atomic gas disks based on new GMRT 21-cm observations of NGC 973 and UGC 4277 and re-reduced archival HI data of NGC 5907, NGC 5529, IC 2531 and NGC 4217. Potential degeneracies be...
An Introduction to the Interacting Boson Model of the Atomic Nucleus, Part I
Pfeifer, Walter
2002-01-01
This work introduces to the Interacting Boson Model, which was created in 1974 by F. Iachello and A. Arima and then extend by numerous papers. Many-body configurations with s- and d-boson states are described and creation- and annihilation-operators for bosons are introduced. States with defined angular momentum are dealt with and the Hamilton operator of the IBM1-model is expressed in terms of Casimir operators. Level energies and electromagnetic transition probabilities are compared with measured data. A short introduction to Lie algebras and their application to the IBM1-model are given. In the IBM2-model protons and neutrons are treated separately and in IBFM single nucleons are added to the boson model. Comparison with experimental results.
An Introduction to the Interacting Boson Model of the Atomic Nucleus. Part II
Pfeifer, Walter
2002-01-01
This work introduces to the Interacting Boson Model, which was created in 1974 by F. Iachello and A. Arima and then extended by numerous papers. Many-body configurations with s- and d-boson states are described and creation- and annihilation-operators for bosons are introduced. States with defined angular momentum are dealt with and the Hamilton operator of the IBM1-model is expressed in terms of Casimir operators. Level energies and electromagnetic transition probabilities are compared with measured data. A short introduction to Lie algebras and their application to the IBM1-model are given. In the IBM2-model protons and neutrons are treated separately and in IBFM single nucleons are added to the boson model. Comparison with experimental results.
International Nuclear Information System (INIS)
We will first present a development of the fundamental principles of atom interferometers. Next we will discuss a few of the various methods now available to split and recombine atomic De Broglie waves, with special emphasis on atom interferometers based on optical pulses. We will also be particularly concerned with high precision interferometers with long measurement times such those made with atomic fountains. The application of atom interferometry to the measurement of the acceleration due to gravity will be detailed. We will also develop the atom interferometry based on adiabatic transfer and we will apply it to the measurement of the photon recoil in the case of the Doppler shift of an atomic resonance caused by the momentum recoil from an absorbed photon. Finally the outlook of future developments will be given. (A.C.)
Surzhykov, Andrey; Koval, Peter; Fritzsche, Stephan
2005-01-01
Today, the 'hydrogen atom model' is known to play its role not only in teaching the basic elements of quantum mechanics but also for building up effective theories in atomic and molecular physics, quantum optics, plasma physics, or even in the design of semiconductor devices. Therefore, the analytical as well as numerical solutions of the hydrogen-like ions are frequently required both, for analyzing experimental data and for carrying out quite advanced theoretical studies. In order to support a fast and consistent access to these (Coulomb-field) solutions, here we present the DIRAC program which has been developed originally for studying the properties and dynamical behavior of the (hydrogen-like) ions. In the present version, a set of MAPLE procedures is provided for the Coulomb wave and Green's functions by applying the (wave) equations from both, the nonrelativistic and relativistic theory. Apart from the interactive access to these functions, moreover, a number of radial integrals are also implemented in the DIRAC program which may help the user to construct transition amplitudes and cross sections as they occur frequently in the theory of ion-atom and ion-photon collisions. Program summaryTitle of program:DIRAC Catalogue number: ADUQ Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUQ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Computer for which the program is designed and has been tested: All computers with a license of the computer algebra package MAPLE [1] Program language used: Maple 8 and 9 No. of lines in distributed program, including test data, etc.:2186 No. of bytes in distributed program, including test data, etc.: 162 591 Distribution format: tar gzip file CPC Program Library subprograms required: None Nature of the physical problem: Analytical solutions of the hydrogen atom are widely used in very different fields of physics [2,3]. Despite of the rather simple structure
Michaud, Georges; Richer, Jacques
2015-01-01
This book gives an overview of atomic diffusion, a fundamental physical process, as applied to all types of stars, from the main sequence to neutron stars. The superficial abundances of stars as well as their evolution can be significantly affected. The authors show where atomic diffusion plays an essential role and how it can be implemented in modelling. In Part I, the authors describe the tools that are required to include atomic diffusion in models of stellar interiors and atmospheres. An important role is played by the gradient of partial radiative pressure, or radiative acceleration, which is usually neglected in stellar evolution. In Part II, the authors systematically review the contribution of atomic diffusion to each evolutionary step. The dominant effects of atomic diffusion are accompanied by more subtle effects on a large number of structural properties throughout evolution. One of the goals of this book is to provide the means for the astrophysicist or graduate student to evaluate the importanc...
What dislocation modelling at the atomic scale tell us about the strength of MgSiO3 perovskite
Kraych, A.
2015-12-01
Heat transfer through the mantle is carried by convection, which involves plastic flow of the mantle constituents. The plasticity of (Mg,Fe,Al)(Si,Al)O3 Bridgmanite, the main constituent of the lower mantle, is therefore crucial to understand the Earth's dynamics. Its deformation occurs at extreme pressure and temperature conditons (from 30 to 140 GPa, 2000 to 3000 K) and very low strain rate (from 10-12 to 10-16 s-1), the latter being impossible to reach experimentally. Here we calculate the strength of MgSiO3 perovskite (Mg-Pv), by modelling [100] and [010] dislocations at the atomic scale with molecular statics calculation. To assess the mobility of these dislocations under the conjugate action of stress and temperature, we describe their behaviour into a kink-pair model. We develop therefore a velocity model informed by atomistic calculations, taking into account P, T, stress and deformation strain-rate. We show that our model is consistent with deformation experiments on perovskite (see figure), and can also be used to calculate the strength of Mg-Pv induced by dislocation creep at natural strain rate relevant to the mantle.
Po, Hoi Chun; Zhou, Qi
2015-08-01
Bosons have a natural instinct to condense at zero temperature. It is a long-standing challenge to create a high-dimensional quantum liquid that does not exhibit long-range order at the ground state, as either extreme experimental parameters or sophisticated designs of microscopic Hamiltonians are required for suppressing the condensation. Here we show that synthetic gauge fields for ultracold atoms, using either the Raman scheme or shaken lattices, provide physicists a simple and practical scheme to produce a two-dimensional algebraic quantum liquid at the ground state. This quantum liquid arises at a critical Lifshitz point, where a two-dimensional quartic dispersion emerges in the momentum space, and many fundamental properties of two-dimensional bosons are changed in its proximity. Such an ideal simulator of the quantum Lifshitz model allows experimentalists to directly visualize and explore the deconfinement transition of topological excitations, an intriguing phenomenon that is difficult to access in other systems.
Quantum-kinetic modeling of electron release in low-energy surface collisions of atoms and molecules
Energy Technology Data Exchange (ETDEWEB)
Marbach, Johannes
2012-09-20
In this work we present a theoretical description of electron release in the collision of atomic and molecular projectiles with metallic and especially dielectric surfaces. The associated electron yield, the secondary electron emission coefficient, is an important input parameter for numerical simulations of dielectric barrier discharges and other bounded low-temperature gas discharges. The available reference data for emission coefficients is, however, very sparse and often uncertain, especially for molecular projectiles. With the present work we aim to contribute to the filling of these gaps by providing a flexible and easy-to-use model that allows for a convenient calculation of the emission coefficient and related quantities for a wide range of projectile-surface systems and the most dominant reaction channels.
Lima, H.; Couto dos Santos, M. A.
2016-09-01
In this work, based on fundamental physics and chemistry (charge distribution, electronegativity, induced dipole moment), we are introducing an analytical expression for Zeff and a general way of calculating the crystal packing factor, p, of any ionic material. By using the average separation between the atomic and crystal(ionic) radii of the interacting ions, we are postulating an effective distance(Rij) between the positive and the negative centre of charge. When compared to the available experimental data, predictions within 20% have been obtained to Zeff of materials applied to dosimetry. In photonics, the increasing behaviour of the refractive index with Zeff is confirmed. By combining crystal field and effective charge models, we have predicted Zeff of the Eu2O3 within the range of available experimental data.
Prasai, Binay; Wilson, A. R.; Wiley, B. J.; Ren, Y.; Petkov, Valeri
2015-10-01
The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au100-xPdx (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when ``tuned up'' against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design.The extent to which current theoretical modeling alone can
How Modelling of Crystal Defects at the Atomic Scale can Provide Information on Seismic Anisotropy
Cordier, P.; Carrez, P.; Goryaeva, A.; Gouriet, K.; Hirel, P.; Kraych, A.; Ritterbex, S.
2014-12-01
Seismic anisotropy represents one of the few sources of information about flow in the mantle that takes place at timescales that are barely accessible at human timescales. Seismic waves travelling through rocks at the speed of sound can reveal flow lines frozen in rocks over hundreds of million years. The interpretation of seismic anisotropy also needs to bridge length-scales since crystal defects are responsible for the plastic anisotropy that align crystals in a deforming rock thus revealing elastic anisotropy at the macroscopic scale. Knowing the easiest slip systems for a given crystal structure is thus the fundamental information needed. To obtain it we propose the following approach based on multiscale numerical modeling. As a first approach, we calculate generalized stacking faults which inform us about the easiest shear paths imposed by the crystal chemistry. This leads to a short list of potential slip systems for which lattice friction will be calculated. A further selection will be done by modeling the core structures of screw dislocations. The tendency for core spreading of screw dislocations impose a selection on potential glide planes which is further validated by modeling corresponding edge dislocations and their respective mobilities. Finally, we model the mobility of these dislocations under the conjugate influence of stress and temperature using the kink-pair model which is based on the activation enthalpy of the critical configuration which allows a dislocation to glide from one stable position to the next. The output of this model is the so-called critical resolved shear stress which is the onset of plastic glide at a given temperature and strain rate. Comparison between slip systems provides constraints on the plastic anisotropy. Examples are presented among the major phases of the Earth's mantle.
Gaussian Schell Source as Model for Slit-Collimated Atomic and Molecular Beams
McMorran, Ben
2008-01-01
We show how to make a Gaussian Schell-model (GSM) beam. Then we compare the intensity profile, the transverse coherence width and the divergence angle of a GSM beam with those same properties of a beam that is collimated with two hard-edged slits. This work offers an intuitive way to understand various interferometer designs, and we compare our results with data.
Error sources in atomic force microscopy for dimensional measurements: Taxonomy and modeling
DEFF Research Database (Denmark)
Marinello, F.; Voltan, A.; Savio, E.;
2010-01-01
: 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...
EINSTEIN, SCHROEDINGER, AND ATOM
Directory of Open Access Journals (Sweden)
Trunev A. P.
2014-03-01
Full Text Available In this paper, we consider gravitation theory in multidimensional space. The model of the metric satisfying the basic requirements of quantum theory is proposed. It is shown that gravitational waves are described by the Liouville equation and the Schrodinger equation as well. The solutions of the Einstein equations describing the stationary states of arbitrary quantum and classical systems with central symmetry have been obtained. Einstein’s atom model has been developed, and proved that atoms and atomic nuclei can be represented as standing gravitational waves
Young, Peter R; Landi, Enrico; Del Zanna, Giulio; Mason, Helen
2015-01-01
The CHIANTI atomic database was first released in 1996 and has had a huge impact on the analysis and modeling of emissions from astrophysical plasmas. The database has continued to be updated, with version 8 released in 2015. Atomic data for modeling the emissivities of 246 ions and neutrals are contained in CHIANTI, together with data for deriving the ionization fractions of all elements up to zinc. The different types of atomic data are summarized here and their formats discussed. Statistics on the impact of CHIANTI to the astrophysical community are given and examples of the diverse range of applications are presented.
International Nuclear Information System (INIS)
Research activities in atomic physics at Lawrence Berkeley Laboratory during 1976 are described. Topics covered include: experiments on stored ions; test for parity violation in neutral weak currents; energy conservation and astrophysics; atomic absorption spectroscopy, atomic and molecular detectors; theoretical studies of quantum electrodynamics and high-z ions; atomic beam magnetic resonance; radiative decay from the 23Po,2 levels of helium-like argon; quenching of the metastable 2S/sub 1/2/ state of hydrogen-like argon in an external electric field; and lifetime of the 23Po level of helium-like krypton
Prasai, Binay; Wilson, A R; Wiley, B J; Ren, Y; Petkov, Valeri
2015-11-14
The extent to which current theoretical modeling alone can reveal real-world metallic nanoparticles (NPs) at the atomic level was scrutinized and demonstrated to be insufficient and how it can be improved by using a pragmatic approach involving straightforward experiments is shown. In particular, 4 to 6 nm in size silica supported Au(100-x)Pd(x) (x = 30, 46 and 58) explored for catalytic applications is characterized structurally by total scattering experiments including high-energy synchrotron X-ray diffraction (XRD) coupled to atomic pair distribution function (PDF) analysis. Atomic-level models for the NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modeling Sutton-Chen (SC) method. Models are matched against independent experimental data and are demonstrated to be inaccurate unless their theoretical foundation, i.e. the SC method, is supplemented with basic yet crucial information on the length and strength of metal-to-metal bonds and, when necessary, structural disorder in the actual NPs studied. An atomic PDF-based approach for accessing such information and implementing it in theoretical modeling is put forward. For completeness, the approach is concisely demonstrated on 15 nm in size water-dispersed Au particles explored for bio-medical applications and 16 nm in size hexane-dispersed Fe48Pd52 particles explored for magnetic applications as well. It is argued that when "tuned up" against experiments relevant to metals and alloys confined to nanoscale dimensions, such as total scattering coupled to atomic PDF analysis, rather than by mere intuition and/or against data for the respective solids, atomic-level theoretical modeling can provide a sound understanding of the synthesis-structure-property relationships in real-world metallic NPs. Ultimately this can help advance nanoscience and technology a step closer to producing metallic NPs by rational design. PMID:26463562
Bloemen, S; Aerts, C; Dupret, M A; Østensen, R H; Degroote, P; Müller-Ringat, E; Rauch, T
2014-01-01
We have computed a new grid of evolutionary subdwarf B star (sdB) models from the start of central He burning, taking into account atomic diffusion due to radiative levitation, gravitational settling, concentration diffusion, and thermal diffusion. We have computed the non-adiabatic pulsation properties of the models and present the predicted p-mode and g-mode instability strips. In previous studies of the sdB instability strips, artificial abundance enhancements of Fe and Ni were introduced in the pulsation driving layers. In our models, the abundance enhancements of Fe and Ni occur naturally, eradicating the need to use artificial enhancements. We find that the abundance increases of Fe and Ni were previously underestimated and show that the instability strip predicted by our simulations solves the so-called blue edge problem of the subdwarf B star g-mode instability strip. The hottest known g-mode pulsator, KIC 10139564, now resides well within the instability strip {even when only modes with low spherical...
Bloemen, S.; Hu, H.; Aerts, C.; Dupret, M. A.; Østensen, R. H.; Degroote, P.; Müller-Ringat, E.; Rauch, T.
2014-09-01
We have computed a new grid of evolutionary subdwarf B star (sdB) models from the start of central He burning, taking into account atomic diffusion due to radiative levitation, gravitational settling, concentration diffusion, and thermal diffusion. We have computed the non-adiabatic pulsation properties of the models and present the predicted p-mode and g-mode instability strips. In previous studies of the sdB instability strips, artificial abundance enhancements of Fe and Ni were introduced in the pulsation driving layers. In our models, the abundance enhancements of Fe and Ni occur naturally, eradicating the need to use artificial enhancements. We find that the abundance increases of Fe and Ni were previously underestimated and show that the instability strip predicted by our simulations solves the so-called blue edge problem of the subdwarf B star g-mode instability strip. The hottest known g-mode pulsator, KIC 10139564, now resides well within the instability strip even when only modes with low spherical degrees (l ≤ 2) are considered. Appendix A is available in electronic form at http://www.aanda.org
Constitution and model. The quantum theory of Bohr and imagining the atom
Hon, Giora
2014-01-01
The quantum theory of Bohr has roots in the theories of Rutherford and J. J. Thomson on the one hand, and that of Nicholson on the other. We note that Bohr neither presented the theories of Rutherford and Thomson faithfully, nor did he refer to the theory of Nicholson in its own terms. The contrasting attitudes towards these antecedent theories is telling and reveals the philosophical disposition of Bohr. We argue that Bohr intentionally avoided the concept of model as inappropriate for describing his proposed theory. Bohr had no problem in referring to the works of others as 'models', thus separating his theory from previous theories. He was interested in uncovering 'a little piece of reality'.
Quantum-Atomic-Continuum-Coupled Model for Mechanical Behaviors in Micro-nano Simulations
Han, Tiansi; Cui, JunZhi
2014-01-01
For the numerical simulations of physical and mechanical behaviors of materials at the micro-nano scale, a coupled model with the effect of local quantum is presented in this paper. Unlike traditional methods, the transition region is not needed since the non-local mechanical effects and the constitutive relations are naturally involved by first principle density functional calculations. In order to identify and calculate the mechanical quantities at different scales, some necessary assumptio...
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
Directory of Open Access Journals (Sweden)
Xiaojun Xu
2015-01-01
Full Text Available While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM and small angle X-ray scattering (SAXS have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair.
Energy Technology Data Exchange (ETDEWEB)
Elrawemi, Mohamed, E-mail: Mohamed.elrawemi@hud.ac.uk [EPSRC Centre for Innovative Manufacturing in Advanced Metrology, School of Computing and Engineering, University of Huddersfield, Huddersfield (United Kingdom); Blunt, Liam; Fleming, Leigh [EPSRC Centre for Innovative Manufacturing in Advanced Metrology, School of Computing and Engineering, University of Huddersfield, Huddersfield (United Kingdom); Bird, David, E-mail: David.Bird@uk-cpi.com [Centre for Process Innovation Limited, Sedgefield, County Durham (United Kingdom); Robbins, David [Centre for Process Innovation Limited, Sedgefield, County Durham (United Kingdom); Sweeney, Francis [EPSRC Centre for Innovative Manufacturing in Advanced Metrology, School of Computing and Engineering, University of Huddersfield, Huddersfield (United Kingdom)
2014-11-03
Transparent barrier films such as Al{sub 2}O{sub 3} used for prevention of oxygen and/or water vapour permeation are the subject of increasing research interest when used for the encapsulation of flexible photovoltaic modules. However, the existence of micro-scale defects in the barrier surface topography has been shown to have the potential to facilitate water vapour ingress, thereby reducing cell efficiency and causing internal electrical shorts. Previous work has shown that small defects (≤ 3 μm lateral dimension) were less significant in determining water vapour ingress. In contrast, larger defects (≥ 3 μm lateral dimension) seem to be more detrimental to the barrier functionality. Experimental results based on surface topography segmentation analysis and a model presented in this paper will be used to test the hypothesis that the major contributing defects to water vapour transmission rate are small numbers of large defects. The model highlighted in this study has the potential to be used for gaining a better understanding of photovoltaic module efficiency and performance. - Highlights: • A model of water vapour permeation through barrier defects is presented. • The effect of the defects on the water vapour permeability is investigated. • Defect density correlates with water vapour permeability. • Large defects may dominate the permeation properties of the barrier film.
Dynamics of atom-atom correlations in the Fermi problem
Borrelli, Massimo; Sabín, Carlos; Adesso, Gerardo; Plastina, Francesco; Maniscalco, Sabrina
2012-01-01
We present a detailed perturbative study of the dynamics of several types of atom-atom correlations in the famous Fermi problem. This is an archetypal model to study micro-causality in the quantum domain, where two atoms, one initially excited and the other prepared in its ground state, interact with the vacuum electromagnetic field. The excitation can be transferred to the second atom via a flying photon, and various kinds of quantum correlations between the two are generated during this pro...
Modeling Primary Atomization of Liquid Fuels using a Multiphase DNS/LES Approach
Energy Technology Data Exchange (ETDEWEB)
Arienti, Marco [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Oefelein, Joe [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Doisneau, Francois [Sandia National Lab. (SNL-CA), Livermore, CA (United States)
2016-08-01
As part of a Laboratory Directed Research and Development project, we are developing a modeling-and-simulation capability to study fuel direct injection in automotive engines. Predicting mixing and combustion at realistic conditions remains a challenging objective of energy science. And it is a research priority in Sandia’s mission-critical area of energy security, being also relevant to many flows in defense and climate. High-performance computing applied to this non-linear multi-scale problem is key to engine calculations with increased scientific reliability.
Physicists' approach to studying socio-economic inequalities: Can humans be modelled as atoms?
Sharma, Kiran
2016-01-01
A brief overview of the models and data analyses of income, wealth, consumption distributions by the physicists, are presented here. It has been found empirically that the distributions of income and wealth possess fairly robust features, like the bulk of both the income and wealth distributions seem to reasonably fit both the log-normal and Gamma distributions, while the tail of the distribution fits well to a power law (as first observed by sociologist Pareto). We also present our recent studies of the unit-level expenditure on consumption across multiple countries and multiple years, where it was found that there exist invariant features of consumption distribution: the bulk is log-normally distributed, followed by a power law tail at the limit. The mechanisms leading to such inequalities and invariant features for the distributions of socio-economic variables are not well-understood. We also present some simple models from physics and demonstrate how they can be used to explain some of these findings and ...
Mass Predictions of Atomic Nuclei in the Infinite Nuclear Matter Model
Nayak, R C
2012-01-01
We present here the mass excesses, binding energies, one- and two- neutron, one and two- proton and \\alpha-particle separation energies of 6727 nuclei in the ranges 4 \\leq Z \\leq 120 and 8 \\leq A \\leq 303 calculated in the infinite nuclear matter model. Compared to our predictions of 1999 mass table, the present ones are obtained using larger data base of 2003 mass table of Wapstra and Audi and resorting to higher accuracy in the solutions of the \\eta-differential equations of the INM model. The local energy \\eta's supposed to carry signature of the characteristic properties of nuclei are found to possess the predictive capability. In fact \\eta-systematics reveal new magic numbers in the drip-line regions giving rise to new islands of stability supported by relativistic mean field theoretic calculations. This is a manifestation of a new phenomenon where shell-effect overcomes the instability due to repulsive components of the nucleon-nucleon force broadening the stability peninsula. The two-neutron separation...
Applying a one-dimensional PDR model to the Taurus molecular cloud and its atomic envelope
Heiner, J S
2012-01-01
In this contribution, we test our previously published one-dimensional PDR model for deriving total hydrogen volume densities from HI column density measurements in extragalactic regions by applying it to the Taurus molecular cloud, where its predictions can be compared to available data. Also, we make the first direct detailed comparison of our model to CO(1-0) and far-infrared emission. Using an incident UV flux G0 of 4.25 ({\\chi} = 5) throughout the main body of the cloud, we derive total hydrogen volume densities of \\approx 430 cm-3, consistent with the extensive literature available on Taurus. The distribution of the volume densities shows a log-normal shape with a hint of a power-law shape on the high density end. We convert our volume densities to H2 column densities assuming a cloud depth of 5 parsec and compare these column densities to observed CO emission. We find a slope equivalent to a CO conversion factor relation that is on the low end of reported values for this factor in the literature (0.9 x...
Born, Max
1989-01-01
The Nobel Laureate's brilliant exposition of the kinetic theory of gases, elementary particles, the nuclear atom, wave-corpuscles, atomic structure and spectral lines, electron spin and Pauli's principle, quantum statistics, molecular structure and nuclear physics. Over 40 appendices, a bibliography, numerous figures and graphs.
Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.
2016-09-01
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an
Modeling of damages induced after photoactivation of heavy atoms incorporated at DNA
International Nuclear Information System (INIS)
The photo activation begins to be used for the treatment of certain cancers because it allows a more precise tumor irradiation and a reduction of the combined chemotherapy. A calculation model has been developed to simulate the photoactivation, the Auger effect and the X fluorescence, the transport of all these particles in a core particle and allowing the evaluation of primary DNA damages. The first experimental studies have shown the efficiency of the Cisplatin photo activated around its peak of the K photoabsorption. Here are presented the monte Carlo simulations of all these physical and chemical events, from the creation of particles until about 10-8 second. The yields of DNA strand breaks are deduced by using the direct ionizations of DNA and the reactions of species created during the radiolysis of surrounding water. (N.C.)
Size effects and strain localization in atomic-scale cleavage modeling.
Elsner, B A M; Müller, S
2015-09-01
In this work, we study the adhesion and decohesion of Cu(1 0 0) surfaces using density functional theory (DFT) calculations. An upper stress to surface decohesion is obtained via the universal binding energy relation (UBER), but the model is limited to rigid separation of bulk-terminated surfaces. When structural relaxations are included, an unphysical size effect arises if decohesion is considered to occur as soon as the strain energy equals the energy of the newly formed surfaces. We employ the nudged elastic band (NEB) method to show that this size effect is opposed by a size-dependency of the energy barriers involved in the transition. Further, we find that the transition occurs via a localization of bond strain in the vicinity of the cleavage plane, which resembles the strain localization at the tip of a sharp crack that is predicted by linear elastic fracture mechanics. PMID:26219654
Size effects and strain localization in atomic-scale cleavage modeling
International Nuclear Information System (INIS)
In this work, we study the adhesion and decohesion of Cu(1 0 0) surfaces using density functional theory (DFT) calculations. An upper stress to surface decohesion is obtained via the universal binding energy relation (UBER), but the model is limited to rigid separation of bulk-terminated surfaces. When structural relaxations are included, an unphysical size effect arises if decohesion is considered to occur as soon as the strain energy equals the energy of the newly formed surfaces. We employ the nudged elastic band (NEB) method to show that this size effect is opposed by a size-dependency of the energy barriers involved in the transition. Further, we find that the transition occurs via a localization of bond strain in the vicinity of the cleavage plane, which resembles the strain localization at the tip of a sharp crack that is predicted by linear elastic fracture mechanics. (paper)
Mass predictions of atomic nuclei in the infinite nuclear matter model
Nayak, R. C.; Satpathy, L.
2012-07-01
We present here the mass excesses, binding energies, one- and two-neutron, one- and two-proton and α-particle separation energies of 6727 nuclei in the ranges 4≤Z≤120 and 8≤A≤303 calculated in the infinite nuclear matter model. Compared to our predictions of 1999 mass table, the present ones are obtained using larger data base of 2003 mass table of Wapstra and Audi and resorting to higher accuracy in the solutions of the η-differential equations of the INM model. The local energy η's supposed to carry signature of the characteristic properties of nuclei are found to possess the predictive capability. In fact η-systematics reveal new magic numbers in the drip-line regions giving rise to new islands of stability supported by relativistic mean field theoretic calculations. This is a manifestation of a new phenomenon where shell-effect overcomes the instability due to repulsive components of the nucleon-nucleon force broadening the stability peninsula. The two-neutron separation energy-systematics derived from the present mass predictions reveal a general new feature for the existence of islands of inversion in the exotic neutron-rich regions of nuclear landscape, apart from supporting the presently known islands around 31Na and 62Ti. The five global parameters representing the properties of infinite nuclear matter, the surface, the Coulomb and the pairing terms are retained as per our 1999 mass table. The root-mean-square deviation of the present mass-fit to 2198 known masses is 342 keV, while the mean deviation is 1.3 keV, reminiscent of no left-over systematic effects. This is a substantive improvement over our 1999 mass table having rms deviation of 401 keV and mean deviation of 9 keV for 1884 data nuclei.
Directory of Open Access Journals (Sweden)
Li Yuqin
2014-01-01
Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.
Energy Technology Data Exchange (ETDEWEB)
Nguyen, Hung T. [BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States); Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States); Case, David A., E-mail: case@biomaps.rutgers.edu [BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States); Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854 (United States)
2014-12-14
A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb{sup +} and Sr{sup 2+}) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein–Zernike equations, with results from the Kovalenko–Hirata closure being closest to experiment for the cases studied here.
Ahmed, Maqsood; Nassour, Ayoub; Noureen, Sajida; Lecomte, Claude; Jelsch, Christian
2016-02-01
The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.
Average atom model based on Quantum Hyper-Netted Chain method
Chihara, Junzo
2016-06-01
The study shows how to define, without any ad hoc assumption, the average ion charge ZI in the electron-ion model for plasmas and liquid metals: this definition comes out of the condition that a plasma consisting of electrons and nuclei can be described as an electron-ion mixture. Based on this definition of the average ion charge, the Quantum Hyper-Netted Chain (QHNC) method takes account of the thermal ionization and the resonant-state contribution to the bound electrons forming an ion. On the other hand, Blenski and Cichocki (2007) have derived a formula to determine the uniform electron density in a plasma as an electron-ion mixture by using the variational method with the help of the local density approximation. Without use of any approximation, we derived the formula determining the electron density in an extended form on the basis of the density functional theory. This formula is shown to be valid also for the QHNC method.
Atomic scale modeling of defect production and microstructure evolution in irradiated metals
Energy Technology Data Exchange (ETDEWEB)
Diaz de la Rubia, T.; Soneda, N.; Shimomura, Y. [Lawrence Livermore National Lab., CA (United States)] [and others
1997-04-01
Irradiation effects in materials depend in a complex way on the form of the as-produced primary damage state and its spatial and temporal evolution. Thus, while collision cascades produce defects on a time scale of tens of picosecond, diffusion occurs over much longer time scales, of the order of seconds, and microstructure evolution over even longer time scales. In this report the authors present work aimed at describing damage production and evolution in metals across all the relevant time and length scales. They discuss results of molecular dynamics simulations of displacement cascades in Fe and V. They show that interstitial clusters are produced in cascades above 5 keV, but not vacancy clusters. Next, they discuss the development of a kinetic Monte Carlo model that enables calculations of damage evolution over much longer time scales (1000`s of s) than the picosecond lifetime of the cascade. They demonstrate the applicability of the method by presenting predictions on the fraction of freely migrating defects in {alpha}Fe during irradiation at 600 K.
Atomic-level description of protein-lipid interactions using an accelerated membrane model.
Baylon, Javier L; Vermaas, Josh V; Muller, Melanie P; Arcario, Mark J; Pogorelov, Taras V; Tajkhorshid, Emad
2016-07-01
Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein-membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics simulations offer a suitable approach to study protein-lipid interactions; however, the slow dynamics of the lipids often prevents sufficient sampling of specific membrane-protein interactions in atomistic simulations. To increase lipid dynamics while preserving the atomistic detail of protein-lipid interactions, in the highly mobile membrane-mimetic (HMMM) model the membrane core is replaced by an organic solvent, while short-tailed lipids provide a nearly complete representation of natural lipids at the organic solvent/water interface. Here, we present a brief introduction and a summary of recent applications of the HMMM to study different membrane proteins, complementing the experimental characterization of the presented systems, and we offer a perspective of future applications of the HMMM to study other classes of membrane proteins. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26940626
Atomic kinetic Monte Carlo modeling of multi-component Fe dilute alloys under irradiation
International Nuclear Information System (INIS)
The ageing of pressure vessel steels under radiation has been correlated with the formation of more or less dilute solute clusters which are investigated in this work using a multi-scale approach based on ab initio and atomistic kinetic Monte Carlo (AKMC) simulations. The microstructure evolution of Fe alloys is modeled by AKMC on a lattice, using pair interactions adjusted on DFT (Density Functional Theory) calculations. Several substitutional elements (Cu, Ni, Mn, Si, P) and foreign interstitials (C, N) are taken into account to describe the alloy. The point defect created by the irradiation, i.e. the vacancies and self interstitials have a tendency to form clusters. The evolution of these clusters is governed by the migration energy of the individual point defects which is very heavy in terms of computing time due to the large number of AKMC steps required. The structure of all the possible objects that can form is complex and some optimized and accelerated methods will be presented. The results obtained are in agreement with the experimental trends and indicate that the formation of solute clusters takes place via segregation mechanisms on the point defect clusters
Interacting atoms in optical lattices
Mentink, Johan; Kokkelmans, Servaas
2008-01-01
We propose an easy to use model to solve for interacting atoms in an optical lattice. This model allows for the whole range of weakly to strongly interacting atoms, and it includes the coupling between relative and center-of-mass motion via anharmonic lattice terms. We apply this model to a high-precision spin dynamics experiment, and we discuss the corrections due to atomic interactions and the anharmonic coupling. Under suitable experimental conditions, energy can be transferred between the...
Directory of Open Access Journals (Sweden)
Graves N.
2013-01-01
Full Text Available A model is proposed for the hydrogen atom in which the electron is an objectively real particle orbiting at very near to light speed. The model is based on the postulate that certain velocity terms associated with orbiting bodies can be considered as being af- fected by relativity. This leads to a model for the atom in which the stable electron orbits are associated with orbital velocities where Gamma is n /α , leading to the idea that it is Gamma that is quantized and not angular momentum as in the Bohr and other models. The model provides a mechanism which leads to quantization of energy levels within the atom and also provides a simple mechanical explanation for the Fine Struc- ture Constant. The mechanism is closely associated with the Sampling theorem and the related phenomenon of aliasing developed in the mid-20th century by engineers at Bell labs.
Kaplan, David E.; Krnjaic, Gordan Z.; Rehermann, Keith R.; Wells, Christopher M.
2009-01-01
We propose that dark matter is dominantly comprised of atomic bound states. We build a simple model and map the parameter space that results in the early universe formation of hydrogen-like dark atoms. We find that atomic dark matter has interesting implications for cosmology as well as direct detection: Protohalo formation can be suppressed below $M_{proto} \\sim 10^3 - 10^6 M_{\\odot}$ for weak scale dark matter due to Ion-Radiation interactions in the dark sector. Moreover, weak-scale dark a...
International Nuclear Information System (INIS)
This book is an introduction to modern physics for undergraduate students of physics or students of related fields. After an introduction to the wave-particle dualism the structure of atoms is considered with regards to atomic models. Then the foundations of quantum mechanics are introduced with regards to their application to atomic structure calculations. Thereafter the chemical bond and the molecular structure are discussed. Then classical and quantum statistical mechanics are introduced. Thereafter the crystal binding, the crystal structure, and the specific heat of solids are considered. Finally the band theory of solids is briefly introduced. Every chapter contains exercise problems. (HSI)
Energy Technology Data Exchange (ETDEWEB)
Zemskova, Varvara [Department of Marine Sciences, University of North Carolina at Chapel Hill, 3202 Venable Hall, CB 3300, Chapel Hill, NC 27599-3300 (United States); Garaud, Pascale [Department of Applied Mathematics and Statistics, Baskin School of Engineering, University of California at Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 (United States); Deal, Morgan; Vauclair, Sylvie [Institut de Recherche en Astrophysique et Planétologie, 14 avenue Edouard Belin, Université de Toulouse, F-31400-Toulouse (France)
2014-11-10
Iron-rich layers are known to form in the stellar subsurface through a combination of gravitational settling and radiative levitation. Their presence, nature, and detailed structure can affect the excitation process of various stellar pulsation modes and must therefore be modeled carefully in order to better interpret Kepler asteroseismic data. In this paper, we study the interplay between atomic diffusion and fingering convection in A-type stars, as well as its role in the establishment and evolution of iron accumulation layers. To do so, we use a combination of three-dimensional idealized numerical simulations of fingering convection (which neglect radiative transfer and complex opacity effects) and one-dimensional realistic stellar models. Using the three-dimensional simulations, we first validate the mixing prescription for fingering convection recently proposed by Brown et al. (within the scope of the aforementioned approximation) and identify what system parameters (total mass of iron, iron diffusivity, thermal diffusivity, etc.) play a role in the overall evolution of the layer. We then implement the Brown et al. prescription in the Toulouse-Geneva Evolution Code to study the evolution of the iron abundance profile beneath the stellar surface. We find, as first discussed by Théado et al., that when the concurrent settling of helium is ignored, this accumulation rapidly causes an inversion in the mean molecular weight profile, which then drives fingering convection. The latter mixes iron with the surrounding material very efficiently, and the resulting iron layer is very weak. However, taking helium settling into account partially stabilizes the iron profile against fingering convection, and a large iron overabundance can accumulate. The opacity also increases significantly as a result, and in some cases it ultimately triggers dynamical convection. The direct effects of radiative acceleration on the dynamics of fingering convection (especially in the
Zemskova, Varvara; Garaud, Pascale; Deal, Morgan; Vauclair, Sylvie
2014-11-01
Iron-rich layers are known to form in the stellar subsurface through a combination of gravitational settling and radiative levitation. Their presence, nature, and detailed structure can affect the excitation process of various stellar pulsation modes and must therefore be modeled carefully in order to better interpret Kepler asteroseismic data. In this paper, we study the interplay between atomic diffusion and fingering convection in A-type stars, as well as its role in the establishment and evolution of iron accumulation layers. To do so, we use a combination of three-dimensional idealized numerical simulations of fingering convection (which neglect radiative transfer and complex opacity effects) and one-dimensional realistic stellar models. Using the three-dimensional simulations, we first validate the mixing prescription for fingering convection recently proposed by Brown et al. (within the scope of the aforementioned approximation) and identify what system parameters (total mass of iron, iron diffusivity, thermal diffusivity, etc.) play a role in the overall evolution of the layer. We then implement the Brown et al. prescription in the Toulouse-Geneva Evolution Code to study the evolution of the iron abundance profile beneath the stellar surface. We find, as first discussed by Théado et al., that when the concurrent settling of helium is ignored, this accumulation rapidly causes an inversion in the mean molecular weight profile, which then drives fingering convection. The latter mixes iron with the surrounding material very efficiently, and the resulting iron layer is very weak. However, taking helium settling into account partially stabilizes the iron profile against fingering convection, and a large iron overabundance can accumulate. The opacity also increases significantly as a result, and in some cases it ultimately triggers dynamical convection. The direct effects of radiative acceleration on the dynamics of fingering convection (especially in the
Le Coq, Yann; Thywissen, Joseph H.; Rangwala, Sadiq A.; Gerbier, Fabrice; Richard, Simon; Delannoy, Guillaume; Bouyer, Philippe; Aspect, Alain
2001-01-01
We measure the angular divergence of a quasi-continuous, rf-outcoupled, free-falling atom laser as a function of the outcoupling frequency. The data is compared to a Gaussian-beam model of laser propagation that generalizes the standard formalism of photonic lasers. Our treatment includes diffraction, magnetic lensing, and interaction between the atom laser and the condensate. We find that the dominant source of divergence is the condensate-laser interaction.
Leenaarts, J; Carlsson, M; Uitenbroek, H; de Pontieu, B
2013-01-01
NASA's Interface Region Imaging Spectrograph (IRIS) space mission will study how the solar atmosphere is energized. IRIS contains an imaging spectrograph that covers the Mg II h&k lines as well as a slit-jaw imager centered at Mg II k. Understanding the observations will require forward modeling of Mg II h&k line formation from 3D radiation-MHD models. This paper is the first in a series where we undertake this forward modeling. We discuss the atomic physics pertinent to h&k line formation, present a quintessential model atom that can be used in radiative transfer computations and discuss the effect of partial redistribution (PRD) and 3D radiative transfer on the emergent line profiles. We conclude that Mg II h&k can be modeled accurately with a 4-level plus continuum Mg II model atom. Ideally radiative transfer computations should be done in 3D including PRD effects. In practice this is currently not possible. A reasonable compromise is to use 1D PRD computations to model the line profile up ...
International Nuclear Information System (INIS)
This paper describes an experimental and numerical modeling on microscopic droplet behaviors and macroscopic atomization characteristics of diesel and bio-diesel fuels under the conditions of air cross-flow. In order to obtain the experimental air-assisted-droplet behavior and breakup characteristics, deformation ratio, droplet trajectory, and droplet size distribution were investigated quantitatively for different droplet breakup mechanisms. In order to assess prediction accuracies of the original spray models contained in the standard CFD code and validate the currently modified and suggested models, the computations were implemented using the KIVA-3V code with a three dimensional computational mesh and compared to the experimental results. Because the original TAB model and droplet drag model tend to predict the unphysical breakup characteristics, to improve the calculation accuracy, the model constants of the droplet motion equation in the TAB model and the droplet drag model were modified and optimized. In addition, a new model for determining the droplet size after breakup is currently suggested, because original model does not consider the frictional flow inside a droplet, resulting in impractical droplet size results. Based on inspections of the measured and calculated results, outcomes of atomization characteristics from modified models give a reasonable droplet deformation rate and also show the appropriate droplet trajectory at the first breakup stage. In the results of droplet breakup and atomization, the modified models give improved prediction accuracy on the droplet size distribution better than the standard models. But there still shows a little discrepancy between calculated and measured droplet size and its distribution pattern. It seems to be caused by the own assumption of the TAB model which is based only on the vibration and breakup mechanism.
International Nuclear Information System (INIS)
In this work, a series of aging treatments has been conducted on AA6111 alloy samples for various times at ambient temperature (so-called natural aging) and at temperatures between 60 and 180 °C (artificially aged). The time at artificial ageing was chosen such that samples with approximately the same yield stress were produced. The microstructures of these alloy samples have been carefully characterized using atom probe tomography together with advanced cluster-finding techniques in order to obtain quantitative information about the changes in distribution of both the solute clusters and early-stage precipitates that are formed. The size distribution of clusters has been mapped onto the glide plane and then the stress necessary for a dislocation to pass through the range of obstacles has been estimated using an areal glide model where the dislocation–obstacle interaction strength has been assumed to be related to the obstacle size on the glide plane. It is demonstrated that the contribution of cluster strengthening during artificial aging at higher temperatures is dominated by the high number density of small clusters (Guinier radius <1 nm), whereas the situation during room temperature natural aging is more complex
Sarkadi, L
2015-01-01
The three-body dynamics of the ionization of the atomic hydrogen by 30 keV antiproton impact has been investigated by calculation of fully differential cross sections (FDCS) using the classical trajectory Monte Carlo (CTMC) method. The results of the calculations are compared with the predictions of quantum mechanical descriptions: The semi-classical time-dependent close-coupling theory, the fully quantal, time-independent close-coupling theory, and the continuum-distorted-wave-eikonal-initial-state model. In the analysis particular emphasis was put on the role of the nucleus-nucleus (NN) interaction played in the ionization process. For low-energy electron ejection CTMC predicts a large NN interaction effect on FDCS, in agreement with the quantum mechanical descriptions. By examining individual particle trajectories it was found that the relative motion between the electron and the nuclei is coupled very weakly with that between the nuclei, consequently the two motions can be treated independently. A simple ...
International Nuclear Information System (INIS)
We check the validity of the frozen-core approximation (FCA) in time-dependent density functional theory (TDDFT) for an atom interacting with a laser field. For this purpose we investigate an exactly solvable 1D model for Li with the help of TDDFT considering different exchange-correlation (XC) functionals. Observables such as the ionisation rate, the energy absorption rate and the dipole expectation value are obtained with and without FCA. Comparisons among the different TDDFT results on one hand and with the exact numerical solution of the time-dependent Schroedinger equation on the other hand show that the propagation of core electrons in time does significantly affect the observables of the valence electron. Additionally, we find a strong dependency of TDDFT observables on the XC functional used even though the values for the ionisation potentials are equal. We conclude that pseudopotentials (which apply the FCA or even bolder approximations) must yield inaccurate results in TDDFT simulations of strong-field ionization even for an otherwise exact XC functional.
Rathore, Bhavna
2015-01-01
The 133.5 nm lines are important observables for the NASA/SMEX mission Interface Region Imaging Spectrograph (IRIS). To make 3D non-LTE radiative transfer computationally feasible it is crucial to have a model atom with as few levels as possible while retaining the main physical processes. We here develop such a model atom and we study the general formation properties of the C II lines. We find that a nine-level model atom of C I-C III with the transitions treated assuming complete frequency redistribution (CRD) suffices to describe the 133.5 nm lines. 3D scattering effects are important for the intensity in the core of the line. The lines are formed in the optically thick regime. The core intensity is formed in layers where the temperature is about 10kK at the base of the transition region. The lines are 1.2-4 times wider than the atomic absorption profile due to the formation in the optically thick regime. The smaller opacity broadening happens for single peak intensity profiles where the chromospheric temp...
El-Orany, Faisal A A
2009-01-01
In this paper, we develop the notion of the linear atomic quantum coupler. This device consists of two modes propagating into two waveguides, each of them includes a localized and/or a trapped atom. These waveguides are placed close enough to allow exchanging energy between them via evanescent waves. Each mode interacts with the atom in the same waveguide in the standard way, i.e. as the Jaynes-Cummings model (JCM), and with the atom-mode in the second waveguide via evanescent wave. We present the Hamiltonian for the system and deduce the exact form for the wavefunction. We investigate the atomic inversions and the second-order correlation function. In contrast to the conventional linear coupler, the atomic quantum coupler is able to generate nonclassical effects. The atomic inversions can exhibit long revival-collapse phenomenon as well as subsidiary revivals based on the competition among the switching mechanisms in the system. Finally, under certain conditions, the system can yield the results of the two-m...
Tavis-Cummings模型中原子的纠缠度%Entanglement of atoms in Tavis-Cummings model
Institute of Scientific and Technical Information of China (English)
董传华; 张亚利
2006-01-01
Entanglement is used to measure correlation between separated subsystems. yon Neumann entropy is used to study evolutions of entanglement of atoms in processes of interaction between atoms with the field prepared in coherent state. The effects of field intensity and detuning on entanglement are investigated. It is shown that the entanglement exhibited oscillations in its evolutions, their amplitudes and mean values decrease with increasing field intensity. Oscillation frequencies increase with detuning, but the maximum values are almost independent of detuning.
International Nuclear Information System (INIS)
An article, The H-Bomb Secret: How We Got It, Why We're Telling It, by Howard Morland was to be published in The Progressive magazine in February, 1979. The government, after learning of the author's and the editors' intention to publish the article and failing to persuade them to voluntarily delete about 20% of the text and all of the diagrams showing how an H-bomb works, requested a court injunction against publication. Acting under the Atomic Energy Act of 1954, US District Court Judge Robert W. Warren granted the government's request on March 26. Events dealing with the case are discussed in this publication. Section 1, Progressive Hydrogen Bomb Case, is discussed under the following: Court Order Blocking Magazine Report; Origins of the Howard Morland Article; Author's Motives, Defense of Publication; and Government Arguments Against Disclosure. Section 2, Access to Atomic Data Since 1939, contains information on need for secrecy during World War II; 1946 Atomic Energy Act and its effects; Soviet A-Bomb and the US H-Bomb; and consequences of 1954 Atomic Energy Act. Section 3, Disputed Need for Atomic Secrecy, contains papers entitled: Lack of Studies on H-Bomb Proliferation; Administration's Position on H-Bombs; and National Security Needs vs Free Press
Loring, FH
2014-01-01
Summarising the most novel facts and theories which were coming into prominence at the time, particularly those which had not yet been incorporated into standard textbooks, this important work was first published in 1921. The subjects treated cover a wide range of research that was being conducted into the atom, and include Quantum Theory, the Bohr Theory, the Sommerfield extension of Bohr's work, the Octet Theory and Isotopes, as well as Ionisation Potentials and Solar Phenomena. Because much of the material of Atomic Theories lies on the boundary between experimentally verified fact and spec
Faroque, Muhammad Umer; Yousuf, Sammer; Zafar, Salman; Choudhary, M Iqbal; Ahmed, Maqsood
2016-05-01
Biotransformation is the structural modification of compounds using enzymes as the catalysts and it plays a key role in the synthesis of pharmaceutically important compounds. 10β,17β-Dihydroxy-17α-methylestr-4-en-3-one dihydrate, C19H28O3·2H2O, was obtained from the fungal biotransformation of methyloestrenolone. The structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results from the two refinements have been compared. The ELMAM2 refinement has been found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution.
Energy Technology Data Exchange (ETDEWEB)
Nishikawa, T. [Okayama Univ. (Japan). Faculty of Engineering; Kawachi, T.; Nishihara, K.; Fujimoto, T.
1995-09-01
We have assessed atomic data for lithium-like ions for the purpose of constructing a reliable collisional-radiative model. We show several examples of the atomic data for aluminum and oxygen ions, and comparison of data from several sources is done in detail. For ions with nuclear charge z, the scaling formulas and fitting parameters, which are based on the data of oxygen ions, are presented. By use of these data, we have constructed two collisional-radiative models: the one for aluminum ions and the one for ions according to the scaling for z. The population inversion and the amplification gain of the soft x-ray laser lines in the recombining aluminum plasma are calculated for several electron temperatures. We also examine the effects of ion collisions for {Delta}n=0 transitions on the excited level populations.
Peach, G; Beams, T J; Peach, Gillian; Whittingham, Ian B; Beams, Timothy J
2002-01-01
A novel modified oscillator method of calculating energy eigenvalues for colliding ultracold atoms tightly confined in harmonic potentials is presented and applied to trapped spin-polarized metastable helium atoms. The perturbed harmonic oscillator problem is characterized by a long asymptotic region beyond the effective range of the interatomic potential, and a very efficient method for integrating inwards through this outer region is developed. The calculated eigenvalues for states with $l=0$ agree closely with those computed directly from the radial Schr\\"{o}dinger equation for the trapped atoms using a discrete variable method, and with those computed self-consistently from an energy-dependent effective scattering length. Finally, the self-consistent method is generalized to collisions with $l \
International Nuclear Information System (INIS)
Among the mainly interesting parameters of an atomic vapour laser isotope separation process is the ionization yield. This parameter can be controlled as long as the laser beam spatial intensity distribution and temporal shape are well defined and not subjected to unexpected disturbing effects such as coherent propagation phenomena, leading to spatial and temporal reshaping with hot spots and pulse lengthening and delays. On an other hand, economical considerations require optically thick atomic columns which can favour such effect. In this work is studied the photoionization yield in atomic thulium vapour when propagation effects occur. Experimental results are compared with those of a coherent propagation code describing a four level system and including inhomogeneous broadening as well as degeneracies. A three step photoionization scheme is chosen
International Nuclear Information System (INIS)
Among the interesting parameters of an atomic vapor laser isotope separation process is the ionization yield. This parameter can be controlled as long as the laser beam spatial intensity distribution and temporal shape are well defined and not subjected to unexpected disturbing effects such as coherent propagation phenomena, leading to spatial and temporal reshaping with hot spots and pulse lengthening and delays. On the other hand, economic considerations require optically thick atomic columns which can favor such effects. In this work, the authors study the photoionization yield in atomic thulium vapor when propagation effects occur. The authors compare their experimental results with those of a coherent propagation code describing a four level system and including inhomogeneous broadening as well as degeneracies. They choose a three step photoionization scheme whose main parameters are given
International Nuclear Information System (INIS)
Though density functional theory is already developed in useful practical numerical forms, no explicit simple ground-state energy density functional exists. Here, towards establishing such a theory, we present the ground-state energy of the Crandall et al.'s two-electron spin-compensated model atom in terms of ∇2ρ(r)/ρ(r) evaluated at r=0, where ρ(r) is the electron density.
Ionization of Atoms and the Thomas-Fermi Model for the Electric Field in Crystal Planar Channels
Institute of Scientific and Technical Information of China (English)
LIU Ying-Tai; ZHANG Qi-Ren; GAO Chun-Yuan
2002-01-01
The electric field in the crystal planar channels is studied by the Thomas Fermi method. The Thomas-Fermi equation and the corresponding boundary conditions are derived for the crystal planar channels. The numericalsolution for the electric field in the channels between (110) planes of the single crystal silicon and the critical angles ofchannelling protons in them are shown. Reasonable agreements with the experimental data are obtained. The resultsshow that the Thomas-Fermi method for the crystal works well in this study, and a microscopic research of the channelelectric field with the contribution of all atoms and the atomic ionization being taken into account is practical.
Light scattering from dense cold atomic media
Zhu, Bihui; Ye, Jun; Rey, Ana Maria
2016-01-01
We theoretically study the propagation of light through a cold atomic medium, where the effects of motion, laser intensity, atomic density, and polarization can all modify the properties of the scattered light. We present two different microscopic models: the "coherent dipole model" and the "random walk model", both suitable for modeling recent experimental work done in large atomic arrays in the low light intensity regime. We use them to compute relevant observables such as the linewidth, peak intensity and line center of the emitted light. We further develop generalized models that explicitly take into account atomic motion. Those are relevant for hotter atoms and beyond the low intensity regime. We show that atomic motion can lead to drastic dephasing and to a reduction of collective effects, together with a distortion of the lineshape. Our results are applicable to model a full gamut of quantum systems that rely on atom-light interactions including atomic clocks, quantum simulators and nanophotonic system...
Saidi, Wissam A; Norman, Patrick
2016-07-14
The van der Waals C6 coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C6 ∝ N(2.2) as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N(2.75) as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes by fitting against accurate ab initio calculations. This model shows that C6 ∝ N(2.8), which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole-dipole term scales almost linearly with the number of carbon atoms.
Saidi, Wissam A.; Norman, Patrick
2016-07-01
The van der Waals C6 coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C6 ∝ N2.2 as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N2.75 as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes by fitting against accurate ab initio calculations. This model shows that C6 ∝ N2.8, which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole-dipole term scales almost linearly with the number of carbon atoms.
Levashov, Valentin A.
2015-01-01
It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of t...
International Nuclear Information System (INIS)
To calculate the ion fractional abundance of every charge state with the short computation time, we tried to build a suitable model for describing atomic processes. In 1982, Busquet proposed a mixed model, where he introduced two superlevels. They are related to a ground state and a ionized state, respectively, and the local-thermodynamic equilibrium (LET) is assumed over the excited states with the ionized state. In order to treat the atomic processes more accurately, we introduce the three superlevels which are the ground state, the first excited state and ionized state. The transition rates between them are evaluated by using Burguess formula which is used in the rate equations. The present model (Extended Mixed Model; EMM) gives results closer to the collisional-radiative model (CRM) than the original mixed model. The emissivity calculated by average-ion model (AIM) is compared with the one by EMM. The x-ray spectra are also obtained by using the EMM together with the hydrodynamic implosion code HIMICO. (author)
Entropy squeezing for a two-level atom in two-mode Raman coupled model with intrinsic decoherence
Institute of Scientific and Technical Information of China (English)
Zhang Jian; Shao Bin; Zou Jian
2009-01-01
In this paper,we investigate the entropy squeezing for a two-level atom interacting with two quantized fields through Raman coupling.We obtain the dynamical evolution of the total system under the influence of intrinsic decoherence when the two quantized fields are prepared in a two-mode squeezing vacuum state initially.The effects of the field squeezing factor,the two-level atomic transition frequency,the second field frequency and the intrinsic decoherence on the entropy squeezing are discussed.Without intrinsic decoherence,the increase of field squeezing factor can break the entropy squeezing.The two-level atomic transition frequency changes only the period of oscillation but not the strength of entropy squeezing.The influence of the second field frequency is complicated.With the intrinsic decoherence taken into consideration,the results show that the stronger the intrinsic decoherence is,the more quickly the entropy squeezing will disappear.The increase of the atomic transition frequency can hasten the disappearance of entropy squeezing.
International Nuclear Information System (INIS)
Highlights: ► In this study we model the adsorption of the superheavy element 113 on gold surfaces. ► The binding energy of element 113 and thallium is calculated for cluster models. ► For many different binding sites, element 113 binds weaker by 90 ± 15 kJ/mol. - Abstract: The adsorption of thallium and element 113 atoms on a gold surface has been modelled by cluster calculations. Quasirelativistic two-component density functional calculations that include spin–orbit coupling self-consistently have been used together with spin-dependent effective core potentials. The validity of this method is demonstrated by comparisons with high-level wave function based calculations on the hetero-dimers AuTl and Au(113). New basis sets had to be generated because standard basis sets optimized for scalar-relativistic calculations are too inflexible to describe the different behaviour of the atomic sub-shells that result from the spin–orbit interaction. The topmost layer of gold atoms within the cluster was allowed to fully relax upon adsorption, and different adsorption sites (on-top, hollow, and bridge) on the (1 0 0) and (1 1 1) surfaces were considered. Spin–orbit coupling reduces the surface binding energies of an element 113 atom much more than it does for Tl, such that the binding energy of element 113 to the gold cluster, as compared to Tl, is reduced by 90 ± 15 kJ/mol in most cases. Together with the experimental result for thallium, this allows an estimate of the adsorption temperature of element 113 in thermochromatography experiments.
Crease, Robert P.
2009-01-01
The American composer John Adams uses opera to dramatize controversial current events. His 1987 work Nixon in China was about the landmark meeting in 1972 between US President Richard Nixon and Chairman Mao Zedong of China; The Death of Klinghoffer (1991) was a musical re-enactment of an incident in 1985 when Palestinian terrorists kidnapped and murdered a wheelchair-bound Jewish tourist on a cruise ship. Adams's latest opera, Doctor Atomic, is also tied to a controversial event: the first atomic-bomb test in Alamogordo, New Mexico, on 16 June 1945. The opera premièred in San Francisco in 2005, had a highly publicized debut at the Metropolitan Opera in New York in 2008, and will have another debut on 25 February - with essentially the same cast - at the English National Opera in London.
Energy Technology Data Exchange (ETDEWEB)
Livingston, A.E.; Kukla, K.; Cheng, S. [Univ. of Toledo, OH (United States)] [and others
1995-08-01
In a collaboration with the Atomic Physics group at Argonne and the University of Toledo, the Atomic Physics group at the University of Notre Dame is measuring the fine structure transition energies in highly-charged lithium-like and helium-like ions using beam-foil spectroscopy. Precise measurements of 2s-2p transition energies in simple (few-electron) atomic systems provide stringent tests of several classes of current atomic- structure calculations. Analyses of measurements in helium-like Ar{sup 16+} have been completed, and the results submitted for publication. A current goal is to measure the 1s2s{sup 3}S{sub 1} - 1s2p{sup 3}P{sub 0} transition wavelength in helium-like Ni{sup 26+}. Measurements of the 1s2s{sup 2}S{sub 1/2} - 1s2p{sup 2}P{sub 1/2,3/2} transition wavelengths in lithium-like Kr{sup 33+} is planned. Wavelength and lifetime measurements in copper-like U{sup 63+} are also expected to be initiated. The group is also participating in measurements of forbidden transitions in helium-like ions. A measurement of the lifetime of the 1s2s{sup 3}S{sub 1} state in Kr{sup 34+} was published recently. In a collaboration including P. Mokler of GSI, Darmstadt, measurements have been made of the spectral distribution of the 2E1 decay continuum in helium-like Kr{sup 34+}. Initial results have been reported and further measurements are planned.
Conformal atoms in Supergravity
Jankowski, Jakub
2016-01-01
In this note, we summarize recent attempts to construct holographic models of atoms and lattices in the context of applications to solid state physics. The simplest setup turned out to impose strong constraints on the choice of matter interactions of dual gravitational theory.
Zhou, Chong-Wen; Simmie, John M; Pitz, William J; Curran, Henry J
2016-09-15
Theoretical aspects of the development of a chemical kinetic model for the pyrolysis and combustion of a cyclic ketone, cyclopentanone, are considered. Calculated thermodynamic and kinetic data are presented for the first time for the principal species including 2- and 3-oxo-cyclopentyl radicals, which are in reasonable agreement with the literature. These radicals can be formed via H atom abstraction reactions by Ḣ and Ö atoms and ȮH, HȮ2, and ĊH3 radicals, the rate constants of which have been calculated. Abstraction from the β-hydrogen atom is the dominant process when ȮH is involved, but the reverse holds true for HȮ2 radicals. The subsequent β-scission of the radicals formed is also determined, and it is shown that recent tunable VUV photoionization mass spectrometry experiments can be interpreted in this light. The bulk of the calculations used the composite model chemistry G4, which was benchmarked in the simplest case with a coupled cluster treatment, CCSD(T), in the complete basis set limit. PMID:27558073
Polarized atomic hydrogen beam
Energy Technology Data Exchange (ETDEWEB)
Chan, N.; Crowe, D.M.; Lubell, M.S.; Tang, F.C.; Vasilakis, A.; Mulligan, F.J.; Slevin, J.
1988-12-01
We describe the design and operating characteristics of a simple polarized atomic hydrogen beam particularly suitable for applications to crossed beams experiments. In addition to experimental measurements, we present the results of detailed computer models, using Monte-Carlo ray tracing techniques, optical analogs, and phase-space methods, that not only provide us with a confirmation of our measurement, but also allow us to characterize the density, polarization, and atomic fraction of the beam at all points along its path. As a subsidiary result, we also present measurements of the relative and absolute efficiencies of the V/G Supavac mass analyzer for masses 1 and 2.
Happer, William; Walker, Thad
2010-01-01
Covering the most important knowledge on optical pumping of atoms, this ready reference is backed by numerous examples of modelling computation for optical pumped systems. The authors show for the first time that modern scientific computing software makes it practical to analyze the full, multilevel system of optically pumped atoms. To make the discussion less abstract, the authors have illustrated key points with sections of MATLAB codes. To make most effective use of contemporary mathematical software, it is especially useful to analyze optical pumping situations in the Liouville spa
Atomic CP-violating polarizability
Ravaine, Boris; Kozlov, M. G.; Derevianko, Andrei
2005-01-01
Searches for CP violating effects in atoms and molecules provide important constrains on competing extensions to the standard model of elementary particles. In particular, CP violation in an atom leads to the CP-odd (T,P-odd) polarizability $\\beta^\\mathrm{CP}$: a magnetic moment $\\mu^\\mathrm{CP}$ is induced by an electric field $\\mathcal{E}_0$ applied to an atom, $\\mu^\\mathrm{CP} = \\beta^\\mathrm{CP} \\mathcal{E}_0 $. We estimate the CP-violating polarizability for rare-gas (diamagnetic) atoms ...
Atomic toposes and countable categoricity
Caramello, Olivia
2008-01-01
We give a model-theoretic characterization of the class of geometric theories classified by an atomic topos having enough points; in particular, we show that every complete geometric theory classified by an atomic topos is countably categorical. Some applications are also discussed.
Ionization of Atoms and the Thomas－Fermi Model for the Electric Field in Crystal Planar Channels
Institute of Scientific and Technical Information of China (English)
LIUYing－Tai; ZHANGQi－Ren; 等
2002-01-01
The electric field in the crystal planar channels is studied by the Thomas-Fermi method.The ThomasFermi equation and the corresponding boundary conditions are derived for the crystal palanar channels,The numerical solution for the elctric field in the channels between(110) Planes of the single crystal silicaon and the critical angles of channelling protons in them are shown.Reasonable agreements with the experimental data are obtained.The results show that the Thomas-Fermi method for the crystal works well in this study,and a microscopic research of the channel electric field with the contribution of all atoms and the atomic ionization being taken into account is practical.
Experiments in cold atom optics towards precision atom interferometry
Aveline, David C.
Atom optics has been a highly active field of research with many scientific breakthroughs over the past two decades, largely due to successful advances in laser technology, microfabrication techniques, and the development of laser cooling and trapping of neutral atoms. This dissertation details several atom optics experiments with the motivation to develop tools and techniques for precision atom wave interferometry. It provides background information about atom optics and the fundamentals behind laser cooling and trapping, including basic techniques for cold gas thermometry and absorptive detection of atoms. A brief overview of magnetic trapping and guiding in tight wire-based traps is also provided before the experimental details are presented. We developed a novel laser source of 780 nm light using frequency-doubled 1560 nm fiber amplifier. This laser system provided up to a Watt of tunable frequency stabilized light for two Rb laser cooling and trapping experiments. One system generates Bose-Einstein condensates in an optical trap while the second is based on atom chip magnetic traps. The atom chip system, detailed in this thesis, was designed and built to develop the tools necessary for transport and loading large numbers of cold atoms and explore the potential for guided atom interferometry. Techniques and results from this experiment are presented, including an efficient magnetic transport and loading method to deliver cold atom to atom chip traps. We also developed a modeling tool for the magnetic fields formed by coiled wire geometries, as well as planar wire patterns. These models helped us design traps and determine adiabatic transportation of cold atoms between macro-scale traps and micro-traps formed on atom chips. Having achieved near unity transfer efficiency, we demonstrated that this approach promises to be a consistent method for loading large numbers of atoms into micro-traps. Furthermore, we discuss an in situ imaging technique to investigate
Bright Solitons in an Atomic Tunnel Array with Either Attractive or Repulsive Atom-Atom Interactions
Institute of Scientific and Technical Information of China (English)
YANG Xiao-Xue; YOU Jun; WU Ying
2004-01-01
@@ Taking a coherent state representation, we derive the nonlinear Schrodinger-type differential-difference equations from the quantized model of an array of traps containing Bose-Einstein condensates and linked by the tunnelling process among the adjacent traps. It is shown that no matter whether two-body interactions among atoms are repulsive or attractive, a nearly uniform atom distribution can evolve into a bright soliton-type localized ensemble of atoms and a lump of atom distribution can also be smeared out by redistributing atoms among traps under appropriate initial phase differences of atoms in adjacent traps. These two important features originate from the tailoring effect of the initial phase conditions in coherent tunnelling processes, which differs crucially from the previous tailoring effect coming mainly from the periodicity of optical lattices.
Paulraj, D.; Swamynathan, S.; Madhaiyan, M.
2012-11-01
Web Service composition has become indispensable as a single web service cannot satisfy complex functional requirements. Composition of services has received much interest to support business-to-business (B2B) or enterprise application integration. An important component of the service composition is the discovery of relevant services. In Semantic Web Services (SWS), service discovery is generally achieved by using service profile of Ontology Web Languages for Services (OWL-S). The profile of the service is a derived and concise description but not a functional part of the service. The information contained in the service profile is sufficient for atomic service discovery, but it is not sufficient for the discovery of composite semantic web services (CSWS). The purpose of this article is two-fold: first to prove that the process model is a better choice than the service profile for service discovery. Second, to facilitate the composition of inter-organisational CSWS by proposing a new composition method which uses process ontology. The proposed service composition approach uses an algorithm which performs a fine grained match at the level of atomic process rather than at the level of the entire service in a composite semantic web service. Many works carried out in this area have proposed solutions only for the composition of atomic services and this article proposes a solution for the composition of composite semantic web services.
Atom Skimmers and Atom Lasers Utilizing Them
Hulet, Randall; Tollett, Jeff; Franke, Kurt; Moss, Steve; Sackett, Charles; Gerton, Jordan; Ghaffari, Bita; McAlexander, W.; Strecker, K.; Homan, D.
2005-01-01
Atom skimmers are devices that act as low-pass velocity filters for atoms in thermal atomic beams. An atom skimmer operating in conjunction with a suitable thermal atomic-beam source (e.g., an oven in which cesium is heated) can serve as a source of slow atoms for a magneto-optical trap or other apparatus in an atomic-physics experiment. Phenomena that are studied in such apparatuses include Bose-Einstein condensation of atomic gases, spectra of trapped atoms, and collisions of slowly moving atoms. An atom skimmer includes a curved, low-thermal-conduction tube that leads from the outlet of a thermal atomic-beam source to the inlet of a magneto-optical trap or other device in which the selected low-velocity atoms are to be used. Permanent rare-earth magnets are placed around the tube in a yoke of high-magnetic-permeability material to establish a quadrupole or octupole magnetic field leading from the source to the trap. The atoms are attracted to the locus of minimum magnetic-field intensity in the middle of the tube, and the gradient of the magnetic field provides centripetal force that guides the atoms around the curve along the axis of the tube. The threshold velocity for guiding is dictated by the gradient of the magnetic field and the radius of curvature of the tube. Atoms moving at lesser velocities are successfully guided; faster atoms strike the tube wall and are lost from the beam.
Peng, Junhui; Zhang, Zhiyong
2016-07-01
Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1–3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.
Peng, Junhui; Zhang, Zhiyong
2016-07-01
Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.
Decoherence Spectroscopy for Atom Interferometry
Directory of Open Access Journals (Sweden)
Raisa Trubko
2016-08-01
Full Text Available Decoherence due to photon scattering in an atom interferometer was studied as a function of laser frequency near an atomic resonance. The resulting decoherence (contrast-loss spectra will be used to calibrate measurements of tune-out wavelengths that are made with the same apparatus. To support this goal, a theoretical model of decoherence spectroscopy is presented here along with experimental tests of this model.
Bhadoriya, Kamlendra Singh; Sharma, Mukesh C.; Jain, Shailesh V.
2015-02-01
Icmt enzymes are of particular importance in the post-translational modification of proteins that are involved in the regulation of cell growth. Thus, effective Icmt inhibitors may be of significant therapeutic importance in oncogenesis. To determine the structural requirements responsible for high affinity of previously reported amino derivatives of indole as Icmt inhibitors, a successful pharmacophore generation and atom-based 3D-QSAR analysis have been carried out. The best four-point pharmacophore model with four features HHRR: two hydrophobic groups (H) and two aromatic rings (R) as pharmacophore features was developed by PHASE module of Schrodinger suite. In this study, highly predictive 3D-QSAR models have been developed for Icmt inhibition using HHRR.191 hypothesis. The pharmacophore hypothesis yielded a 3D-QSAR model with good partial least-square (PLS) statistics results. The validation of the PHASE model was done by dividing the dataset into training and test set. The statistically significant the four-point pharmacophore hypothesis yielded a 3D-QSAR model with good PLS statistics results (R2 = 0.9387, Q2 = 0.8132, F = 114.8, SD = 0.1567, RMSE = 0.2682, Pearson-R = 0.9147). The generated model showed excellent predictive power, with a correlation coefficient of Q2 = 0.8132. The results of ligand-based pharmacophore hypothesis and atom-based 3D-QSAR provide detailed structural insights as well as highlights important binding features of novel amino derivatives of indole as Icmt inhibitors which can afford guidance for the rational drug design of novel, potent and promising Icmt inhibitors with enhanced potencies and may prove helpful for further lead optimization and virtual screening.
Energy Technology Data Exchange (ETDEWEB)
Mohammadi, M [Department of Physics, Islamic Azad University-Shahreza Branch, Shahreza, Isfahan (Iran, Islamic Republic of)], E-mail: majid471702@yahoo.com
2009-07-28
The effective mass that approximately describes the influence of a classical homogeneous gravitational field on an interacting atom-radiation field system is determined within the framework of the Jaynes-Cummings model. By taking into account both the atomic motion and the gravitational field, a full quantum treatment of the internal and external dynamics of the atom is presented. By exactly solving the Schroedinger equation in the interaction picture, the evolving state of the system is found. The influence of a classical homogeneous gravitational field on the energy eigenvalues, the effective mass of the atom-radiation field system and the Wigner distribution of the radiation field are studied, when the initial condition is such that the radiation field is prepared in a coherent state and the two-level atom is in a coherent superposition of the excited and ground states.
Directory of Open Access Journals (Sweden)
Vincent Frappier
2014-04-01
Full Text Available Normal mode analysis (NMA methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.
International Nuclear Information System (INIS)
upgrowing during the time of the first atomic bomb test in August 1949. For 90Sr and other nuclides observed the annual effective doses 1995 have been calculated. However, dose reconstruction for the older inhabitants directly affected by the aboverground atomic weapons tests remains difficult. Two simple models to account for part of the total dose received are presented in this paper. (orig.)
Daw, Murray S.; Mills, Michael J.
2003-01-01
We report on the progress made during the first year of the project. Most of the progress at this point has been on the theoretical and computational side. Here are the highlights: (1) A new code, tailored for high-end desktop computing, now combines modern Accelerated Dynamics (AD) with the well-tested Embedded Atom Method (EAM); (2) The new Accelerated Dynamics allows the study of relatively slow, thermally-activated processes, such as diffusion, which are much too slow for traditional Molecular Dynamics; (3) We have benchmarked the new AD code on a rather simple and well-known process: vacancy diffusion in copper; and (4) We have begun application of the AD code to the diffusion of vacancies in ordered intermetallics.
Shepherd, Gordon G.; Cho, Young-Min; Fomichev, Victor I.; Martynenko, Oleg V.
2016-09-01
Thermospheric atomic oxygen concentrations have been retrieved from observations by the Wind Imaging Interferometer (WINDII) O+(2P→2D) 732 and 733 nm emissions and are compared with results obtained by the Global Ultraviolet Imager (GUVI). Although the observations compared were taken ten years apart, the periods were selected on the basis of solar activity, using the Canadian Ionosphere and Atmosphere Model (C-IAM) to bridge the time gap. Results from all of these were compared with those from the Naval Research Laboratory Mass Spectrometer and Incoherent Scatter (NRLMSISE-00) model. Comparisons were made on the basis of F10.7 solar flux, day of year, local time, season, latitude and longitude. The WINDII local time variations showed enhanced values for the Northern spring season. Latitude and longitude plots showed smooth variations for NRLMSISE-00 and large variations for both WINDII and GUVI observations; in particular a depression in atomic oxygen concentration around 40 °S latitude and 100 °E longitude that is tentatively identified with a longitudinal wave 1 that does not propagate in local time but has an annual variation. The averaged values showed the WINDII values to be 0.75 that of NRLMSISE-00 compared with 0.80 for GUVI. Thus the WINDII values agreed with those of GUVI to within 6%, although taken 10 years apart.
Kharlamov, V S; Hou, M
2002-01-01
The slowing down of Ni sub 3 Al clusters on a Al, Ni and Ni sub 3 Al (1 1 1) surfaces is studied by atomic scale modelling. The semi-grand canonical metropolis Monte Carlo is used for the preparation of isolated clusters at thermodynamic equilibrium. The cluster deposition on the surface is studied in detail by classical Molecular Dynamics simulations that include a model to account for electron-phonon coupling. Long- and short-range orders in the cluster are evaluated as functions of temperature in an impact energy range between 0 and 1.5 eV/atom. The interaction between the Ni sub 3 Al cluster and an Al surface is characterised low short range (chemical) disorder. No sizeable epitaxy is found, subsequent to the impact. In contrast, in the case of Ni and Ni sub 3 Al substrates, which are harder materials than aluminium, the chemical disorder is higher and epitaxial accommodation is possible. With these substrates, chemical disorder in the cluster is an increasing function of the impact energy, as well as of ...
Energy Technology Data Exchange (ETDEWEB)
Es-sebbar, Et; C-Gazeau, M; Benilan, Y; Jolly, A [LISA, Universites Paris-Est Creteil Val de Marne (UPEC) and Paris Denis Diderot, CNRS-UMR 7583, 61, avenue du General de Gaulle, 94010 Creteil Cedex (France); Pintassilgo, C D, E-mail: essebbar@lisa.univ-paris12.f [Instituto de Plasmas e Fusao Nuclear-Laboratorio Associado, Instituto Superior Tecnico, 1049-001 Lisboa (Portugal)
2010-08-25
Following a first study on a late afterglow in flowing pure nitrogen post discharge, we report new two-photon absorption laser-induced fluorescence (TALIF) measurements of the absolute ground-state atomic nitrogen density N({sup 4}S) and investigate the influence of methane introduced downstream from the discharge by varying the CH{sub 4} mixing ratio from 0% up to 50%. The N ({sup 4}S) maximum density is about 2.2 x 10{sup 15} cm{sup -3} in pure N{sub 2} for a residence time of 22 ms and does not change significantly for methane mixing ratio up to {approx}15%, while above, a drastic decrease is observed. The influence of the residence time has been studied. A kinetic model has been developed to determine the elementary processes responsible for the evolution of the N ({sup 4}S) density in N{sub 2}/CH{sub 4} late afterglow. This model shows the same decrease as the experimental results even though absolute density values are always larger by about a factor of 3. In the late afterglow three-body recombination dominates the loss of N ({sup 4}S) atoms whatever the CH{sub 4} mixing ratio. For high CH{sub 4} mixing ratio, the destruction process through collisions with CH{sub 3}, H{sub 2}CN and NH becomes important and is responsible for the observed decrease of the N ({sup 4}S) density.
Directory of Open Access Journals (Sweden)
Hua Wong
Full Text Available In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.
Energy Technology Data Exchange (ETDEWEB)
Roy, Kunal, E-mail: kunalroy_in@yahoo.com; Das, Rudra Narayan
2013-06-15
Highlights: • Ionic liquids are not intrinsically ‘green chemicals’ and require toxicological assessment. • Predictive QSTR models have been developed for toxicity of ILs to Daphnia magna. • Simple two dimensional descriptors were used to reduce the computational burden. • Discriminant and regression based models showed appreciable predictivity and reproducibility. • The extracted features can be explored in designing novel environmentally-friendly agents. -- Abstract: Ionic liquids have been judged much with respect to their wide applicability than their considerable harmful effects towards the living ecosystem which has been observed in many instances. Hence, toxicological introspection of these chemicals by the development of predictive mathematical models can be of good help. This study presents an attempt to develop predictive classification and regression models correlating the structurally derived chemical information of a group of 62 diverse ionic liquids with their toxicity towards Daphnia magna and their interpretation. We have principally used the extended topochemical atom (ETA) indices along with various topological non-ETA and thermodynamic parameters as independent variables. The developed quantitative models have been subjected to extensive statistical tests employing multiple validation strategies from which acceptable results have been reported. The best models obtained from classification and regression studies captured necessary structural information on lipophilicity, branching pattern, electronegativity and chain length of the cationic substituents for explaining ecotoxicity of ionic liquids towards D. magna. The derived information can be successfully used to design better ionic liquid analogues acquiring the qualities of a true eco-friendly green chemical.
Manipulating nanoscale atom-atom interactions with cavity QED
Pal, Arpita; Deb, Bimalendu
2016-01-01
We theoretically explore manipulation of interactions between excited and ground state atoms at nanoscale separations by cavity quantum electrodynamics (CQED). We develop an adiabatic molecular dressed state formalism and show that it is possible to generate Fano-Feshbach resonances between ground and long-lived excited-state atoms inside a cavity. The resonances are shown to arise due to non-adiabatic coupling near a pseudo-crossing between the dressed state potentials. We illustrate our results with a model study using fermionic $^{171}$Yb atoms in a two-modal cavity. Our study is important for manipulation of interatomic interactions at low energy by cavity field.
Near relativistic study of bound levels in atoms. Application to alkaline atoms
Energy Technology Data Exchange (ETDEWEB)
Varade, A.; Delgado-Barrio, G.; Villarreal, P. (Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Inst. de Estructura de la Materia)
1985-01-01
A model is described for the calculation of the atomic binding energies. The Pauli equation has been solved with a local potential. The results for alkaline atoms are reported here and compared with the perturbative calculation and experimental data.
Collision-produced atomic states
International Nuclear Information System (INIS)
The last 10-15 years have witnessed the development of a new, powerful class of experimental techniques for atomic collision studies, allowing partial or complete determination of the state of the atoms after a collision event, i.e. the full set of quantum-mechanical scattering amplitudes or - more generally - the density matrix describing the system. Evidently, such studies, involving determination of alignment and orientation parameters, provide much more severe tests of state-of-the-art scattering theories than do total or differential cross section measurements which depend on diagonal elements of the density matrix. The off-diagonal elements give us detailed information about the shape and dynamics of the atomic states. Therefore, close studies of collision-produced atomic states are currently leading to deeper insights into the fundamental physical mechanisms governing the dynamics of atomic collision events. The first part of the lectures deals with the language used to describe atomic states, while the second part presents a selection of recent results for model systems which display fundamental aspects of the collision physics in particularly instructive ways. I shall here restrict myself to atom-atom collisions. The discussion will be focused on states decaying by photon emission though most of the ideas can be easily modified to include electron emission as well. (orig./AH)
Energy Technology Data Exchange (ETDEWEB)
Fujita E.; Cohen, B.W.; Polyansky, D.E.; Achord, P.; Cabelli, D.; Muckerman, J.T.; Tanaka, K.; Thummel, R.P.; Zong, R.
2012-01-01
Two isomers, [Ru(1)]{sup 2+} (Ru = Ru(bpy){sub 2}, bpy = 2,2{prime}-bipyridine, 1 = 2-(pyrid-2{prime}-yl)-1-azaacridine) and [Ru(2)]{sup 2+} (2 = 3-(pyrid-2{prime}-yl)-4-azaacridine), are bio-inspired model compounds containing the nicotinamide functionality and can serve as precursors for the photogeneration of C-H hydrides for studying reactions pertinent to the photochemical reduction of metal-C{sub 1} complexes and/or carbon dioxide. While it has been shown that the structural differences between the azaacridine ligands of [Ru(1)]{sup 2+} and [Ru(2)]{sup 2+} have a significant effect on the mechanism of formation of the hydride donors, [Ru(1HH)]{sup 2+} and [Ru(2HH)]{sup 2+}, in aqueous solution, we describe the steric implications for proton, net-hydrogen-atom and net-hydride transfer reactions in this work. Protonation of [Ru(2{sup {sm_bullet}-})]{sup +} in aprotic and even protic media is slow compared to that of [Ru(1{sup {sm_bullet}-})]{sup +}. The net hydrogen-atom transfer between *[Ru(1)]{sup 2+} and hydroquinone (H{sub 2}Q) proceeds by one-step EPT, rather than stepwise electron-proton transfer. Such a reaction was not observed for *[Ru(2)]{sup 2+} because the non-coordinated N atom is not easily available for an interaction with H{sub 2}Q. Finally, the rate of the net hydride ion transfer from [Ru(1HH)]{sup 2+} to [Ph{sub 3}C]{sup +} is significantly slower than that of [Ru(2HH)]{sup 2+} owing to steric congestion at the donor site.
Design Rules for Non-Atomic Implementations of PRS
Papadantonakis, Karl
2005-01-01
Martin Synthesis yields quasi--delay-insensitive (QDI) circuits, expressed in production--rule-set (PRS) form. Under an atomic circuit evaluation model, these circuits are provably correct. However, not all physical circuit implementations provide the atomic transitions needed to satisfy the atomic circuit model. This can cause operational failures in real circuits, as we illustrate. Nonetheless, circuits with non-atomic transitions can faithfully implement the atomic circuit model when comb...
Korchuganova, Olesya A.; Thuvander, Mattias; Aleev, Andrey A.; Rogozhkin, Sergey V.; Boll, Torben; Kulevoy, Timur V.
2016-08-01
Nanostructure evolution during ion irradiation of two thermally aged binary Fee22Cr alloys has been investigated using atom probe tomography. Specimens aged at 500 °C for 50 and 200 h were irradiated by 5.6 MeV Fe ions at room temperature up to fluences of 0.3 × 1015 ions/cm2 and 1 × 1015 ions/cm2. The effect of irradiation on the material nanostructure was examined at a depth of 1 μm from the irradiated surface. The analysis of Cr radial concentration functions reveals that dense α‧-phase precipitates in the 200 h aged alloy become diffuse and thereby larger when subjected to irradiation. On the other hand, less Cr-enriched precipitates in the alloy aged for 50 h are less affected. The CreCr pair correlation function analysis shows that matrix inhomogeneity decreases under irradiation. Irradiation leads to a decrease in the number density of diffuse clusters, whereas in the case of well-developed precipitates it remains unchanged.
Schiltz, M; Dumas, P; Ennifar, E; Flensburg, C; Paciorek, W; Vonrhein, C; Bricogne, G
2004-06-01
The case of a brominated RNA crystal structure determination in which standard three-wavelength MAD phasing was unsuccessful because of fast X-ray-induced debromination was reinvestigated [Ennifar et al. (2002), Acta Cryst. D58, 1262-1268]. It was found that if the data are kept unmerged and if a dose-stamp is associated with each reflection measurement, dose-dependent occupancies can be refined for the Br atoms. Such a parametrization has been implemented in the macromolecular phasing program SHARP. Refining such dose-dependent occupancies on an unmerged data set gave a dramatic improvement, even for SAD phases from only the first wavelength (peak), and resulted in a good electron-density map after solvent flattening. The adverse effect of radiation damage has been turned into a beneficial one. The crucial difference is made by the use of unmerged data: phasing power is generated through the intensity differences of symmetry-related reflections recorded at different doses, i.e. corresponding to different states of the X-ray-induced debromination. This approach should prove useful in all situations of experimental phasing where site-specific radiation damage occurs unavoidably and undesirably and not only in cases in which radiation damage is purposely being created in order to demonstrate its potential usefulness. PMID:15159561
AtomPy: an open atomic-data curation environment
Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka
2014-06-01
We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.
Yi-Xiang, Yu; Ye, Jinwu; Zhang, CunLin
2016-08-01
Four standard quantum optics models, that is, the Rabi, Dicke, Jaynes-Cummings, and Tavis-Cummings models, were proposed by physicists many decades ago. Despite their relative simple forms and many previous theoretical works, their physics at a finite N , especially inside the superradiant regime, remain unknown. In this work, by using the strong-coupling expansion and exact diagonalization (ED), we study the Z2-U(1 ) Dicke model with independent rotating-wave coupling g and counterrotating-wave coupling g' at a finite N . This model includes the four standard quantum optics models as its various special limits. We show that in the superradiant phase, the system's energy levels are grouped into doublets with even and odd parity. Any anisotropy β =g'/g ≠1 leads to the oscillation of parities in both the ground and excited doublets as the atom-photon coupling strength increases. The oscillations will be pushed to the infinite coupling strength in the isotropic Z2 limit β =1 . We find nearly perfect agreement between the strong-coupling expansion and the ED in the superradiant regime when β is not too small. We also compute the photon correlation functions, squeezing spectrum, and number correlation functions that can be measured by various standard optical techniques.
Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal
2016-11-01
Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study, pharmacophore and atom-based 3D-QSAR studies were carried out for pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC50 ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2 )= .9949), cross validation coefficient (Q(2 )= .7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R(2) value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.
Inner-shell corrections to the Bethe stopping-power formula evaluated from a realistic atomic model
International Nuclear Information System (INIS)
Generalized oscillator strengths for K- and L-shell ionization have been calculated using a central potential derived from the Hartree-Slater model. In cases in which an ejected electron carries low kinetic energies, sizable differences with hydrogenic-model calculations are evident
Bhardwaj, Anil
2012-01-01
The green (5577 \\AA) and red-doublet (6300, 6364 \\AA) lines are prompt emissions of metastable oxygen atoms in the $^1$S and $^1$D states, respectively, that have been observed in several comets. The value of intensity ratio of green to red-doublet (G/R ratio) of 0.1 has been used as a benchmark to identify the parent molecule of oxygen lines as H$_2$O. A coupled chemistry-emission model is developed to study the production and loss mechanisms of O($^1$S) and O($^1$D) atoms and the generation of red and green lines in the coma of C/1996 B2 Hyakutake. The G/R ratio depends not only on photochemistry, but also on the projected area observed for cometary coma, which is a function of the dimension of the slit used and geocentric distance of the comet. Calculations show that the contribution of photodissociation of H$_2$O to the green (red) line emission is 30 to 70% (60 to 90%), while CO$_2$ and CO are the next potential sources contributing 25 to 50% ($<$5%). The ratio of the photo-production rate of O($^1$S)...
Ishikawa, Atsushi; Nakatsuji, Hiroshi
2013-08-01
O1s core-electron binding energies (CEBE) of the atomic oxygens on different Ag surfaces were investigated by the symmetry adapted cluster-configuration interaction (SAC-CI) method combined with the dipped adcluster model, in which the electron exchange between bulk metal and adsorbate is taken into account properly. Electrophilic and nucleophilic oxygens (O(elec) and O(nuc)) that might be important for olefin epoxidation in a low-oxygen coverage condition were focused here. We consider the O1s CEBE as a key property to distinguish the surface oxygen states, and series of calculation was carried out by the Hartree-Fock, Density functional theory, and SAC/SAC-CI methods. The experimental information and our SAC/SAC-CI results indicate that O(elec) is the atomic oxygen adsorbed on the fcc site of Ag(111) and that O(nuc) is the one on the reconstructed added-row site of Ag(110) and that one- and two-electron transfers occur, respectively, to the O(elec) and O(nuc) adclusters from the silver surface.
Sommer, H. T.; Marnicio, R. J.
1983-06-01
The theory of a two-phase flow in a rotating cup atomizer is described. The analysis considers the separation of the solid and liquid media thus realistically modeling the flow of two layers along the inner cup wall: a slurry of increasing solids concentration and a supernatent liquid layer. The analysis is based on the earlier work of Hinze and Milborn (1950) which addressed the flow within a rotary cup for a homogeneous liquid. The superimposition of a settling velocity under conditions of high centrifugal acceleration permits the extended analysis of the separation of the two phases. Appropriate boundary conditions have been applied to the film's free surface and the cup wall and to match the flow characteristics at the liquid-slurry interface. The changing slurry viscosity, increasing nonlinearly with growing solid loading, was also considered. A parameter study illustrates the potential for a cup design to provide optimal slurry and liquid film thicknesses for effective atomization.
Atomic Energy Basics, Understanding the Atom Series.
Atomic Energy Commission, Oak Ridge, TN. Div. of Technical Information.
This booklet is part of the "Understanding the Atom Series," though it is a later edition and not included in the original set of 51 booklets. A basic survey of the principles of nuclear energy and most important applications are provided. These major topics are examined: matter has molecules and atoms, the atom has electrons, the nucleus,…
A polarized atomic hydrogen beam
Chan, N; Crowe, D.M.; Lubell, M. S.; Tang, F.C.; Vasilakis, A.; Mulligan, F. J.; Slevin, J.
1988-01-01
We describe the design and operating characteristics of a simple polarized atomic hydrogen beam particularly suitable for applications to crossed beams experiments. In addition to experimental measurements, we present the results of detailed computer models, using Monte-Carlo ray tracing techniques, optical analogs, and phase-space methods, that not only provide us with a confirmation of our measurement, but also allow us to characterize the density, polarization, and atomic fraction of the b...
International Nuclear Information System (INIS)
This book is written to teach atom structure in very easy way. It is divided into nine chapters, which indicates what is the components of matter? when we divide matter continuously, it becomes atom, what did atom look like? particles comprised of matter is not only atom, discover of particles comprised of atom, symbol of element, various radiation, form alchemy to nuclear transmutation, shape of atom is evolving. It also has various pictures in each chapters to explain easily.
Energy Technology Data Exchange (ETDEWEB)
Lim, Suh Yeon
2006-08-15
This book is written to teach atom structure in very easy way. It is divided into nine chapters, which indicates what is the components of matter? when we divide matter continuously, it becomes atom, what did atom look like? particles comprised of matter is not only atom, discover of particles comprised of atom, symbol of element, various radiation, form alchemy to nuclear transmutation, shape of atom is evolving. It also has various pictures in each chapters to explain easily.
International Nuclear Information System (INIS)
13CH4 , 12CD4 or 12CH4 gases were puffed into the crown (top) of lower single-null divertor plasmas in DIII-D using toroidally symmetric injection, constituting a particularly simple experiment to interpret. The resulting CI (9094.83 A) wavelength profiles were measured with a high resolution spectrometer. For a wide variety of plasma conditions, the shape of the profile was nearly constant, and could be approximately represented by a shifted gaussian distribution, corresponding to a temperature of the C-atoms of <1 eV. DIVIMP code analysis reported here, based on the recent Janev-Reiter database/model for methane breakup, has produced sufficiently close matches to these experimental CI profiles, to provide reasonable confidence that the controlling processes have been included
Energy Technology Data Exchange (ETDEWEB)
Stangeby, P.C. [University of Toronto, Institute for Aerospace Studies, 4925 Dufferin Street, Toronto, Ont., M3H 5T6 (Canada)]. E-mail: stangeby@fusion.gat.com; McLean, A.G. [University of Toronto, Institute for Aerospace Studies, 4925 Dufferin Street, Toronto, Ont., M3H 5T6 (Canada); Elder, J.D. [University of Toronto, Institute for Aerospace Studies, 4925 Dufferin Street, Toronto, Ont., M3H 5T6 (Canada); Brooks, N.H. [General Atomics, San Diego, CA 92186-5608 (United States); West, W.P. [General Atomics, San Diego, CA 92186-5608 (United States); Reiter, D. [Institut fuer Plasmaphysik Forschungszentrum, Juelich GmbH 52425, Juelich (Germany)
2007-06-15
{sup 13}CH{sub 4} , {sup 12}CD{sub 4} or {sup 12}CH{sub 4} gases were puffed into the crown (top) of lower single-null divertor plasmas in DIII-D using toroidally symmetric injection, constituting a particularly simple experiment to interpret. The resulting CI (9094.83 A) wavelength profiles were measured with a high resolution spectrometer. For a wide variety of plasma conditions, the shape of the profile was nearly constant, and could be approximately represented by a shifted gaussian distribution, corresponding to a temperature of the C-atoms of <1 eV. DIVIMP code analysis reported here, based on the recent Janev-Reiter database/model for methane breakup, has produced sufficiently close matches to these experimental CI profiles, to provide reasonable confidence that the controlling processes have been included.
Thinking on the Theory of Bohr Atom Model%对玻尔原子模型理论的若干思考
Institute of Scientific and Technical Information of China (English)
兰花艳; 朱平
2013-01-01
In this paper,we use the survey techniques to get the students’difficulties of learn-ing the Bohr's theory.On this basis,the physical nature and the inner relations of Bohr atom model theory are analyzed deeply in order to solve the students’confusions in learning the theory.%通过调查的方法了解学生学习玻尔理论的困难，在此基础上，对玻尔理论的物理本质和内在联系进行了深入的分析研究，以解决学生在学习该理论时的困惑。
International Nuclear Information System (INIS)
Fossil fuels, especially coal, can support the energy demands of the world for centuries to come, if the environmental problems associated with CO(sub 2) emissions can be overcome. Permanent and safe methods for CO(sub 2) capture and disposal/storage need to be developed. Mineralization of stationary-source CO(sub 2) emissions as carbonates can provide such safe capture and long-term sequestration. Mg-rich lamellar hydroxide mineral carbonation is a leading process candidate, which generates the stable naturally occurring mineral magnesite (MgCO(sub 3)) and water. Key to process cost and viability are the carbonation reaction rate and its degree of completion. This process, which involves simultaneous dehydroxylation and carbonation is very promising, but far from optimized. In order to optimize the dehydroxylation/carbonation process, an atomic-level understanding of the mechanisms involved is needed. In this investigation Mg(OH)(sub 2) was selected as a model Mg-rich lamellar hydrocide carbonation feedstock material due to its chemical and structural simplicity. Since Mg(OH)(sub 2) dehydroxylation is intimately associated with the carbonation process, its mechanisms are also of direct interest in understanding and optimizing the process. The aim of the current innovative concepts project is to develop a specialized advanced computational methodology to complement the ongoing experimental inquiry of the atomic level processes involved in CO(sub 2) mineral sequestration. The ultimate goal is to integrate the insights provided by detailed predictive simulations with the data obtained from optical microscopy, FESEM, ion beam analysis, SIMS, TGA, Raman, XRD, and C and H elemental analysis. The modeling studies are specifically designed to enhance the synergism with, and complement the analysis of, existing mineral-CO(sub 2) reaction process studies being carried out under DOE UCR Grant DE-FG2698-FT40112. Direct contact between the simulations and the experimental
Energy Technology Data Exchange (ETDEWEB)
Bhardwaj, Anil; Raghuram, Susarla, E-mail: bhardwaj_spl@yahoo.com, E-mail: anil_bhardwaj@vssc.gov.in, E-mail: raghuramsusarla@gmail.com [Space Physics Laboratory, Vikram Sarabhai Space Centre, Trivandrum 695022 (India)
2012-03-20
The green (5577 Angstrom-Sign ) and red-doublet (6300, 6364 Angstrom-Sign ) lines are prompt emissions of metastable oxygen atoms in the {sup 1}S and {sup 1}D states, respectively, that have been observed in several comets. The value of the intensity ratio of green to red-doublet (G/R ratio) of 0.1 has been used as a benchmark to identify the parent molecule of oxygen lines as H{sub 2}O. A coupled chemistry-emission model is developed to study the production and loss mechanisms of the O({sup 1}S) and O({sup 1}D) atoms and the generation of red and green lines in the coma of C/1996 B2 Hyakutake. The G/R ratio depends not only on photochemistry, but also on the projected area observed for cometary coma, which is a function of the dimension of the slit used and the geocentric distance of the comet. Calculations show that the contribution of photodissociation of H{sub 2}O to the green (red) line emission is 30%-70% (60%-90%), while CO{sub 2} and CO are the next potential sources contributing 25%-50% (<5%). The ratio of the photoproduction rate of O({sup 1} S) to O({sup 1} D) would be around 0.03 ({+-}0.01) if H{sub 2}O is the main source of oxygen lines, whereas it is {approx}0.6 if the parent is CO{sub 2}. Our calculations suggest that the yield of O({sup 1} S) production in the photodissociation of H{sub 2}O cannot be larger than 1%. The model-calculated radial brightness profiles of the red and green lines and G/R ratios are in good agreement with the observations made on the comet Hyakutake in 1996 March.
Bhardwaj, Anil; Raghuram, Susarla
2012-03-01
The green (5577 Å) and red-doublet (6300, 6364 Å) lines are prompt emissions of metastable oxygen atoms in the 1 S and 1 D states, respectively, that have been observed in several comets. The value of the intensity ratio of green to red-doublet (G/R ratio) of 0.1 has been used as a benchmark to identify the parent molecule of oxygen lines as H2O. A coupled chemistry-emission model is developed to study the production and loss mechanisms of the O(1 S) and O(1 D) atoms and the generation of red and green lines in the coma of C/1996 B2 Hyakutake. The G/R ratio depends not only on photochemistry, but also on the projected area observed for cometary coma, which is a function of the dimension of the slit used and the geocentric distance of the comet. Calculations show that the contribution of photodissociation of H2O to the green (red) line emission is 30%-70% (60%-90%), while CO2 and CO are the next potential sources contributing 25%-50% (<5%). The ratio of the photoproduction rate of O(1 S) to O(1 D) would be around 0.03 (±0.01) if H2O is the main source of oxygen lines, whereas it is ~0.6 if the parent is CO2. Our calculations suggest that the yield of O(1 S) production in the photodissociation of H2O cannot be larger than 1%. The model-calculated radial brightness profiles of the red and green lines and G/R ratios are in good agreement with the observations made on the comet Hyakutake in 1996 March.
Cold Matter Assembled Atom-by-Atom
Endres, Manuel; Keesling, Alexander; Levine, Harry; Anschuetz, Eric R; Krajenbrink, Alexandre; Senko, Crystal; Vuletic, Vladan; Greiner, Markus; Lukin, Mikhail D
2016-01-01
The realization of large-scale fully controllable quantum systems is an exciting frontier in modern physical science. We use atom-by-atom assembly to implement a novel platform for the deterministic preparation of regular arrays of individually controlled cold atoms. In our approach, a measurement and feedback procedure eliminates the entropy associated with probabilistic trap occupation and results in defect-free arrays of over 50 atoms in less than 400 ms. The technique is based on fast, real-time control of 100 optical tweezers, which we use to arrange atoms in desired geometric patterns and to maintain these configurations by replacing lost atoms with surplus atoms from a reservoir. This bottom-up approach enables controlled engineering of scalable many-body systems for quantum information processing, quantum simulations, and precision measurements.
A linear atomic quantum coupler
Energy Technology Data Exchange (ETDEWEB)
El-Orany, Faisal A A [Department of Mathematics and computer Science, Faculty of Science, Suez Canal University 41522, Ismailia (Egypt); Wahiddin, M R B, E-mail: el_orany@hotmail.co, E-mail: faisal.orany@mimos.m, E-mail: mridza@mimos.m [Cyberspace Security Laboratory, MIMOS Berhad, Technology Park Malaysia, 57000 Kuala Lumpur (Malaysia)
2010-04-28
In this paper we develop the notion of the linear atomic quantum coupler. This device consists of two modes propagating into two waveguides, each of which includes a localized atom. These waveguides are placed close enough to allow exchange of energy between them via evanescent waves. Each mode interacts with the atom in the same waveguide in the standard way as the Jaynes-Cummings model (JCM) and with the atom-mode system in the second waveguide via the evanescent wave. We present the Hamiltonian for this system and deduce its wavefunction. We investigate the atomic inversions and the second-order correlation function. In contrast to the conventional coupler the atomic quantum coupler is able to generate nonclassical effects. The atomic inversions can exhibit a long revival-collapse phenomenon as well as subsidiary revivals based on the competition among the switching mechanisms in the system. Finally, under certain conditions the system can yield the results of the two-mode JCM.
Dzuba, V A; Sushkov, O P
1997-01-01
A semi-empirical calculation of the 6s - 7s Stark amplitude $\\alpha$ in Cs has been performed using the most accurate measurements and calculations of the electromagnetic amplitudes available. This is then used to extract the parameters of the electroweak theory from experimental data. The results are: (80)_{theor}$, deviation from the Standard model $S = -1.0(.3)_{exp} (1.0)_{theor}$ and limit on the mass of the extra Z-boson in SO(10) model $M_{Z_x} > 550 GeV$.
Indian Academy of Sciences (India)
B Jayaram; Priyanka Dhingra; Bharat Lakhani; Shashank Shekhar
2012-01-01
Protein folding, considered to be the holy grail of molecular biology, remains intractable even after six decades since the report of the first crystal structure. Over 70,000 X-ray and NMR structures are now available in protein structural repositories and no physico-chemical solution is in sight. Molecular simulation methodologies have evolved to a stage to provide a computational solution to the tertiary structures of small proteins. Knowledge base driven methodologies are maturing in predicting the tertiary structures of query sequences which share high similarities with sequences of known structures in the databases. The void region thus seems to be medium (> 100 amino acid residues) to large proteins with no sequence homologs in the databases and hence which has become a fertile ground for the genesis of hybrid models which exploit local similarities together with ab initio models to arrive at reasonable predictions.We describe here the development of Bhageerath an ab initio model and Bhageerath-H a hybrid model and present a critique on the current status of prediction of protein tertiary structures.
Gouveia, Amanda F.; Ferrer, Mateus M.; Sambrano, Júlio R.; Andrés, Juan; Longo, Elson
2016-09-01
In this communication, a systematic study of the surface structure, including energy management during morphological transformations of tetragonal phase of LaVO4, has been carried out. For this study, we combined experimental findings and first-principles calculations to develop a Wulff construction model. Our findings can help further understand the synthetic control of crystal shape via tuning of surface chemistry.
DEFF Research Database (Denmark)
Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit;
2012-01-01
in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable...
Coffee Cup Atomic Force Microscopy
Ashkenaz, David E.; Hall, W. Paige; Haynes, Christy L.; Hicks, Erin M.; McFarland, Adam D.; Sherry, Leif J.; Stuart, Douglas A.; Wheeler, Korin E.; Yonzon, Chanda R.; Zhao, Jing; Godwin, Hilary A.; Van Duyne, Richard P.
2010-01-01
In this activity, students use a model created from a coffee cup or cardstock cutout to explore the working principle of an atomic force microscope (AFM). Students manipulate a model of an AFM, using it to examine various objects to retrieve topographic data and then graph and interpret results. The students observe that movement of the AFM…
Energy Technology Data Exchange (ETDEWEB)
Migunov, V., E-mail: v.migunov@fz-juelich.de; Dunin-Borkowski, R. E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C) and Peter Grünberg Institute (PGI), Forschungszentrum Jülich, D-52425 Jülich (Germany); London, A. [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Farle, M. [Fakultät für Physik and Center of Nanointegration (CeNIDE), Universität Duisburg-Essen, D-47048 Duisburg (Germany)
2015-04-07
The one-dimensional charge density distribution along an electrically biased Fe atom probe needle is measured using a model-independent approach based on off-axis electron holography in the transmission electron microscope. Both the mean inner potential and the magnetic contribution to the phase shift are subtracted by taking differences between electron-optical phase images recorded with different voltages applied to the needle. The measured one-dimensional charge density distribution along the needle is compared with a similar result obtained using model-based fitting of the phase shift surrounding the needle. On the assumption of cylindrical symmetry, it is then used to infer the three-dimensional electric field and electrostatic potential around the needle with ∼10 nm spatial resolution, without needing to consider either the influence of the perturbed reference wave or the extension of the projected potential outside the field of view of the electron hologram. The present study illustrates how a model-independent approach can be used to measure local variations in charge density in a material using electron holography in the presence of additional contributions to the phase, such as those arising from changes in mean inner potential and specimen thickness.
Sub-atom shot noise Faraday imaging of ultracold atom clouds
Kristensen, Mick A; Pedersen, Poul L; Klempt, Carsten; Sherson, Jacob F; Arlt, Jan J; Hilliard, Andrew J
2016-01-01
We demonstrate that a dispersive imaging technique based on the Faraday effect can measure the atom number in a large, ultracold atom cloud with a precision below the atom shot noise level. The minimally destructive character of the technique allows us to take multiple images of the same cloud, which enables sub-atom shot noise measurement precision of the atom number and allows for an in situ determination of the measurement precision. We have developed a noise model that quantitatively describes the noise contributions due to photon shot noise in the detected light and the noise associated with single atom loss. This model contains no free parameters and is calculated through an analysis of the fluctuations in the acquired images. For clouds containing $N \\sim 5 \\times 10^6$ atoms, we achieve a precision more than a factor of two below the atom shot noise level.
Aoiz, F J; González-Lezana, T; Sáez Rábanos, V
2008-09-01
A detailed comparison of statistical models based on the quasiclassical trajectory (SQCT) and quantum mechanical (SQM) methods is presented in this work for the C((1)D)+H(2), S((1)D)+H(2), O((1)D)+H(2) and N((2)D)+H(2) insertion reactions. Reaction probabilities, integral (ICS) and differential (DCS) cross sections at different levels of product's state resolution are shown and discussed for these reactions. The agreement is in most cases excellent and indicates that the effect of tunneling through the centrifugal barrier is negligible. However, if there exists a dynamical barrier, as in the case of the N((2)D)+H(2) reaction, some of the SQM results can be slightly different than those calculated with the SQCT model. The rationale of the observed similarities and discrepancies can be traced back to the specific topologies of the potential energy surfaces for each of the reactions examined. The SQCT model is sensitive enough to show the relatively small inaccuracies resulting from the decoupling inherent to the centrifugal sudden approximation when used in the SQM calculations. In addition, the effect of ignoring the parity conservation is also examined. This effect is in general minor except in particular cases such as the DCS from initial rotational state j=0, which requires, in order to reproduce the sharp forward and backward peaks, the explicit conservation of parity.
Smiar, Karen; Mendez, J. D.
2016-01-01
Molecular model kits have been used in chemistry classrooms for decades but have seen very little recent innovation. Using 3D printing, three sets of physical models were created for a first semester, introductory chemistry course. Students manipulated these interactive models during class activities as a supplement to existing teaching tools for…
Stable atomic hydrogen: Polarized atomic beam source
International Nuclear Information System (INIS)
We have carried out experiments with stable atomic hydrogen with a view to possible applications in polarized targets or polarized atomic beam sources. Recent results from the stabilization apparatus are described. The first stable atomic hydrogen beam source based on the microwave extraction method (which is being tested ) is presented. The effect of the stabilized hydrogen gas density on the properties of the source is discussed. (orig.)
International Nuclear Information System (INIS)
This article has dealt with the development and modeling of various contact theories for biological nanoparticles shaped as cylinders and circular crowned rollers for application in the manipulation of different biological micro/nanoparticles based on Atomic Force Microscope. First, the effective contact forces were simulated, and their impact on contact mechanics simulation was investigated. In the next step, the Hertz contact model was simulated and compared for gold and DNA nanoparticles with the three types of spherical, cylindrical, and circular crowned roller type contact geometries. Then by reducing the length of the cylindrical section in the circular crowned roller geometry, the geometry of the body was made to approach that of a sphere, and the results were compared for DNA nanoparticles. To anticipatory validate the developed theories, the results of the cylindrical and the circular crowned roller contacts were compared with the results of the existing spherical contact simulations. Following the development of these contact models for the manipulation of various biological micro/nanoparticles, the cylindrical and the circular crowned roller type contact theories were modeled based on the theories of Lundberg, Dowson, Nikpur, Heoprich, and Hertz for the manipulation of biological micro/nanoparticles. Then, for a more accurate validation, the results obtained from the simulations were compared with those obtained by the finite element method and with the experimental results available in previous articles. The previous research works on the simulation of nanomanipulation have mainly investigated the contact theories used in the manipulation of spherical micro/nanoparticles. However since in real biomanipulation situations, biological micro/nanoparticles of more complex shapes need to be displaced in biological environments, this article therefore has modeled and compared, for the first time, different contact theories for use in the biomanipulation of
Energy Technology Data Exchange (ETDEWEB)
Manos Mavrikakis; James A. Dumesic; Amit A. Gokhale; Rahul P. Nabar; Calvin H. Bartholomew; Hu Zou; Brian Critchfield
2005-03-22
Efforts during this first year focused on four areas: (1) searching/summarizing published FTS mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) construction of mass spectrometer-TPD and Berty CSTR reactor systems; (3) preparation and characterization of unsupported iron and alumina-supported iron catalysts at various iron loadings (4) Determination of thermochemical parameters such as binding energies of reactive intermediates, heat of FTS elementary reaction steps, and kinetic parameters such as activation energies, and frequency factors of FTS elementary reaction steps on a number of model surfaces. Literature describing mechanistic and kinetic studies of Fischer-Tropsch synthesis on iron catalysts was compiled in a draft review. Construction of the mass spectrometer-TPD system is 90% complete and of a Berty CSTR reactor system 98% complete. Three unsupported iron catalysts and three alumina-supported iron catalysts were prepared by nonaqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2}, thus ideal for kinetic and mechanistic studies. The alumina-supported iron catalysts will be used for kinetic and mechanistic studies. In the coming year, adsorption/desorption properties, rates of elementary steps, and global reaction rates will be measured for these catalysts, with and without promoters, providing a database for understanding effects of dispersion, metal loading, and support on elementary kinetic parameters and for validation of computational models that incorporate effects of surface structure and promoters. Furthermore, using state-of-the-art self-consistent Density Functional Theory (DFT) methods, we have extensively studied the thermochemistry and kinetics of various elementary steps on
International Nuclear Information System (INIS)
The multi-element Zr-based bio-alloys are optimized for reaching lower Young's modulus and magnetic susceptibility by introducing the cluster-plus-glue-atom model to realize the composition design. A general cluster formulas of [(Mo,Sn)–(Zr,Ti)14]Nbx (x=1, 3) was obtained from the model and alloy rods with a diameter of 3 mm were prepared by copper-mold suction-casting processing. The β structural stabilities of the designed alloys were studied by the valence electron concentration (VEC). Among the β-Zr alloys, the [(Mo0.5Sn0.5)–Zr14]Nb1 (Zr87.5Nb6.25Mo3.13Sn3.13 at%) and [(Mo0.5Sn0.5)–(Zr13Ti)]Nb1 (Zr81.25Nb6.25Ti6.25Mo3.13Sn3.13 at%) alloys, corresponding to the lower β stability limit, display lower Young's moduli (77–79 GPa), lowest magnetic susceptibilities (2.12×10−6–2.13×10−6 cm3 g−1), as well as higher Vickers hardness (288–311 HV)
Bera, Swapna; Kar, Rajiv K; Mondal, Susanta; Pahan, Kalipada; Bhunia, Anirban
2016-09-01
Cell-penetrating peptides (CPPs) have shown promise in nonpermeable therapeutic drug delivery, because of their ability to transport a variety of cargo molecules across the cell membranes and their noncytotoxicity. Drosophila antennapedia homeodomain-derived CPP penetratin (RQIKIWFQNRRMKWKK), being rich in positively charged residues, has been increasingly used as a potential drug carrier for various purposes. Penetratin can breach the tight endothelial network known as the blood-brain barrier (BBB), permitting treatment of several neurodegenerative maladies, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. However, a detailed structural understanding of penetratin and its mechanism of action is lacking. This study defines structural features of the penetratin-derived peptide, DK17 (DRQIKIWFQNRRMKWKK), in several model membranes and describes a membrane-induced conformational transition of the DK17 peptide in these environments. A series of biophysical experiments, including high-resolution nuclear magnetic resonance spectroscopy, provides the three-dimensional structure of DK17 in different membranes mimicking the BBB or total brain lipid extract. Molecular dynamics simulations support the experimental results showing preferential binding of DK17 to particular lipids at atomic resolution. The peptide conserves the structure of the subdomain spanning residues Ile6-Arg11, despite considerable conformational variation in different membrane models. In vivo data suggest that the wild type, not a mutated sequence, enters the central nervous system. Together, these data highlight important structural and functional attributes of DK17 that could be utilized in drug delivery for neurodegenerative disorders. PMID:27532224
Extension of Mediema's Macroscopic Atom Model to the Elements of Group 16 (O, S, Se, Te ,Po)
Energy Technology Data Exchange (ETDEWEB)
Neuhausen, J.; Eichler, B
2003-09-01
A consistent set of Miedema-parameters has been developed for the elements of the chalcogen group (Group 16 of the periodic table of the elements: 0, S, Se, Te, Po) from ab-initio quantum-mechanical calculations as weIl as empirical correlations. Using this parameter set thermochemical properties such as enthalpies of formation of solid metal chalcogenides, partial molar enthalpies of solution of chalcogens in liquid and solid metaIs, partial molar enthalpies of evaporation of the chalcogens from liquid metal solution into the monoatomic gaseous state, partial molar enthalpies of adsorption of chalcogenides on metal surfaces at zero coverage and partial molar enthalpies of segregation of the chalcogens in trace amounts within solid metal matrices have been calculated. These properties are compared with available experimental data and discussed with an emphasis on the periodic behaviour of the elements. The model calculations show that a description of the thermochemical properties of the chalcogens using the semi-empirical Miedema approach is possible. The calculated properties can serve as a basis for the prediction of the chemical interactions for metal-chalcogen combinations that have not been studied experimentally so far. (author)
Advances in atomic spectroscopy
Sneddon, J
2000-01-01
This fifth volume of the successful series Advances in Atomic Spectroscopy continues to discuss and investigate the area of atomic spectroscopy.It begins with a description of the use of various atomic spectroscopic methods and applications of speciation studies in atomic spectroscopy. The emphasis is on combining atomic spectroscopy with gas and liquid chromatography. In chapter two the authors describe new developments in tunable lasers and the impact they will have on atomic spectroscopy. The traditional methods of detection, such as photography and the photomultiplier, and how they are being replaced by new detectors is discussed in chapter three. The very active area of glow discharge atomic spectrometry is presented in chapter four where, after a brief introduction and historical review, the use of glow discharge lamps for atomic spectroscopy and mass spectrometry are discussed. Included in this discussion is geometry and radiofrequency power. The future of this source in atomic spectroscopy is also dis...
Atomic and molecular manipulation
Mayne, Andrew J
2011-01-01
Work with individual atoms and molecules aims to demonstrate that miniaturized electronic, optical, magnetic, and mechanical devices can operate ultimately even at the level of a single atom or molecule. As such, atomic and molecular manipulation has played an emblematic role in the development of the field of nanoscience. New methods based on the use of the scanning tunnelling microscope (STM) have been developed to characterize and manipulate all the degrees of freedom of individual atoms and molecules with an unprecedented precision. In the meantime, new concepts have emerged to design molecules and substrates having specific optical, mechanical and electronic functions, thus opening the way to the fabrication of real nano-machines. Manipulation of individual atoms and molecules has also opened up completely new areas of research and knowledge, raising fundamental questions of "Optics at the atomic scale", "Mechanics at the atomic scale", Electronics at the atomic scale", "Quantum physics at the atomic sca...
Light scattering from dense cold atomic media
Zhu, Bihui; Cooper, John; Ye, Jun; Rey, Ana Maria
2016-08-01
We theoretically study the propagation of light through a cold atomic medium, where the effects of motion, laser intensity, atomic density, and polarization can all modify the properties of the scattered light. We present two different microscopic models: the "coherent dipole model" and the "random-walk model", both suitable for modeling recent experimental work done in large atomic arrays in the low-light-intensity regime. We use them to compute relevant observables such as the linewidth, peak intensity, and line center of the emitted light. We further develop generalized models that explicitly take into account atomic motion. Those are relevant for hotter atoms and beyond the low-intensity regime. We show that atomic motion can lead to drastic dephasing and to a reduction of collective effects, together with a distortion of the line shape. Our results are applicable to model a full gamut of quantum systems that rely on atom-light interactions, including atomic clocks, quantum simulators, and nanophotonic systems.
Energy Technology Data Exchange (ETDEWEB)
Favalli, Renata Cristina
2002-07-01
The aim of the present work is to numerically simulate the behaviour of the drying system for several sets of operating conditions in order to improve and optimize this process. However, the mathematical modeling adopted here can be employed to simulate other systems such as the processes that occur in liquid-fueled engines with direct spray injection and ceramic spraying for hard surfacing. Then, mathematical and physical models were established to simulate the interaction of continuous and disperse phases in drying processes of ceramic slurries. Solving the set of governing coupled partial differential equations, it is possible to study the influence of drying air on the atomized droplets of alumina slurry, and vice-versa. The materials used as continuous and disperse phase, air and alumina slurry respectively, are representative since any kind of gas and slurry can be used if its thermodynamic and transport properties are known. Several experimental tests were carried out in a spray dryer in the 'Laboratorio de Insumos', at IPEN - Instituto de Pesquisas Energeticas e Nucleares for different sets of operating conditions: initial temperature of the drying air, the gas flow rate, the slurry feed rate and atomiser configuration among others. Measurements of the wet and the dry bulb temperatures were made in some experimental tests to allow the calculations of the air humidity. The dynamic pressure were also measured in order to determine the gas flow rate. Some samples of the material used in the tile industry and of the one produced at IPEN were analysed to determine: the morphology of the atomized material and the range of granules diameter through scanning electron microscopy; the amount of pores and the bulk density through porosimetry; the residual moisture of the material through thermogravimetry; and the granulometric distribution of granules and particles through laser diffraction. Important information about the process and the final material are
Wang, Chia-Yu; Barrow, Lloyd H.
2013-01-01
The purpose of the study was to explore students' conceptual frameworks of models of atomic structure and periodic variations, chemical bonding, and molecular shape and polarity, and how these conceptual frameworks influence their quality of explanations and ability to shift among chemical representations. This study employed a purposeful sampling…
Miller, M
1986-01-01
The ORNL Atom Probe is a microanalytical tool for studies in materials science. The instrument is a combination of a customized version of the vacuum system of the VG FIM-100 atom probe, an ORNL-designed microcomputer-controlled digital timing system, and a double curved CEMA Imaging Atom Probe detector. The atom probe combines four instruments into one - namely a field ion microscope, an energy compensated time-of-flight mass spectrometer, an imaging atom probe, and a pulsed laser atom probe.