ERIC Educational Resources Information Center
Willden, Jeff
2001-01-01
"Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…
Computer Modeling Of Atomization
NASA Technical Reports Server (NTRS)
Giridharan, M.; Ibrahim, E.; Przekwas, A.; Cheuch, S.; Krishnan, A.; Yang, H.; Lee, J.
1994-01-01
Improved mathematical models based on fundamental principles of conservation of mass, energy, and momentum developed for use in computer simulation of atomization of jets of liquid fuel in rocket engines. Models also used to study atomization in terrestrial applications; prove especially useful in designing improved industrial sprays - humidifier water sprays, chemical process sprays, and sprays of molten metal. Because present improved mathematical models based on first principles, they are minimally dependent on empirical correlations and better able to represent hot-flow conditions that prevail in rocket engines and are too severe to be accessible for detailed experimentation.
Pearson, Ralph G.
1981-01-01
The energies of several two- and three-electron atoms, in both ground states and excited states, are calculated by a very simple semiclassical model. The only change from Bohr's original method is to replace definite orbits by probability distribution functions based on classical dynamics. The energies are better than Hartree-Fock values. There is still a need for an exchange-energy correction. Images PMID:16593047
Stochastic models for atomic clocks
NASA Technical Reports Server (NTRS)
Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.
1983-01-01
For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.
A Quantum Model of Atoms (the Energy Levels of Atoms).
ERIC Educational Resources Information Center
Rafie, Francois
2001-01-01
Discusses the model for all atoms which was developed on the same basis as Bohr's model for the hydrogen atom. Calculates the radii and the energies of the orbits. Demonstrates how the model obeys the de Broglie's hypothesis that the moving electron exhibits both wave and particle properties. (Author/ASK)
"Electronium": A Quantum Atomic Teaching Model.
ERIC Educational Resources Information Center
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Outlines an alternative atomic model to the probability model, the descriptive quantum atomic model Electronium. Discusses the way in which it is intended to support students in learning quantum-mechanical concepts. (Author/MM)
Nagaoka's atomic model and hyperfine interactions.
Inamura, Takashi T
2016-01-01
The prevailing view of Nagaoka's "Saturnian" atom is so misleading that today many people have an erroneous picture of Nagaoka's vision. They believe it to be a system involving a 'giant core' with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka's model is exactly the same as Rutherford's. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure. PMID:27063182
The Hydrogen Atom: The Rutherford Model
NASA Astrophysics Data System (ADS)
Tilton, Homer Benjamin
1996-06-01
Early this century Ernest Rutherford established the nuclear model of the hydrogen atom, presently taught as representing the best visual model after modification by Niels Bohr and Arnold Sommerfeld. It replaced the so-called "plum pudding" model of J. J. Thomson which held sway previously. While the Rutherford model represented a large step forward in our understanding of the hydrogen atom, questions remained, and still do.
The Completeness Criterion in Atomic Modeling
NASA Astrophysics Data System (ADS)
Liedahl, Duane A.
2000-10-01
I discuss two variations on the completeness theme in atomic modeling; missing lines as they affect the performance of spectral synthesis codes, and missing configurations as they affect the theoretical emissivities of bright lines, with emphasis on the latter. It is shown that the detrimental effects of working with incomplete atomic models can overshadow those brought about by working with less-than-perfect atomic rates. Atomic models can be brought up to an acceptable level of completeness in a fairly straightforward manner, and on a reasonably short timescale, whereas the long-term goal of comprehensive accuracy is unlikely to be reached on the timescale of the current generation of X-ray observatories. A near-term, albeit imperfect, solution is to hybridize atomic models used to synthesize spectra. A hybrid atomic model is one for which a large-scale atomic model, in which completeness is achieved at the expense of accuracy, is augmented with more accurate atomic quantities as they become available.
Atomic modeling of the plasma EUV sources
NASA Astrophysics Data System (ADS)
Sasaki, Akira; Sunahara, Atsushi; Furukawa, Hiroyuki; Nishihara, Katsunobu; Nishikawa, Takeshi; Koike, Fumihiro; Tanuma, Hajime
2009-09-01
We present the development of population kinetics models for tin plasmas that can be employed to design an EUV source for microlithography. The atomic kinetic code is constrained for the requirement that the model must be able to calculate spectral emissivity and opacity that can be used in radiation hydrodynamic simulations. Methods to develop compact and reliable atomic model with an appropriate set of atomic states are discussed. Specifically, after investigation of model dependencies and comparison experiment, we improve the effect of configuration interaction and the treatment of satellite lines. Using the present atomic model we discuss the temperature and density dependencies of the emissivity, as well as conditions necessary to obtain high efficiency EUV power at λ = 13.5 nm.
Ion-Atom and Atom-Atom Collisional Processes and Modeling of Stellar Atmospheres
NASA Astrophysics Data System (ADS)
Mihajlov, A. A.; Ignjatovic, Lj. M.; Sreckovic, V. A.; Dimitrijevic, M. S.; Dimitrijevic, M. S.
2015-09-01
We report the results obtained in our previous works on the influence of two groups of collisional processes (ion--atom and atom--atom) on the optical and kinetic properties of weakly ionised plasma. The first group includes radiative processes of the photodissociation/association type and radiative charge exchange, the second one -- chemi-ionisation/recombination processes. The effect of the radiative processed is assessed by comparing their intensities with those of the known competing processed in application to the solar photosphere and to the photospheres of DB white dwarfs. The studied chemi-ionisation/recombination processes are considered from the viewpoint of their influence on the populations of the excited states of the hydrogen atom (the Sun and an M-type red dwarf with an effective temperature of 3800~K) and helium atom (DB white dwarfs). The effect of these processes on the populations of the excited states of the hydrogen atom has been studied using the PHOENIX code, which generates the model of the considered atmosphere. The reported results demonstrate the unquestionable influence of the considered radiative and chemi- ionisation/recombination processes on the optical properties and on the kinetics of the weakly ionised layers in stellar atmospheres. It can be expected that the reported results will be a sufficient reason for including these processes in the models of stellar atmospheres.
Tight Binding Models in Cold Atoms Physics
NASA Astrophysics Data System (ADS)
Zakrzewski, J.
2007-05-01
Cold atomic gases placed in optical lattice potentials offer a unique tool to study simple tight binding models. Both the standard cases known from the condensed matter theory as well as novel situations may be addressed. Cold atoms setting allows for a precise control of parameters of the systems discussed, stimulating new questions and problems. The attempts to treat disorder in a controlled fashion are addressed in detail.
A Newtonian Model of the Hydrogen Atom
NASA Astrophysics Data System (ADS)
Espinosa, James; Woodyard, James
2010-03-01
Classical physics was deemed useless in atomic physics in the early 1900's by the vast majority of the physics community. There were multiple problems that were believed to be insoluble, such as blackbody radiation and the photoelectric and Compton effects. Another outstanding problem had been the explanation of atomic spectra. By the 1920's, a very powerful theory called quantum mechanics was created which explained all atomic experiments. Nevertheless, a few physicists, most notably Albert Einstein, rejected this theory on the grounds that it did not give a complete description of the microscopic world. Another more radical view held by Walter Ritz is that Newtonian physics is applicable to all of atomic physics. Over the last couple of years, we have presented classical explanations of many of the ``insoluble'' problems given by textbooks. We will present a model of the hydrogen atom that stays within the framework of Newton. Using only the assumption that the stable building blocks of matter are the electron, positron, and neutrino, we will deduce the following results from our model: orbital stability, line spectra, and scattering cross sections for electrons and protons. We will also qualitatively demonstrate how to explain the lifetime of excited states.
Atomic Data Applications for Supernova Modeling
NASA Astrophysics Data System (ADS)
Fontes, Christopher J.
2013-06-01
The modeling of supernovae (SNe) incorporates a variety of disciplines, including hydrodynamics, radiation transport, nuclear physics and atomic physics. These efforts require numerical simulation of the final stages of a star's life, the supernova explosion phase, and the radiation that is subsequently emitted by the supernova remnant, which can occur over a time span of tens of thousands of years. While there are several different types of SNe, they all emit radiation in some form. The measurement and interpretation of these spectra provide important information about the structure of the exploding star and the supernova engine. In this talk, the role of atomic data is highlighted as iit pertains to the modeling of supernova spectra. Recent applications [1,2] involve the Los Alamos OPLIB opacity database, which has been used to provide atomic opacities for modeling supernova plasmas under local thermodynamic equilibrium (LTE) conditions. Ongoing work includes the application of atomic data generated by the Los Alamos suite of atomic physics codes under more complicated, non-LTE conditions [3]. As a specific, recent example, a portion of the x-ray spectrum produced by Tycho's supernova remnant (SN 1572) will be discussed [4]. [1] C.L. Fryer et al, Astrophys. J. 707, 193 (2009). [2] C.L. Fryer et al, Astrophys. J. 725, 296 (2009). [3] C.J. Fontes et al, Conference Proceedings for ICPEAC XXVII, J. of Phys: Conf. Series 388, 012022 (2012). [4] K.A. Eriksen et al, Presentation at the 2012 AAS Meeting (Austin, TX). (This work was performed under the auspices of the U.S. Department of Energy by Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396.)
Optical analogs of model atoms in fields
Milonni, P.W.
1991-05-02
The equivalence of the paraxial wave equation to a time-dependent Schroedinger equation is exploited to construct optical analogs of model atoms in monochromatic fields. The approximation of geometrical optics provides the analog of the corresponding classical mechanics. Optical analogs of Rabi oscillations, photoionization, stabilization, and the Kramers-Henneberger transformation are discussed. One possibility for experimental realization of such optical analogs is proposed. These analogs may be useful for studies of quantum chaos'' when the ray trajectories are chaotic. 9 refs.
A Green's function quantum average atom model
Starrett, Charles Edward
2015-05-21
A quantum average atom model is reformulated using Green's functions. This allows integrals along the real energy axis to be deformed into the complex plane. The advantage being that sharp features such as resonances and bound states are broadened by a Lorentzian with a half-width chosen for numerical convenience. An implementation of this method therefore avoids numerically challenging resonance tracking and the search for weakly bound states, without changing the physical content or results of the model. A straightforward implementation results in up to a factor of 5 speed-up relative to an optimized orbital based code.
Atom-Role-Based Access Control Model
NASA Astrophysics Data System (ADS)
Cai, Weihong; Huang, Richeng; Hou, Xiaoli; Wei, Gang; Xiao, Shui; Chen, Yindong
Role-based access control (RBAC) model has been widely recognized as an efficient access control model and becomes a hot research topic of information security at present. However, in the large-scale enterprise application environments, the traditional RBAC model based on the role hierarchy has the following deficiencies: Firstly, it is unable to reflect the role relationships in complicated cases effectively, which does not accord with practical applications. Secondly, the senior role unconditionally inherits all permissions of the junior role, thus if a user is under the supervisor role, he may accumulate all permissions, and this easily causes the abuse of permission and violates the least privilege principle, which is one of the main security principles. To deal with these problems, we, after analyzing permission types and role relationships, proposed the concept of atom role and built an atom-role-based access control model, called ATRBAC, by dividing the permission set of each regular role based on inheritance path relationships. Through the application-specific analysis, this model can well meet the access control requirements.
NASA Technical Reports Server (NTRS)
Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.
1992-01-01
The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.
Making It Visual: Creating a Model of the Atom
ERIC Educational Resources Information Center
Pringle, Rose M.
2004-01-01
This article describes a lesson in which students construct Bohr's planetary model of the atom. Niels Bohr's atomic model provides a framework for discussing with middle and high school students the historical development of our understanding of the structure of the atom. The model constructed in this activity will enable students to visualize the…
Computer Model Of Fragmentation Of Atomic Nuclei
NASA Technical Reports Server (NTRS)
Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.
1995-01-01
High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.
Atomic Models for Motional Stark Effects Diagnostics
Gu, M F; Holcomb, C; Jayakuma, J; Allen, S; Pablant, N A; Burrell, K
2007-07-26
We present detailed atomic physics models for motional Stark effects (MSE) diagnostic on magnetic fusion devices. Excitation and ionization cross sections of the hydrogen or deuterium beam traveling in a magnetic field in collisions with electrons, ions, and neutral gas are calculated in the first Born approximation. The density matrices and polarization states of individual Stark-Zeeman components of the Balmer {alpha} line are obtained for both beam into plasma and beam into gas models. A detailed comparison of the model calculations and the MSE polarimetry and spectral intensity measurements obtained at the DIII-D tokamak is carried out. Although our beam into gas models provide a qualitative explanation for the larger {pi}/{sigma} intensity ratios and represent significant improvements over the statistical population models, empirical adjustment factors ranging from 1.0-2.0 must still be applied to individual line intensities to bring the calculations into full agreement with the observations. Nevertheless, we demonstrate that beam into gas measurements can be used successfully as calibration procedures for measuring the magnetic pitch angle through {pi}/{sigma} intensity ratios. The analyses of the filter-scan polarization spectra from the DIII-D MSE polarimetry system indicate unknown channel and time dependent light contaminations in the beam into gas measurements. Such contaminations may be the main reason for the failure of beam into gas calibration on MSE polarimetry systems.
Operation of the computer model for microenvironment atomic oxygen exposure
NASA Technical Reports Server (NTRS)
Bourassa, R. J.; Gillis, J. R.; Gruenbaum, P. E.
1995-01-01
A computer model for microenvironment atomic oxygen exposure has been developed to extend atomic oxygen modeling capability to include shadowing and reflections. The model uses average exposure conditions established by the direct exposure model and extends the application of these conditions to treat surfaces of arbitrary shape and orientation.
Atomic Oscillator Strengths for Stellar Atmosphere Modeling
NASA Astrophysics Data System (ADS)
Ruffoni, Matthew; Pickering, Juliet C.
2015-08-01
In order to correctly model stellar atmospheres, fundamental atomic data must be available to describe atomic lines observed in their spectra. Accurate, laboratory-measured oscillator strengths (f-values) for Fe peak elements in neutral or low-ionisation states are particularly important for determining chemical abundances.However, advances in astronomical spectroscopy in recent decades have outpaced those in laboratory astrophysics, with the latter frequently being overlooked at the planning stages of new projects. As a result, numerous big-budget astronomy projects have been, and continue to be hindered by a lack of suitable, accurately-measured reference data to permit the analysis of expensive astronomical spectra; a problem only likely to worsen in the coming decades as spectrographs at new facilities increasingly move to infrared wavelengths.At Imperial College London - and in collaboration with NIST, Wisconsin University and Lund University - we have been working with the astronomy community in an effort to provide new accurately-measured f-values for a range of projects. In particular, we have been working closely with the Gaia-ESO (GES) and SDSS-III/APOGEE surveys, both of which have discovered that many lines that would make ideal candidates for inclusion in their analyses have poorly defined f-values, or are simply absent from the database. Using high-resolution Fourier transform spectroscopy (R ~ 2,000,000) to provide atomic branching fractions, and combining these with level lifetimes measured with laser induced fluorescence, we have provided new laboratory-measured f-values for a range of Fe-peak elements, most recently including Fe I, Fe II, and V I. For strong, unblended lines, uncertainties are as low as ±0.02 dex.In this presentation, I will describe how experimental f-values are obtained in the laboratory and present our recent work for GES and APOGEE. In particular, I will also discuss the strengths and limitations of current laboratory
Project Physics Text 5, Models of the Atom.
ERIC Educational Resources Information Center
Harvard Univ., Cambridge, MA. Harvard Project Physics.
Basic atomic theories are presented in this fifth unit of the Project Physics text for use by senior high students. Chemical basis of atomic models in the early years of the 18th Century is discussed n connection with Dalton's theory, atomic properties, and periodic tables. The discovery of electrons is described by using cathode rays, Millikan's…
An atomic model for neutral and singly ionized uranium
NASA Technical Reports Server (NTRS)
Maceda, E. L.; Miley, G. H.
1979-01-01
A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.
Two Dimensional Non-commutative Space and Rydberg Atom Model
NASA Astrophysics Data System (ADS)
Chung, Won Sang
2015-06-01
In this paper we consider the case of only space-space non-commutativity in two dimension. We also discuss the Rydberg atom model in this space and use the linear realization of the coordinate and momentum operators to solve the Schrödinger equation for the Rydberg atom through the standard perturbation method. Finally, the thermodynamics for the Rydberg atom model is discussed.
Perturbed atoms in molecules and solids: The PATMOS model
NASA Astrophysics Data System (ADS)
Røeggen, Inge; Gao, Bin
2013-09-01
A new computational method for electronic-structure studies of molecules and solids is presented. The key element in the new model - denoted the perturbed atoms in molecules and solids model - is the concept of a perturbed atom in a complex. The basic approximation of the new model is unrestricted Hartree Fock (UHF). The UHF orbitals are localized by the Edmiston-Ruedenberg procedure. The perturbed atoms are defined by distributing the orbitals among the nuclei in such a way that the sum of the intra-atomic UHF energies has a minimum. Energy corrections with respect to the UHF energy, are calculated within the energy incremental scheme. The most important three- and four-electron corrections are selected by introducing a modified geminal approach. Test calculations are performed on N2, Li2, and parallel arrays of hydrogen atoms. The character of the perturbed atoms is illustrated by calculations on H2, CH4, and C6H6.
Perturbed atoms in molecules and solids: The PATMOS model.
Røeggen, Inge; Gao, Bin
2013-09-01
A new computational method for electronic-structure studies of molecules and solids is presented. The key element in the new model - denoted the perturbed atoms in molecules and solids model - is the concept of a perturbed atom in a complex. The basic approximation of the new model is unrestricted Hartree Fock (UHF). The UHF orbitals are localized by the Edmiston-Ruedenberg procedure. The perturbed atoms are defined by distributing the orbitals among the nuclei in such a way that the sum of the intra-atomic UHF energies has a minimum. Energy corrections with respect to the UHF energy, are calculated within the energy incremental scheme. The most important three- and four-electron corrections are selected by introducing a modified geminal approach. Test calculations are performed on N2, Li2, and parallel arrays of hydrogen atoms. The character of the perturbed atoms is illustrated by calculations on H2, CH4, and C6H6. PMID:24028099
"Piekara's Chair": Mechanical Model for Atomic Energy Levels.
ERIC Educational Resources Information Center
Golab-Meyer, Zofia
1991-01-01
Uses the teaching method of models or analogies, specifically the model called "Piekara's chair," to show how teaching classical mechanics can familiarize students with the notion of energy levels in atomic physics. (MDH)
Proposed reference models for atomic oxygen in the terrestrial atmosphere
NASA Technical Reports Server (NTRS)
Llewellyn, E. J.; Mcdade, I. C.; Lockerbie, M. D.
1989-01-01
A provisional Atomic Oxygen Reference model was derived from average monthly ozone profiles and the MSIS-86 reference model atmosphere. The concentrations are presented in tabular form for the altitude range 40 to 130 km.
The Quantum Atomic Model "Electronium": A Successful Teaching Tool.
ERIC Educational Resources Information Center
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Focuses on the quantum atomic model Electronium. Outlines the Bremen teaching approach in which this model is used, and analyzes the learning of two students as they progress through the teaching unit. (Author/MM)
Developing Models: What is the Atom Really Like?
ERIC Educational Resources Information Center
Records, Roger M.
1982-01-01
Five atomic theory activities feasible for high school students to perform are described based on the following models: (1) Dalton's Uniform Sphere Model; (2) Thomson's Raisin Pudding Model; (3) Rutherford's Nuclear Model; (4) Bohr's Energy Level Model, and (5) Orbital Model from quantum mechanics. (SK)
Early atomic models - from mechanical to quantum (1904-1913)
NASA Astrophysics Data System (ADS)
Baily, C.
2013-01-01
A complete history of early atomic models would fill volumes, but a reasonably coherent tale of the path from mechanical atoms to the quantum can be told by focusing on the relevant work of three great contributors to atomic physics, in the critically important years between 1904 and 1913: J.J. Thomson, Ernest Rutherford and Niels Bohr. We first examine the origins of Thomson's mechanical atomic models, from his ethereal vortex atoms in the early 1880's, to the myriad "corpuscular" atoms he proposed following the discovery of the electron in 1897. Beyond qualitative predictions for the periodicity of the elements, the application of Thomson's atoms to problems in scattering and absorption led to quantitative predictions that were confirmed by experiments with high-velocity electrons traversing thin sheets of metal. Still, the much more massive and energetic α-particles being studied by Rutherford were better suited for exploring the interior of the atom, and careful measurements on the angular dependence of their scattering eventually allowed him to infer the existence of an atomic nucleus. Niels Bohr was particularly troubled by the radiative instability inherent to any mechanical atom, and succeeded in 1913 where others had failed in the prediction of emission spectra, by making two bold hypotheses that were in contradiction to the laws of classical physics, but necessary in order to account for experimental facts.
100th anniversary of Bohr's model of the atom.
Schwarz, W H Eugen
2013-11-18
In the fall of 1913 Niels Bohr formulated his atomic models at the age of 27. This Essay traces Bohr's fundamental reasoning regarding atomic structure and spectra, the periodic table of the elements, and chemical bonding. His enduring insights and superseded suppositions are also discussed. PMID:24123759
Project Physics Tests 5, Models of the Atom.
ERIC Educational Resources Information Center
Harvard Univ., Cambridge, MA. Harvard Project Physics.
Test items relating to Project Physics Unit 5 are presented in this booklet. Included are 70 multiple-choice and 23 problem-and-essay questions. Concepts of atomic model are examined on aspects of relativistic corrections, electron emission, photoelectric effects, Compton effect, quantum theories, electrolysis experiments, atomic number and mass,…
Modeling of atom-diatom scattering. Technical report
Sindoni, J.M.
1992-05-30
This report entails the work performed on modeling atom-diatom scattering processes utilizing the Impulse Approach (IA). Results of the model, obtained with a computer code, have proven to be in remarkable agreement with laboratory measurements for several atom-diatom scattering systems. Two scattering systems, in particular, that were successfully modeled and compared to measurements were Ar-KBr and Ar-CsF. The IA model provided an explanation for the rapid deactivation evident in the Ar-KBr system. Experimental results in the Ar-CsF experiment that could not be explained by conventional models were also successfully modeled using the IA. Results fit the experimental observations.
Detailed atomic modeling of Sn plasmas for the EUV source
NASA Astrophysics Data System (ADS)
Sasaki, A.; Sunahara, A.; Nishihawra, K.; Nishikawa, T.; Koike, F.; Tanuma, H.
2008-05-01
An atomic model of Sn plasmas is developed to calculate coefficients of radiative transfer, based on the calculated atomic data using the Hullac code. We find that the emission spectrum and conversion efficiency depend critically on the wavelength and spectral structure of the 4d-4f transition arrays. Satellite lines, which have a significant contribution to the emission, are determined after iterative calculations by changing the number of levels in the atomic model. We also correct transition wavelengths through comparison with experiments. Using the present emissivity and opacity, the radiation hydrodynamics simulation will be carried out toward the optimization of the EUV source.
A liquid drop model for embedded atom method cluster energies
NASA Technical Reports Server (NTRS)
Finley, C. W.; Abel, P. B.; Ferrante, J.
1996-01-01
Minimum energy configurations for homonuclear clusters containing from two to twenty-two atoms of six metals, Ag, Au, Cu, Ni, Pd, and Pt have been calculated using the Embedded Atom Method (EAM). The average energy per atom as a function of cluster size has been fit to a liquid drop model, giving estimates of the surface and curvature energies. The liquid drop model gives a good representation of the relationship between average energy and cluster size. As a test the resulting surface energies are compared to EAM surface energy calculations for various low-index crystal faces with reasonable agreement.
Alpha-cluster model of atomic nuclei
NASA Astrophysics Data System (ADS)
Sosin, Zbigniew; Błocki, Jan; Kallunkathariyil, Jinesh; Łukasik, Jerzy; Pawłowski, Piotr
2016-05-01
The description of a nuclear system in its ground state and at low excitations based on the equation of state (EoS) around normal density is presented. In the expansion of the EoS around the saturation point, additional spin polarization terms are taken into account. These terms, together with the standard symmetry term, are responsible for the appearance of the α-like clusters in the ground-state configurations of the N = Z even-even nuclei. At the nuclear surface these clusters can be identified as alpha particles. A correction for the surface effects is introduced for atomic nuclei. Taking into account an additional interaction between clusters the binding energies and sizes of the considered nuclei are very accurately described. The limits of the EoS parameters are established from the properties of the α, 3He and t particles.
Modeling sympathetic cooling of molecules by ultracold atoms
NASA Astrophysics Data System (ADS)
Lim, Jongseok; Frye, Matthew D.; Hutson, Jeremy M.; Tarbutt, M. R.
2015-11-01
We model sympathetic cooling of ground-state CaF molecules by ultracold Li and Rb atoms. The molecules are moving in a microwave trap, while the atoms are trapped magnetically. We calculate the differential elastic cross sections for CaF-Li and CaF-Rb collisions, using model Lennard-Jones potentials adjusted to give typical values for the s -wave scattering length. Together with trajectory calculations, these differential cross sections are used to simulate the cooling of the molecules, the heating of the atoms, and the loss of atoms from the trap. We show that a hard-sphere collision model based on an energy-dependent momentum transport cross section accurately predicts the molecule cooling rate but underestimates the rates of atom heating and loss. Our simulations suggest that Rb is a more effective coolant than Li for ground-state molecules, and that the cooling dynamics is less sensitive to the exact value of the s -wave scattering length when Rb is used. Using realistic experimental parameters, we find that molecules can be sympathetically cooled to 100 μ K in about 10 s. By applying evaporative cooling to the atoms, the cooling rate can be increased and the final temperature of the molecules can be reduced to 1 μ K within 30 s.
Surface Adsorption in Nonpolarizable Atomic Models.
Whitmer, Jonathan K; Joshi, Abhijeet A; Carlton, Rebecca J; Abbott, Nicholas L; de Pablo, Juan J
2014-12-01
Many ionic solutions exhibit species-dependent properties, including surface tension and the salting-out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to develop atomistic models capable of capturing Hofmeister effects rigorously. Importantly, we aim to capture this dependence in computationally cheap "hard" ionic models, which do not exhibit dynamic polarization. To do this, we have performed an investigation detailing the effects of the water model on these properties. Though incredibly important, the role of water models in simulation of ionic solutions and biological systems is essentially unexplored. We quantify this via the ion-dependent surface attraction of the halide series (Cl, Br, I) and, in so doing, determine the relative importance of various hypothesized contributions to ionic surface free energies. Importantly, we demonstrate surface adsorption can result in hard ionic models combined with a thermodynamically accurate representation of the water molecule (TIP4Q). The effect observed in simulations of iodide is commensurate with previous calculations of the surface potential of mean force in rigid molecular dynamics and polarizable density-functional models. Our calculations are direct simulation evidence of the subtle but sensitive role of water thermodynamics in atomistic simulations. PMID:26583244
Enhanced NLTE Atomic Kinetics Modeling Capabilities in HYDRA
NASA Astrophysics Data System (ADS)
Patel, Mehul V.; Scott, Howard A.; Marinak, Michael M.
2014-10-01
In radiation hydrodynamics modeling of ICF targets, an NLTE treatment of atomic kinetics is necessary for modeling high-Z hohlraum wall materials, high-Z dopants mixed in the central gas hotspot, and is potentially needed for accurate modeling of outer layers of the capsule ablator. Over the past several years, the NLTE DCA atomic physics capabilities in the 3D ICF radiation hydrodynamics code HYDRA have been significantly enhanced. The underlying atomic models have been improved, additional kinetics options including the ability to run DCA in cells with dynamic mixing of species has been added, and the computational costs have been significantly reduced using OpenMP threading. To illustrate the improved capabilities, we will show higher fidelity results from simulations of ICF hohlraum energetics, laser irradiated sphere experiments, and ICF capsule implosions. Prepared by LLNL under Contract DE-AC52-07NA27344.
Modelling spectral properties of non-equilibrium atomic hydrogen plasma
NASA Astrophysics Data System (ADS)
D'Ammando, G.; Pietanza, L. D.; Colonna, G.; Longo, S.; Capitelli, M.
2010-02-01
A model to predict the emissivity and absorption coefficient of atomic hydrogen plasma is presented in detail. Non-equilibrium plasma is studied through coupling of the model with a collisional-radiative code for the excited states population as well as with the Boltzmann equation for the electron energy distribution function.
Atomic-scale modeling of cellulose nanocrystals
NASA Astrophysics Data System (ADS)
Wu, Xiawa
Cellulose nanocrystals (CNCs), the most abundant nanomaterials in nature, are recognized as one of the most promising candidates to meet the growing demand of green, bio-degradable and sustainable nanomaterials for future applications. CNCs draw significant interest due to their high axial elasticity and low density-elasticity ratio, both of which are extensively researched over the years. In spite of the great potential of CNCs as functional nanoparticles for nanocomposite materials, a fundamental understanding of CNC properties and their role in composite property enhancement is not available. In this work, CNCs are studied using molecular dynamics simulation method to predict their material' behaviors in the nanoscale. (a) Mechanical properties include tensile deformation in the elastic and plastic regions using molecular mechanics, molecular dynamics and nanoindentation methods. This allows comparisons between the methods and closer connectivity to experimental measurement techniques. The elastic moduli in the axial and transverse directions are obtained and the results are found to be in good agreement with previous research. The ultimate properties in plastic deformation are reported for the first time and failure mechanism are analyzed in details. (b) The thermal expansion of CNC crystals and films are studied. It is proposed that CNC film thermal expansion is due primarily to single crystal expansion and CNC-CNC interfacial motion. The relative contributions of inter- and intra-crystal responses to heating are explored. (c) Friction at cellulose-CNCs and diamond-CNCs interfaces is studied. The effects of sliding velocity, normal load, and relative angle between sliding surfaces are predicted. The Cellulose-CNC model is analyzed in terms of hydrogen bonding effect, and the diamond-CNC model compliments some of the discussion of the previous model. In summary, CNC's material properties and molecular models are both studied in this research, contributing to
Physically representative atomistic modeling of atomic-scale friction
NASA Astrophysics Data System (ADS)
Dong, Yalin
Nanotribology is a research field to study friction, adhesion, wear and lubrication occurred between two sliding interfaces at nano scale. This study is motivated by the demanding need of miniaturization mechanical components in Micro Electro Mechanical Systems (MEMS), improvement of durability in magnetic storage system, and other industrial applications. Overcoming tribological failure and finding ways to control friction at small scale have become keys to commercialize MEMS with sliding components as well as to stimulate the technological innovation associated with the development of MEMS. In addition to the industrial applications, such research is also scientifically fascinating because it opens a door to understand macroscopic friction from the most bottom atomic level, and therefore serves as a bridge between science and engineering. This thesis focuses on solid/solid atomic friction and its associated energy dissipation through theoretical analysis, atomistic simulation, transition state theory, and close collaboration with experimentalists. Reduced-order models have many advantages for its simplification and capacity to simulating long-time event. We will apply Prandtl-Tomlinson models and their extensions to interpret dry atomic-scale friction. We begin with the fundamental equations and build on them step-by-step from the simple quasistatic one-spring, one-mass model for predicting transitions between friction regimes to the two-dimensional and multi-atom models for describing the effect of contact area. Theoretical analysis, numerical implementation, and predicted physical phenomena are all discussed. In the process, we demonstrate the significant potential for this approach to yield new fundamental understanding of atomic-scale friction. Atomistic modeling can never be overemphasized in the investigation of atomic friction, in which each single atom could play a significant role, but is hard to be captured experimentally. In atomic friction, the
The chaotic atom model via a fractal approximation of motion
NASA Astrophysics Data System (ADS)
Agop, M.; Nica, P.; Gurlui, S.; Focsa, C.; Magop, D.; Borsos, Z.
2011-10-01
A new model of the atom is built based on a complete and detailed nonlinear dynamics analysis (complete time series, Poincaré sections, complete phase space, Lyapunov exponents, bifurcation diagrams and fractal analysis), through the correlation of the chaotic-stochastic model with a fractal one. Some specific mechanisms that ensure the atom functionality are proposed: gun, chaotic gun and multi-gun effects for the excited states (the classical analogue of quantum absorption) and the fractalization of the trajectories for the stationary states (a natural way of introducing the quantification).
Model based control of dynamic atomic force microscope
Lee, Chibum; Salapaka, Srinivasa M.
2015-04-15
A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H{sub ∞} control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.
Model based control of dynamic atomic force microscope.
Lee, Chibum; Salapaka, Srinivasa M
2015-04-01
A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments. PMID:25933864
Atmospheric turbulence optical model (ATOM) based on fractal theory
NASA Astrophysics Data System (ADS)
Jaenisch, Holger M.; Handley, James W.; Scoggins, Jim; Carroll, Marvin P.
1994-06-01
An Atmospheric Turbulence Optical Model (ATOM) is presented that used cellular automata (CA) rules as the basis for modeling synthetic phase sheets. This method allows image fracture, scintillation and blur to be correctly models using the principle of convolution with a complex kernel derived from CA rules interaction. The model takes into account the changing distribution of turbules from micro-turbule domination at low altitudes to macro-domination at high altitudes. The wavelength of propagating images (such as a coherent laser beam) and the range are taken into account. The ATOM model is written in standard FORTRAN 77 and enables high-speed in-line calculation of atmospheric effects to be performed without resorting to computationally intensive solutions of Navier Stokes equations or Cn2 profiles.
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
Quan, Wei; Lv, Lin Liu, Baiqi
2014-11-15
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
ATOMIC DATA AND SPECTRAL MODEL FOR Fe III
Bautista, Manuel A.; Ballance, Connor P.; Quinet, Pascal
2010-08-01
We present new atomic data (radiative transitions rates and collision strengths) from large-scale calculations and a non-LTE spectral model for Fe III. This model is in very good agreement with observed astronomical emission spectra, in contrast with previous models that yield large discrepancies in observations. The present atomic computations employ a combination of atomic physics methods, e.g., relativistic Hartree-Fock, the Thomas-Fermi-Dirac potential, and Dirac-Fock computation of A-values and the R-matrix with intermediate coupling frame transformation and the Dirac R-matrix. We study advantages and shortcomings of each method. It is found that the Dirac R-matrix collision strengths yield excellent agreement with observations, much improved over previously available models. By contrast, the transformation of the LS-coupling R-matrix fails to yield accurate effective collision strengths at around 10{sup 4} K, despite using very large configuration expansions, due to the limited treatment of spin-orbit effects in the near-threshold resonances of the collision strengths. The present work demonstrates that accurate atomic data for low-ionization iron-peak species are now within reach.
A Nonlinear Model for Fuel Atomization in Spray Combustion
NASA Technical Reports Server (NTRS)
Liu, Nan-Suey (Technical Monitor); Ibrahim, Essam A.; Sree, Dave
2003-01-01
Most gas turbine combustion codes rely on ad-hoc statistical assumptions regarding the outcome of fuel atomization processes. The modeling effort proposed in this project is aimed at developing a realistic model to produce accurate predictions of fuel atomization parameters. The model involves application of the nonlinear stability theory to analyze the instability and subsequent disintegration of the liquid fuel sheet that is produced by fuel injection nozzles in gas turbine combustors. The fuel sheet is atomized into a multiplicity of small drops of large surface area to volume ratio to enhance the evaporation rate and combustion performance. The proposed model will effect predictions of fuel sheet atomization parameters such as drop size, velocity, and orientation as well as sheet penetration depth, breakup time and thickness. These parameters are essential for combustion simulation codes to perform a controlled and optimized design of gas turbine fuel injectors. Optimizing fuel injection processes is crucial to improving combustion efficiency and hence reducing fuel consumption and pollutants emissions.
Modeling atomic hydrogen diffusion in GaAs
NASA Astrophysics Data System (ADS)
Kagadei, Valerii A.; Nefyodtsev, E.
2004-05-01
The hydrogen diffusion model in GaAs in conditions of an intense flow of penetrating atoms has been developed. It is shown that the formation undersurface diffusion barrier layer from immobile interstitial molecules of hydrogen reduce probability of atoms penetration into crystal and rate of their diffusion in GaAs, and influence on the process of shallow- and/or deep-centers passivation. It is exhibited that the influence of diffusion barrier should be taken into account at optimum mode selection of GaAs structure hydrogenation.
Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules.
Bereau, Tristan; Andrienko, Denis; von Lilienfeld, O Anatole
2015-07-14
Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular interactions. Here we introduce a machine learning model for multipole coefficients of atom types H, C, O, N, S, F, and Cl in any molecular conformation. The model is trained on quantum-chemical results for atoms in varying chemical environments drawn from thousands of organic molecules. Multipoles in systems with neutral, cationic, and anionic molecular charge states are treated with individual models. The models' predictive accuracy and applicability are illustrated by evaluating intermolecular interaction energies of nearly 1,000 dimers and the cohesive energy of the benzene crystal. PMID:26575759
A collisional-radiative average atom model for hot plasmas
Rozsnyai, B.F.
1996-10-17
A collisional-radiative `average atom` (AA) model is presented for the calculation of opacities of hot plasmas not in the condition of local thermodynamic equilibrium (LTE). The electron impact and radiative rate constants are calculated using the dipole oscillator strengths of the average atom. A key element of the model is the photon escape probability which at present is calculated for a semi infinite slab. The Fermi statistics renders the rate equation for the AA level occupancies nonlinear, which requires iterations until the steady state. AA level occupancies are found. Detailed electronic configurations are built into the model after the self-consistent non-LTE AA state is found. The model shows a continuous transition from the non-LTE to the LTE state depending on the optical thickness of the plasma. 22 refs., 13 figs., 1 tab.
Quantum Transport Modeling of Atomic Nanostructures on Silicon
NASA Astrophysics Data System (ADS)
Smeu, Manuel
Surface effects can adversely influence the performance of a nanoelectronic device, but may also lead to new functionality. The focus of this thesis is to theoretically study the role of surfaces in nanoelectronics. Our theoretical analysis is from atomic first principles achieved by combining density functional theory with the Keldysh nonequilibrium Green's function approach. This technique allows for all atoms in a system to be treated on an equal footing without any phenomenological parameters. The first part of the thesis considers conduction through a molecule with no substrate to illustrate the sort of system typically modeled in transport calculations. Two Au electrodes are bridged by a substituted benzenediamine molecule (R = CH3, NH2, OH) where an H atom is removed to form a radical that may behave as a spin filter, depending on the R group. Next is considered a π-stacked line of ethylbenzene molecules on the Si(100) surface, where the Si atoms are explicitly included in the calculation. Although the molecules conduct electrons at certain energies, a channel occurs through the substrate, which can dominate the conductance. The use of substituent groups to modulate the electron transport properties of such wires is also investigated, showing that the conductance of the molecular wire could be tuned to dominate over the substrate. Finally, the conductance of the Si(111)-7 × 7 metallic surface is studied. Inspired by experiments suggesting that atomic steps reduce the surface conductance, the atomic structure and transport properties of such steps are examined, revealing that dimer atom buckling along the step edges is the primary culprit since it leads to an opening of a local band gap at the step.
Exactly solvable models for atom-molecule Hamiltonians.
Dukelsky, J; Dussel, G G; Esebbag, C; Pittel, S
2004-07-30
We present a family of exactly solvable generalizations of the Jaynes-Cummings model involving the interaction of an ensemble of SU(2) or SU(1,1) quasispins with a single boson field. They are obtained from the trigonometric Richardson-Gaudin models by replacing one of the SU(2) or SU(1,1) degrees of freedom by an ideal boson. The application to a system of bosonic atoms and molecules is reported. PMID:15323678
Atomic scale modeling of boron transient diffusion in silicon
Caturla, M. J.; Diaz de la Rubia, T.; Foad, M.; Giles, M.; Johnson, M. D.; Law, M.; Lilak, A.
1998-06-17
We presents results from a predictive atomic level simulation of Boron diffusion in Silicon under a wide variety of implant and annealing conditions. The parameters for this simulation have been extracted from first principle approximation models and molecular dynamics simulations. The results are compared with experiments showing good agreement in all cases. The parameters and reactions used have been implemented into a continuum-level model simulator.
A constructive model potential method for atomic interactions
NASA Technical Reports Server (NTRS)
Bottcher, C.; Dalgarno, A.
1974-01-01
A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.
Modeling of Turbulence Effect on Liquid Jet Atomization
NASA Technical Reports Server (NTRS)
Trinh, H. P.
2007-01-01
Recent studies indicate that turbulence behaviors within a liquid jet have considerable effect on the atomization process. Such turbulent flow phenomena are encountered in most practical applications of common liquid spray devices. This research aims to model the effects of turbulence occurring inside a cylindrical liquid jet to its atomization process. The two widely used atomization models Kelvin-Helmholtz (KH) instability of Reitz and the Taylor analogy breakup (TAB) of O'Rourke and Amsden portraying primary liquid jet disintegration and secondary droplet breakup, respectively, are examined. Additional terms are formulated and appropriately implemented into these two models to account for the turbulence effect. Results for the flow conditions examined in this study indicate that the turbulence terms are significant in comparison with other terms in the models. In the primary breakup regime, the turbulent liquid jet tends to break up into large drops while its intact core is slightly shorter than those without turbulence. In contrast, the secondary droplet breakup with the inside liquid turbulence consideration produces smaller drops. Computational results indicate that the proposed models provide predictions that agree reasonably well with available measured data.
Atomic Data and the Modeling of Supernova Spectra
NASA Astrophysics Data System (ADS)
Fontes, Christopher
2012-06-01
The modeling of supernovae (SNe) incorporates a variety of disciplines, including hydrodynamics, radiation transport, nuclear physics and atomic physics. These efforts require numerical simulation of the final stages of a star's life, the supernova explosion phase, and the radiation that is subsequently emitted by the supernova remnant, which can occur over a time span of tens of thousands of years. While there are several different types of SNe, they all emit radiation in some form. The measurement and interpretation of these spectra provide important information about the structure of the exploding star and the supernova engine. In this talk, the role of atomic data is highlighted as it pertains to the modeling of supernova spectra. Recent applications [1,2] involve the Los Alamos OPLIB opacity database, which has been used to provide atomic opacities for modeling supernova plasmas under local thermodynamic equilibrium (LTE) conditions. Ongoing work includes the application of atomic data generated by the Los Alamos suite of atomic physics codes under more complicated, non-LTE conditions [3]. As a specific, recent example, a portion of the x-ray spectrum produced by Tycho's supernova remnant (SN 1572) will be discussed [4].[4pt] [1] C.L. Fryer et al., Astrophys. J. 707, 193 (2009).[0pt] [2] C.L. Fryer et al., Astrophys. J. 725, 296 (2009).[0pt] [3] C.J. Fontes et al., Conference Proceedings for ICPEAC XXVII (Belfast, Northern Ireland), in press, (2011).[0pt] [4] K.A. Eriksen et al., Presentation at the 2012 AAS Meeting (Austin, TX).
Semirelativistic model for ionization of atomic hydrogen by electron impact
Attaourti, Y.; Taj, S.; Manaut, B.
2005-06-15
We present a semirelativistic model for the description of the ionization process of atomic hydrogen by electron impact in the first Born approximation by using the Darwin wave function to describe the bound state of atomic hydrogen and the Sommerfeld-Maue wave function to describe the ejected electron. This model, accurate to first order in Z/c in the relativistic correction, shows that, even at low kinetic energies of the incident electron, spin effects are small but not negligible. These effects become noticeable with increasing incident electron energies. All analytical calculations are exact and our semirelativistic results are compared with the results obtained in the nonrelativistic Coulomb Born approximation both for the coplanar asymmetric and the binary coplanar geometries.
Empirical model of atomic nitrogen in the upper thermosphere
NASA Technical Reports Server (NTRS)
Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.
1977-01-01
Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.
Extended Bose-Hubbard models with ultracold magnetic atoms
NASA Astrophysics Data System (ADS)
Baier, S.; Mark, M. J.; Petter, D.; Aikawa, K.; Chomaz, L.; Cai, Z.; Baranov, M.; Zoller, P.; Ferlaino, F.
2016-04-01
The Hubbard model underlies our understanding of strongly correlated materials. Whereas its standard form only comprises interactions between particles at the same lattice site, extending it to encompass long-range interactions is predicted to profoundly alter the quantum behavior of the system. We realize the extended Bose-Hubbard model for an ultracold gas of strongly magnetic erbium atoms in a three-dimensional optical lattice. Controlling the orientation of the atomic dipoles, we reveal the anisotropic character of the onsite interaction and hopping dynamics and their influence on the superfluid-to-Mott insulator quantum phase transition. Moreover, we observe nearest-neighbor interactions, a genuine consequence of the long-range nature of dipolar interactions. Our results lay the groundwork for future studies of exotic many-body quantum phases.
Generalized Kronig-Penney model for ultracold atomic quantum systems
NASA Astrophysics Data System (ADS)
Negretti, A.; Gerritsma, R.; Idziaszek, Z.; Schmidt-Kaler, F.; Calarco, T.
2014-10-01
We study the properties of a quantum particle interacting with a one-dimensional structure of equidistant scattering centers. We derive an analytical expression for the dispersion relation and for the Bloch functions in the presence of both even and odd scattering waves within the pseudopotential approximation. This generalizes the well-known solid-state physics textbook result known as the Kronig-Penney model. Our generalized model can be used to describe systems such as degenerate Fermi gases interacting with ions or with another neutral atomic species confined in an optical lattice, thus enabling the investigation of polaron or Kondo physics within a simple formalism. We focus our attention on the specific atom-ion system and compare our findings with quantum defect theory. Excellent agreement is obtained within the regime of validity of the pseudopotential approximation. This enables us to derive a Bose-Hubbard Hamiltonian for a degenerate quantum Bose gas in a linear chain of ions.
Extended Bose-Hubbard models with ultracold magnetic atoms.
Baier, S; Mark, M J; Petter, D; Aikawa, K; Chomaz, L; Cai, Z; Baranov, M; Zoller, P; Ferlaino, F
2016-04-01
The Hubbard model underlies our understanding of strongly correlated materials. Whereas its standard form only comprises interactions between particles at the same lattice site, extending it to encompass long-range interactions is predicted to profoundly alter the quantum behavior of the system. We realize the extended Bose-Hubbard model for an ultracold gas of strongly magnetic erbium atoms in a three-dimensional optical lattice. Controlling the orientation of the atomic dipoles, we reveal the anisotropic character of the onsite interaction and hopping dynamics and their influence on the superfluid-to-Mott insulator quantum phase transition. Moreover, we observe nearest-neighbor interactions, a genuine consequence of the long-range nature of dipolar interactions. Our results lay the groundwork for future studies of exotic many-body quantum phases. PMID:27124454
Charged Neutrinos and Atoms in the Standard Model
NASA Astrophysics Data System (ADS)
Takasugi, E.; Tanaka, M.
1992-03-01
The possibility of the charge quantization in the standard model is examined in the absence of the ``generation as copies'' rule. It is shown that neutrinos and atoms can have mini-charges, while neutron is neutral. If a triplet Higgs boson is introduced, neutrinos have masses. Two neutrinos form a Konopinski-Mahmoud Dirac particle and the other becomes a Majorana particle due to the hidden local anomaly free U(1) symmetry.
AtomDB and PyAtomDB: Atomic Data and Modelling Tools for High Energy and Non-Maxwellian Plasmas
NASA Astrophysics Data System (ADS)
Foster, Adam; Smith, Randall K.; Brickhouse, Nancy S.; Cui, Xiaohong
2016-04-01
The release of AtomDB 3 included a large wealth of inner shell ionization and excitation data allowing accurate modeling of non-equilibrium plasmas. We describe the newly calculated data and compare it to published literature data. We apply the new models to existing supernova remnant data such as W49B and N132D. We further outline progress towards AtomDB 3.1, including a new energy-dependent charge exchange cross sections.We present newly developed models for the spectra of electron-electron bremsstrahlung and those due to non-Maxwellian electron distributions.Finally, we present our new atomic database access tools, released as PyAtomDB, allowing powerful use of the underlying fundamental atomic data as well as the spectral emissivities.
Modeling of Turbulence Effects on Liquid Jet Atomization and Breakup
NASA Technical Reports Server (NTRS)
Trinh, Huu P.; Chen, C. P.
2005-01-01
Recent experimental investigations and physical modeling studies have indicated that turbulence behaviors within a liquid jet have considerable effects on the atomization process. This study aims to model the turbulence effect in the atomization process of a cylindrical liquid jet. Two widely used models, the Kelvin-Helmholtz (KH) instability of Reitz (blob model) and the Taylor-Analogy-Breakup (TAB) secondary droplet breakup by O Rourke et al, are further extended to include turbulence effects. In the primary breakup model, the level of the turbulence effect on the liquid breakup depends on the characteristic scales and the initial flow conditions. For the secondary breakup, an additional turbulence force acted on parent drops is modeled and integrated into the TAB governing equation. The drop size formed from this breakup regime is estimated based on the energy balance before and after the breakup occurrence. This paper describes theoretical development of the current models, called "T-blob" and "T-TAB", for primary and secondary breakup respectivety. Several assessment studies are also presented in this paper.
A Comprehensive X-Ray Absorption Model for Atomic Oxygen
NASA Technical Reports Server (NTRS)
Gorczyca, T. W.; Bautista, M. A.; Hasoglu, M. F.; Garcia, J.; Gatuzz, E.; Kaastra, J. S.; Kallman, T. R.; Manson, S. T.; Mendoza, C.; Raassen, A. J. J.; de Vries, C. P.; Zatsarinny, O.
2013-01-01
An analytical formula is developed to accurately represent the photoabsorption cross section of atomic Oxygen for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects, that accurately predict the absorption oscillator strengths below threshold and merge consistently and continuously to the above-threshold cross section. Further, minor adjustments are made to the threshold energies in order to reliably align the atomic Rydberg resonances after consideration of both experimental and observed line positions. At energies far below or above the K-edge region, the formulation is based on both outer- and inner-shell direct photoionization, including significant shake-up and shake-off processes that result in photoionization-excitation and double-photoionization contributions to the total cross section. The ultimate purpose for developing a definitive model for oxygen absorption is to resolve standing discrepancies between the astronomically observed and laboratory-measured line positions, and between the inferred atomic and molecular oxygen abundances in the interstellar medium from XSTAR and SPEX spectral models.
ERIC Educational Resources Information Center
Liguori, Lucia
2014-01-01
Atomic orbital theory is a difficult subject for many high school and beginning undergraduate students, as it includes mathematical concepts not yet covered in the school curriculum. Moreover, it requires certain ability for abstraction and imagination. A new atomic orbital model "the chocolate shop" created "by" students…
Atomic collision processes for modelling cool star spectra
NASA Astrophysics Data System (ADS)
Barklem, Paul
2015-05-01
The abundances of chemical elements in cool stars are very important in many problems in modern astrophysics. They provide unique insight into the chemical and dynamical evolution of the Galaxy, stellar processes such as mixing and gravitational settling, the Sun and its place in the Galaxy, and planet formation, to name a just few examples. Modern telescopes and spectrographs measure stellar spectral lines with precision of order 1 per cent, and planned surveys will provide such spectra for millions of stars. However, systematic errors in the interpretation of observed spectral lines leads to abundances with uncertainties greater than 20 per cent. Greater precision in the interpreted abundances should reasonably be expected to lead to significant discoveries, and improvements in atomic data used in stellar atmosphere models play a key role in achieving such advances in precision. In particular, departures from the classical assumption of local thermodynamic equilibrium (LTE) represent a significant uncertainty in the modelling of stellar spectra and thus derived chemical abundances. Non-LTE modelling requires large amounts of radiative and collisional data for the atomic species of interest. I will focus on inelastic collision processes due to electron and hydrogen atom impacts, the important perturbers in cool stars, and the progress that has been made. I will discuss the impact on non-LTE modelling, and what the modelling tells us about the types of collision processes that are important and the accuracy required. More specifically, processes of fundamentally quantum mechanical nature such as spin-changing collisions and charge transfer have been found to be very important in the non-LTE modelling of spectral lines of lithium, oxygen, sodium and magnesium.
Atomic mechanism of internal friction in a model metallic glass
NASA Astrophysics Data System (ADS)
Yu, Hai-Bin; Samwer, Konrad
2014-10-01
Internal friction (IF) describes the ability of materials to damp out mechanical oscillations. It is a crucial engineering parameter and also conveys unique microscopic information about structural defects, transport phenomena, and phase transformations in solids. While IF predominately results from lattice defects in crystalline materials, the origin of IF remains unclear in disordered materials, like metallic glasses. In this paper, we study the atomic rearrangements that govern IF in a model metallic glass, via numerical simulations of dynamical mechanical spectroscopy together with structural analysis. We identify cooperative and avalanchelike thermal-driven excitations as an underlying mechanism and demonstrate a linearlike relation between the concentrations of these excitations and the values of IF. Structurally, these excitations can be hindered, and thus suppress IF, by slow atoms that usually associate with full icosahedral symmetry. Our results also provide practical guides in tuning IF in metallic glasses from atomistic perspectives.
Theoretical model for electrophilic oxygen atom insertion into hydrocarbons
Bach, R.D.; Su, M.D. ); Andres, J.L. Wayne State Univ., Detroit, MI ); McDouall, J.J.W. )
1993-06-30
A theoretical model suggesting the mechanistic pathway for the oxidation of saturated-alkanes to their corresponding alcohols and ketones is described. Water oxide (H[sub 2]O-O) is employed as a model singlet oxygen atom donor. Molecular orbital calculations with the 6-31G basis set at the MP2, QCISD, QCISD(T), CASSCF, and MRCI levels of theory suggest that oxygen insertion by water oxide occurs by the interaction of an electrophilic oxygen atom with a doubly occupied hydrocarbon fragment orbital. The electrophilic oxygen approaches the hydrocarbon along the axis of the atomic carbon p orbital comprising a [pi]-[sub CH(2)] or [pi]-[sub CHCH(3)] fragment orbital to form a carbon-oxygen [sigma] bond. A concerted hydrogen migration to an adjacent oxygen lone pair of electrons affords the alcohol insertion product in a stereoselective fashion with predictable stereochemistry. Subsequent oxidation of the alcohol to a ketone (or aldehyde) occurs in a similar fashion and has a lower activation barrier. The calculated (MP4/6-31G*//MP2/6-31G*) activation barriers for oxygen atom insertion into the C-H bonds of methane, ethane, propane, butane, isobutane, and methanol are 10.7, 8.2, 3.9, 4.8, 4.5, and 3.3 kcal/mol, respectively. We use ab initio molecular orbital calculations in support of a frontier MO theory that provides a unique rationale for both the stereospecificity and the stereoselectivity of insertion of electrophilic oxygen and related electrophiles into the carbon-hydrogen bond. 13 refs., 7 figs., 2 tabs.
Bohr model and dimensional scaling analysis of atoms and molecules
NASA Astrophysics Data System (ADS)
Urtekin, Kerim
It is generally believed that the old quantum theory, as presented by Niels Bohr in 1913, fails when applied to many-electron systems, such as molecules, and nonhydrogenic atoms. It is the central theme of this dissertation to display with examples and applications the implementation of a simple and successful extension of Bohr's planetary model of the hydrogenic atom, which has recently been developed by an atomic and molecular theory group from Texas A&M University. This "extended" Bohr model, which can be derived from quantum mechanics using the well-known dimentional scaling technique is used to yield potential energy curves of H2 and several more complicated molecules, such as LiH, Li2, BeH, He2 and H3, with accuracies strikingly comparable to those obtained from the more lengthy and rigorous "ab initio" computations, and the added advantage that it provides a rather insightful and pictorial description of how electrons behave to form chemical bonds, a theme not central to "ab initio" quantum chemistry. Further investigation directed to CH, and the four-atom system H4 (with both linear and square configurations), via the interpolated Bohr model, and the constrained Bohr model (with an effective potential), respectively, is reported. The extended model is also used to calculate correlation energies. The model is readily applicable to the study of molecular species in the presence of strong magnetic fields, as is the case in the vicinities of white dwarfs and neutron stars. We find that magnetic field increases the binding energy and decreases the bond length. Finally, an elaborative review of doubly coupled quantum dots for a derivation of the electron exchange energy, a straightforward application of Heitler-London method of quantum molecular chemistry, concludes the dissertation. The highlights of the research are (1) a bridging together of the pre- and post quantum mechanical descriptions of the chemical bond (Bohr-Sommerfeld vs. Heisenberg-Schrodinger), and
Bohr model and dimensional scaling analysis of atoms and molecules
NASA Astrophysics Data System (ADS)
Svidzinsky, Anatoly; Chen, Goong; Chin, Siu; Kim, Moochan; Ma, Dongxia; Murawski, Robert; Sergeev, Alexei; Scully, Marlan; Herschbach, Dudley
It is generally believed that the old quantum theory, as presented by Niels Bohr in 1913, fails when applied to few electron systems, such as the H2 molecule. Here we review recent developments of the Bohr model that connect it with dimensional scaling procedures adapted from quantum chromodynamics. This approach treats electrons as point particles whose positions are determined by optimizing an algebraic energy function derived from the large-dimension limit of the Schrödinger equation. The calculations required are simple yet yield useful accuracy for molecular potential curves and bring out appealing heuristic aspects. We first examine the ground electronic states of H2, HeH, He2, LiH, BeH and Li2. Even a rudimentary Bohr model, employing interpolation between large and small internuclear distances, gives good agreement with potential curves obtained from conventional quantum mechanics. An amended Bohr version, augmented by constraints derived from Heitler-London or Hund-Mulliken results, dispenses with interpolation and gives substantial improvement for H2 and H3. The relation to D-scaling is emphasized. A key factor is the angular dependence of the Jacobian volume element, which competes with interelectron repulsion. Another version, incorporating principal quantum numbers in the D-scaling transformation, extends the Bohr model to excited S states of multielectron atoms. We also discuss kindred Bohr-style applications of D-scaling to the H atom subjected to superstrong magnetic fields or to atomic anions subjected to high frequency, superintense laser fields. In conclusion, we note correspondences to the prequantum bonding models of Lewis and Langmuir and to the later resonance theory of Pauling, and discuss prospects for joining D-scaling with other methods to extend its utility and scope.
Minimal non-Abelian model of atomic dark matter
NASA Astrophysics Data System (ADS)
Choquette, Jeremie; Cline, James M.
2015-12-01
A dark sector resembling the Standard Model, where the abundance of matter is explained by baryon and lepton asymmetries and stable constituents bind to form atoms, is a theoretically appealing possibility. We show that a minimal model with a hidden SU(2) gauge symmetry broken to U(1), with a Dirac fermion doublet, suffices to realize this scenario. Supplemented with a dark Higgs doublet that gets no vacuum expectation value, we readily achieve the dark matter asymmetry through leptogenesis. The model can simultaneously have three portals to the Standard Model, through the Higgs, non-Abelian kinetic mixing, and the heavy neutrino, with interesting phenomenology for direct and collider searches, as well as cosmologically relevant dark matter self-interactions. Exotic bound states consisting of two fermions and a doubly charged vector boson can exist in one phase of the theory.
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.
Laury, Marie L; Wang, Lee-Ping; Pande, Vijay S; Head-Gordon, Teresa; Ponder, Jay W
2015-07-23
A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model. PMID:25683601
Using colloids to model atomic thin film growth
NASA Astrophysics Data System (ADS)
Ganapathy, Rajesh; Buckley, Mark; Cohen, Itai
2009-03-01
We epitaxially grow colloidal thin films by sedimenting micron sized colloidal particles on a microfabricated substrate. The attractive interaction between the colloids, induced by a depletant polymer, leads to the nucleation of islands that grow and coalesce with one another. We use confocal microscopy and particle tracking to study the dynamics of the colloidal particles as they diffuse, aggregate and rearrange configurations during deposition. The saturation island density is estimated as a function of the deposition rate and depletant concentration. We find that our results are in excellent agreement with those obtained from atomic deposition experiments suggesting that our system can be used to model various phenomena that occur in atomic thin film growth. Furthermore, we quantify the Ehrlich-Schwoebel step edge barrier by using holographic optical tweezers to create artificial islands and study the dynamics of colloidal monomers placed on the edge of these islands. Owing to the short-range of the attractive interaction in our system, the origin of the step edge barrier in colloids is strikingly different from atoms.
Assessment of Some Atomization Models Used in Spray Calculations
NASA Technical Reports Server (NTRS)
Raju, M. S.; Bulzin, Dan
2011-01-01
The paper presents the results from a validation study undertaken as a part of the NASA s fundamental aeronautics initiative on high altitude emissions in order to assess the accuracy of several atomization models used in both non-superheat and superheat spray calculations. As a part of this investigation we have undertaken the validation based on four different cases to investigate the spray characteristics of (1) a flashing jet generated by the sudden release of pressurized R134A from cylindrical nozzle, (2) a liquid jet atomizing in a subsonic cross flow, (3) a Parker-Hannifin pressure swirl atomizer, and (4) a single-element Lean Direct Injector (LDI) combustor experiment. These cases were chosen because of their importance in some aerospace applications. The validation is based on some 3D and axisymmetric calculations involving both reacting and non-reacting sprays. In general, the predicted results provide reasonable agreement for both mean droplet sizes (D32) and average droplet velocities but mostly underestimate the droplets sizes in the inner radial region of a cylindrical jet.
Modeling atomization processes in high-pressure vaporizing sprays
NASA Astrophysics Data System (ADS)
Reitz, Rolf D.
The theoretical basis and numerical implementation of KIVA, a multidimensional computer code for the simulation of atomization and vaporization processes in the injection of a liquid through a round hole into a compressed gas, are described. KIVA is based on the blob-injection model of Reitz and Diwakar (1987), taking into account the effects of liquid inertia, surface tension, and the aerodynamic forces on the jet, as well as drop collision and coalescence and the effect of drops on turbulence in the gas. The predictions of KIVA for different injection regimes are compared with published experimental data in extensive graphs, and good agreement is demonstrated.
Quantitative Modeling of Single Atom High Harmonic Generation
Gordon, Ariel; Kaertner, Franz X.
2005-11-25
It is shown by comparison with numerical solutions of the Schroedinger equation that the three step model (TSM) of high harmonic generation (HHG) can be improved to give a quantitatively reliable description of the process. Excellent agreement is demonstrated for the H atom and the H{sub 2}{sup +} molecular ion. It is shown that the standard TSM heavily distorts the HHG spectra, especially of H{sub 2}{sup +}, and an explanation is presented for this behavior. Key to the improvement is the use of the Ehrenfest theorem in the TSM.
A comprehensive X-ray absorption model for atomic oxygen
Gorczyca, T. W.; Bautista, M. A.; Mendoza, C.; Hasoglu, M. F.; García, J.; Gatuzz, E.; Kaastra, J. S.; Raassen, A. J. J.; De Vries, C. P.; Kallman, T. R.; Manson, S. T.; Zatsarinny, O.
2013-12-10
An analytical formula is developed to accurately represent the photoabsorption cross section of O I for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects, that accurately predict the absorption oscillator strengths below threshold and merge consistently and continuously to the above-threshold cross section. Further, minor adjustments are made to the threshold energies in order to reliably align the atomic Rydberg resonances after consideration of both experimental and observed line positions. At energies far below or above the K-edge region, the formulation is based on both outer- and inner-shell direct photoionization, including significant shake-up and shake-off processes that result in photoionization-excitation and double-photoionization contributions to the total cross section. The ultimate purpose for developing a definitive model for oxygen absorption is to resolve standing discrepancies between the astronomically observed and laboratory-measured line positions, and between the inferred atomic and molecular oxygen abundances in the interstellar medium from XSTAR and SPEX spectral models.
Low energy neutral atoms in the earth's magnetosphere: Modeling
Moore, K.R.; McComas, D.J.; Funsten, H.O.; Thomsen, M.F.
1992-01-01
Detection of low energy neutral atoms (LENAs) produced by the interaction of the Earth's geocorona with ambient space plasma has been proposed as a technique to obtain global information about the magnetosphere. Recent instrumentation advances reported previously and in these proceedings provide an opportunity for detecting LENAs in the energy range of <1 keV to {approximately}50 keV. In this paper, we present results from a numerical model which calculates line of sight LENA fluxes expected at a remote orbiting spacecraft for various magnetospheric plasma regimes. This model uses measured charge exchange cross sections, either of two neural hydrogen geocorona models, and various empirical modes of the ring current and plasma sheet to calculate the contribution to the integrated directional flux from each point along the line of sight of the instrument. We discuss implications for LENA imaging of the magnetosphere based on these simulations. 22 refs.
Numerical modeling for primary atomization of liquid jets
NASA Technical Reports Server (NTRS)
Przekwas, A. J.; Chuech, S. G.; Singhal, A. K.
1989-01-01
In the proposed numerical model for primary atomization, surface-wave dispersion equations are solved in conjunction with the jet-embedding technique of solving mean flow equations of a liquid jet. Linear and approximate nonlinear models have been considered. In each case, the dispersion equation is solved over the whole wavelength spectrum to predict drop sizes, frequency, and liquid-mass breakup rates without using any empirical constants. The present model has been applied to several low-speed and high-speed jets. For the high-speed case (the LOX/H2 coaxial injector of the Space Shuttle Main Engine Preburner), predicted drop sizes and liquid breakup rates are in good agreement with the results of the CICM code, which have been calibrated against measured data.
Chapman, Michael S.; Trzynka, Andrew; Chapman, Brynmor K.
2013-01-01
When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5–2.5 Å at resolutions of 4.5–6 Å. PMID:23376441
Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K
2013-04-01
When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. PMID:23376441
Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N
2009-05-01
Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035
A generalized model of atomic processes in dense plasmas
NASA Astrophysics Data System (ADS)
Chung, Hyun-Kyung; Chen, M.; Ciricosta, O.; Vinko, S.; Wark, J.; Lee, R. W.
2015-11-01
A generalized model of atomic processes in plasmas, FLYCHK, has been developed over a decade to provide experimentalists fast and simple but reasonable predictions of atomic properties of plasmas. For a given plasma condition, it provides charge state distributions and spectroscopic properties, which have been extensively used for experimental design and data analysis and currently available through NIST web site. In recent years, highly transient and non-equilibrium plasmas have been created with X-ray free electron lasers (XFEL). As high intensity x-rays interact with matter, the inner-shell electrons are ionized and Auger electrons and photo electrons are generated. With time, electrons participate in the ionization processes and collisional ionization by these electrons dominates photoionization as electron density increases. To study highly complex XFEL produced plasmas, SCFLY, an extended version of FLYCHK code has been used. The code accepts the time-dependent history of x-ray energy and intensity to compute population distribution and ionization distribution self-consistently with electron temperature and density assuming an instantaneous equilibration. The model and its applications to XFEL experiments will be presented as well as its limitations.
Model of spacecraft atomic oxygen and solar exposure microenvironments
NASA Technical Reports Server (NTRS)
Bourassa, R. J.; Pippin, H. G.
1993-01-01
Computer models of environmental conditions in Earth orbit are needed for the following reasons: (1) derivation of material performance parameters from orbital test data, (2) evaluation of spacecraft hardware designs, (3) prediction of material service life, and (4) scheduling spacecraft maintenance. To meet these needs, Boeing has developed programs for modeling atomic oxygen (AO) and solar radiation exposures. The model allows determination of AO and solar ultraviolet (UV) radiation exposures for spacecraft surfaces (1) in arbitrary orientations with respect to the direction of spacecraft motion, (2) overall ranges of solar conditions, and (3) for any mission duration. The models have been successfully applied to prediction of experiment environments on the Long Duration Exposure Facility (LDEF) and for analysis of selected hardware designs for deployment on other spacecraft. The work on these models has been reported at previous LDEF conferences. Since publication of these reports, a revision has been made to the AO calculation for LDEF, and further work has been done on the microenvironments model for solar exposure.
Four-component united-atom model of bitumen.
Hansen, J S; Lemarchand, Claire A; Nielsen, Erik; Dyre, Jeppe C; Schrøder, Thomas
2013-03-01
We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From the stress autocorrelation function, the shear viscosity and shear modulus are evaluated, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin, and resinous oil tend to form nano-aggregates. The characteristic dynamical relaxation time of these aggregates is larger than that of the homogeneously distributed parts of the system, leading to strong dynamical heterogeneity. PMID:23485314
Four-component united-atom model of bitumen
NASA Astrophysics Data System (ADS)
Hansen, J. S.; Lemarchand, Claire A.; Nielsen, Erik; Dyre, Jeppe C.; Schrøder, Thomas
2013-03-01
We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From the stress autocorrelation function, the shear viscosity and shear modulus are evaluated, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin, and resinous oil tend to form nano-aggregates. The characteristic dynamical relaxation time of these aggregates is larger than that of the homogeneously distributed parts of the system, leading to strong dynamical heterogeneity.
Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF
NASA Technical Reports Server (NTRS)
Banks, Bruce A.; Degroh, Kim K.; Auer, Bruce M.; Gebauer, Linda; Edwards, Jonathan L.
1993-01-01
Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) assists in understanding of the mechanisms involved. Thus the reliability of predicting in-space durability of materials based on ground laboratory testing should be improved. A computational model which simulates atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of an assumed mechanistic behavior of atomic oxygen interaction based on in-space atomic oxygen erosion of unprotected polymers and ground laboratory atomic oxygen interaction with protected polymers, prediction of atomic oxygen interaction with protected polymers on LDEF was accomplished. However, the results of these predictions are not consistent with the observed LDEF results at defect sites in protected polymers. Improved agreement between observed LDEF results and predicted Monte Carlo modeling can be achieved by modifying of the atomic oxygen interactive assumptions used in the model. LDEF atomic oxygen undercutting results, modeling assumptions, and implications are presented.
Independent-particle models for light negative atomic ions
NASA Technical Reports Server (NTRS)
Ganas, P. S.; Talman, J. D.; Green, A. E. S.
1980-01-01
For the purposes of astrophysical, aeronomical, and laboratory application, a precise independent-particle model for electrons in negative atomic ions of the second and third period is discussed. The optimum-potential model (OPM) of Talman et al. (1979) is first used to generate numerical potentials for eight of these ions. Results for total energies and electron affinities are found to be very close to Hartree-Fock solutions. However, the OPM and HF electron affinities both depart significantly from experimental affinities. For this reason, two analytic potentials are developed whose inner energy levels are very close to the OPM and HF levels but whose last electron eigenvalues are adjusted precisely with the magnitudes of experimental affinities. These models are: (1) a four-parameter analytic characterization of the OPM potential and (2) a two-parameter potential model of the Green, Sellin, Zachor type. The system O(-) or e-O, which is important in upper atmospheric physics is examined in some detail.
SLIMP: Strong laser interaction model package for atoms and molecules
NASA Astrophysics Data System (ADS)
Zhang, Bin; Zhao, Zengxiu
2015-07-01
We present the SLIMP package, which provides an efficient way for the calculation of strong-field ionization rate and high-order harmonic spectra based on the single active electron approximation. The initial states are taken as single-particle orbitals directly from output files of the general purpose quantum chemistry programs GAMESS, Firefly and Gaussian. For ionization, the molecular Ammosov-Delone-Krainov theory, and both the length gauge and velocity gauge Keldysh-Faisal-Reiss theories are implemented, while the Lewenstein model is used for harmonic spectra. Furthermore, it is also efficient for the evaluation of orbital coordinates wavefunction, momentum wavefunction, orbital dipole moment and calculation of orbital integrations. This package can be applied to quite large basis sets and complex molecules with many atoms, and is implemented to allow easy extensions for additional capabilities.
Simulating and Modeling Transport Through Atomically Thin Membranes
NASA Astrophysics Data System (ADS)
Ostrowski, Joseph; Eaves, Joel
2014-03-01
The world is running out of clean portable water. The efficacy of water desalination technologies using porous materials is a balance between membrane selectivity and solute throughput. These properties are just starting to be understood on the nanoscale, but in the limit of atomically thin membranes it is unclear whether one can apply typical continuous time random walk models. Depending on the size of the pore and thickness of the membrane, mass transport can range from single stochastic passage events to continuous flow describable by the usual hydrodynamic equations. We present a study of mass transport through membranes of various pore geometries using reverse nonequilibrium simulations, and analyze transport rates using stochastic master equations.
Atomic scale modelling of hexagonal structured metallic fission product alloys
Middleburgh, S. C.; King, D. M.; Lumpkin, G. R.
2015-01-01
Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)—making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperatures. The variation of Mo content was modelled to understand the change in alloy structure and behaviour with fuel burnup (Mo molar content decreases in these alloys as burnup increases). The predicted structures compare extremely well with experimentally ascertained values. Vacancy formation energies and the behaviour of extrinsic defects (including iodine and xenon) in the epsilon phase were also investigated to further understand the impact that the metallic precipitates have on fuel performance. PMID:26064629
Atomic-level models of the bacterial carboxysome shell
Tanaka, S.; Kerfeld, C.A.; Sawaya, M.R.; Cai, F.; Heinhorst, S.; Cannon, G.C.; Yeates, T.O.
2008-06-03
The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.
Atomic-scale simulations of atomic and molecular mobility in models of interstellar ice
NASA Astrophysics Data System (ADS)
Andersson, Stefan
The mobility of atoms and molecular radicals at ice-covered dust particles controls the surprisingly rich chemistry of circumstellar and interstellar environments, where a large number of different organic molecules have been observed. Both thermal and non-thermal processes, for instance caused by UV radiation, have been inferred to play important roles in this chemistry. A growing number of experimental studies support previously suggested mechanisms and add to the understanding of possible astrochemical processes. Simulations, of both experiments and astrophysical environments, aid in interpreting experiments and suggesting important mechanisms. Still, the exact mechanisms behind the mobility of species in interstellar ice are far from fully understood. We have performed calculations at the molecular level on the mobility of H atoms and OH radicals at water ice surfaces of varying morphology. Calculations of binding energies and diffusion barriers of H atoms at crystalline and amorphous ice surfaces show that the experimentally observed slower diffusion at amorphous ice is due to considerably stronger binding energies and higher diffusion barriers than at crystalline ice. These results are in excellent agreement with recent experiments. It was also found that quantum tunneling is important for H atom mobility below 10 K. The binding energies and diffusion barriers of OH radicals at crystalline ice have been studied using the ONIOM(QM:AMOEBA) approach. Results indicate that OH diffusion over crystalline ice, contrary to the case of H atoms, might be slower at crystalline ice than at amorphous ice, due to a higher surface density of stronger binding sites at crystalline ice. We have also performed molecular dynamics simulations of the photoexcitation of vapor-deposited water at a range of surface temperatures. These results support that the experimentally observed desorption of H atoms following UV excitation is best explained by release of H atoms from
A computer model for liquid jet atomization in rocket thrust chambers
NASA Astrophysics Data System (ADS)
Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Yang, H. Q.; Ibrahim, E.; Chuech, S.; Przekwas, A. J.
1991-12-01
The process of atomization has been used as an efficient means of burning liquid fuels in rocket engines, gas turbine engines, internal combustion engines, and industrial furnaces. Despite its widespread application, this complex hydrodynamic phenomenon has not been well understood, and predictive models for this process are still in their infancy. The difficulty in simulating the atomization process arises from the relatively large number of parameters that influence it, including the details of the injector geometry, liquid and gas turbulence, and the operating conditions. In this study, numerical models are developed from first principles, to quantify factors influencing atomization. For example, the surface wave dynamics theory is used for modeling the primary atomization and the droplet energy conservation principle is applied for modeling the secondary atomization. The use of empirical correlations has been minimized by shifting the analyses to fundamental levels. During applications of these models, parametric studies are performed to understand and correlate the influence of relevant parameters on the atomization process. The predictions of these models are compared with existing experimental data. The main tasks of this study were the following: development of a primary atomization model; development of a secondary atomization model; development of a model for impinging jets; development of a model for swirling jets; and coupling of the primary atomization model with a CFD code.
Atomic Models of Strong Solids Interfaces Viewed as Composite Structures
NASA Astrophysics Data System (ADS)
Staffell, I.; Shang, J. L.; Kendall, K.
2014-02-01
This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture energy of a composite interface is needed. Using an interface model based on atomic interaction forces, it is shown that a single layer of contaminant atoms between the matrix and the reinforcement can reduce the interface fracture energy by an order of magnitude, giving a large delamination effect. The paper also looks to a future in which cars will be made largely from composite materials. Radical improvements in automobile design are necessary because the number of cars worldwide is predicted to double. This paper predicts gains in fuel economy by suggesting a new theory of automobile fuel consumption using an adaptation of Coulomb's friction law. It is demonstrated both by experiment and by theoretical argument that the energy dissipated in standard vehicle tests depends only on weight. Consequently, moving from metal to fibre construction can give a factor 2 improved fuel economy performance, roughly the same as moving from a petrol combustion drive to hydrogen fuel cell propulsion. Using both options together can give a factor 4 improvement, as demonstrated by testing a composite car using the ECE15 protocol.
Atomic-orbital expansion model for describing ion-atom collisions at intermediate and low energies
Lin, C.D.; Fritsch, W.
1983-01-01
In the description of inelastic processes in ion-atom collisions at moderate energies, the semiclassical close-coupling method is well established as the standard method. Ever since the pioneering work on H/sup +/ + H in the early 60's, the standard procedure is to expand the electronic wavefunction in terms of molecular orbitals (MO) or atomic orbitals (AO) for describing collisions at, respectively, low or intermediate velocities. It has been recognized since early days that traveling orbitals are needed in the expansions in order to represent the asymptotic states in the collisions correctly. While the adoption of such traveling orbitals presents no conceptual difficulties for expansions using atomic orbitals, the situation for molecular orbitals is less clear. In recent years, various forms of traveling MO's have been proposed, but conflicting results for several well-studied systems have been reported.
One-dimensional extended Hubbard model in the atomic limit
NASA Astrophysics Data System (ADS)
Mancini, F.; Mancini, F. P.
2008-06-01
We present the exact solution of the one-dimensional extended Hubbard model in the atomic limit within the Green’s function and equations of motion formalism. We provide a comprehensive and systematic analysis of the model by considering all the relevant response and correlation functions as well as thermodynamic quantities in the whole parameters space. At zero temperature we identify four phases in the plane (U,n) ( U is the on-site potential and n is the filling) and relative phase transitions as well as different types of charge ordering. These features are endorsed by investigating at T=0 the chemical potential and pertinent local correlators, the particle and double occupancy correlation functions, the entropy, and by studying the behavior in the limit T→0 of the charge and spin susceptibilities. A detailed study of the thermodynamic quantities is also presented at finite temperature. This study evidences that a finite-range order persists for a wide range of the temperature, as shown by the behavior of the correlation functions and by the two-peak structure exhibited by the charge susceptibility and by the entropy. Moreover, the equations of motion formalism, together with the use of composite operators, allows us to exactly determine the set of elementary excitations. As a result, the density of states can be determined and a detailed analysis of the specific heat allows for identifying the excitations and for ascribing its two-peak structure to a redistribution of the charge density.
Magnetic-sublevel atomic kinetics modeling for line polarization spectroscopy
Hakel, P.; Mancini, R. C.
2004-01-01
We discuss the mechanism of polarized X-ray line emission in plasmas, its connection to plasma anisotropy, and introduce an atomic kinetics model and code (POLAR) based on the population kinetics of magnetic sublevels. POLAR represents a multi-level, multi-process approach to the problem of polarized spectra in plasmas, and hence it is well suited for plasma applications where cascade effects and alignment transfer can become important. Polarization degrees of X-ray spectral lines computed with POLAR were successfully benchmarked against calculations done with other formalisms, and experimental results obtained at the EBIT facility of Lawrence Livermore National Laboratory. We also investigated the polarization of He-like Si X-ray satellite lines as spectral signatures of anisotropy in the electron distribution function. A comprehensive modeling study was performed taking into account hydrodynamics and electron kinetics. We find that two satellite lines connecting singlet states develop a noticeable polarization while the triplet lines remain unpolarized. These results suggest a scenario where triplet lines could be used as a reference while the singlets could be used as polarized markers of plasma anisotropy.
Secondary Students' Mental Models of Atoms and Molecules: Implications for Teaching Chemistry.
ERIC Educational Resources Information Center
Harrison, Allan G.; Treagust, David F.
1996-01-01
Examines the reasoning behind views of atoms and molecules held by students (n=48) and investigates how mental models may assist or hamper further instruction in chemistry. Reports that students prefer models of atoms and molecules that depict them as discrete, concrete structures. Recommends that teachers develop student modeling skills and…
Development of a phenomenological model for coal slurry atomization
Dooher, J.P.
1995-11-01
Highly concentrated suspensions of coal particles in water or alternate fluids appear to have a wide range of applications for energy production. For enhanced implementation of coal slurry fuel technology, an understanding of coal slurry atomization as a function coal and slurry properties for specific mechanical configurations of nozzle atomizers should be developed.
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
NASA Technical Reports Server (NTRS)
Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.
1993-01-01
The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.
Improving the Ni I atomic model for solar and stellar atmospheric models
Vieytes, M. C.; Fontenla, J. M. E-mail: johnf@digidyna.com
2013-06-01
Neutral nickel (Ni I) is abundant in the solar atmosphere and is one of the important elements that contribute to the emission and absorption of radiation in the spectral range between 1900 and 3900 Å. Previously, the Solar Radiation Physical Modeling (SRPM) models of the solar atmosphere only considered a few levels of this species. Here, we improve the Ni I atomic model by taking into account 61 levels and 490 spectral lines. We compute the populations of these levels in full NLTE using the SRPM code and compare the resulting emerging spectrum with observations. The present atomic model significantly improves the calculation of the solar spectral irradiance at near-UV wavelengths, which is important for Earth atmospheric studies, and particularly for ozone chemistry.
Operation of the computer model for direct atomic oxygen exposure of Earth satellites
NASA Technical Reports Server (NTRS)
Bourassa, R. J.; Gruenbaum, P. E.; Gillis, J. R.; Hargraves, C. R.
1995-01-01
One of the primary causes of material degradation in low Earth orbit (LEO) is exposure to atomic oxygen. When atomic oxygen molecules collide with an orbiting spacecraft, the relative velocity is 7 to 8 km/sec and the collision energy is 4 to 5 eV per atom. Under these conditions, atomic oxygen may initiate a number of chemical and physical reactions with exposed materials. These reactions contribute to material degradation, surface erosion, and contamination. Interpretation of these effects on materials and the design of space hardware to withstand on-orbit conditions requires quantitative knowledge of the atomic oxygen exposure environment. Atomic oxygen flux is a function of orbit altitude, the orientation of the orbit plan to the Sun, solar and geomagnetic activity, and the angle between exposed surfaces and the spacecraft heading. We have developed a computer model to predict the atomic oxygen exposure of spacecraft in low Earth orbit. The application of this computer model is discussed.
Coupling of an average-atom model with a collisional-radiative equilibrium model
Faussurier, G. Blancard, C.; Cossé, P.
2014-11-15
We present a method to combine a collisional-radiative equilibrium model and an average-atom model to calculate bound and free electron wavefunctions in hot dense plasmas by taking into account screening. This approach allows us to calculate electrical resistivity and thermal conductivity as well as pressure in non local thermodynamic equilibrium plasmas. Illustrations of the method are presented for dilute titanium plasma.
'Bubble chamber model' of fast atom bombardment induced processes.
Kosevich, Marina V; Shelkovsky, Vadim S; Boryak, Oleg A; Orlov, Vadim V
2003-01-01
A hypothesis concerning FAB mechanisms, referred to as a 'bubble chamber FAB model', is proposed. This model can provide an answer to the long-standing question as to how fragile biomolecules and weakly bound clusters can survive under high-energy particle impact on liquids. The basis of this model is a simple estimation of saturated vapour pressure over the surface of liquids, which shows that all liquids ever tested by fast atom bombardment (FAB) and liquid secondary ion mass spectrometry (SIMS) were in the superheated state under the experimental conditions applied. The result of the interaction of the energetic particles with superheated liquids is known to be qualitatively different from that with equilibrium liquids. It consists of initiation of local boiling, i.e., in formation of vapour bubbles along the track of the energetic particle. This phenomenon has been extensively studied in the framework of nuclear physics and provides the basis for construction of the well-known bubble chamber detectors. The possibility of occurrence of similar processes under FAB of superheated liquids substantiates a conceptual model of emission of secondary ions suggested by Vestal in 1983, which assumes formation of bubbles beneath the liquid surface, followed by their bursting accompanied by release of microdroplets and clusters as a necessary intermediate step for the creation of molecular ions. The main distinctive feature of the bubble chamber FAB model, proposed here, is that the bubbles are formed not in the space and time-restricted impact-excited zone, but in the nearby liquid as a 'normal' boiling event, which implies that the temperature both within the bubble and in the droplets emerging on its burst is practically the same as that of the bulk liquid sample. This concept can resolve the paradox of survival of intact biomolecules under FAB, since the part of the sample participating in the liquid-gas transition via the bubble mechanism has an ambient temperature
Fast and accurate modeling of molecular atomization energies with machine learning.
Rupp, Matthias; Tkatchenko, Alexandre; Müller, Klaus-Robert; von Lilienfeld, O Anatole
2012-02-01
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of ∼10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves. PMID:22400967
NASA Astrophysics Data System (ADS)
Jin, Lin; Auerbach, Scott M.; Monson, Peter A.
2011-04-01
We present an atomic lattice model for studying the polymerization of silicic acid in sol-gel and related processes for synthesizing silica materials. Our model is based on Si and O atoms occupying the sites of a body-centered-cubic lattice, with all atoms arranged in SiO4 tetrahedra. This is the simplest model that allows for variation in the Si-O-Si angle, which is largely responsible for the versatility in silica polymorphs. The model describes the assembly of polymerized silica structures starting from a solution of silicic acid in water at a given concentration and pH. This model can simulate related materials—chalcogenides and clays—by assigning energy penalties to particular ring geometries in the polymerized structures. The simplicity of this approach makes it possible to study the polymerization process to higher degrees of polymerization and larger system sizes than has been possible with previous atomistic models. We have performed Monte Carlo simulations of the model at two concentrations: a low density state similar to that used in the clear solution synthesis of silicalite-1, and a high density state relevant to experiments on silica gel synthesis. For the high concentration system where there are NMR data on the temporal evolution of the Qn distribution, we find that the model gives good agreement with the experimental data. The model captures the basic mechanism of silica polymerization and provides quantitative structural predictions on ring-size distributions in good agreement with x-ray and neutron diffraction data.
Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I.
NASA Technical Reports Server (NTRS)
Bautista, M. A.; Fivet, V.; Quinet, P.; Dunn, J.; Gull, T. R.; Kallman, T. R.; Mendoza, C.
2013-01-01
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data.We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of Oiii and Fe ii and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe ii]. Key words: atomic data - atomic processes - line: formation - methods: data analysis - molecular data - molecular processes - techniques: spectroscopic
Project Physics Reader 5, Models of the Atom.
ERIC Educational Resources Information Center
Harvard Univ., Cambridge, MA. Harvard Project Physics.
As a supplement to Project Physics Unit 5, a collection of articles is presented in this reader for student browsing. Nine excerpts are given under the following headings: failure and success, Einstein, Mr. Tompkins and simultaneity, parable of the surveyors, outside and inside the elevator, the teacher and the Bohr theory of atom, Dirac and Born,…
Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness
ERIC Educational Resources Information Center
Park, Eun Jung; Light, Gregory
2009-01-01
Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…
A simple model for optical capture of atoms in strong magnetic quadrupole fields
NASA Astrophysics Data System (ADS)
Haubrich, D.; Höpe, A.; Meschede, D.
1993-10-01
The radiative capture of cesium atoms from the gas phase in a magnetooptic trap with strong magnetic field gradients is studied. A simplified analytic model is used to derive an upper limit for capture velocities. The resulting scaling law agrees well with the observed number of atoms and with the density as a function of field gradient.
Atomic charges for modeling metal–organic frameworks: Why and how
Hamad, Said Balestra, Salvador R.G.; Bueno-Perez, Rocio; Calero, Sofia; Ruiz-Salvador, A. Rabdel
2015-03-15
Atomic partial charges are parameters of key importance in the simulation of Metal–Organic Frameworks (MOFs), since Coulombic interactions decrease with the distance more slowly than van der Waals interactions. But despite its relevance, there is no method to unambiguously assign charges to each atom, since atomic charges are not quantum observables. There are several methods that allow the calculation of atomic charges, most of them starting from the electronic wavefunction or the electronic density or the system, as obtained with quantum mechanics calculations. In this work, we describe the most common methods employed to calculate atomic charges in MOFs. In order to show the influence that even small variations of structure have on atomic charges, we present the results that we obtained for DMOF-1. We also discuss the effect that small variations of atomic charges have on the predicted structural properties of IRMOF-1. - Graphical abstract: We review the different method with which to calculate atomic partial charges that can be used in force field-based calculations. We also present two examples that illustrate the influence of the geometry on the calculated charges and the influence of the charges on structural properties. - Highlights: • The choice of atomic charges is crucial in modeling adsorption and diffusion in MOFs. • Methods for calculating atomic charges in MOFs are reviewed. • We discuss the influence of the framework geometry on the calculated charges. • We discuss the influence of the framework charges on structural the properties.
Mg I as a probe of the solar chromosphere - The atomic model
NASA Technical Reports Server (NTRS)
Mauas, Pablo J.; Avrett, Eugene H.; Loeser, Rudolf
1988-01-01
This paper presents a complete atomic model for Mg I line synthesis, where all the atomic parameters are based on recent experimental and theoretical data. It is shown how the computed profiles at 4571 A and 5173 A are influenced by the choice of these parameters and the number of levels included in the model atom. In addition, observed profiles of the 5173 A b2 line and theoretical profiles for comparison (based on a recent atmospheric model for the average quiet sun) are presented.
Plasma injection and atomic physics models for use in particle simulation codes
Procassini, R.J. California Univ., Berkeley, CA . Electronics Research Lab.)
1991-06-12
Models of plasma injection (creation) and charged/neutral atomic physics which are suitable for incorporation into particle simulation codes are described. Both planar and distributed source injection models are considered. Results obtained from planar injection into a collisionless plasma-sheath region are presented. The atomic physics package simulates the charge exchange and impact ionization interactions which occur between charged particles and neutral atoms in a partially-ionized plasma. These models are applicable to a wide range of problems, from plasma processing of materials to transport in the edge region of a tokamak plasma. 18 refs., 6 figs.
Modeling Linear and Cyclic PKS Intermediates through Atom Replacement
2015-01-01
The mechanistic details of many polyketide synthases (PKSs) remain elusive due to the instability of transient intermediates that are not accessible via conventional methods. Here we report an atom replacement strategy that enables the rapid preparation of polyketone surrogates by selective atom replacement, thereby providing key substrate mimetics for detailed mechanistic evaluations. Polyketone mimetics are positioned on the actinorhodin acyl carrier protein (actACP) to probe the underpinnings of substrate association upon nascent chain elongation and processivity. Protein NMR is used to visualize substrate interaction with the actACP, where a tetraketide substrate is shown not to bind within the protein, while heptaketide and octaketide substrates show strong association between helix II and IV. To examine the later cyclization stages, we extended this strategy to prepare stabilized cyclic intermediates and evaluate their binding by the actACP. Elongated monocyclic mimics show much longer residence time within actACP than shortened analogs. Taken together, these observations suggest ACP-substrate association occurs both before and after ketoreductase action upon the fully elongated polyketone, indicating a key role played by the ACP within PKS timing and processivity. These atom replacement mimetics offer new tools to study protein and substrate interactions and are applicable to a wide variety of PKSs. PMID:25406716
Metelkin, E. V.; Ryazanov, A. I. Semenov, E. V.
2008-09-15
A new theoretical model is developed for the investigation of atomic collision cascades and subcascades in irradiated solids consisting of atoms of a single type. The model is based on an analytical description of the elastic collisions between moving atoms knocked out of the crystal lattice sites and the immobile atoms of the lattice. The description is based on the linear kinetic Boltzmann equation describing the retardation of primary recoil atoms (PRAs) in irradiated solids. The laws of conservation for the total number and the kinetic energy of moving atoms, which follow from the kinetic Boltzmann equation, are analyzed using the proposed model. An analytical solution is obtained for the stationary kinetic Boltzmann equation, which describes the retardation of PRAs for a given source responsible for their production. A kinetic equation for the moving atoms and the corresponding laws of conservation are also analyzed with allowance for the binding energy of atoms at the crystal lattice sites. A criterion for determining the threshold energy of subcascade formation in irradiated solids is formulated. Based on this criterion, the threshold energy of subcascade formation is calculated using the Thomas-Fermi potential. Formulas are presented for determining the mean size and number of subcascades formed in a solid as functions of the PRA energy.
NASA Technical Reports Server (NTRS)
Banks, Bruce A.; Stueber, Thomas J.; Norris, Mary Jo
1998-01-01
A Monte Carlo computational model has been developed which simulates atomic oxygen attack of protected polymers at defect sites in the protective coatings. The parameters defining how atomic oxygen interacts with polymers and protective coatings as well as the scattering processes which occur have been optimized to replicate experimental results observed from protected polyimide Kapton on the Long Duration Exposure Facility (LDEF) mission. Computational prediction of atomic oxygen undercutting at defect sites in protective coatings for various arrival energies was investigated. The atomic oxygen undercutting energy dependence predictions enable one to predict mass loss that would occur in low Earth orbit, based on lower energy ground laboratory atomic oxygen beam systems. Results of computational model prediction of undercut cavity size as a function of energy and defect size will be presented to provide insight into expected in-space mass loss of protected polymers with protective coating defects based on lower energy ground laboratory testing.
Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.
Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M
2016-09-21
We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model. PMID:27420398
Modeling Atoms and Molecules: A New Lesson for Upper Elementary and Middle School Students.
ERIC Educational Resources Information Center
Schwaner, Terry D.; And Others
1994-01-01
Describes a study involving 86 fifth-grade science students to enhance their understandings of basic biological chemistry. Contains a lesson that allows students to build models of atoms and molecules. (ZWH)
Computational model for noncontact atomic force microscopy: energy dissipation of cantilever
NASA Astrophysics Data System (ADS)
Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M.
2016-09-01
We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.
Atomic bomb survivors and the sigmoidal response model
Kondo, S.
1994-12-31
Epidemiological data on health effects of low-level radiation based on 40-yr followup studies of 75000 atomic bomb survivors and 35000 control people show that there were no measurable risks from low-level radiation in regard to noncancer diseases, genetic, teratogenic, and carcinogenic effects. However, seemingly sigmoidal responses of bomb radiation-induced cancers, which must have been caused by tumorigenic mutations contradict experimental results that mutations linearly increase with increase in radiation dose. An explanation is proposed for this superficial contradiction.
Invited review article: The statistical modeling of atomic clocks and the design of time scales.
Levine, Judah; Ibarra-Manzano, O
2012-02-01
I will show how the statistical models that are used to describe the performance of atomic clocks are derived from their internal design. These statistical models form the basis for time scales, which are used to define international time scales such as International Atomic Time and Coordinated Universal Time. These international time scales are realized by ensembles of clocks at national laboratories such as the National Institute of Standards and Technology, and I will describe how ensembles of atomic clocks are characterized and managed. PMID:22380071
Invited Review Article: The statistical modeling of atomic clocks and the design of time scales
Levine, Judah
2012-02-15
I will show how the statistical models that are used to describe the performance of atomic clocks are derived from their internal design. These statistical models form the basis for time scales, which are used to define international time scales such as International Atomic Time and Coordinated Universal Time. These international time scales are realized by ensembles of clocks at national laboratories such as the National Institute of Standards and Technology, and I will describe how ensembles of atomic clocks are characterized and managed.
NASA Astrophysics Data System (ADS)
Jung, Hyunseung; in, Chihun; Choi, Hyunyong; Lee, Hojin
2014-06-01
Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems.
Jung, Hyunseung; In, Chihun; Choi, Hyunyong; Lee, Hojin
2014-01-01
Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems. PMID:24910144
A simple model of molecular imaging with noncontact atomic force microscopy
NASA Astrophysics Data System (ADS)
Moll, Nikolaj; Gross, Leo; Mohn, Fabian; Curioni, Alessandro; Meyer, Gerhard
2012-08-01
Using functionalized tips, the atomic resolution of a single organic molecule can be achieved by noncontact atomic force microscopy (nc-AFM) operating in the regime of short-ranged repulsive Pauli forces. To theoretically describe the atomic contrast in such AFM images, we propose a simple model in which the Pauli repulsion is assumed to follow a power law as a function of the probed charge density. As the exponent in this power law is found to be largely independent of the sample molecule, our model provides a general method for simulating atomically resolved AFM images of organic molecules. For a single perylene-tetracarboxylic-dianhydride (PTCDA) molecule imaged with a CO-terminated tip, we find excellent agreement with the experimental data. Our model eliminates the need to take into account the full tip and sample system and therefore reduces computational cost by three orders of magnitude.
Nonlinear Jaynes–Cummings model for two interacting two-level atoms
NASA Astrophysics Data System (ADS)
de los Santos-Sánchez, O.; González-Gutiérrez, C.; Récamier, J.
2016-08-01
In this work we examine a nonlinear version of the Jaynes–Cummings model for two identical two-level atoms allowing for Ising-like and dipole–dipole interplays between them. The model is said to be nonlinear in the sense that it can incorporate both a general intensity-dependent interaction between the atomic system and the cavity field and/or the presence of a nonlinear medium inside the cavity. As an example, we consider a particular type of atom-field coupling based upon the so-called Buck–Sukumar model and a lossless Kerr-like cavity. We describe the possible effects of such features on the evolution of some quantities of current interest, such as atomic excitation, purity, concurrence, the entropy of the field and the evolution of the latter in phase space.
NASA Astrophysics Data System (ADS)
Tsivilskiy, I. V.; Nagulin, K. Yu.; Gilmutdinov, A. Kh.
2016-02-01
A full three-dimensional nonstationary numerical model of graphite electrothermal atomizers of various types is developed. The model is based on solution of a heat equation within solid walls of the atomizer with a radiative heat transfer and numerical solution of a full set of Navier-Stokes equations with an energy equation for a gas. Governing equations for the behavior of a discrete phase, i.e., atomic particles suspended in a gas (including gas-phase processes of evaporation and condensation), are derived from the formal equations molecular kinetics by numerical solution of the Hertz-Langmuir equation. The following atomizers test the model: a Varian standard heated electrothermal vaporizer (ETV), a Perkin Elmer standard THGA transversely heated graphite tube with integrated platform (THGA), and the original double-stage tube-helix atomizer (DSTHA). The experimental verification of computer calculations is carried out by a method of shadow spectral visualization of the spatial distributions of atomic and molecular vapors in an analytical space of an atomizer.
Kinetic modeling of primary and secondary oxygen atom fluxes at 1 AU
NASA Astrophysics Data System (ADS)
Balyukin, Igor; Katushkina, Olga; Alexashov, Dmitry; Izmodenov, Vladislav
2016-07-01
The first quantitative measurements of the interstellar heavy (oxygen and neon) neutral atoms obtained on the IBEX spacecraft were presented in Park et al. (ApJS, 2015). Qualitative analysis of these data shows that the secondary component of the interstellar oxygen atoms was also measured along with the primary interstellar atoms. This component is formed near the heliopause due to process of charge exchange of interstellar oxygen ions with hydrogen atoms and its existence in the heliosphere was previously predicted theoretically (Izmodenov et al, 1997, 1999, 2001). Quantitative analysis of fluxes of interstellar heavy neutral atoms is only possible with the help of a model which takes into account both filtration of the primary and origin of the secondary interstellar oxygen in the region of interaction of the solar wind with the local interstellar medium as well as a detailed simulation of the motion of interstellar atoms inside the heliosphere. This simulation must take into account the temporal and heliolatitudinal dependences of ionization, the process of charge exchange with the protons of the solar wind and the effect of the solar gravitational attraction. This paper presents the results of modeling interstellar oxygen and neon atoms in the heliospheric shock layer and inside the heliosphere based on a new three-dimensional kinetic-MHD model of the solar wind interaction with the local interstellar medium (Izmodenov and Alexashov, ApJS, 2015) and the comparison of this results with the data obtained on the IBEX spacecraft.
NASA Astrophysics Data System (ADS)
Farrell, Kathryn; Oden, J. Tinsley
2014-07-01
Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and
YUP.SCX: Coaxing Atomic Models into Medium Resolution Electron Density Maps
Tan, Robert K.-Z.; Devkota, Batsal; Harvey, Stephen C.
2008-01-01
The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33 Å, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments. PMID:18572416
Models of atoms in plasmas based on common formalism for bound and free electrons
NASA Astrophysics Data System (ADS)
Blenski, T.; Piron, R.; Caizergues, C.; Cichocki, B.
2013-12-01
Atom-in-plasma models: Thomas-Fermi (TF) and INFERNO, AJCI and VAAQP, that use the same formalism for all electrons are briefly described and analyzed from the point of view of their thermodynamic consistence. While the TF and VAAQP models may be derived from variational principle and respect the virial theorem, it appears that two earlier quantum extensions of the quasi-classical TF model, INFERNO and AJCI, are not fully variational. The problems of the two latter approaches are analyzed from the point of view of the VAAQP model. However all quantum models seem to give unrealistic description of atoms in plasma at low temperature and high plasma densities. These difficulties are connected with the Wigner-Seitz cavity approach to non-central ions that is present in all considered models. Comparison of some equation-of-state data from TF, INFERNO and VAAQP models are shown on a chosen example. We report also on the status of our research on the frequency-dependent linear-response theory of atoms in plasma. A new Ehrenfest-type sum rule, originally proposed in the quantum VAAQP model, was proven in the case of the response of the TF atom with the Bloch hydrodynamics (TFB) and checked by numerical example. The TFB case allows one to have a direct insight into the rather involved mathematics of the self-consistent linear response calculations in situations when both the central atom and its plasma vicinity are perturbed by an electric field.
NASA Astrophysics Data System (ADS)
Wheeldon, Ruth
2012-06-01
Chemistry students' explanations of ionisation energy phenomena often involve a number of non-scientific or inappropriate ideas being used to form causality arguments. Research has attributed this to many science teachers using these ideas themselves (Tan and Taber, in J Chem Educ 86(5):623-629, 2009). This research extends this work by considering which atomic models are used in pre-service teachers' explanations and how that relates to the causality ideas expressed. Thirty-one pre-service teachers were interviewed. Each was asked to describe and explain four different atomic representations (Rutherford, Electron cloud micrograph, Bohr and Schrödinger types) in as much detail as they could. They also provided an explanation for the subsequent ionisation energy values for an oxygen atom and identified which representations were helpful in explaining the values. Significantly, when pre-service teachers only used Bohr type representations, they did not use repelling electron ideas in their explanations. However, arguments that were based on electron-electron repulsion used features from Schrödinger type atoms. These findings suggest that many pre-service teachers need to develop their atomic modelling skills so that they select and use models more expertly and that subsequent ionisation explanations offer a context in which to explore different atomic models' limitations and their deployment as explanatory resources.
NASA Astrophysics Data System (ADS)
O'Sullivan, Colm
2016-03-01
The role of "semi-classical" (Bohr-Sommerfeld) and "semi-quantum-mechanical" (atomic orbital) models in the context of the teaching of atomic theory is considered. It is suggested that an appropriate treatment of such models can serve as a useful adjunct to quantum mechanical study of atomic systems.
Efficient Nonlinear Atomization Model for Thin 3D Free Liquid Films
NASA Astrophysics Data System (ADS)
Mehring, Carsten
2007-03-01
Reviewed is a nonlinear reduced-dimension thin-film model developed by the author and aimed at the prediction of spray formation from thin films such as those found in gas-turbine engines (e.g., prefilming air-blast atomizers), heavy-fuel-oil burners (e.g., rotary-cup atomizers) and in the paint industry (e.g., flat-fan atomizers). Various implementations of the model focusing on different model-aspects, i.e., effect of film geometry, surface tension, liquid viscosity, coupling with surrounding gas-phase flow, influence of long-range intermolecular forces during film rupture are reviewed together with a validation of the nonlinear wave propagation characteristics predicted by the model for inviscid planar films using a two-dimensional vortex- method. An extension and generalization of the current nonlinear film model for implementation into a commercial flow- solver is outlined.
UNCERTAINTIES IN ATOMIC DATA AND THEIR PROPAGATION THROUGH SPECTRAL MODELS. I
Bautista, M. A.; Fivet, V.; Quinet, P.; Dunn, J.; Gull, T. R.; Kallman, T. R.; Mendoza, C.
2013-06-10
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data. We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of O III and Fe II and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe II].
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
Reasoning with Atomic-Scale Molecular Dynamic Models
ERIC Educational Resources Information Center
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Optical Pattern Formation in Spatially Bunched Atoms: A Self-Consistent Model and Experiment
NASA Astrophysics Data System (ADS)
Schmittberger, Bonnie L.; Gauthier, Daniel J.
2014-05-01
The nonlinear optics and optomechanical physics communities use different theoretical models to describe how optical fields interact with a sample of atoms. There does not yet exist a model that is valid for finite atomic temperatures but that also produces the zero temperature results that are generally assumed in optomechanical systems. We present a self-consistent model that is valid for all atomic temperatures and accounts for the back-action of the atoms on the optical fields. Our model provides new insights into the competing effects of the bunching-induced nonlinearity and the saturable nonlinearity. We show that it is crucial to keep the fifth and seventh-order nonlinearities that arise when there exists atomic bunching, even at very low optical field intensities. We go on to apply this model to the results of our experimental system where we observe spontaneous, multimode, transverse optical pattern formation at ultra-low light levels. We show that our model accurately predicts our experimentally observed threshold for optical pattern formation, which is the lowest threshold ever reported for pattern formation. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.
NASA Astrophysics Data System (ADS)
Park, Eun Jung
The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced
[Application of model 4650 type I compressor atomizer in bronchial challenge test].
Yuan, Y; Wang, Y; Zeng, J; He, T
2000-06-01
This study was directed to the feasibility of applying a simple atomizer-model 4650 type I (abbrev. M)-to bronchial challenge test. 92 cases of asthma were divided into 3 groups randomly. All of them were subjected to the bronchial challenge test by M atomizer, and by standard Dosimeter atomizer (abbrev. D) as a comparison. In the test by M atomizer, the times for inspiring challenging medicine were 1, 1.5 and 2 minutes for the 3 groups respectively, while the time for D atomizer was 1 minute for all. The results showed no significant differences (P > 0.2-0.5) between the two atomizers in the 3 groups, their values were linear correlated. When the inspiring time was 1 minute for both M and D, the test needed a higher concentration of challenging medicine for M than for D, their coefficient of correlation (r = 0.285) was relatively low. When inspiring time postponed to 1.5 minute for M, the difference in medicine concentration between M and D was smallest (-0.075 g/L), r = 0.665. However, a further postponed inspiring time to 2 minute for M reversely broadened their difference. These results indicated that the efficiency of M atomizer was a little lower than that of D, postponing the inspiring time for M could make up this weakness. A 1.5 minute inspiring time for M atomizer was the suggestion. Some modifications on M atomizer were done by us for a better efficiency, and the cheap and popular M atomizer could be a good replacement in bronchial challenge test. PMID:12515156
Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling
NASA Astrophysics Data System (ADS)
Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki
2015-12-01
Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene.Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene. Electronic supplementary information (ESI) available: Three TEM movies, additional TEM data corresponding to movies, calculated models, and lifetime results. See DOI: 10.1039/c5nr05913e
Fast Three-Dimensional Method of Modeling Atomic Oxygen Undercutting of Protected Polymers
NASA Technical Reports Server (NTRS)
Snyder, Aaron; Banks, Bruce A.
2002-01-01
A method is presented to model atomic oxygen erosion of protected polymers in low Earth orbit (LEO). Undercutting of protected polymers by atomic oxygen occurs in LEO due to the presence of scratch, crack or pin-window defects in the protective coatings. As a means of providing a better understanding of undercutting processes, a fast method of modeling atomic-oxygen undercutting of protected polymers has been developed. Current simulation methods often rely on computationally expensive ray-tracing procedures to track the surface-to-surface movement of individual "atoms." The method introduced in this paper replaces slow individual particle approaches by substituting a model that utilizes both a geometric configuration-factor technique, which governs the diffuse transport of atoms between surfaces, and an efficient telescoping series algorithm, which rapidly integrates the cumulative effects stemming from the numerous atomic oxygen events occurring at the surfaces of an undercut cavity. This new method facilitates the systematic study of three-dimensional undercutting by allowing rapid simulations to be made over a wide range of erosion parameters.
Theoretical modeling of laser-induced plasmas using the ATOMIC code
NASA Astrophysics Data System (ADS)
Colgan, James; Johns, Heather; Kilcrease, David; Judge, Elizabeth; Barefield, James, II; Clegg, Samuel; Hartig, Kyle
2014-10-01
We report on efforts to model the emission spectra generated from laser-induced breakdown spectroscopy (LIBS). LIBS is a popular and powerful method of quickly and accurately characterizing unknown samples in a remote manner. In particular, LIBS is utilized by the ChemCam instrument on the Mars Science Laboratory. We model the LIBS plasma using the Los Alamos suite of atomic physics codes. Since LIBS plasmas generally have temperatures of somewhere between 3000 K and 12000 K, the emission spectra typically result from the neutral and singly ionized stages of the target atoms. We use the Los Alamos atomic structure and collision codes to generate sets of atomic data and use the plasma kinetics code ATOMIC to perform LTE or non-LTE calculations that generate level populations and an emission spectrum for the element of interest. In this presentation we compare the emission spectrum from ATOMIC with an Fe LIBS laboratory-generated plasma as well as spectra from the ChemCam instrument. We also discuss various physics aspects of the modeling of LIBS plasmas that are necessary for accurate characterization of the plasma, such as multi-element target composition effects, radiation transport effects, and accurate line shape treatments. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.
ERIC Educational Resources Information Center
Sunyono; Yuanita, L.; Ibrahim, M.
2015-01-01
The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…
Everyone Wants to Be a Model Teacher: Part III: Extensions to Atomic Structures and Bonding.
ERIC Educational Resources Information Center
Schrader, C. L.
1985-01-01
Describes activities in which students: (1) propose creative atomic models that account for observed properties and predict additional experimental data; (2) calculate empirical formulas for 27 binary compounds; (3) propose a model to explain why certain elements have certain valences; and (4) arrange hypothetical elements into a periodic chart.…
ERIC Educational Resources Information Center
Battino, Rubin
1983-01-01
Describes the design, construction, and use of oversize lecture-demonstration atomic/molecular models. These models appeal to both concrete and formal operational students. Also describes construction and use of an "spdf" sandwich board and an experiment using attribute blocks. (JN)
A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.
Genheden, Samuel; Essex, Jonathan W
2015-10-13
We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264
Mathematical modelling of the liquid atomization process by cocurrent gas flow
NASA Astrophysics Data System (ADS)
Arkhipov, V. A.; Boiko, V. M.; Goldin, V. D.; Maslov, E. A.; Orlov, S. E.; Poplavskiy, S. V.; Usanina, A. S.; Zharova, I. K.
2016-04-01
This paper focuses on the physical-mathematical model of liquid atomization in the spray pattern of an ejection nozzle. A flow field of a gas phase behind the nozzle section is computed using the Ansys Fluent package. Dynamics of molten metal droplets in the gas phase within a trajectory approach is calculated. Using the presented model, numerical calculation results are given.
Re-examination of an early model of two-electron atoms
NASA Astrophysics Data System (ADS)
Wesenberg, G. E.; Noid, D. W.; Delos, J. B.
1985-07-01
A classical model for the helium atom, originally proposed in 1920 by Irving Langmuir, is re-examined. This model gives surprisingly good energies over a wide range of nuclear charges. In the limit of very large nuclear charge, agreement with the Wilson-Sommerfeld quantization rules is seen. A discussion of stable and unstable orbits is given.
Nano Goes to School: A Teaching Model of the Atomic Force Microscope
ERIC Educational Resources Information Center
Planinsic, Gorazd; Kovac, Janez
2008-01-01
The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…
Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation
NASA Technical Reports Server (NTRS)
Willey, Ronald J.
1993-01-01
Five kinetic models are compared for their ability to predict recombination coefficients for oxygen and nitrogen atoms over high-temperature reusable surface insulation (HRSI). Four of the models are derived using Rideal-Eley or Langmuir-Hinshelwood catalytic mechanisms to describe the reaction sequence. The fifth model is an empirical expression that offers certain features unattainable through mechanistic description. The results showed that a four-parameter model, with temperature as the only variable, works best with data currently available. The model describes recombination coefficients for oxygen and nitrogen atoms for temperatures from 300 to 1800 K. Kinetic models, with atom concentrations, demonstrate the influence of atom concentration on recombination coefficients. These models can be used for the prediction of heating rates due to catalytic recombination during re-entry or aerobraking maneuvers. The work further demonstrates a requirement for more recombination experiments in the temperature ranges of 300-1000 K, and 1500-1850 K, with deliberate concentration variation to verify model requirements.
Expansion of the USDA ARS Aerial Application spray atomization models
Technology Transfer Automated Retrieval System (TEKTRAN)
An effort is underway to update the USDA ARS aerial spray nozzle models using new droplet sizing instrumen-tation and measurement techniques. As part of this effort, the applicable maximum airspeed is being increased from 72 to 80 m/s to provide guidance to applicators when using new high speed air...
Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen
NASA Technical Reports Server (NTRS)
Banks, Bruce A.; Miller, Sharon K.
2004-01-01
Atomic oxygen is one of the predominant constituents of Earth's upper atmosphere. It is created by the photodissociation of molecular oxygen (O2) into single O atoms by ultraviolet radiation. It is chemically very reactive because a single O atom readily combines with another O atom or with other atoms or molecules that can form a stable oxide. The effects of atomic oxygen on the external surfaces of spacecraft in low Earth orbit can have dire consequences for spacecraft life, and this is a well-known and much studied problem. Much less information is known about the effects of atomic oxygen on the internal surfaces of spacecraft. This degradation can occur when openings in components of the spacecraft exterior exist that allow the entry of atomic oxygen into regions that may not have direct atomic oxygen attack but rather scattered attack. Openings can exist because of spacecraft venting, microwave cavities, and apertures for Earth viewing, Sun sensors, or star trackers. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft were simulated at the NASA Glenn Research Center by using Monte Carlo computational techniques. A two-dimensional model was used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of the distance into a parallel-walled cavity. The model allows the atomic oxygen arrival direction, the Maxwell Boltzman temperature, and the ram energy to be varied along with the interaction parameters of the degree of recombination upon impact with polymer or nonreactive surfaces, the initial reaction probability, the reaction probability dependence upon energy and angle of attack, degree of specularity of scattering of reactive and nonreactive surfaces, and the degree of thermal accommodation upon impact with reactive and non-reactive surfaces to be varied to allow the model to produce atomic oxygen erosion geometries that replicate actual experimental results from space. The degree of
Collisional radiative average atom code based on a relativistic Screened Hydrogenic Model
NASA Astrophysics Data System (ADS)
Benita, A. J.; Mínguez, E.; Mendoza, M. A.; Rubiano, J. G.; Gil, J. M.; Rodríguez, R.; Martel, P.
2015-03-01
A steady-state and time-dependent collisional-radiative ''average-atom'' (AA) model (ATMED CR) is presented for the calculation of atomic and radiative properties of plasmas for a wide range of laboratory and theoretical conditions: coronal, local thermodynamic equilibrium or nonlocal thermodynamic equilibrium, optically thin or thick plasmas and photoionized plasmas. The radiative and collisional rates are a set of analytical approximations that compare well with more sophisticated quantum treatment of atomic rates that yield fast calculations. The atomic model is based on a new Relativistic Screened Hydrogenic Model (NRSHM) with a set of universal screening constants including nlj-splitting that has been obtained by fitting to a large database of ionization potentials and excitation energies compiled from the National Institute of Standards and Technology (NIST) database and the Flexible Atomic Code (FAC). The model NRSHM has been validated by comparing the results with ionization energies, transition energies and wave functions computed using sophisticated self-consistent codes and experimental data. All the calculations presented in this work were performed using ATMED CR code.
Planar hydrogen-like atom in inhomogeneous magnetic fields: Exactly or quasi-exactly solvable models
NASA Astrophysics Data System (ADS)
Liu, Liyan; Hao, Qinghai
2015-05-01
We use a simple mathematical method to solve the problem of a two-dimensional hydrogen-like atom in the inhomogeneous magnetic fields B = ( k/ r)z and B = ( k/ r 3)z. We construct a Hamiltonian that takes the same form as the Hamiltonian of a hydrogen-like atom in the homogeneous magnetic fields and obtain the energy spectrum by comparing the Hamiltonians. The results show that the whole spectrum of the atom in the magnetic field B = ( k/ r)z can be obtained, and the problem is exactly solvable in this case. We find analytic solutions of the Schrödinger equation for the atom in the magnetic field B = ( k/ r 3)z for particular values of the magnetic strength k and thus present a quasi-exactly solvable model.
NASA Astrophysics Data System (ADS)
Gorokhov, A. V.; Sinaiski, I. E.
2006-03-01
The Jaynes-Cummings model (JCM) of two-level atom interacting with the photon mode in ideal cavity plays an essential role in modern quantum optics. In previous papers 1,2 an exact form of density matrix of the JCM with fixed atom position and photons dissipation was found. Here, taking into account the classical motion of the atom through the cavity, it is considered a case of nonideal cavity with zero temperature. We have obtained an exact expression for density matrix and calculated photon spectra and spectra of the mean number of photons in a cavity and and time dependencies of some values relevant for the one-atom maser theory.
Numerical Modeling of Turbulence Effects within an Evaporating Droplet in Atomizing Sprays
NASA Technical Reports Server (NTRS)
Balasubramanyam, M. S.; Chen, C. P.; Trinh, H. P.
2006-01-01
A new approach to account for finite thermal conductivity and turbulence effects within atomizing liquid sprays is presented in this paper. The model is an extension of the T-blob and T-TAB atomization/spray model of Trinh and Chen (2005). This finite conductivity model is based on the two-temperature film theory, where the turbulence characteristics of the droplet are used to estimate the effective thermal diffhsivity within the droplet phase. Both one-way and two-way coupled calculations were performed to investigate the performance of this model. The current evaporation model is incorporated into the T-blob atomization model of Trinh and Chen (2005) and implemented in an existing CFD Eulerian-Lagrangian two-way coupling numerical scheme. Validation studies were carried out by comparing with available evaporating atomization spray experimental data in terms of jet penetration, temperature field, and droplet SMD distribution within the spray. Validation results indicate the superiority of the finite-conductivity model in low speed parallel flow evaporating spray.
NASA Astrophysics Data System (ADS)
Lüdde, Hans Jürgen; Achenbach, Alexander; Kalkbrenner, Thilo; Jankowiak, Hans-Christian; Kirchner, Tom
2016-04-01
A new model to account for geometric screening corrections in an independent-atom-model description of ion-molecule collisions is introduced. The ion-molecule cross sections for net capture and net ionization are represented as weighted sums of atomic cross sections with weight factors that are determined from a geometric model of overlapping cross section areas. Results are presented for proton collisions with targets ranging from diatomic to complex polyatomic molecules. Significant improvement compared to simple additivity rule results and in general good agreement with experimental data are found. The flexibility of the approach opens up the possibility to study more detailed observables such as orientation-dependent and charge-state-correlated cross sections for a large class of complex targets ranging from biomolecules to atomic clusters.
Masses of atomic nuclei in the infinite nuclear matter model
Satpathy, L.; Nayak, R.C.
1988-07-01
We present mass excesses of 3481 nuclei in the range 18less than or equal toAless than or equal to267 using the infinite nuclear matter model based on the Hugenholtz-Van Hove theorem. In this model the ground-state energy of a nucleus of asymmetry ..beta.. is considered equivalent to the energy of a perfect sphere made up of the infinite nuclear matter of the same asymmetry plus the residual energy due to shell effects, deformation, etc., called the local energy eta. In this model there are two kinds of parameters: global and local. The five global parameters characterizing the properties of the above sphere are determined by fitting the mass of all nuclei (756) in the recent mass table of Wapstra et al. having error bar less than 30 keV. The local parameters are determined for 25 regions each spanning 8 or 10 A values. The total number of parameters including the five global ones is 238. The root-mean-square deviation for the calculated masses from experiment is 397 keV for the 1572 nuclei used in the least-squares fit. copyright 1988 Academic Press, Inc.
An atomic model of brome mosaic virus using direct electron detection and real-space optimization
NASA Astrophysics Data System (ADS)
Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah
2014-09-01
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.
An atomic model of brome mosaic virus using direct electron detection and real-space optimization.
Wang, Zhao; Hryc, Corey F; Bammes, Benjamin; Afonine, Pavel V; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F; Adams, Paul D; Chiu, Wah
2014-01-01
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. PMID:25185801
An atomic model of brome mosaic virus using direct electron detection and real-space optimization
Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah
2014-01-01
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. PMID:25185801
NASA Astrophysics Data System (ADS)
Ling, Yue; Zaleski, Stéphane; Institut Jean Le Rond d'Alembert Team
2014-11-01
Numerical simulation is conducted to investigate the drop formation and evolution in gas-assisted atomization. The atomizer consists of two parallel planar jets: the fast gas jet and the slow liquid jet. Due to the shear between gas and liquid streams, the liquid-gas interface is unstable, and this eventually leads to full atomization. A fundamental challenge in atomization simulations is the existence of multiple length scales involved. In order to accurately capture both the gas-liquid interface instability and the drop dynamics, a multi-scale multiphase flow simulation strategy is proposed. In the present model, the gas-liquid interface is resolved by the Volume-of-Fluid (VOF) method, while the small drops are represented by Lagrangian point-particle (LPP) models. Particular attention is paid on validating the coupling and conversion between LPP and VOF. The present model is validated by comparing with direct numerical simulation (DNS) results and also experimental data. The simulation results show complex coupling between the interface instability and the turbulent gas jet, which in turn influence the formation and evolution of the drops formed in atomization. ANR-11-MONU-0011.
The LANL atomic kinetics modeling effort and its application to W plasmas
Colgan, James; Abdallah, Joseph; Fontes, Christopher; Zhang, Honglin
2010-12-10
This is the work of the LANL group on atomic kinetics modelling. There are various levels of detail in the LANL suite of atomic physics codes: (1) Non-relativistic configuration average kinetics (nl{sup w}) + UTA spectra, (2) Relativistic configuration average kinetics (nlj{sup w}) + UTA spectra, (3) Mixed UTA (MUTA) - configuration average kinetics and spectra composed of mixture of UTAs and fine-structure features and (4) Fine-structure levels. The LANL suite of atomic physics codes consists of 5 codes: (1) CATS/RATS atomic structure codes (semi-relativistic Cowan code or Dirac-Fock-Slater code), (2) ACE collisional excitation code (Plane-wave Born, Columb-Born and distorted-wave methods) and (3) GIPPER ionization code (scaled-hydrogenic and distorted-wave methods). An on-line version of the codes is available at http://aphysics2.lanl.gov/tempweb. ATOMIC kinetics modelling code uses the atomic data for LTE or NLTE population kinetics models and spectral modelling of a broad range of plasma applications. The mixed UTA (MUTA) approach was developed for the spectra of complex ions and the results are in very good agreement with the Sandia-Z Iron opacity experiments. The LANL configuration-average/MUTA calculations were applied to tungsten problems of the non-LTE kinetics code comparison workshops. The LANL group plans to perform much larger calculations to assess the accuracy of the older results and to investigate low-temperature tungsten processes relevant to the divertor modelling.
NASA Astrophysics Data System (ADS)
Brecht, A. S.; Bougher, S. W.; Gérard, J.-C.; Soret, L.
2012-02-01
Nightglow emissions provide insight into the global thermospheric circulation, specifically in the transition region (˜70-120 km). The O 2 IR nightglow statistical map created from Venus Express (VEx) Visible and InfraRed Thermal Imaging Spectrometer (VIRTIS) observations has been used to deduce a three-dimensional atomic oxygen density map. In this study, the National Center of Atmospheric Research (NCAR) Venus Thermospheric General Circulation Model (VTGCM) is utilized to provide a self-consistent global view of the atomic oxygen density distribution. More specifically, the VTGCM reproduces a 2D nightside atomic oxygen density map and vertical profiles across the nightside, which are compared to the VEx atomic oxygen density map. Both the simulated map and vertical profiles are in close agreement with VEx observations within a ˜30° contour of the anti-solar point. The quality of agreement decreases past ˜30°. This discrepancy implies the employment of Rayleigh friction within the VTGCM may be an over-simplification for representing wave drag effects on the local time variation of global winds. Nevertheless, the simulated atomic oxygen vertical profiles are comparable with the VEx profiles above 90 km, which is consistent with similar O 2 ( 1Δ) IR nightglow intensities. The VTGCM simulations demonstrate the importance of low altitude trace species as a loss for atomic oxygen below 95 km. The agreement between simulations and observations provides confidence in the validity of the simulated mean global thermospheric circulation pattern in the lower thermosphere.
Laser-induced photofragmentation of triethylaluminum: Modeling H-atom production
NASA Astrophysics Data System (ADS)
Brum, Jeffrey L.; Deshmukh, Subhash; Koplitz, Brent
1990-12-01
A rate-equation approach is presented that models H-atom formation during the pulsed laser photolysis of a triethyl metal compound, the specific case being triethylaluminum excited at 193 nm. An excimer laser initiates the chemistry under collisionless conditions, and H atoms are produced that are detected using two-photon (121.6+364.7 nm) ionization. Experimentally, the H-atom intensity is monitored as a function of photolysis laser power. Mechanistically, the primary photodissociation step is postulated to involve cleavage of the metal-carbon bond, thereby producing an ethyl radical. This species can then either: (1) form C2H4 and H directly; or (2) absorb an additional photon and produce an H-atom photofragment. The rate equations and their solutions allow one to calculate how H-atom production should vary as a function of photolysis laser power, and the interplay between the two H-atom production channels is calculated for various absorption cross sections and dissociation rates. A comparison with experimental power dependence data suggests that an overall one-photon dissociation process predominates under the experimental conditions actually used.
Modeling the Reaction of Fe Atoms with CCl4
Camaioni, Donald M.; Ginovska, Bojana; Dupuis, Michel
2009-01-05
The reaction of zero-valent iron with carbon tetrachloride (CCl4) in gas phase was studied using density functional theory. Temperature programmed desorption experiments over a range of Fe and CCl4 coverages on a FeO(111) surface, demonstrate a rich surface chemistry with several reaction products (C2Cl4, C2Cl6, OCCl2, CO, FeCl2, FeCl3) observed. The reactivity of Fe and CCl4 was studied under three stoichiometries, one Fe with one CCl4, one Fe with two CCl4 molecules and two Fe with one CCl4, modeling the environment of the experimental work. The electronic structure calculations give insight into the reactions leading to the experimentally observed products and suggest that novel Fe-C-Cl containing species are important intermediates in these reactions. The intermediate complexes are formed in highly exothermic reactions, in agreement with the experimentally observed reactivity with the surface at low temperature (30 K). This initial survey of the reactivity of Fe with CCl4 identifies some potential reaction pathways that are important in the effort to use Fe nano-particles to differentiate harmful pathways that lead to the formation of contaminants like chloroform (CHCl3) from harmless pathways that lead to products such as formate (HCO2-) or carbon oxides in water and soil. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.
NASA Astrophysics Data System (ADS)
Yin, Cong; Lin, Zheng-Zhe; Li, Min; Tang, Hao
2016-04-01
A condensing potential (CP) model was established for predicting the geometric structure of two-dimensional (2D) atomic islands on crystal surfaces. To further verify the CP model, statistical molecular dynamics simulations are performed to investigate the trapping adatom process of atomic island steps on Pt (111). According to the detailed analysis on the adatom trapping process, the CP model should be a universal theory to understand the shape of the 2D atomic islands on crystal surfaces.
Building a pseudo-atomic model of the anaphase-promoting complex
Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; Fonseca, Paula C. A. da; Barford, David
2013-11-01
This article describes an example of molecular replacement in which atomic models are used to interpret electron-density maps determined using single-particle electron-microscopy data. The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14–15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.
A model of optical trapping cold atoms using a metallic nano wire with surface plasmon effect
NASA Astrophysics Data System (ADS)
Thi Phuong Lan, Nguyen; Thi Nga, Do; Viet, Nguyen Ai
2016-06-01
In this work, we construct a new model of optical trapping cold atoms with a metallic nano wire by using surface plasmon effect generated by strong field of laser beams. Using the skin effect, we send a strong oscillated electromagnetic filed through the surface of a metallic nano wire. The local field generated by evanescent effect creates an effective attractive potential near the surface of metallic nano wires. The consideration of some possible boundary and frequency conditions might lead to non-trivial bound state solution for a cold atom. We discus also the case of the laser reflection optical trap with shell-core design, and compare our model with another recent schemes of cold atom optical traps using optical fibers and carbon nanotubes.
Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model.
Kao, Hsiu-Fen; Lo, Ikai; Chiang, Jih-Chen; Chen, Chun-Nan; Wang, Wan-Tsang; Hsu, Yu-Chi; Ren, Chung-Yuan; Lee, Meng-En; Wu, Chieh-Lung; Gau, Ming-Hong
2012-10-17
We develop a 16-band atomic bond-orbital model (16ABOM) to compute the spin splitting induced by bulk inversion asymmetry in zincblende materials. This model is derived from the linear combination of atomic-orbital (LCAO) scheme such that the characteristics of the real atomic orbitals can be preserved to calculate the spin splitting. The Hamiltonian of 16ABOM is based on a similarity transformation performed on the nearest-neighbor LCAO Hamiltonian with a second-order Taylor expansion k at the Γ point. The spin-splitting energies in bulk zincblende semiconductors, GaAs and InSb, are calculated, and the results agree with the LCAO and first-principles calculations. However, we find that the spin-orbit coupling between bonding and antibonding p-like states, evaluated by the 16ABOM, dominates the spin splitting of the lowest conduction bands in the zincblende materials. PMID:23014503
Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model
NASA Astrophysics Data System (ADS)
Kao, Hsiu-Fen; Lo, Ikai; Chiang, Jih-Chen; Chen, Chun-Nan; Wang, Wan-Tsang; Hsu, Yu-Chi; Ren, Chung-Yuan; Lee, Meng-En; Wu, Chieh-Lung; Gau, Ming-Hong
2012-10-01
We develop a 16-band atomic bond-orbital model (16ABOM) to compute the spin splitting induced by bulk inversion asymmetry in zincblende materials. This model is derived from the linear combination of atomic-orbital (LCAO) scheme such that the characteristics of the real atomic orbitals can be preserved to calculate the spin splitting. The Hamiltonian of 16ABOM is based on a similarity transformation performed on the nearest-neighbor LCAO Hamiltonian with a second-order Taylor expansion over \\vec{k} at the Γ point. The spin-splitting energies in bulk zincblende semiconductors, GaAs and InSb, are calculated, and the results agree with the LCAO and first-principles calculations. However, we find that the spin-orbit coupling between bonding and antibonding p-like states, evaluated by the 16ABOM, dominates the spin splitting of the lowest conduction bands in the zincblende materials.
Transport-theoretic model for the electron-proton-hydrogen atom aurora. I. Theory
Basu, B.; Jasperse, J.R; Strickland, D.J.
1993-12-01
The first self-consistent transport-theoretic model for the combined electron-proton-hydrogen atom aurora is presented. This is needed for accurate modeling of the diffuse aurora, particularly in the midnight sector, for which a statistical study indicates that the proton contribution to the total auroral energy flux is (on the average) about 20 to 25% of that of the electrons. As a result, the ionization yield as well as the yields of many emission features will be underestimated (on the average) by about the same percentage if the proton-hydrogen atom contributions are neglected. The model presented here can also be used to study a pure electron aurora or a pure proton-hydrogen atom aurora by choosing the appropriate boundary conditions, namely, by setting the incident flux of one or the other particle population equal to zero. In the latter case, the new feature of the present model is the rigorous transport-theoretic treatment of the contributions to ionization rates and to emission rates and yields from the secondary electrons produced by protons and hydrogen atoms. A coupled set of three linear transport equations is presented. Protons and hydrogen atoms are coupled only to each other through charge-changing (charge exchange and stripping) collisions, while the electrons are coupled to both protons and hydrogen atoms through the secondary electrons that they produce. Source functions for the secondary electrons produced by the three primary particle populations are compared and contrasted, and the numerical methods for solving the coupled transport equations are described. Finally, formulas for calculating pertinent aurora-related quantities from the particle fluxes are given. 66 refs., 9 figs., 2 tabs.
UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions
Siebert, Xavier; Navaza, Jorge
2009-01-01
Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30–10 Å range and sometimes even beyond 10 Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/. PMID:19564685
Elliott, Simon D; Dey, Gangotri; Maimaiti, Yasheng; Ablat, Hayrensa; Filatova, Ekaterina A; Fomengia, Glen N
2016-07-01
Recent progress in the simulation of the chemistry of atomic layer deposition (ALD) is presented for technologically important materials such as alumina, silica, and copper metal. Self-limiting chemisorption of precursors onto substrates is studied using density functional theory so as to determine reaction pathways and aid process development. The main challenges for the future of ALD modeling are outlined. PMID:26689290
Atomic Dipole Squeezing in the Correlated Two-Mode Two-Photon Jaynes-Cummings Model
NASA Technical Reports Server (NTRS)
Dong, Zhengchao; Zhao, Yonglin
1996-01-01
In this paper, we study the atomic dipole squeezing in the correlated two-mode two-photon JC model with the field initially in the correlated two-mode SU(1,1) coherent state. The effects of detuning, field intensity and number difference between the two field modes are investigated through numerical calculation.
NASA Astrophysics Data System (ADS)
El-Orany, Faisal A. A.
2006-11-01
In this paper, we study the evolution of two two-level atoms interacting with a single-mode quantized radiation field, namely, the two-atom multiphoton Jaynes-Cummings model (JCM). We assume that the field and the atoms are initially prepared in the superposition of displaced number states and excited atomic states, respectively. For this system, we investigate the atomic inversion, Wigner function, phase distribution and entanglement. We show that for symmetric (asymmetric) atoms, the system can generate asymmetric (symmetric) cat states at a quarter of the revival time. Furthermore, the degrees of entanglement for the field-atoms and the one-atom-remainder tangles depend on the rate of energy flow between the parties. The interference in phase space decreases the degree of entanglement in the bipartite.
NASA Astrophysics Data System (ADS)
Murakami, I.; Sakaue, H. A.; Suzuki, C.; Kato, D.; Goto, M.; Tamura, N.; Sudo, S.; Morita, S.
2015-09-01
Quantitative tungsten study with reliable atomic modeling is important for successful achievement of ITER and fusion reactors. We have developed tungsten atomic modeling for understanding the tungsten behavior in fusion plasmas. The modeling is applied to the analysis of tungsten spectra observed from plasmas of the large helical device (LHD) with tungsten pellet injection. We found that extreme ultraviolet (EUV) emission of W24+ to W33+ ions at 1.5-3.5 nm are sensitive to electron temperature and useful to examine the tungsten behavior in edge plasmas. We can reproduce measured EUV spectra at 1.5-3.5 nm by calculated spectra with the tungsten atomic model and obtain charge state distributions of tungsten ions in LHD plasmas at different temperatures around 1 keV. Our model is applied to calculate the unresolved transition array (UTA) seen at 4.5-7 nm tungsten spectra. We analyze the effect of configuration interaction on population kinetics related to the UTA structure in detail and find the importance of two-electron-one-photon transitions between 4p54dn+1- 4p64dn-14f. Radiation power rate of tungsten due to line emissions is also estimated with the model and is consistent with other models within factor 2.
Mathematical Modeling of Ultracold Few-Body Processes in Atomic Traps
NASA Astrophysics Data System (ADS)
Melezhik, V. S.
2016-02-01
We discuss computational aspects of the developed mathematical models for ultracold few-body processes in atomic traps. The key element of the elaborated computational schemes is a nondirect product discrete variable representation (npDVR) we have suggested and applied to the time-dependent and stationary Schrödinger equations with a few spatial variables. It turned out that this approach is very effcient in quantitative analysis of low-dimensional ultracold few-body systems arising in confined geometry of atomic traps. The effciency of the method is demonstrated here on two examples. A brief review is also given of novel results obtained recently.
Berry phase in a two-atom Jaynes-Cummings model with Kerr medium
NASA Astrophysics Data System (ADS)
Bu, Shen-Ping; Zhang, Guo-Feng; Liu, Jia; Chen, Zi-Yu
2008-12-01
The Jaynes-Cummings model (JCM) is an very important model for describing interaction between quantized electromagnetic fields and atoms in cavity quantum electrodynamics (QED). This model is generalized in many different directions since it predicts many novel quantum effects that can be verified by modern physics experimental technologies. In this paper, the Berry phase and entropy of the ground state for arbitrary photon number n of a two-atom Jaynes-Cummings model with Kerr-like medium are investigated. It is found that there is some correspondence between their images, especially the existence of a curve in the Δ-ɛ plane along which the energy, Berry phase and entropy all reach their special values. So it is available for detecting entanglement by applying Berry phase.
A robust all-atom model for LCAT generated by homology modeling[S
Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.
2015-01-01
LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A2 (PLA2) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15–20 Å relative to PLA2. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport. PMID:25589508
Estimation of the adequacy of the fractal model of the atomic structure of amorphous silicon
Golodenko, A. B.
2010-01-15
A method of constructing a fractal model of noncrystalline solid substance is considered using the example of amorphous silicon. In systems of iteration functions, the physical meaning of dihedral and valence angles of the elementary crystallographic cell is assigned to arguments. The model adequacy is estimated by the radial distribution function, the atomic structure density, the distribution of valence and dihedral angles, and the density of dangling interatomic bonds.
An attempt for modeling the atmospheric transport of 3H around Kakrapar Atomic Power Station.
Patra, A K; Nankar, D P; Joshi, C P; Venkataraman, S; Sundar, D; Hegde, A G
2008-01-01
Prediction of downwind tritium air concentrations in the environment around Kakrapar Atomic Power Station (KAPS) was studied on the basis of Gaussian plume dispersion model. The tritium air concentration by field measurement [measured tritium air concentrations in the areas adjacent to KAPS] were compared with the theoretically calculated values (predicted) to validate the model. This approach will be useful in evaluating environmental radiological impacts due to pressurised heavy water reactors. PMID:18664562
Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep
2015-02-01
Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed. PMID:25393218
Influence of the plasma environment on atomic structure using an ion-sphere model
NASA Astrophysics Data System (ADS)
Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel
2015-09-01
Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene
2015-09-28
An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.
Modeling the Formation of Tropical Rings of Atomic Bromine and Iodine
NASA Astrophysics Data System (ADS)
Saiz-Lopez, A.; Fernandez, R.; Salawitch, R. J.; Kinnison, D. E.; Lamarque, J. F.; Ordoñez, C.; Gomez Martin, J. C.; Tilmes, S.
2014-12-01
Very short-lived (VSL) bromo- and iodocarbons are produced at a prodigious rate by ocean biology and these source compounds (SGVSL), together with their degradation inorganic products (PGVSL), are lofted by vigorous convection to the tropical tropopause layer (TTL). Using a state-of-the-art photochemical mechanism within a global model, we investigate the partitioning and loading of reactive inorganic halogens within the TTL. The specific low ozone and low temperature conditions of this region of the atmosphere changes the steady-state between halogen atoms and oxides, making the atoms the dominant species. We suggest that this leads to the formation of two daytime "tropical rings" of both atomic bromine and iodine that circle the tropics with the sun. In addition to a description of this photochemical phenomenon, this communication the partitioning of inorganic halogen reservoirs within the TTL and assess its relevance for the injection of bromine to stratosphere.
Modeling the formation of tropical rings of atomic bromine and iodine
NASA Astrophysics Data System (ADS)
Saiz-Lopez, Alfonso; Fernandez, Rafael; Gomez Martin, Juan Carlos; Salawitch, Ross; Kinnison, Douglas; Lamarque, Jean-Francois; Tilmes, Simone
2015-04-01
Very short-lived (VSL) bromo- and iodocarbons are produced at a prodigious rate by ocean biology and these source compounds (SGVSL), together with their degradation inorganic products (PGVSL), are lofted by vigorous convection to the tropical tropopause layer (TTL). Using a state-of-the-art photochemical mechanism within a global model, we investigate the partitioning and loading of reactive inorganic halogens within the TTL. The specific low ozone and low temperature conditions of this region of the atmosphere changes the steady-state between halogen atoms and oxides, making the atoms the dominant species. We suggest that this leads to the formation of two daytime "tropical rings" of both atomic bromine and iodine that circle the tropics with the sun. In addition to a description of this photochemical phenomenon, this communication the partitioning of inorganic halogen reservoirs within the TTL and assess its relevance for the injection of bromine to stratosphere.
Adsorption and recombination of hydrogen atoms on a model graphite surface. [in interstellar space
NASA Technical Reports Server (NTRS)
Aronowitz, S.; Chang, S.
1985-01-01
The adsorption and recombination of atomic hydrogen on a model graphite grain have been examined in a series of calculations in which a modified, iterative, extended Hueckel program was used. The hydrogen atom is found to be chemisorbed at a site with a zero-point binding energy of 0.7 eV and at an equilibrium distance of 2.25 A above the site. Despite a barrier of about 0.4 eV between adjacent sites, calculations suggest that at temperatures as low as 10 K, an H atom will tunnel through to adjacent sites in less than one nanosecond. However, a potential barrier to the recombination of two hydrogen atoms has been found which displays high sensitivity to the mutual arrangement of the two hydrogen atoms with respect to the graphite surface. Results show that at very low temperatures, recombinations can occur only by tunneling. Consistent with experiment, the region in which H2 begins to form exhibits a repulsive potential with respect to possible chemisorption of the incipient H2 entity.
Collisional radiative model for heavy atoms in hot non-local-thermodynamical-equilibrium plasmas
NASA Astrophysics Data System (ADS)
Bar-Shalom, A.; Oreg, J.; Klapisch, M.
1997-07-01
A collisional radiative model for calculating non-local-thermodynamical-equilibrium (non-LTE) spectra of heavy atoms in hot plasmas has been developed, taking into account the numerous excited and autoionizing states. This model uses superconfigurations as effective levels with an iterative procedure which converges to the detailed configuration spectrum. The non-LTE opacities and emissivities may serve as a reliable benchmark for simpler on-line models in hydrodynamic code simulations. The model is tested against detailed configuration calculations of selenium and is applied to non-LTE optically thin plasma of lutetium.
Modeling the heating and atomic kinetics of a photoionized neon plasma experiment
NASA Astrophysics Data System (ADS)
Lockard, Tom E.
Motivated by gas cell photoionized plasma experiments performed by our group at the Z facility of Sandia National Laboratories, we discuss in this dissertation a modeling study of the heating and ionization of the plasma for conditions characteristic of these experiments. Photoionized plasmas are non-equilibrium systems driven by a broadband x-ray radiation flux. They are commonly found in astrophysics but rarely seen in the laboratory. Several modeling tools have been employed: (1) a view-factor computer code constrained with side x-ray power and gated monochromatic image measurements of the z-pinch radiation, to model the time-history of the photon-energy resolved x-ray flux driving the photoionized plasma, (2) a Boltzmann self-consistent electron and atomic kinetics model to simulate the electron distribution function and configuration-averaged atomic kinetics, (3) a radiation-hydrodynamics code with inline non-equilibrium atomic kinetics to perform a comprehensive numerical simulation of the experiment and plasma heating, and (4) steady-state and time-dependent collisional-radiative atomic kinetics calculations with fine-structure energy level description to assess transient effects in the ionization and charge state distribution of the plasma. The results indicate that the photon-energy resolved x-ray flux impinging on the front window of the gas cell is very well approximated by a linear combination of three geometrically-diluted Planckian distributions. Knowledge of the spectral details of the x-ray drive turned out to be important for the heating and ionization of the plasma. The free electrons in the plasma thermalize quickly relative to the timescales associated with the time-history of the x-ray drive and the plasma atomic kinetics. Hence, electrons are well described by a Maxwellian energy distribution of a single temperature. This finding is important to support the application of a radiation-hydrodynamic model to simulate the experiment. It is found
A Monte Carlo model for seeded atomic flows in the transition regime
Longo, S. Diomede, P.
2009-06-01
A simple model for the numerical determination of separation effects in seeded atomic gas flows is presented. The model is based on the known possibility to provide a statistically convergent estimate of the exact solution for a linear transport equation using the test particle Monte Carlo method. Accordingly, the flow field of the main gas is preliminary calculated and as a second step the linear transport equations obtained by fixing the target distribution in the collision term of the Boltzmann equation for both main and minority components are solved. Both solutions are based on appropriately devised test particle Monte Carlo methods. The second step, the critical one in evaluating the separation effects, is exact and thereby completely free of numerical diffusion. The model is described in details and illustrated by 2D test cases of atomic separation in shock fronts.
ERIC Educational Resources Information Center
Polat-Yaseen, Zeynep
2012-01-01
This study was designed for two major goals, which are to describe students' mental models about atom concept from 6th to 8th grade and to compare students' mental models with visual representations of atom in textbooks. Qualitative and quantitative data were collected with 4 open-ended questions including drawings which were quantified using the…
Influence of the plasma environment on atomic structure using an ion-sphere model
Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel
2015-09-03
Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe^{22+}, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy
Klocke, Michael
2016-01-01
Summary A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively. PMID:27335760
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.
Klocke, Michael; Wolf, Dietrich E
2016-01-01
A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively. PMID:27335760
Influence of the plasma environment on atomic structure using an ion-sphere model
Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel
2015-09-03
Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less
Tunable two-dimensional arrays of single Rydberg atoms for realizing quantum Ising models.
Labuhn, Henning; Barredo, Daniel; Ravets, Sylvain; de Léséleuc, Sylvain; Macrì, Tommaso; Lahaye, Thierry; Browaeys, Antoine
2016-06-30
Spin models are the prime example of simplified many-body Hamiltonians used to model complex, strongly correlated real-world materials. However, despite the simplified character of such models, their dynamics often cannot be simulated exactly on classical computers when the number of particles exceeds a few tens. For this reason, quantum simulation of spin Hamiltonians using the tools of atomic and molecular physics has become a very active field over the past years, using ultracold atoms or molecules in optical lattices, or trapped ions. All of these approaches have their own strengths and limitations. Here we report an alternative platform for the study of spin systems, using individual atoms trapped in tunable two-dimensional arrays of optical microtraps with arbitrary geometries, where filling fractions range from 60 to 100 per cent. When excited to high-energy Rydberg D states, the atoms undergo strong interactions whose anisotropic character opens the way to simulating exotic matter. We illustrate the versatility of our system by studying the dynamics of a quantum Ising-like spin-1/2 system in a transverse field with up to 30 spins, for a variety of geometries in one and two dimensions, and for a wide range of interaction strengths. For geometries where the anisotropy is expected to have small effects on the dynamics, we find excellent agreement with ab initio simulations of the spin-1/2 system, while for strongly anisotropic situations the multilevel structure of the D states has a measurable influence. Our findings establish arrays of single Rydberg atoms as a versatile platform for the study of quantum magnetism. PMID:27281203
Why has the bohr-sommerfeld model of the atom been ignoredby general chemistry textbooks?
Niaz, Mansoor; Cardellini, Liberato
2011-12-01
Bohr's model of the atom is considered to be important by general chemistry textbooks. A major shortcoming of this model was that it could not explain the spectra of atoms containing more than one electron. In order to increase the explanatory power of the model, Sommerfeld hypothesized the existence of elliptical orbits. This study has the following objectives: 1) Formulation of criteria based on a history and philosophy of science framework; and 2) Evaluation of university-level general chemistry textbooks based on the criteria, published in Italy and U.S.A. Presentation of a textbook was considered to be "satisfactory" if it included a description of the Bohr-Sommerfeld model along with diagrams of the elliptical orbits. Of the 28 textbooks published in Italy that were analyzed, only five were classified as "satisfactory". Of the 46 textbooks published in U.S.A., only three were classified as "satisfactory". This study has the following educational implications: a) Sommerfeld's innovation (auxiliary hypothesis) by introducing elliptical orbits, helped to restore the viability of Bohr's model; b) Bohr-Sommerfeld's model went no further than the alkali metals, which led scientists to look for other models; c) This clearly shows that scientific models are tentative in nature; d) Textbook authors and chemistry teachers do not consider the tentative nature of scientific knowledge to be important; e) Inclusion of the Bohr-Sommerfeld model in textbooks can help our students to understand how science progresses. PMID:24061142
Observation of antiferromagnetic correlations in the Hubbard model with ultracold atoms.
Hart, Russell A; Duarte, Pedro M; Yang, Tsung-Lin; Liu, Xinxing; Paiva, Thereza; Khatami, Ehsan; Scalettar, Richard T; Trivedi, Nandini; Huse, David A; Hulet, Randall G
2015-03-12
Ultracold atoms in optical lattices have great potential to contribute to a better understanding of some of the most important issues in many-body physics, such as high-temperature superconductivity. The Hubbard model--a simplified representation of fermions moving on a periodic lattice--is thought to describe the essential details of copper oxide superconductivity. This model describes many of the features shared by the copper oxides, including an interaction-driven Mott insulating state and an antiferromagnetic (AFM) state. Optical lattices filled with a two-spin-component Fermi gas of ultracold atoms can faithfully realize the Hubbard model with readily tunable parameters, and thus provide a platform for the systematic exploration of its phase diagram. Realization of strongly correlated phases, however, has been hindered by the need to cool the atoms to temperatures as low as the magnetic exchange energy, and also by the lack of reliable thermometry. Here we demonstrate spin-sensitive Bragg scattering of light to measure AFM spin correlations in a realization of the three-dimensional Hubbard model at temperatures down to 1.4 times that of the AFM phase transition. This temperature regime is beyond the range of validity of a simple high-temperature series expansion, which brings our experiment close to the limit of the capabilities of current numerical techniques, particularly at metallic densities. We reach these low temperatures using a compensated optical lattice technique, in which the confinement of each lattice beam is compensated by a blue-detuned laser beam. The temperature of the atoms in the lattice is deduced by comparing the light scattering to determinant quantum Monte Carlo simulations and numerical linked-cluster expansion calculations. Further refinement of the compensated lattice may produce even lower temperatures which, along with light scattering thermometry, would open avenues for producing and characterizing other novel quantum states of
Atomic density functional and diagram of structures in the phase field crystal model
NASA Astrophysics Data System (ADS)
Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.
2016-02-01
The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindrical tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.
Computational model for non-LTE atomic process in laser produced plasmas
NASA Astrophysics Data System (ADS)
Takabe, Hideaki; Nishikawa, Takeshi
1994-02-01
A computational model for simulating hydro-radiation phenomena has been studied relating to the partially ionized gold plasma produced by irradiation of intense laser light. The screened hydrogenic model with l-splitting effect and the average ion model are used to determine the atomic state of gold ions in the collisional radiative equilibrium. A statistical method is used to evaluate the spectral opacity and emissivity due to the clusters of line transitions. The x-ray conversion rate and spectrum calculated with the hydrodynamic code ILESTA coupled with opacity and emissivity are compared with those observed experimentally.
Atom-field entanglement in the Jaynes-Cummings model without rotating wave approximation
NASA Astrophysics Data System (ADS)
Mirzaee, M.; Batavani, M.
2015-04-01
In this paper, we present a structure for obtaining the exact eigenfunctions and eigenvalues of the Jaynes-Cummings model (JCM) without the rotating wave approximation (RWA). We study the evolution of the system in the strong coupling region using the time evolution operator without RWA. The entanglement of the system without RWA is investigated using the Von Neumann entropy as an entanglement measure. It is interesting that in the weak coupling regime, the population of the atomic levels and Von Neumann entropy without RWA model shows a good agreement with the RWA whereas in strong coupling domain, the results of these two models are quite different.
Spatial Distributions of Metal Atoms During Carbon SWNTs Formation: Measurements and Modelling
NASA Technical Reports Server (NTRS)
Cau, M.; Dorval, N.; Attal-Tretout, B.; Cochon, J. L.; Loiseau, A.; Farhat, S.; Hinkov, I.; Scott, C. D.
2004-01-01
Experiments and modelling have been undertaken to clarify the role of metal catalysts during single-wall carbon nanotube formation. For instance, we wonder whether the metal catalyst is active as an atom, a cluster, a liquid or solid nanoparticle [1]. A reactor has been developed for synthesis by continuous CO2-laser vaporisation of a carbon-nickel-cobalt target in laminar helium flow. The laser induced fluorescence technique [2] is applied for local probing of gaseous Ni, Co and CZ species throughout the hot carbon flow of the target heated up to 3500 K. A rapid depletion of C2 in contrast to the spatial extent of metal atoms is observed in the plume (Fig. 1). This asserts that C2 condenses earlier than Ni and Co atoms.[3, 4]. The depletion is even faster when catalysts are present. It may indicate that an interaction between metal atoms and carbon dimers takes place in the gas as soon as they are expelled from the target surface. Two methods of modelling are used: a spatially I-D calculation developed originally for the arc process [5], and a zero-D time dependent calculation, solving the chemical kinetics along the streamlines [6]. The latter includes Ni cluster formation. The peak of C2 density is calculated close to the target surface where the temperature is the highest. In the hot region, C; is dominant. As the carbon products move away from the target and mix with the ambient helium, they recombine into larger clusters, as demonstrated by the peak of C5 density around 1 mm. The profile of Ni-atom density compares fairly well with the measured one (Fig. 2). The early increase is due to the drop of temperature, and the final decrease beyond 6 mm results from Ni cluster formation at the eutectic temperature (approx.1600 K).
Atomization modeling in a multiphase flow environment and comparison with experiments
NASA Technical Reports Server (NTRS)
Liang, P. Y.; Schuman, M. D.
1990-01-01
An atomization model based on Reitz's instability wave analysis has been implemented into the ARICC3D multiphase CFD combustion code. Preliminary test runs with cold non-evaporating liquid jet and coaxial gas-liquid atomization cases appeared to have verified basic performance of the model, generating realistic-looking sprays. Furthermore, the extended liquid jet is explicitly resolved, and predicted jet lengths agree well with classical correlations. Fair agreement with test data is obtained for predicted spray tip penetrations and liquid mass flux radial distributions, with obvious room for improvement. Some numerical problems also appear to have resulted with the current implementation when low gas Mach number and high liquid velocities are involved.
NASA Astrophysics Data System (ADS)
Wu, X.; Sha, W.
2008-12-01
In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.
NASA Astrophysics Data System (ADS)
Lüdde, H. J.; Achenbach, A.; Kalkbrenner, T.; Jankowiak, H. C.; Kirchner, T.
2016-05-01
A recently introduced model to account for geometric screening corrections in an independent-atom-model description of ion-molecule collisions is applied to proton collisions from amino acids and DNA and RNA nucleobases. The correction coefficients are obtained from using a pixel counting method (PCM) for the exact calculation of the effective cross sectional area that emerges when the molecular cross section is pictured as a structure of (overlapping) atomic cross sections. This structure varies with the relative orientation of the molecule with respect to the projectile beam direction and, accordingly, orientation-independent total cross sections are obtained from averaging the pixel count over many orientations. We present net capture and net ionization cross sections over wide ranges of impact energy and analyze the strength of the screening effect by comparing the PCM results with Bragg additivity rule cross sections and with experimental data where available. Work supported by NSERC, Canada.
Na, Hyuntae; Jernigan, Robert L.; Song, Guang
2015-01-01
Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491
NASA Astrophysics Data System (ADS)
Di Rocco, Héctor O.; Lanzini, Fernando
2016-04-01
The correction to the Coulomb repulsion between two electrons due to the exchange of a transverse photon, referred to as the Breit interaction, as well as the main quantum electrodynamics contributions to the atomic energies (self-energy and vacuum polarization), are calculated using the recently formulated relativistic screened hydrogenic model. Comparison with the results of multiconfiguration Dirac-Hartree-Fock calculations and experimental X- ray energies is made.
Quantum phase transitions in an interacting atom-molecule boson model
Santos, G.; Foerster, A.; Mattei, E.; Dahmen, S. R.; Links, J.
2010-06-15
We study the quantum phase transitions of a model that describes the interconversion of interacting bosonic atoms and molecules. Using a classical analysis, we identify a threshold coupling line separating a molecular phase and a mixed phase. Through studies of the energy gap, von Neumann entanglement entropy, and fidelity, we give evidence that this line is associated with a boundary line in the ground-state phase diagram of the quantum system.
NASA Astrophysics Data System (ADS)
Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina
2016-07-01
Atomic oxygen (AO) of the upper atmosphere is one of the most important space factors that can cause degradation of spacecraft surface. In our previous mathematical model the Monte Carlo method and the "large particles" approximation were used for simulating processes of polymer etching under the influence of AO [1]. The interaction of enlarged AO particles with the polymer was described in terms of probabilities of reactions such as etching of polymer and specular and diffuse scattering of the AO particles on polymer. The effects of atomic oxygen on protected polymers and microfiller containing composites were simulated. The simulation results were in quite good agreement with the results of laboratory experiments on magnetoplasmadynamic accelerator of the oxygen plasma of SINP MSU [2]. In this paper we present a new model that describes the reactions of AO interactions with polymeric materials in more detail. Reactions of formation and further emission of chemical compounds such as CO, CO _{2}, H _{2}O, etc. cause the modification of the chemical composition of the polymer and change the probabilities of its consequent interaction with the AO. The simulation results are compared with the results of previous simulation and with the results of laboratory experiments. The reasons for the differences between the results of natural experiments on spacecraft, laboratory experiments and simulations are discussed. N. Chirskaya, M. Samokhina, Computer modeling of polymer structures degradation under the atomic oxygen exposure, WDS'12 Proceedings of Contributed Papers: Part III - Physics, Matfyzpress Prague, 2012, pp. 30-35. E. Voronina, L. Novikov, V. Chernik, N. Chirskaya, K. Vernigorov, G. Bondarenko, and A. Gaidar, Mathematical and experimental simulation of impact of atomic oxygen of the earth's upper atmosphere on nanostructures and polymer composites, Inorganic Materials: Applied Research, 2012, vol. 3, no. 2, pp. 95-101.
McElfresh, Mike; Baesu, Eveline; Balhorn, Rod; Belak, James; Allen, Michael J.; Rudd, Robert E.
2002-01-01
The goal of this work is to study the properties of living cells and cell membranes by using atomic force microscopy. During atomic force microscopy (AFM) measurement, there is a strong mechanical coupling between the AFM tip and the cell. The purpose of this paper is to present a model of the overall mechanical response of the cell that allows us to separate out the mechanical response of the cell from the local surface interactions we wish to quantify. These local interactions include recognition (or binding) events between molecules bound to an AFM tip (e.g., an antibody) and molecules or receptors on the cell surface (e.g., the respective antigen). The computational model differs from traditional Hertzian contact models by explicitly taking into account the mechanics of the biomembrane and cytoskeleton. The model also accounts for the mechanical response of the living cell during arbitrary deformation. The indentation of a bovine sperm cell is used to test the validity of this model, and further experiments are proposed to fully parameterize the model. PMID:11983924
NASA Technical Reports Server (NTRS)
Kostelecky, V. Alan
1993-01-01
Atomic supersymmetry is a quantum-mechanical supersymmetry connecting the properties of different atoms and ions. A short description of some established results in the subject are provided and a few recent developments are discussed including the extension to parabolic coordinates and the calculation of Stark maps using supersymmetry-based models.
Atomic-scale modeling of particle size effects for the oxygen reduction reaction on Pt.
Tritsaris, G. A.; Greeley, J.; Rossmeisl, J.; Norskov, J. K.
2011-07-01
We estimate the activity of the oxygen reduction reaction on platinum nanoparticles of sizes of practical importance. The proposed model explicitly accounts for surface irregularities and their effect on the activity of neighboring sites. The model reproduces the experimentally observed trends in both the specific and mass activities for particle sizes in the range between 2 and 30 nm. The mass activity is calculated to be maximized for particles of a diameter between 2 and 4 nm. Our study demonstrates how an atomic-scale description of the surface microstructure is a key component in understanding particle size effects on the activity of catalytic nanoparticles.
NASA Astrophysics Data System (ADS)
Porter, R. L.; Bauman, R. P.; MacAdam, K. B.; Ferland, G. J.
2004-12-01
We have completed the development of a new model helium atom for the spectra simulation code Cloudy. All relevant astrophysically significant processes are included, and the spectrum is solved self-consistently with the thermal and ionization structure of the simulated system. We present here an overview of the differences that distinguish our model from those by previous authors. We also compare predicted case B emissivities with those from previous works. The differences will have significant consequences for the interpretation of spectra of a wide variety of systems. We also explore deviations from the case B approximation and present an estimate of the primordial helium abundance.
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
NASA Astrophysics Data System (ADS)
Yang, Yantao; Cui, Junzhi; Han, Tiansi
2016-04-01
Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.
Intrinsic chirp of attosecond pulses: Single-atom model versus experiment
Kazamias, S.; Balcou, Ph.
2004-06-01
We demonstrate and evaluate the importance of an intrinsic chirp inherent to attosecond pulse creation accompanying high-order harmonic generation in recently published experimental data by Dinu et al. [Phys. Rev. Lett. 91, 063901 (2003)]. We present an analytical model, from which the atomic origin of the harmonic chirp is clearly understood. Moreover, the behavior of the chirp as a function of experimental parameters such as laser intensity is inferred. The comparison between our model and the experimental data provides us with useful information about the conditions in which the high-order harmonics is generated.
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
NASA Astrophysics Data System (ADS)
Yang, Yantao; Cui, Junzhi; Han, Tiansi
2016-08-01
Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.
Yang-Baxter integrable models in experiments: from condensed matter to ultracold atoms
NASA Astrophysics Data System (ADS)
Batchelor, Murray T.; Foerster, Angela
2016-04-01
The Yang-Baxter equation has long been recognised as the masterkey to integrability, providing the basis for exactly solved models which capture the fundamental physics of a number of realistic classical and quantum systems. In this article we provide an introductory survey of the impact of Yang-Baxter integrable models on experiments in condensed matter physics and ultracold atoms. A number of prominent examples are covered, including the hard-hexagon model, the Heisenberg spin chain, the transverse quantum Ising chain, a spin ladder model, the Lieb-Liniger Bose gas, the Gaudin-Yang Fermi gas and the two-site Bose-Hubbard model. The review concludes by pointing to some other recent developments with promise for further progress.
Testing the validity of the International Atomic Energy Agency (IAEA) safety culture model.
López de Castro, Borja; Gracia, Francisco J; Peiró, José M; Pietrantoni, Luca; Hernández, Ana
2013-11-01
This paper takes the first steps to empirically validate the widely used model of safety culture of the International Atomic Energy Agency (IAEA), composed of five dimensions, further specified by 37 attributes. To do so, three independent and complementary studies are presented. First, 290 students serve to collect evidence about the face validity of the model. Second, 48 experts in organizational behavior judge its content validity. And third, 468 workers in a Spanish nuclear power plant help to reveal how closely the theoretical five-dimensional model can be replicated. Our findings suggest that several attributes of the model may not be related to their corresponding dimensions. According to our results, a one-dimensional structure fits the data better than the five dimensions proposed by the IAEA. Moreover, the IAEA model, as it stands, seems to have rather moderate content validity and low face validity. Practical implications for researchers and practitioners are included. PMID:24076304
NASA Astrophysics Data System (ADS)
Rozsnyai, Balazs F.
2012-03-01
We use a "self-consistent average atom" (SCAA) model to compute shock Hugoniots for aluminum, iron, molybdenum, strontium, barium and thulium. The pressures and energies include relativistic effects. We make comparisons with the Thomas-Fermi-Dirac (TFD) model and with the available experimental data including pressures, shock and particle speeds and energy deposition. The connection between the usage of the "average atom" (AA) model and "detailed configuration accounting" (DCA) is discussed in the Appendix.
Fullerene film on metal surface: Diffusion of metal atoms and interface model
Li, Wen-jie; Li, Hai-Yang; Li, Hong-Nian; Wang, Peng; Wang, Xiao-Xiong; Wang, Jia-Ou; Wu, Rui; Qian, Hai-Jie; Ibrahim, Kurash
2014-05-12
We try to understand the fact that fullerene film behaves as n-type semiconductor in electronic devices and establish a model describing the energy level alignment at fullerene/metal interfaces. The C{sub 60}/Ag(100) system was taken as a prototype and studied with photoemission measurements. The photoemission spectra revealed that the Ag atoms of the substrate diffused far into C{sub 60} film and donated electrons to the molecules. So the C{sub 60} film became n-type semiconductor with the Ag atoms acting as dopants. The C{sub 60}/Ag(100) interface should be understood as two sub-interfaces on both sides of the molecular layer directly contacting with the substrate. One sub-interface is Fermi level alignment, and the other is vacuum level alignment.
NASA Astrophysics Data System (ADS)
Balzer, Karsten; Bauch, Sebastian; Bonitz, Michael
2010-04-01
In this contribution, we discuss the finite-element discrete variable representation (FE-DVR) of the nonequilibrium Green's function and its implications on the description of strongly inhomogeneous quantum systems. In detail, we show that the complementary features of FEs and the DVR allow for a notably more efficient solution of the two-time Schwinger/Keldysh/Kadanoff-Baym equations compared to a general basis approach. Particularly, the use of the FE-DVR leads to an essential speedup in computing the self-energies. As atomic and molecular examples we consider the He atom and the linear version of H+3 in one spatial dimension. For these closed-shell models we, in Hartree-Fock and second Born approximation, compute the ground-state properties and compare with the exact findings obtained from the solution of the few-particle time-dependent Schrödinger equation.
An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water
Stauffer, D.; Dragneva, N.; Floriano, W. B.; Rubel, O.; Mawhinney, R. C.; Fanchini, G.; French, S.
2014-07-28
Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
Tung, Chang-Shung; Joseph, Simpson; Sanbonmatsu, Kevin Y
2002-10-01
Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit. We find that the tertiary structure of the ribosome core, including the A-, P- and E-sites, is highly conserved. The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome. PMID:12244297
Average-atom model combined with the hypernetted chain approximation applied to warm dense matter.
Hou, Yong; Bredow, Richard; Yuan, Jianmin; Redmer, Ronald
2015-03-01
We have combined the average-atom model with the hypernetted chain approximation (AAHNC) to describe the electronic and ionic structure in the warm dense matter regime. On the basis of the electronic and ionic structures, the x-ray Thomson scattering (XRTS) spectrum is calculated using the random-phase approximation. While the electronic structure is described within the average-atom model, the effects of other ions on the electronic structure are considered using an integral equation method of the theory of liquids, namely the hypernetted chain approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution. Finally, the electronic and ionic structures are determined self-consistently. The XRTS spectrum is calculated according to the Chihara formula, where the scattering contributions are divided into three components: elastic, bound-free, and free-free. Comparison of the present AAHNC results with other theoretical models and experimental data shows very good agreement. Thus the AAHNC model can give a reasonable description of the electronic and ionic structure in warm dense matter. PMID:25871231
Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment
Joseph, Agnel Praveen; Malhotra, Sony; Burnley, Tom; Wood, Chris; Clare, Daniel K.; Winn, Martyn; Topf, Maya
2016-01-01
As the resolutions of Three Dimensional Electron Microscopic reconstructions of biological macromolecules are being improved, there is a need for better fitting and refinement methods at high resolutions and robust approaches for model assessment. Flex-EM/MODELLER has been used for flexible fitting of atomic models in intermediate-to-low resolution density maps of different biological systems. Here, we demonstrate the suitability of the method to successfully refine structures at higher resolutions (2.5–4.5 Å) using both simulated and experimental data, including a newly processed map of Apo-GroEL. A hierarchical refinement protocol was adopted where the rigid body definitions are relaxed and atom displacement steps are reduced progressively at successive stages of refinement. For the assessment of local fit, we used the SMOC (segment-based Manders’ overlap coefficient) score, while the model quality was checked using the Qmean score. Comparison of SMOC profiles at different stages of refinement helped in detecting regions that are poorly fitted. We also show how initial model errors can have significant impact on the goodness-of-fit. Finally, we discuss the implementation of Flex-EM in the CCP-EM software suite. PMID:26988127
Joseph, Agnel Praveen; Malhotra, Sony; Burnley, Tom; Wood, Chris; Clare, Daniel K; Winn, Martyn; Topf, Maya
2016-05-01
As the resolutions of Three Dimensional Electron Microscopic reconstructions of biological macromolecules are being improved, there is a need for better fitting and refinement methods at high resolutions and robust approaches for model assessment. Flex-EM/MODELLER has been used for flexible fitting of atomic models in intermediate-to-low resolution density maps of different biological systems. Here, we demonstrate the suitability of the method to successfully refine structures at higher resolutions (2.5-4.5Å) using both simulated and experimental data, including a newly processed map of Apo-GroEL. A hierarchical refinement protocol was adopted where the rigid body definitions are relaxed and atom displacement steps are reduced progressively at successive stages of refinement. For the assessment of local fit, we used the SMOC (segment-based Manders' overlap coefficient) score, while the model quality was checked using the Qmean score. Comparison of SMOC profiles at different stages of refinement helped in detecting regions that are poorly fitted. We also show how initial model errors can have significant impact on the goodness-of-fit. Finally, we discuss the implementation of Flex-EM in the CCP-EM software suite. PMID:26988127
Quantum model for double ionization of atoms in strong laser fields
NASA Astrophysics Data System (ADS)
Prauzner-Bechcicki, Jakub S.; Sacha, Krzysztof; Eckhardt, Bruno; Zakrzewski, Jakub
2008-07-01
We discuss double ionization of atoms in strong laser pulses using a reduced dimensionality model. Following the insight obtained from an analysis of the classical mechanics of the process, we confine each electron to move along the lines that point towards the two-particle Stark saddle in the presence of a field. The resulting effective two-dimensional model is similar to the aligned electron model, but it enables correlated escape of electrons with equal momenta, as observed experimentally. The time-dependent solution of the Schrödinger equation allows us to discuss in detail the time dynamics of the ionization process, the formation of electronic wave packets, and the development of the momentum distribution of the outgoing electrons. In particular, we are able to identify the rescattering process, simultaneous direct double ionization during the same field cycle, as well as other double ionization processes. We also use the model to study the phase dependence of the ionization process.
Charge-state-dependent energy loss of slow ions. II. Statistical atom model
NASA Astrophysics Data System (ADS)
Wilhelm, Richard A.; Möller, Wolfhard
2016-05-01
A model for charge-dependent energy loss of slow ions is developed based on the Thomas-Fermi statistical model of atoms. Using a modified electrostatic potential which takes the ionic charge into account, nuclear and electronic energy transfers are calculated, the latter by an extension of the Firsov model. To evaluate the importance of multiple collisions even in nanometer-thick target materials we use the charge-state-dependent potentials in a Monte Carlo simulation in the binary collision approximation and compare the results to experiment. The Monte Carlo results reproduce the incident charge-state dependence of measured data well [see R. A. Wilhelm et al., Phys. Rev. A 93, 052708 (2016), 10.1103/PhysRevA.93.052708], even though the experimentally observed charge exchange dependence is not included in the model.
From deep TLS validation to ensembles of atomic models built from elemental motions
Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; Fraser, James S.; Adams, Paul D.
2015-07-28
The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy severalmore » conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.« less
From deep TLS validation to ensembles of atomic models built from elemental motions
Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; Fraser, James S.; Adams, Paul D.
2015-07-28
The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
Mazzarella, G.; Giampaolo, S. M.; Illuminati, F.
2006-01-15
For systems of interacting, ultracold spin-zero neutral bosonic atoms, harmonically trapped and subject to an optical lattice potential, we derive an Extended Bose Hubbard (EBH) model by developing a systematic expansion for the Hamiltonian of the system in powers of the lattice parameters and of a scale parameter, the lattice attenuation factor. We identify the dominant terms that need to be retained in realistic experimental conditions, up to nearest-neighbor interactions and nearest-neighbor hoppings conditioned by the on-site occupation numbers. In the mean field approximation, we determine the free energy of the system and study the phase diagram both at zero and at finite temperature. At variance with the standard on site Bose Hubbard model, the zero-temperature phase diagram of the EBH model possesses a dual structure in the Mott insulating regime. Namely, for specific ranges of the lattice parameters, a density wave phase characterizes the system at integer fillings, with domains of alternating mean occupation numbers that are the atomic counterparts of the domains of staggered magnetizations in an antiferromagnetic phase. We show as well that in the EBH model, a zero-temperature quantum phase transition to pair superfluidity is, in principle, possible, but completely suppressed at the lowest order in the lattice attenuation factor. Finally, we determine the possible occurrence of the different phases as a function of the experimentally controllable lattice parameters.
From deep TLS validation to ensembles of atomic models built from elemental motions
Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; Fraser, James S.; Adams, Paul D.
2015-07-28
Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
Partial ionization in dense plasmas: comparisons among average-atom density functional models.
Murillo, Michael S; Weisheit, Jon; Hansen, Stephanie B; Dharma-wardana, M W C
2013-06-01
Nuclei interacting with electrons in dense plasmas acquire electronic bound states, modify continuum states, generate resonances and hopping electron states, and generate short-range ionic order. The mean ionization state (MIS), i.e, the mean charge Z of an average ion in such plasmas, is a valuable concept: Pseudopotentials, pair-distribution functions, equations of state, transport properties, energy-relaxation rates, opacity, radiative processes, etc., can all be formulated using the MIS of the plasma more concisely than with an all-electron description. However, the MIS does not have a unique definition and is used and defined differently in different statistical models of plasmas. Here, using the MIS formulations of several average-atom models based on density functional theory, we compare numerical results for Be, Al, and Cu plasmas for conditions inclusive of incomplete atomic ionization and partial electron degeneracy. By contrasting modern orbital-based models with orbital-free Thomas-Fermi models, we quantify the effects of shell structure, continuum resonances, the role of exchange and correlation, and the effects of different choices of the fundamental cell and boundary conditions. Finally, the role of the MIS in plasma applications is illustrated in the context of x-ray Thomson scattering in warm dense matter. PMID:23848795
Wang, Junmei; Cieplak, Piotr; Li, Jie; Hou, Tingjun; Luo, Ray; Duan, Yong
2011-01-01
In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, i.e. whether the interactions of two atoms that form bond, bond angle and dihedral angle are turned off or scaled down. When 1-2 (bonded), 1-3 (separated by two bonds) interactions are turned off and/or 1-4 (separated by three bonds) interactions are scaled down, all the models including the Applequist model achieved similar performance: the average percentage errors (APE) ranges from 1.15% to 1.23%, and The average unsigned errors (AUE) ranges from 0.143 to 0.158 Å3. When the short-range 1-2, 1-3 and full 1-4 terms are taken into account (Set D models), the APE ranges from 1.30% to 1.58% for the three Thole models whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å3 for the three Thole models, compared to 0.446 Å3 for the Applequist model. Further assessement using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact more accurate than the models developed using this particular data set (Set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy. PMID:21391553
Wang, Junmei; Cieplak, Piotr; Li, Jie; Hou, Tingjun; Luo, Ray; Duan, Yong
2011-03-31
In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, that is, whether the interactions of two atoms that form the bond, bond angle, and dihedral angle are turned off or scaled down. When 1-2 (bonded) and 1-3 (separated by two bonds) interactions are turned off, 1-4 (separated by three bonds) interactions are scaled down, or both, all models including the Applequist model achieved similar performance: the average percentage error (APE) ranges from 1.15 to 1.23%, and the average unsigned error (AUE) ranges from 0.143 to 0.158 Å(3). When the short-range 1-2, 1-3, and full 1-4 terms are taken into account (set D models), the APE ranges from 1.30 to 1.58% for the three Thole models, whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å(3) for the three Thole models, compared with 0.446 Å(3) for the Applequist model. Further assessment using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact have smaller errors than the models developed using this particular data set (set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy. PMID:21391553
NASA Astrophysics Data System (ADS)
Chaney, Andrea; Espinosa, James; Espinosa, James
2006-10-01
At the turn of the twentieth century, physicists and chemists were developing atomic models. Some of the phenomena that they had to explain were the periodic table, the stability of the atom, and the emission spectra. Niels Bohr is known as making the first modern picture that accounted for these. Unknown to much of the physics community is the work of Walter Ritz. His model explained more emission spectra and predates Bohr's work. We will fit several spectra using Ritz's magnetic model for the atom. The problems of stability and chemical periodicity will be shown to be challenges that this model has difficulty solving, but we will present some potentially useful adaptations to the Ritzian atom that can account for them.
Why Do We Believe that an Atom Is Colourless? Reflections about the Teaching of the Particle Model.
ERIC Educational Resources Information Center
Albanese, Alessandro; Vicentini, Matilde
1997-01-01
Highlights students' ideas about the particle model of matter and its use. Discusses the atomic model in teaching and the rules of the particle modeling game. Demonstrates how a complete understanding of the rules of the model construction yields guidelines for didactic practice. Focuses on problems connected with visual communication through…
NASA Astrophysics Data System (ADS)
Baldus, Sabrina; Schröder, Daniel; Bibinov, Nikita; Schulz-von der Gathen, Volker; Awakowicz, Peter
2015-06-01
Cold atmospheric pressure plasmas are a promising alternative therapy for treatment of chronic wounds, as they have already shown in clinical trials. In this study an air dielectric barrier discharge (DBD) developed for therapeutic use in dermatology is characterized with respect to the plasma produced reactive oxygen species, namely atomic oxygen and ozone, which are known to be of great importance to wound healing. To understand the plasma chemistry of the applied DBD, xenon-calibrated two-photon laser-induced fluorescence spectroscopy and optical absorption spectroscopy are applied. The measured spatial distributions are shown and compared to each other. A model of the afterglow chemistry based on optical emission spectroscopy is developed to cross-check the measurement results and obtain insight into the dynamics of the considered reactive oxygen species. The atomic oxygen density is found to be located mostly between the electrodes with a maximum density of {{n}\\text{O}}=6× {{10}16} cm-3 . Time resolved measurements reveal a constant atomic oxygen density between two high voltage pulses. The ozone is measured up to 3 mm outside the active plasma volume, reaching a maximum value of {{n}{{\\text{O}3}}}=3× {{10}16} cm-3 between the electrodes.
Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.
Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi
2015-03-17
Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase. PMID:25730881
Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges
Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi
2015-01-01
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 Ca2+-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 Ca2+-binding sites of Ca2+-ATPase and that of the iron atom in the heme in catalase. PMID:25730881
Quantum simulation of the Hubbard model with dopant atoms in silicon
Salfi, J.; Mol, J. A.; Rahman, R.; Klimeck, G.; Simmons, M. Y.; Hollenberg, L. C. L.; Rogge, S.
2016-01-01
In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose–Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model. PMID:27094205
Atomic spin-chain realization of a model for quantum criticality
NASA Astrophysics Data System (ADS)
Toskovic, R.; van den Berg, R.; Spinelli, A.; Eliens, I. S.; van den Toorn, B.; Bryant, B.; Caux, J.-S.; Otte, A. F.
2016-07-01
The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum computing and spintronic devices; on the other hand, they can be used as fundamental building blocks for the realization of textbook many-body quantum models, illustrating key concepts such as quantum phase transitions, topological order or frustration as a function of system size. Here, we use low-temperature scanning tunnelling microscopy to construct arrays of magnetic atoms on a surface, designed to behave like spin-1/2 XXZ Heisenberg chains in a transverse field, for which a quantum phase transition from an antiferromagnetic to a paramagnetic phase is predicted in the thermodynamic limit. Site-resolved measurements on these finite-size realizations reveal a number of sudden ground state changes when the field approaches the critical value, each corresponding to a new domain wall entering the chains. We observe that these state crossings become closer for longer chains, suggesting the onset of critical behaviour. Our results present opportunities for further studies on quantum behaviour of many-body systems, as a function of their size and structural complexity.
Quantum simulation of the Hubbard model with dopant atoms in silicon
NASA Astrophysics Data System (ADS)
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.
Quantum simulation of the Hubbard model with dopant atoms in silicon.
Salfi, J; Mol, J A; Rahman, R; Klimeck, G; Simmons, M Y; Hollenberg, L C L; Rogge, S
2016-01-01
In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose-Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model. PMID:27094205
Coqblin-Schrieffer model for an ultracold gas of ytterbium atoms with metastable state
NASA Astrophysics Data System (ADS)
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
Peach, Gillian; Whittingham, Ian B.; Beams, Timothy J.
2004-09-01
We analyze a system of two colliding ultracold atoms under strong harmonic confinement from the viewpoint of quantum defect theory and formulate a generalized self-consistent method for determining the allowed energies. We also present two highly efficient computational methods for determining the bound state energies and eigenfunctions of such systems. The perturbed harmonic oscillator problem is characterized by a long asymptotic region beyond the effective range of the interatomic potential. The first method, which is based on quantum defect theory and is an adaptation of a technique developed by one of the authors (G.P.) for highly excited states in a modified Coulomb potential, is very efficient for integrating through this outer region. The second method is a direct numerical solution of the radial Schroedinger equation using a discrete variable representation of the kinetic energy operator and a scaled radial coordinate grid. The methods are applied to the case of trapped spin-polarized metastable helium atoms. The calculated eigenvalues agree very closely for the two methods, and with the eigenvalues computed using the generalized self-consistent method.
Temperature dependence of elastic constants of embedded-atom models of palladium
Wolf, R.J.; Mansour, K.A.; Lee, M.W. ); Ray, J.R. )
1992-10-01
The elastic constants of fcc palladium are calculated as a function of temperature for four different embedded-atom-method (EAM) models and compared to experimental values. Two of these EAM models have been derived by other workers whereas two of the models are new. Because of the elastic anomaly near 120 K, in the shear constant [ital C][sub 44] of Pd, the use of this zero-temperature elastic constant to determine the Pd EAM potential leads to errors in the calculated [ital C][sub 44] above the Debye temperature of 280 K where the potentials are to be used. To correct this behavior we determine the EAM potential in the two new EAM models so that [ital C][sub 44] is in much better agreement with the experimental value above the Debye temperature. Interestingly in both of these new models the melting temperature is significantly higher and in better agreement with the experimental value of 1825 K. One of our models uses a conventional EAM third-neighbor interaction model whereas our other model is a fifth-neighbor interaction model.
Observation of Antiferromagnetic Correlations in the Hubbard Model with Ultracold Atoms
NASA Astrophysics Data System (ADS)
Hulet, Randall
2015-03-01
Ultracold atoms on optical lattices form a versatile platform for studying many-body physics, with the potential of addressing some of the most important issues in strongly correlated matter. Progress, however, has been stymied by an inability to create sufficiently low temperatures in an optical lattice. In this talk, I will present our experimental results on the characterization of the three-dimensional Hubbard model near half-filling, realized using two spin-states of fermionic atomic lithium (6Li). We have developed a compensated optical lattice that has enabled, for the first time, the achievement of temperatures that are below the tunneling energy, t. We use in-situ imaging to extract the central density of the gas, and to determine its local compressibility. For intermediate to strong interactions, we observe the emergence of a density plateau and a reduction of the compressibility, indicative of the formation of a Mott insulator. Comparisons to state-of-the-art numerical simulations of the Hubbard model over a wide range of interactions set an upper limit for the temperature T < t. The Hubbard model is known to exhibit antiferromagnetism at temperatures below the Néel temperature TN. We have detected antiferromagnetic correlations in this system by spin-sensitive Bragg scattering of light. We deduce the temperature of the atoms in the lattice by comparing the light scattering to determinantal quantum Monte Carlo and numerical linked-cluster expansion calculations to find that T / t = 0 . 51 +/- 0 . 06 , corresponding to 1 . 4TN. Further refinement of the compensated lattice may produce even lower temperatures which, along with light scattering thermometry, have important implications for achieving other novel quantum states of matter. Supported by DARPA/ARO, ONR, NSF.
A Strongly-Coupled Average Atom Model for Warm Dense Mixtures
NASA Astrophysics Data System (ADS)
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.
Spin-dependent Hubbard model and a quantum phase transition in cold atoms
Liu, W. Vincent; Wilczek, Frank; Zoller, Peter
2004-09-01
We describe an experimental protocol for introducing spin-dependent lattice structure in a cold atomic Fermi gas using lasers. It can be used to realize Hubbard models whose hopping parameters depend on spin and whose interaction strength can be controlled with an external magnetic field. We suggest that exotic superfluidities will arise in this framework. An especially interesting possibility is a class of states that support coexisting superfluid and normal components, even at zero temperature. The quantity of normal component varies with external parameters. We discuss some aspects of the quantum phase transition that arises at the point where it vanishes.
Landau Zener scenario in a trapped atomic gas: multi-level multi-particle model
NASA Astrophysics Data System (ADS)
Fai, Lukong Cornelius; Tchoffo, Martin; Jipdi, Michael Nana
2015-07-01
The paper investigates multi-level and multi-particle Landau-Zener problem applying the dynamic matrix approach. The Landau Zener transitions are observed to depend sensitively on the frequency, phase of interaction and number of levels and particles. The dynamic behaviour of atomic trapped gas is solved for one particle model that permits to deduce different probabilities for particular initial conditions. The generalization of the probabilities permits to solve any multi-level system with an arbitrary number of particles and controlled particle transitions.
An All-Atom Model of the Structure of Human Copper Transporter 1
Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.
2013-01-01
Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840
Paraskevas, Paschalis D; Sabbe, Maarten K; Reyniers, Marie-Françoise; Papayannakos, Nikos G; Marin, Guy B
2014-10-01
Hydrogen-abstraction reactions play a significant role in thermal biomass conversion processes, as well as regular gasification, pyrolysis, or combustion. In this work, a group additivity model is constructed that allows prediction of reaction rates and Arrhenius parameters of hydrogen abstractions by hydrogen atoms from alcohols, ethers, esters, peroxides, ketones, aldehydes, acids, and diketones in a broad temperature range (300-2000 K). A training set of 60 reactions was developed with rate coefficients and Arrhenius parameters calculated by the CBS-QB3 method in the high-pressure limit with tunneling corrections using Eckart tunneling coefficients. From this set of reactions, 15 group additive values were derived for the forward and the reverse reaction, 4 referring to primary and 11 to secondary contributions. The accuracy of the model is validated upon an ab initio and an experimental validation set of 19 and 21 reaction rates, respectively, showing that reaction rates can be predicted with a mean factor of deviation of 2 for the ab initio and 3 for the experimental values. Hence, this work illustrates that the developed group additive model can be reliably applied for the accurate prediction of kinetics of α-hydrogen abstractions by hydrogen atoms from a broad range of oxygenates. PMID:25209711
Low energy neutral atoms in the earth`s magnetosphere: Modeling
Moore, K.R.; McComas, D.J.; Funsten, H.O.; Thomsen, M.F.
1992-06-01
Detection of low energy neutral atoms (LENAs) produced by the interaction of the Earth`s geocorona with ambient space plasma has been proposed as a technique to obtain global information about the magnetosphere. Recent instrumentation advances reported previously and in these proceedings provide an opportunity for detecting LENAs in the energy range of <1 keV to {approximately}50 keV. In this paper, we present results from a numerical model which calculates line of sight LENA fluxes expected at a remote orbiting spacecraft for various magnetospheric plasma regimes. This model uses measured charge exchange cross sections, either of two neural hydrogen geocorona models, and various empirical modes of the ring current and plasma sheet to calculate the contribution to the integrated directional flux from each point along the line of sight of the instrument. We discuss implications for LENA imaging of the magnetosphere based on these simulations. 22 refs.
Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains
NASA Technical Reports Server (NTRS)
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.
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
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
Nuclear magnetic resonance parameters of atomic xenon dissolved in Gay-Berne model liquid crystal
NASA Astrophysics Data System (ADS)
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 κ=4.4 , κ'=20.0 , and μ=ν=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 Xe129/131 shielding and Xe131 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
Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2013-09-13
Recently, the possibility of quantum simulation of dynamical gauge fields was pointed out by using a system of cold atoms trapped on each link in an optical lattice. However, to implement exact local gauge invariance, fine-tuning the interaction parameters among atoms is necessary. In the present Letter, we study the effect of violation of the U(1) local gauge invariance by relaxing the fine-tuning of the parameters and showing that a wide variety of cold atoms is still a faithful quantum simulator for a U(1) gauge-Higgs model containing a Higgs field sitting on sites. The clarification of the dynamics of this gauge-Higgs model sheds some light upon various unsolved problems, including the inflation process of the early Universe. We study the phase structure of this model by Monte Carlo simulation and also discuss the atomic characteristics of the Higgs phase in each simulator. PMID:24074102
A cluster expansion model for predicting activation barrier of atomic processes
Rehman, Tafizur; Jaipal, M.; Chatterjee, Abhijit
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.
ERIC Educational Resources Information Center
Harrison, Allan G.; Treagust, David F.
2000-01-01
Reports in detail on a year-long case study of multiple-model use at grade 11. Suggests that students who socially negotiated the shared and unshared attributes of common analogical models for atoms, molecules, and chemical bonds used these models more consistently in their explanations. (Author/CCM)
Benchmarking atomic physics models for magnetically confined fusion plasma physics experiments
NASA Astrophysics Data System (ADS)
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.)
NASA Astrophysics Data System (ADS)
Bertolus, Marjorie; Freyss, Michel; Dorado, Boris; Martin, Guillaume; Hoang, Kiet; Maillard, Serge; Skorek, Richard; Garcia, Philippe; Valot, Carole; Chartier, Alain; Van Brutzel, Laurent; Fossati, Paul; Grimes, Robin W.; Parfitt, David C.; Bishop, Clare L.; Murphy, Samuel T.; Rushton, Michael J. D.; Staicu, Dragos; Yakub, Eugen; Nichenko, Sergii; Krack, Matthias; Devynck, Fabien; Ngayam-Happy, Raoul; Govers, Kevin; Deo, Chaitanya S.; Behera, Rakesh K.
2015-07-01
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 UO2, 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.
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. PMID:24778944
Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa
2014-01-01
Summary 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. PMID:24778944
Finite element modeling of atomic force microscopy cantilever dynamics during video rate imaging
Howard-Knight, J. P.; Hobbs, J. K.
2011-04-01
A dynamic finite element model has been constructed to simulate the behavior of low spring constant atomic force microscope (AFM) cantilevers used for imaging at high speed without active feedback as in VideoAFM. The model is tested against experimental data collected at 20 frame/s and good agreement is found. The complex dynamics of the cantilever, consisting of traveling waves coming from the tip sample interaction, reflecting off the cantilever-substrate junction, and interfering with new waves created at the tip, are revealed. The construction of the image from this resulting nonequilibrium cantilever deflection is also examined. Transient tip-sample forces are found to reach values up to 260 nN on a calibration grid sample, and the maximum forces do not always correspond to the position of steepest features as a result of energy stored in the cantilever.
3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils.
Ciesielski, Peter N; Matthews, James F; Tucker, Melvin P; Beckham, Gregg T; Crowley, Michael F; Himmel, Michael E; Donohoe, Bryon S
2013-09-24
Fundamental insights into the macromolecular architecture of plant cell walls will elucidate new structure-property relationships and facilitate optimization of catalytic processes that produce fuels and chemicals from biomass. Here we introduce computational methodology to extract nanoscale geometry of cellulose microfibrils within thermochemically treated biomass directly from electron tomographic data sets. We quantitatively compare the cell wall nanostructure in corn stover following two leading pretreatment strategies: dilute acid with iron sulfate co-catalyst and ammonia fiber expansion (AFEX). Computational analysis of the tomographic data is used to extract mathematical descriptions for longitudinal axes of cellulose microfibrils from which we calculate their nanoscale curvature. These nanostructural measurements are used to inform the construction of atomistic models that exhibit features of cellulose within real, process-relevant biomass. By computational evaluation of these atomic models, we propose relationships between the crystal structure of cellulose Iβ and the nanoscale geometry of cellulose microfibrils. PMID:23988022
An analytic technique for statistically modeling random atomic clock errors in estimation
NASA Technical Reports Server (NTRS)
Fell, P. J.
1981-01-01
Minimum variance estimation requires that the statistics of random observation errors be modeled properly. If measurements are derived through the use of atomic frequency standards, then one source of error affecting the observable is random fluctuation in frequency. This is the case, for example, with range and integrated Doppler measurements from satellites of the Global Positioning and baseline determination for geodynamic applications. An analytic method is presented which approximates the statistics of this random process. The procedure starts with a model of the Allan variance for a particular oscillator and develops the statistics of range and integrated Doppler measurements. A series of five first order Markov processes is used to approximate the power spectral density obtained from the Allan variance.
NASA Astrophysics Data System (ADS)
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.
MacFarlane, Joseph J
2009-08-07
This Final Report summarizes work performed under DOE STTR Phase II Grant No. DE-FG02-05ER86258 during the project period from August 2006 to August 2009. The project, “Development of Spectral and Atomic Models for Diagnosing Energetic Particle Characteristics in Fast Ignition Experiments,” was led by Prism Computational Sciences (Madison, WI), and involved collaboration with subcontractors University of Nevada-Reno and Voss Scientific (Albuquerque, NM). In this project, we have: Developed and implemented a multi-dimensional, multi-frequency radiation transport model in the LSP hybrid fluid-PIC (particle-in-cell) code [1,2]. Updated the LSP code to support the use of accurate equation-of-state (EOS) tables generated by Prism’s PROPACEOS [3] code to compute more accurate temperatures in high energy density physics (HEDP) plasmas. Updated LSP to support the use of Prism’s multi-frequency opacity tables. Generated equation of state and opacity data for LSP simulations for several materials being used in plasma jet experimental studies. Developed and implemented parallel processing techniques for the radiation physics algorithms in LSP. Benchmarked the new radiation transport and radiation physics algorithms in LSP and compared simulation results with analytic solutions and results from numerical radiation-hydrodynamics calculations. Performed simulations using Prism radiation physics codes to address issues related to radiative cooling and ionization dynamics in plasma jet experiments. Performed simulations to study the effects of radiation transport and radiation losses due to electrode contaminants in plasma jet experiments. Updated the LSP code to generate output using NetCDF to provide a better, more flexible interface to SPECT3D [4] in order to post-process LSP output. Updated the SPECT3D code to better support the post-processing of large-scale 2-D and 3-D datasets generated by simulation codes such as LSP. Updated atomic physics modeling to provide for
A computer code for calculations in the algebraic collective model of the atomic nucleus
NASA Astrophysics Data System (ADS)
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.
HELIOS-CR A 1-D radiation-magnetohydrodynamics code with inline atomic kinetics modeling
NASA Astrophysics Data System (ADS)
Macfarlane, J. J.; Golovkin, I. E.; Woodruff, P. R.
2006-05-01
HELIOS-CR is a user-oriented 1D radiation-magnetohydrodynamics code to simulate the dynamic evolution of laser-produced plasmas and z-pinch plasmas. It includes an in-line collisional-radiative (CR) model for computing non-LTE atomic level populations at each time step of the hydrodynamics simulation. HELIOS-CR has been designed for ease of use, and is well-suited for experimentalists, as well as graduate and undergraduate student researchers. The energy equations employed include models for laser energy deposition, radiation from external sources, and high-current discharges. Radiative transport can be calculated using either a multi-frequency flux-limited diffusion model, or a multi-frequency, multi-angle short characteristics model. HELIOS-CR supports the use of SESAME equation of state (EOS) tables, PROPACEOS EOS/multi-group opacity data tables, and non-LTE plasma properties computed using the inline CR modeling. Time-, space-, and frequency-dependent results from HELIOS-CR calculations are readily displayed with the HydroPLOT graphics tool. In addition, the results of HELIOS simulations can be post-processed using the SPECT3D Imaging and Spectral Analysis Suite to generate images and spectra that can be directly compared with experimental measurements. The HELIOS-CR package runs on Windows, Linux, and Mac OSX platforms, and includes online documentation. We will discuss the major features of HELIOS-CR, and present example results from simulations.
Chang, Christopher H.; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon
2007-01-01
The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H2 from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20 kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H2 evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2. PMID:17660315
How Sommerfeld extended Bohr's model of the atom (1913-1916)
NASA Astrophysics Data System (ADS)
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.
Non-local correlation and quantum discord in two atoms in the non-degenerate model
Mohamed, A.-B.A.
2012-12-15
By using geometric quantum discord (GQD) and measurement-induced nonlocality (MIN), quantum correlation is investigated for two atoms in the non-degenerate two-photon Tavis-Cummings model. It is shown that there is no asymptotic decay for MIN while asymptotic decay exists for GQD. Quantum correlations can be strengthened by introducing the dipole-dipole interaction. The evolvement period of quantum correlation gets shorter with the increase in the dipole-dipole parameter. It is found that there exists not only quantum nonlocality without entanglement but also quantum nonlocality without quantum discord. Also, the MIN and GQD are raised rather than entanglement, and also with weak initial entanglement, there are MIN and entanglement in a interval of death quantum discord. - Highlights: Black-Right-Pointing-Pointer Geometric quantum discord (GQD) and measurement induced nonlocality (MIN) are used to investigate the correlations of two two-level atoms. Black-Right-Pointing-Pointer There is no asymptotic decay for MIN while asymptotic decay exists for GQD. Black-Right-Pointing-Pointer Quantum correlations can be strengthened by introducing the dipole-dipole interaction. Black-Right-Pointing-Pointer There exists not only quantum nonlocality without entanglement but also without discord. Black-Right-Pointing-Pointer Weak initial entanglement leads to MIN and entanglement in intervals of death discord.
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. PMID:27303797
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
ERIC Educational Resources Information Center
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…
Li, Xueming; Brunner, Matthias J.; Xu, Chunfu; Conticello, Vincent; Egelman, Edward; Marlovits, Thomas; Cheng, Yifan; Baker, David
2015-01-01
Direct electron detectors have made it possible to generate electron density maps at near atomic resolution using cryo-electron microscopy single particle reconstructions. Critical current questions include how best to build models into these maps, how high quality a map is required to generate an accurate model, and how to cross-validate models in a system independent way. We describe a modeling approach that integrates Monte Carlo optimization with local density guided moves, Rosetta all-atom refinement, and real space B-factor fitting, yielding accurate models from experimental maps for three different systems with resolutions 4.5 Å or higher. We characterize model accuracy as a function of data quality, and present a model validation statistic that correlates with model accuracy over the three test systems. PMID:25707030
A model for energy transfer in collisions of atoms with highly excited molecules.
Houston, Paul L; Conte, Riccardo; Bowman, Joel M
2015-05-21
A model for energy transfer in the collision between an atom and a highly excited target molecule has been developed on the basis of classical mechanics and turning point analysis. The predictions of the model have been tested against the results of trajectory calculations for collisions of five different target molecules with argon or helium under a variety of temperatures, collision energies, and initial rotational levels. The model predicts selected moments of the joint probability distribution, P(Jf,ΔE) with an R(2) ≈ 0.90. The calculation is efficient, in most cases taking less than one CPU-hour. The model provides several insights into the energy transfer process. The joint probability distribution is strongly dependent on rotational energy transfer and conservation laws and less dependent on vibrational energy transfer. There are two mechanisms for rotational excitation, one due to motion normal to the intermolecular potential and one due to motion tangential to it and perpendicular to the line of centers. Energy transfer is found to depend strongly on the intermolecular potential and only weakly on the intramolecular potential. Highly efficient collisions are a natural consequence of the energy transfer and arise due to collisions at "sweet spots" in the space of impact parameter and molecular orientation. PMID:25907301
Methodology to set up accurate OPC model using optical CD metrology and atomic force microscopy
NASA Astrophysics Data System (ADS)
Shim, Yeon-Ah; Kang, Jaehyun; Lee, Sang-Uk; Kim, Jeahee; Kim, Keeho
2007-03-01
For the 90nm node and beyond, smaller Critical Dimension(CD) control budget is required and the ways to control good CD uniformity are needed. Moreover Optical Proximity Correction(OPC) for the sub-90nm node demands more accurate wafer CD data in order to improve accuracy of OPC model. Scanning Electron Microscope (SEM) is the typical method for measuring CD until ArF process. However SEM can give serious attack such as shrinkage of Photo Resist(PR) by burning of weak chemical structure of ArF PR due to high energy electron beam. In fact about 5nm CD narrowing occur when we measure CD by using CD-SEM in ArF photo process. Optical CD Metrology(OCD) and Atomic Force Microscopy(AFM) has been considered to the method for measuring CD without attack of organic materials. Also the OCD and AFM measurement system have the merits of speed, easiness and accurate data. For model-based OPC, the model is generated using CD data of test patterns transferred onto the wafer. In this study we discuss to generate accurate OPC model using OCD and AFM measurement system.
Henderson, M.G.; Reeves, G.D.; Moore, K.R.; Spence, H.E.; Jorgensen, A.M.; Fennell, J.F.; Blake, J.B.; Roelof, E.C.
1997-12-31
Although the primary function of the CEP-PAD/IPS instrument on Polar is the measurement of energetic ions in-situ, it has also proven to be a very capable Energetic neutral Atom (ENA) imager. Raw ENA images are currently being constructed on a routine basis with a temporal resolution of minutes during both active and quiet times. However, while analyses of these images by themselves provide much information on the spatial distribution and dynamics of the energetic ion population in the ring current, detailed modeling is required to extract the actual ion distributions. In this paper, the authors present the initial results of forward modeling an IPS ENA image obtained during a small geo-magnetic storm on June 9, 1997. The equatorial ion distribution inferred with this technique reproduces the expected large noon/midnight and dawn/dusk asymmetries. The limitations of the model are discussed and a number of modifications to the basic forward modeling technique are proposed which should significantly improve its performance in future studies.
NASA Technical Reports Server (NTRS)
Henderson, M. G.; Reeves, G. D.; Moore, K. R.; Spence, H. E.; Jorgensen, A. M.; Fennell, J. F.; Blake, J. B.; Roelof, E. C.
1999-01-01
Although the primary function of the CEPPAD/IPS instrument on Polar is the measurement of energetic ions in-situ, it has also proven to be a very capable Energetic Neutral Atom (ENA) imager. Raw ENA images are currently being constructed on a routine basis with a temporal resolution of minutes during both active and quiet times. However, while analyses of these images by themselves provide much information on the spatial distribution and dynamics of the energetic ion population in the ring current. detailed modeling is required to extract the actual ion distributions. In this paper. we present the initial results of forward modeling an IPS ENA image obtained during a small geo-magnetic storm on June 9, 1997. The equatorial ion distribution inferred with this technique reproduces the expected large noon/midnight and dawn/dusk asymmetries. The limitations of the model are discussed and a number of modifications to the basic forward modeling technique are proposed which should significantly improve its performance in future studies.
Atomic model of the Thermus thermophilus 70S ribosome developed in silico.
Tung, Chang-Shung; Sanbonmatsu, Kevin Y
2004-10-01
The ribosome is a large molecular complex that consists of at least three ribonucleic acid molecules and a large number of proteins. It translates genetic information from messenger ribonucleic acid and makes protein accordingly. To better understand ribosomal function and provide information for designing biochemical experiments require knowledge of the complete structure of the ribosome. For expanding the structural information of the ribosome, we took on the challenge of developing a detailed Thermus thermophilus ribosomal structure computationally. By combining information derived from the low-resolution x-ray structure of the 70S ribosome (providing the overall fold), high-resolution structures of the ribosomal subunits (providing the local structure), sequences, and secondary structures, we have developed an atomic model of the T. thermophilus ribosome using a homology modeling approach. Our model is stereochemically sound with a consistent single-species sequence. The overall folds of the three ribosomal ribonucleic acids in our model are consistent with those in the low-resolution crystal structure (root mean-square differences are all <1.9 angstroms). The large overall interface area (approximately 2500 angstroms2) of intersubunit bridges B2a, B3, and B5, and the inherent flexibility in regions connecting the contact residues are consistent with these bridges serving as anchoring patches for the ratcheting and rolling motions between the two subunits during translocation. PMID:15454463
NASA Astrophysics Data System (ADS)
Levashov, V. A.
2014-11-01
In order to gain insight into the connection between the vibrational dynamics and the atomic-level Green-Kubo stress correlation function in liquids, we consider this connection in a model crystal instead. Of course, vibrational dynamics in liquids and crystals are quite different and it is not expected that the results obtained on a model crystal should be valid for liquids. However, these considerations provide a benchmark to which the results of the previous molecular dynamics simulations can be compared. Thus, assuming that vibrations are plane waves, we derive analytical expressions for the atomic-level stress correlation functions in the classical limit and analyze them. These results provide, in particular, a recipe for analysis of the atomic-level stress correlation functions in Fourier space and extraction of the wave-vector and frequency-dependent information. We also evaluate the energies of the atomic-level stresses. The energies obtained are significantly smaller than the energies previously determined in molecular dynamics simulations of several model liquids. This result suggests that the average energies of the atomic-level stresses in liquids and glasses are largely determined by the structural disorder. We discuss this result in the context of equipartition of the atomic-level stress energies. Analysis of the previously published data suggests that it is possible to speak about configurational and vibrational contributions to the average energies of the atomic-level stresses in a glass state. However, this separation in a liquid state is problematic. We also introduce and briefly consider the atomic-level transverse current correlation function. Finally, we address the broadening of the peaks in the pair distribution function with increase of distance. We find that the peaks' broadening (by ≈40 % ) occurs due to the transverse vibrational modes, while contribution from the longitudinal modes does not change with distance.
Kaufman-Osborn, Tobin; Chagarov, Evgueni A.; Kummel, Andrew C.
2014-05-28
Passivation, functionalization, and atomic layer deposition nucleation via H{sub 2}O{sub 2}(g) and trimethylaluminum (TMA) dosing was studied on the clean Ge(100) surface at the atomic level using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). Chemical analysis of the surface was performed using x-ray photoelectron spectroscopy, while the bonding of the precursors to the substrate was modeled with density functional theory (DFT). At room temperature, a saturation dose of H{sub 2}O{sub 2}(g) produces a monolayer of a mixture of –OH or –O species bonded to the surface. STS confirms that H{sub 2}O{sub 2}(g) dosing eliminates half-filled dangling bonds on the clean Ge(100) surface. Saturation of the H{sub 2}O{sub 2}(g) dosed Ge(100) surface with TMA followed by a 200 °C anneal produces an ordered monolayer of thermally stable Ge–O–Al bonds. DFT models and STM simulations provide a consistent model of the bonding configuration of the H{sub 2}O{sub 2}(g) and TMA dosed surfaces. STS verifies the TMA/H{sub 2}O{sub 2}/Ge surface has an unpinned Fermi level with no states in the bandgap demonstrating the ability of a Ge–O–Al monolayer to serve as an ideal template for further high-k deposition.
Distributed force probe bending model of critical dimension atomic force microscopy bias
NASA Astrophysics Data System (ADS)
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.
Dislocation-stacking fault tetrahedron interaction: what can we learn from atomic scale modelling.
Osetskiy, Yury N; Stoller, Roger E; Matsukawa, Yoshitaka
2004-01-01
The high number density of stacking fault tetrahedra (SFTs) observed in irradiated fcc metals suggests that they should contribute to radiation-induced hardening and, therefore, taken into account when estimating mechanical properties changes of irradiated materials. The central issue is describing the individual interaction between a moving dislocation and an SFT, which is characterized by a very fine size scale, {approx}100 nm. This scale is amenable to both in situ TEM experiments and large-scale atomic modelling. In this paper we present results of an atomistic simulation of dislocation-SFT interactions using molecular dynamics (MD). The results are compared with observations from in situ deformation experiments. It is demonstrated that in some cases the simulations and experimental observations are quite similar, suggesting a reasonable interpretation of experimental observations.
Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation
Zhang, Qiang; Zhang, Ruiting; Zhao, Ying; Li, HuanHuan; Zhuang, Wei E-mail: gaoyq@pku.edu.cn; Gao, Yi Qin E-mail: gaoyq@pku.edu.cn
2014-05-14
We carried out a series of potential of mean force calculations to study the pairing preferences of a series of model mono-atomic 1:1 ions with evenly varied sizes. The probabilities of forming the contact ion pair (CIP) and the single water separate ion pair (SIP) were presented in the two-dimensional plots with respect to the ion sizes. The pairing preferences reflected in these plots largely agree with the empirical rule of matching ion sizes in the small and big size regions. In the region that the ion sizes are close to the size of the water molecule; however, a significant deviation from this conventional rule is observed. Our further analysis indicated that this deviation originates from the competition between CIP and the water bridging SIP state. The competition is mainly an enthalpy modulated phenomenon in which the existing of the water bridging plays a significant role.
Kubo–Greenwood approach to conductivity in dense plasmas with average atom models
Starrett, C. E.
2016-06-01
In this study, a new formulation of the Kubo–Greenwood conductivity for average atom models is given. The new formulation improves upon previous treatments 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 withmore » 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.« less
Kubo-Greenwood approach to conductivity in dense plasmas with average atom models
NASA Astrophysics Data System (ADS)
Starrett, C. E.
2016-06-01
A new formulation of the Kubo-Greenwood conductivity for average atom models is given. The new formulation improves upon previous treatments 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.
A model for charge transfer in ultracold Rydberg ground-state atomic collisions
NASA Astrophysics Data System (ADS)
Markson, Samuel; Sadeghpour, H. R.
2016-06-01
In excited molecules, the interaction between the covalent Rydberg and ion-pair channels forms a unique class of excited states, in which the infinite manifold of vibrational levels are the equivalent of atomic Rydberg states with a heavy electron mass. Production of the ion-pair states usually requires excitation through one or several interacting Rydberg states; these interacting channels lead to loss of flux, diminishing the rate of ion-pair production. Here, we develop an analytical, asymptotic charge-transfer model for the interaction between ultracold Rydberg molecular states, and employ this method to demonstrate the utility of off-resonant field control over the ion-pair formation, with near unity efficiency.
Alderighi, Michele; Ierardi, Vincenzo; Allegrini, Maria; Fuso, Francesco; Solaro, Roberto
2008-05-01
Investigation of the mechanical properties of materials at the nanoscale is often performed by atomic force microscopy nanoindentation. However, substrates with large surface roughness and heterogeneity demand careful data analysis. This requirement is even more stringent when surface indentations with a typical depth of a few nanometers are produced to test material hardness. Accordingly, we developed a geometrical model of the nanoindenter, which was first validated by measurements on a reference gold sample. Then we used this technique to investigate the mechanical properties of a coating layer made of Balinit C, a commercially available alloy with superior anti-wear features deposited on steel. The reported results support the feasibility of reliable hardness measurements with truly nanosized indents. PMID:18572668
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
A robust all-atom model for LCAT generated by homology modeling.
Segrest, Jere P; Jones, Martin K; Catte, Andrea; Thirumuruganandham, Saravana P
2015-03-01
LCAT is activated by apoA-I to form cholesteryl ester. We combined two structures, phospholipase A2 (PLA2) that hydrolyzes the ester bond at the sn-2 position of oxidized (short) acyl chains of phospholipid, and bacteriophage tubulin PhuZ, as C- and N-terminal templates, respectively, to create a novel homology model for human LCAT. The juxtaposition of multiple structural motifs matching experimental data is compelling evidence for the general correctness of many features of the model: i) The N-terminal 10 residues of the model, required for LCAT activity, extend the hydrophobic binding trough for the sn-2 chain 15-20 Å relative to PLA2. ii) The topography of the trough places the ester bond of the sn-2 chain less than 5 Å from the hydroxyl of the catalytic nucleophile, S181. iii) A β-hairpin resembling a lipase lid separates S181 from solvent. iv) S181 interacts with three functionally critical residues: E149, that regulates sn-2 chain specificity, and K128 and R147, whose mutations cause LCAT deficiency. Because the model provides a novel explanation for the complicated thermodynamic problem of the transfer of hydrophobic substrates from HDL to the catalytic triad of LCAT, it is an important step toward understanding the antiatherogenic role of HDL in reverse cholesterol transport. PMID:25589508
Modelling of 'sub-atomic' contrast resulting from back-bonding on Si(111)-7×7.
Sweetman, Adam; Jarvis, Samuel P; Rashid, Mohammad A
2016-01-01
It has recently been shown that 'sub-atomic' contrast can be observed during NC-AFM imaging of the Si(111)-7×7 substrate with a passivated tip, resulting in triangular shaped atoms [Sweetman et al. Nano Lett. 2014, 14, 2265]. The symmetry of the features, and the well-established nature of the dangling bond structure of the silicon adatom means that in this instance the contrast cannot arise from the orbital structure of the atoms, and it was suggested by simple symmetry arguments that the contrast could only arise from the backbonding symmetry of the surface adatoms. However, no modelling of the system has been performed in order to understand the precise origin of the contrast. In this paper we provide a detailed explanation for 'sub-atomic' contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking similarity to experimental results, and demonstrate how 'sub-atomic' contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms. PMID:27547610
Interaction of a Two-Level Atom with the Morse Potential in the Framework of Jaynes-Cummings Model
NASA Astrophysics Data System (ADS)
Setare R., M.; Sh., Barzanjeh
2009-09-01
A theoretical study of the dynamical behaviors of the interaction between a two-level atom with a Morse potential in the framework of the Jaynes-Cummings model (JCM) is discussed. We show that this system is equivalent to an intensity-dependent coupling between the two-level atom and the non-deformed single-mode radiation field in the presence of an additional nonlinear interaction. We study the dynamical properties of the system such as, atomic population inversion, the probability distribution of cavity-field, the Mandel parameter and atomic dipole squeezing. It is shown how the depth of the Morse potential can be affected by non-classical properties of the system. Moreover, the temporal evolution of the Husimi-distribution function is explored.
NASA Astrophysics Data System (ADS)
Alekseev, N. I.; Luchinin, V. V.; Charykov, N. A.
2013-11-01
The evaporation of silicon atoms during the epitaxial growth of graphene on the singular carbon and silicon faces of silicon carbide SiC was modeled by the semiempirical AM1 and PM3 methods. The analysis was performed for evaporation of atoms both from the open surface of SiC and through the surface of the formed graphene monolayers. The total activation barrier of the evaporation of the silicon atoms, their passage from the graphene cell, and further evaporation from graphene was shown to be lower than the barrier to evaporation of the silicon atom on a free surface of SiC. Passage through graphene is thus not the limiting stage of the process, but contributes significantly to the effective evaporation time.
Mukherjee, Goutam; Patra, Niladri; Barua, Poranjyoti; Jayaram, B
2011-04-15
We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RESP fit charges. The atom types defined span diverse plausible chemical environments of each atom in a molecule. The partial charge on any atom in a given molecule is then assigned by a reference to the look-up table. We tested the sensitivity of the TPACM4 partial charges in estimates of hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. An average error ±1.11 kcal/mol and a correlation coefficient of 0.90 is obtained in the calculated protein-ligand binding free energies vis-à-vis an RMS error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in comparison to experiment. Similar accuracies are realized in predictions of hydrogen bond energies and solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes on the order of milliseconds on a single processor machine to assign partial atomic charges. The TPACM4 programme has been web-enabled and made freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/charge.jsp. PMID:21341292
Rovibrationally Inelastic Atom-Molecule Collision Cross Sections from a Hard Sphere Model
NASA Astrophysics Data System (ADS)
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.
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-01-01
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson’s ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers. PMID:26510769
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-01-01
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers. PMID:26510769
NASA Astrophysics Data System (ADS)
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-10-01
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson’s ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.
Analysis of phase transitions in spin-crossover compounds by using atom - phonon coupling model
NASA Astrophysics Data System (ADS)
Gîndulescu, A.; Rotaru, A.; Linares, J.; Dimian, M.; Nasser, J.
2011-01-01
The spin - crossover compounds (SCO) have become of great interest recently due to their potential applications in memories, sensors, switches, and display devices. These materials are particularly interesting because upon application of heat, light, pressure or other physical stimulus, they feature a phase transition between a low-spin (LS) diamagnetic ground state and a high-spin (HS) paramagnetic state, accompanied in some cases by color change. The phase transition can be discontinuous (with hysteresis), in two steps or gradual. Our analysis is performed by using the atom - phonon coupling (APC) model which considers that neighboring molecules are connected through a spring characterized by an elastic constant depending on molecules electronic state. By associating a fictitious spin to each molecule that has -1 and +1 eigenvalues corresponding to LS and HS levels respectively, an Ising type model can be developed for the analysis of metastable states and phase transitions in spin-crossover compounds. This contribution is aimed at providing a review of our recent results in this area, as well as novel aspects related to SCO compounds behavior at low temperature. In the framework of the APC model, we will discuss about the existence of metastable and unstable states, phase transitions and hysteresis phenomena, as well as their dependence on sample size.
Pan, Dongqing; Chien Jen, Tien; Li, Tao; Yuan, Chris
2014-01-15
This paper characterizes the carrier gas flow in the atomic layer deposition (ALD) vacuum reactor by introducing Lattice Boltzmann Method (LBM) to the ALD simulation through a comparative study of two LBM models. Numerical models of gas flow are constructed and implemented in two-dimensional geometry based on lattice Bhatnagar–Gross–Krook (LBGK)-D2Q9 model and two-relaxation-time (TRT) model. Both incompressible and compressible scenarios are simulated and the two models are compared in the aspects of flow features, stability, and efficiency. Our simulation outcome reveals that, for our specific ALD vacuum reactor, TRT model generates better steady laminar flow features all over the domain with better stability and reliability than LBGK-D2Q9 model especially when considering the compressible effects of the gas flow. The LBM-TRT is verified indirectly by comparing the numerical result with conventional continuum-based computational fluid dynamics solvers, and it shows very good agreement with these conventional methods. The velocity field of carrier gas flow through ALD vacuum reactor was characterized by LBM-TRT model finally. The flow in ALD is in a laminar steady state with velocity concentrated at the corners and around the wafer. The effects of flow fields on precursor distributions, surface absorptions, and surface reactions are discussed in detail. Steady and evenly distributed velocity field contribute to higher precursor concentration near the wafer and relatively lower particle velocities help to achieve better surface adsorption and deposition. The ALD reactor geometry needs to be considered carefully if a steady and laminar flow field around the wafer and better surface deposition are desired.
Aerosol cluster impact and break-up : II. Atomic and Cluster Scale Models.
Lechman, Jeremy B.; Takato, Yoichi
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.
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
Babilas, Rafał
2015-09-15
The atomic structure of Fe{sub 70}Nb{sub 10}B{sub 20} alloy in “as-cast” state and after annealing was investigated using high-energy X-ray diffraction (XRD), Mössbauer spectroscopy (MS) and high resolution transmission electron microscopy (HRTEM). The HRTEM observations allowed to indicate some medium-range order (MRO) regions about 2 nm in size and formation of some kinds of short-range order (SRO) structures represented by atomic clusters with diameter ca. 0.5 nm. The Reverse Monte Carlo (RMC) method basing on the results of XRD measurements was used in modeling the atomic structure of Fe-based alloy. The structural model was described by peak values of partial pair correlation functions and coordination numbers determined by Mössbauer spectroscopy investigations. The three-dimensional configuration box of atoms was obtained from the RMC simulation and the representative Fe-centered clusters were taken from the calculated structure. According to the Gonser et al. approach, the measured spectra of alloy studied were decomposed into 5 subspectra representing average Fe–Fe coordination numbers. Basing on the results of disaccommodation of magnetic permeability, which is sensitive to the short order of the random packing of atoms, it was stated that an occurrence of free volume is not detected after nanocrystallization process. - Highlights: • Atomic cluster model of amorphous structure was proposed for studied glassy alloy. • Short range order (ca. 0.5 nm) regions interpreted as clusters were identified by HREM. • Clusters correspond to coordination numbers (N = 4,6,8,9) calculated by using Gonser approach. • Medium-range order (ca. 2 nm) could be referred to few atomic clusters. • SRO regions are able to grow up as nuclei of crystalline bcc Fe and iron borides. • Crystalline particles have spherical morphology with an average diameter of 20 nm.
Modeling non-local thermodynamic equilibrium plasma using the Flexible Atomic Code data
NASA Astrophysics Data System (ADS)
Han, Bo; Wang, Feilu; Salzmann, David; Zhao, Gang
2015-04-01
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 a rate equation to interpret the plasmas systematically. The Flexible Atomic Code (FAC) supplies all the atomic data needed for RCF, 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 potential emission spectrum. In a preliminary application, RCF successfully reproduced 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
2016-01-01
Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar-Xe, Kr-Xe and Xe-Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal-organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems. PMID:27174162
Van der Waals interactions and the limits of isolated atom models at interfaces
Kawai, Shigeki; Foster, Adam S.; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H.; Jung, Thomas A.; Meyer, Ernst
2016-01-01
Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar–Xe, Kr–Xe and Xe–Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal–organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems. PMID:27174162
Van der Waals interactions and the limits of isolated atom models at interfaces
NASA Astrophysics Data System (ADS)
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.
Nonequilibrium Green's functions and atom-surface dynamics: Simple views from a simple model system
NASA Astrophysics Data System (ADS)
Boström, E.; Hopjan, M.; Kartsev, A.; Verdozzi, C.; Almbladh, C.-O.
2016-03-01
We employ Non-equilibrium Green's functions (NEGF) to describe the real-time dynamics of an adsorbate-surface model system exposed to ultrafast laser pulses. For a finite number of electronic orbitals, the system is solved exactly and within different levels of approximation. Specifically i) the full exact quantum mechanical solution for electron and nuclear degrees of freedom is used to benchmark ii) the Ehrenfest approximation (EA) for the nuclei, with the electron dynamics still treated exactly. Then, using the EA, electronic correlations are treated with NEGF within iii) 2nd Born and with iv) a recently introduced hybrid scheme, which mixes 2nd Born self-energies with non-perturbative, local exchange- correlation potentials of Density Functional Theory (DFT). Finally, the effect of a semi-infinite substrate is considered: we observe that a macroscopic number of de-excitation channels can hinder desorption. While very preliminary in character and based on a simple and rather specific model system, our results clearly illustrate the large potential of NEGF to investigate atomic desorption, and more generally, the non equilibrium dynamics of material surfaces subject to ultrafast laser fields.
Hoshi, M; Endo, S; Takada, J; Ishikawa, M; Nitta, Y; Iwatani, K; Oka, T; Fujita, S; Shizuma, K; Hasai, H
1999-12-01
There has been a large discrepancy between the Dosimetry system 1986 (DS86) and measured data, some of which data in Hiroshima at about 1.5 km ground distance from the hypocenter are about 10 times larger than the calculation. Therefore its causes have long been discussed, since it will change the estimated radiation risks obtained based on the Hiroshima and Nagasaki data. In this study the contradiction was explained by a bare-fission-neutron leakage model through a crack formed at the time of neutron emission. According to the present calculation, the crack has a 3 cm parallel spacing, which is symmetric with respect to the polar axis from the hypocenter to the epicenter of the atomic bomb. We made also an asymmetric opening closing 3/4 of this symmetric geometry, because there are some data which shows asymmetry. In addition, the height of the neutron emission point was elevated 90 m. By using the asymmetric calculation, especially for long distant data located more than 1 km, it was verified that all of the activity data induced by thermal and fast neutrons, were simultaneously explained within the data scattering. The neutron kerma at a typical 1.5 km ground distance increases 3 and 8 times more than DS86 based on the symmetric and asymmetric model, respectively. PMID:10805003
Photon storage in {lambda}-type optically dense atomic media. I. Cavity model
Gorshkov, Alexey V.; Andre, Axel; Lukin, Mikhail D.; Soerensen, Anders S.
2007-09-15
In a recent paper [Gorshkov et al., Phys. Rev. Lett. 98, 123601 (2007)], we used a universal physical picture to optimize and demonstrate equivalence between a wide range of techniques for storage and retrieval of photon wave packets in {lambda}-type atomic media in free space, including the adiabatic reduction of the photon group velocity, pulse-propagation control via off-resonant Raman techniques, and photon-echo-based techniques. In the present paper, we perform the same analysis for the cavity model. In particular, we show that the retrieval efficiency is equal to C/(1+C) independent of the retrieval technique, where C is the cooperativity parameter. We also derive the optimal strategy for storage and, in particular, demonstrate that at any detuning one can store, with the optimal efficiency of C/(1+C), any smooth input mode satisfying TC{gamma}>>1 and a certain class of resonant input modes satisfying TC{gamma}{approx}1, where T is the duration of the input mode and 2{gamma} is the transition linewidth. In the two subsequent papers of the series, we present the full analysis of the free-space model and discuss the effects of inhomogeneous broadening on photon storage.
Cui, Jian; Zhao, Xue-Hong; Wang, Yan; Xiao, Ya-Bing; Jiang, Xue-Hui; Dai, Li
2014-01-01
Flow injection-hydride generation-atomic fluorescence spectrometry was a widely used method in the industries of health, environmental, geological and metallurgical fields for the merit of high sensitivity, wide measurement range and fast analytical speed. However, optimization of this method was too difficult as there exist so many parameters affecting the sensitivity and broadening. Generally, the optimal conditions were sought through several experiments. The present paper proposed a mathematical model between the parameters and sensitivity/broadening coefficients using the law of conservation of mass according to the characteristics of hydride chemical reaction and the composition of the system, which was proved to be accurate as comparing the theoretical simulation and experimental results through the test of arsanilic acid standard solution. Finally, this paper has put a relation map between the parameters and sensitivity/broadening coefficients, and summarized that GLS volume, carrier solution flow rate and sample loop volume were the most factors affecting sensitivity and broadening coefficients. Optimizing these three factors with this relation map, the relative sensitivity was advanced by 2.9 times and relative broadening was reduced by 0.76 times. This model can provide a theoretical guidance for the optimization of the experimental conditions. PMID:24783570
Modeling precursor diffusion and reaction of atomic layer deposition in porous structures
Keuter, Thomas Menzler, Norbert Heribert; Mauer, Georg; Vondahlen, Frank; Vaßen, Robert; Buchkremer, Hans Peter
2015-01-01
Atomic layer deposition (ALD) is a technique for depositing thin films of materials with a precise thickness control and uniformity using the self-limitation of the underlying reactions. Usually, it is difficult to predict the result of the ALD process for given external parameters, e.g., the precursor exposure time or the size of the precursor molecules. Therefore, a deeper insight into ALD by modeling the process is needed to improve process control and to achieve more economical coatings. In this paper, a detailed, microscopic approach based on the model developed by Yanguas-Gil and Elam is presented and additionally compared with the experiment. Precursor diffusion and second-order reaction kinetics are combined to identify the influence of the porous substrate's microstructural parameters and the influence of precursor properties on the coating. The thickness of the deposited film is calculated for different depths inside the porous structure in relation to the precursor exposure time, the precursor vapor pressure, and other parameters. Good agreement with experimental results was obtained for ALD zirconiumdioxide (ZrO{sub 2}) films using the precursors tetrakis(ethylmethylamido)zirconium and O{sub 2}. The derivation can be adjusted to describe other features of ALD processes, e.g., precursor and reactive site losses, different growth modes, pore size reduction, and surface diffusion.
Tight-binding models for ultracold atoms in optical lattices: general formulation and applications
NASA Astrophysics Data System (ADS)
Modugno, Michele; Ibañez-Azpiroz, Julen; Pettini, Giulio
2016-06-01
Tight-binding models for ultracold atoms in optical lattices can be properly defined by using the concept of maximally localized Wannier functions for composite bands. The basic principles of this approach are reviewed here, along with different applications to lattice potentials with two minima per unit cell, in one and two spatial dimensions. Two independent methods for computing the tight-binding coefficients—one ab initio, based on the maximally localized Wannier functions, the other through analytic expressions in terms of the energy spectrum—are considered. In the one dimensional case, where the tight-binding coefficients can be obtained by designing a specific gauge transformation, we consider both the case of quasi resonance between the two lowest bands, and that between s and p orbitals. In the latter case, the role of the Wannier functions in the derivation of an effective Dirac equation is also reviewed. Then, we consider the case of a two dimensional honeycomb potential, with particular emphasis on the Haldane model, its phase diagram, and the breakdown of the Peierls substitution. Tunable honeycomb lattices, characterized by movable Dirac points, are also considered. Finally, general considerations for dealing with the interaction terms are presented.
Non-adiabatic transitions in a model atom subject to a linearly ramped electric field
Price, P.N.
1992-01-01
This work concerns transitions between sets of interacting energy levels that model states of a Rydberg atom in a linearly varying electric field. The model Hamiltonian is derived from consideration of the real physical system, and consists of two sets of diabatic states, whose energies are linear in applied field and which interact via constant coupling. The probabilities of transitions between levels are derived and discussed. Analytical transition probabilities are found for some limiting cases, and numerical results are presented and analyzed. Evidence suggests that the probability of a purely diabatic transition is correctly given by the result of a series of isolated Landau-Zener crossings, even when the assumptions that lead to the Landau-Zener formula do not hold. Numerical evidence also suggests a two-manifold generalization of Demkov's [open quotes]triangle rule[close quotes]: all transitions that are causally forbidden in the case of isolated avoided crossings also have zero probability for the case of overlapping anticrossings.
NASA Astrophysics Data System (ADS)
Kaufman-Osborn, Tobin; Chagarov, Evgueni A.; Park, Sang Wook; Sahu, Bhagawan; Siddiqui, Shariq; Kummel, Andrew C.
2014-12-01
Passivation, functionalization, and atomic layer deposition (ALD) via H2O2(g) and trimethylaluminum (TMA) dosing were studied on the clean Si0.6Ge0.4(001) surface at the atomic level using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). Chemical analysis of the surface was performed with in-situ X-ray photoelectron spectroscopy (XPS) while density functional theory (DFT) was employed to model the bonding of H2O2(g) chemisorbates to the substrate. A room temperature saturation dose of H2O2(g) covers the surface with a monolayer of sbnd OH and sbnd O chemisorbates. XPS and DFT demonstrate that the room temperature H2O2/SiGe surface is composed of only Gesbnd OH and Gesbnd O bonds while annealing induces an atomic layer exchange bringing Si to the surface to bond with sbnd OH or sbnd O while pushing Ge subsurface. The resulting Sisbnd OH and Sisbnd O surface is optimal because it can be used to nucleate high-k ALD and Si dangling bonds are readily passivated by forming gas. After H2O2(g) functionalization, TMA dosing, and a subsequent 230 °C anneal, ordering along the dimer row direction is observed on the surface. STS verifies that the TMA/H2O2/SiGe surface has an unpinned Fermi level with no states in the band gap demonstrating the ability to serve as an ideal template for further high-k deposition.
NASA Technical Reports Server (NTRS)
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.
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
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Kuno, Yoshihito; Kasamatsu, Kenichi; Takahashi, Yoshiro; Ichinose, Ikuo; Matsui, Tetsuo
2015-06-01
Lattice gauge theory has provided a crucial non-perturbative method in studying canonical models in high-energy physics such as quantum chromodynamics. Among other models of lattice gauge theory, the lattice gauge-Higgs model is a quite important one because it describes a wide variety of phenomena/models related to the Anderson-Higgs mechanism, such as superconductivity, the standard model of particle physics, and the inflation process of the early Universe. In this paper, we first show that atomic description of the lattice gauge model allows us to explore real-time dynamics of the gauge variables by using the Gross-Pitaevskii equations. Numerical simulations of the time development of an electric flux reveal some interesting characteristics of the dynamic aspect of the model and determine its phase diagram. Next, to realize a quantum simulator of the U(1) lattice gauge-Higgs model on an optical lattice filled by cold atoms, we propose two feasible methods: (i) Wannier states in the excited bands and (ii) dipolar atoms in a multilayer optical lattice. We pay attention to the constraint of Gauss's law and avoid nonlocal gauge interactions.
The Analog Atomic Force Microscope: Measuring, Modeling, and Graphing for Middle School
ERIC Educational Resources Information Center
Goss, Valerie; Brandt, Sharon; Lieberman, Marya
2013-01-01
using an analog atomic force microscope (A-AFM) made from a cardboard box and mailing tubes. Varying numbers of ping pong balls inside the tubes mimic atoms on a surface. Students use a dowel to make macroscale measurements similar to those of a nanoscale AFM tip as it…
AxBAxB… pulsed atomic layer deposition: Numerical growth model and experiments
NASA Astrophysics Data System (ADS)
Muneshwar, Triratna; Cadien, Ken
2016-02-01
Atomic layer deposition (ALD) is widely used for the fabrication of advanced semiconductor devices and related nanoscale structures. During ALD, large precursor doses (>1000 L per pulse) are often required to achieve surface saturation, of which only a small fraction is utilized in film growth while the rest is pumped from the system. Since the metal precursor constitutes a significant cost of ALD, strategies to enhance precursor utilization are essential for the scaling of ALD processes. In the precursor reaction step, precursor physisorption is restricted by steric hindrance (mA1) from ligands on the precursor molecules. On reaction, some of these ligands are removed as by-products resulting in chemisorbed species with reduced steric hindrance (mA1 → mA2, where mA2 < mA1) and some of the initially hindered surface reaction sites becoming accessible for further precursor physisorption. To utilize these additional reaction sites, we propose a generalized AxBAxB… pulsed deposition where the total precursor dose (ΦA) is introduced as multiple x (x > 1, x ∈ I) short-pulses rather than a single pulse. A numerical first-order surface reaction kinetics growth model is presented and applied to study the effect of AxBAxB… pulsed ALD on the growth per cycle (GPC). The model calculations predict higher GPC for AxBAxB… pulsing than with ABAB… deposition. In agreement with the model predictions, with AxBAxB… pulsed deposition, the GPC was found to increase by ˜46% for ZrN plasma enhanced ALD (PEALD), ˜49% for HfO2 PEALD, and ˜8% for thermal Al2O3 ALD with respect to conventional ABAB… pulsed growth.
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan
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
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
NASA Astrophysics Data System (ADS)
Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H.; Kolinski, Andrzej; Li, Mai Suan
2015-04-01
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.
Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan
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
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
Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom
ERIC Educational Resources Information Center
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…
ERIC Educational Resources Information Center
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…
Dias, M. S.; De Vasconcelos, V.; Mattos, J. R. L.; Jordao, E.
2012-07-01
Formal definitions of convergence, connected-ness and continuity were established to characterize and describe the crystalline solid and its properties as a unified notion in the topological space. In this unified notion, physical and material properties are modeled by means of an intrinsic and invariable form function: the Relative Variational Model. The crystalline solid is assumed an empty space that has been filled with atoms and phonons, i.e., the crystal is built with packages of matter and energy in a regular and orderly repetitive pattern along three orthogonal dimensions of the space. The spatial occupation of the atom in the crystalline structure is determined by its mean vibrational volume, which also defines the lattice parameter or interatomic distance. However, as packages of vibrational energy, phonons can only exist as vibrations of atoms. Any variation of internal energy is in fact the discretized variations of phonon's population. These variations occur in the quantized modes of vibration, and therefore the balance between the frequency and amplitude of vibrations also is a dynamic variable. In this paper, the Relative Variational Model was applied to de-convolutions of frequency spectra of the inelastic neutron scatterings. Some dynamic aspects of atom vibration were presented and evaluated in support to the model's fundamentals. (authors)
A.V.G. Chizmeshya
2002-12-19
/NETL managed National Mineral Sequestration Working Group we have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO{sub 2} mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH){sub 2}. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO{sub 2} mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach will provide a deeper understanding of the key reaction mechanisms than either individual approach can alone. Ab initio techniques will also
A.V.G. Chizmeshya; M.J. McKelvy; G.H. Wolf; R.W. Carpenter; D.A. Gormley; J.R. Diefenbacher; R. Marzke
2006-03-01
significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO2 mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH)2. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO2 mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach has provided a deeper understanding of the key reaction mechanisms than either individual approach can alone. We used ab initio techniques to significantly advance our understanding of atomic-level processes at the solid/solution interface by
A.V.G. Chizmeshya
2003-12-19
/NETL managed National Mineral Sequestration Working Group we have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO{sub 2} mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH){sub 2}. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO{sub 2} mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach will provide a deeper understanding of the key reaction mechanisms than either individual approach can alone. Ab initio techniques will also
Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A
2016-06-01
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229
Relation between elastic modulus and glass softening temperature in the delocalized atom model
NASA Astrophysics Data System (ADS)
Sanditov, B. D.; Sangadiev, S. Sh.; Sanditov, D. S.
2012-09-01
The ratio of softening temperature (glass transition temperature) to elastic modulus ( T g / E) is mainly determined by the limiting elastic deformation of an interatomic bond, which characterizes the transition of a structural microregion from an elastic into a viscous-flow state. In silicate glasses, this transition is caused by the limiting deformation of directed ionic-covalent Si-O-Si bonds. In the case of amorphous hydrocarbons, it is related to the relatively weak intermolecular bonds between regions in chain macromolecules, and the T g / E ratio is significantly higher than in inorganic glasses. In glassy systems of one class, this ratio turns out to be constant ( T g / E ≈ const), and a linear correlation is detected between softening temperature and elastic modulus, which can be explained in terms of the delocalized atom model. The values of T g / E can be used to classify glasses similarly to the well-known Angell classification according to so-called fragility.
Photon storage in {lambda}-type optically dense atomic media. II. Free-space model
Gorshkov, Alexey V.; Andre, Axel; Lukin, Mikhail D.; Soerensen, Anders S.
2007-09-15
In a recent paper [Gorshkov et al., Phys. Rev. Lett. 98, 123601 (2007)], we presented a universal physical picture for describing a wide range of techniques for storage and retrieval of photon wave packets in {lambda}-type atomic media in free space, including the adiabatic reduction of the photon group velocity, pulse-propagation control via off-resonant Raman techniques, and photon-echo based techniques. This universal picture produced an optimal control strategy for photon storage and retrieval applicable to all approaches and yielded identical maximum efficiencies for all of them. In the present paper, we present the full details of this analysis as well some of its extensions, including the discussion of the effects of non-degeneracy of the two lower levels of the {lambda} system. The analysis in the present paper is based on the intuition obtained from the study of photon storage in the cavity model in the preceding paper [Gorshkov et al., previous paper, Phys. Rev. A. 76, 033804 (2007)].
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
2012-01-01
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. PMID:22927375
NASA Technical Reports Server (NTRS)
Snyder, Aaron; Banks, Bruce; Miller, Sharon; Stueber, Thomas; Sechkar, Edward
2001-01-01
A numerical procedure is presented to calculate transmittance degradation caused by contaminant films on spacecraft surfaces produced through the interaction of orbital atomic oxygen (AO) with volatile silicones and hydrocarbons from spacecraft components. In the model, contaminant accretion is dependent on the adsorption of species, depletion reactions due to gas-surface collisions, desorption, and surface reactions between AO and silicone producing SiO(x), (where x is near 2). A detailed description of the procedure used to calculate the constituents of the contaminant layer is presented, including the equations that govern the evolution of fractional coverage by specie type. As an illustrative example of film growth, calculation results using a prototype code that calculates the evolution of surface coverage by specie type is presented and discussed. An example of the transmittance degradation caused by surface interaction of AO with deposited contaminant is presented for the case of exponentially decaying contaminant flux. These examples are performed using hypothetical values for the process parameters.
Relation between elastic modulus and glass softening temperature in the delocalized atom model
Sanditov, B. D.; Sangadiev, S. Sh.; Sanditov, D. S.
2012-09-15
The ratio of softening temperature (glass transition temperature) to elastic modulus (T{sub g}/E) is mainly determined by the limiting elastic deformation of an interatomic bond, which characterizes the transition of a structural microregion from an elastic into a viscous-flow state. In silicate glasses, this transition is caused by the limiting deformation of directed ionic-covalent Si-O-Si bonds. In the case of amorphous hydrocarbons, it is related to the relatively weak intermolecular bonds between regions in chain macromolecules, and the T{sub g}/E ratio is significantly higher than in inorganic glasses. In glassy systems of one class, this ratio turns out to be constant (T{sub g}/E Almost-Equal-To const), and a linear correlation is detected between softening temperature and elastic modulus, which can be explained in terms of the delocalized atom model. The values of T{sub g}/E can be used to classify glasses similarly to the well-known Angell classification according to so-called fragility.
NASA Astrophysics Data System (ADS)
Garcia, Gustavo
2011-10-01
Many radiation applications require detailed energy deposition maps in reduced volumes, typically at the nanoscale. In addition, information about the type of interaction processes taking place in these reduced areas is usually needed. In order to achieve this level of description, single particle tracks, both for primary radiation and secondary generated species, should be simulated upon reasonable physical descriptions of the interaction processes in terms of cross sections and energy loss. In this study we present a Low Energy Particle Track Simulation (LEPTS) Monte Carlo code which is based on experimental and theoretical cross section data we have previously derived as well as on the observed energy loss distribution functions. This model will be applied to the irradiation of atomic (Ar) and molecular (SF6) gases with high energy electrons, positrons and photons by simulating single particle tracks until their final thermalization in the medium. Special attention will be paid to the low energy secondary electrons generated along the tracks. Detailed energy deposition pictures and local radiation effects will be derived from the simulated track structure and compared with direct observations in simple experiments. Acknowledgement to the Spanish Ministry of Science and Innovation (Project FIS2009-10245).
Viewing dynamic interactions of proteins and a model lipid membrane with atomic force microscopy.
Quinn, Anthony S; Rand, Jacob H; Wu, Xiao-Xuan; Taatjes, Douglas J
2013-01-01
The information covered in this chapter will present a model homogenous membrane preparation technique and dynamic imaging procedure that can be successfully applied to more than one type of lipid study and atomic force microscope (AFM) instrument setup. The basic procedural steps have been used with an Asylum Research MFP-3D BIO and the Bruker (formerly, Veeco) BioScope. The AFM imaging protocol has been supplemented by procedures (not to be presented in this chapter) of ellipsometry, standardized western blotting, and dot-blots to verify appropriate purity and activity of all experimental molecular components; excellent purity and activity level of the lipids, proteins, and drug(s) greatly influence the success of imaging experiments in the scanning probe microscopy field. The major goal of the chapter is to provide detailed procedures for sample preparation and operation of the Asylum Research MFP-3D BIO AFM. In addition, one should be cognizant that our comprehensive description in the use of the MFP-3D BIO's functions for successful image acquisitions and analyses is greatly enhanced by Asylum Research's (AR's) accompanying extensive manual(s), technical notes, and AR's users forum. Ultimately, the stepwise protocol and information will allow novice personnel to begin acquiring quality images for processing and analysis with minimal supervision. PMID:23027007
Modeling of the atomic Ne laser in He/Ne/Ar gas mixtures
Jong, W.; Kushner, S.; Kushner, M.J.
1992-12-01
The high pressure atomic Ne laser operates on 4 visible transitions between the 3p and 3s manifolds. There has been renewed interest in this laser due to demonstrated high efficiency lasing at 585 nm in e-beam and fission fragment excited plasmas. A comprehensive computer model for the Ne laser in He/Ne/Ar mixtures has been developed to examine excitation mechanisms. The authors found that direct excitation of the 3p manifold by dissociative recombination of Ne{sub 2}{sup +} is the likely pumping mechanism, while state-selective Penning reactions dominantly relax the lower levels. Comparisons to experiments performed on a short pulsed e-beam excited laser showed that the electron temperature in the afterglow is determined by a slow relaxation of excited states in Ar. Oscillation does not occur until these manifolds are depleted, and the electron temperature falls. Scaling laws for the Ne laser at low pump powers, as obtained using fission fragment excitation, will be discussed.
NASA Astrophysics Data System (ADS)
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.
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
NASA Astrophysics Data System (ADS)
Barettin, Daniele; De Angelis, Roberta; Prosposito, Paolo; Auf der Maur, Matthias; Casalboni, Mauro; Pecchia, Alessandro
2014-05-01
We report on numerical simulations of a zincblende InP surface quantum dot (QD) on \\text{I}{{\\text{n}}_{0.48}}\\text{G}{{\\text{a}}_{0.52}}\\text{P} buffer. Our model is strictly based on experimental structures, since we extrapolated a three-dimensional dot directly by atomic force microscopy results. Continuum electromechanical, \\vec{k}\\;\\cdot \\;\\vec{p} bandstructure and optical calculations are presented for this realistic structure, together with benchmark calculations for a lens-shape QD with the same radius and height of the extrapolated dot. Interesting similarities and differences are shown by comparing the results obtained with the two different structures, leading to the conclusion that the use of a more realistic structure can provide significant improvements in the modeling of QDs fact, the remarkable splitting for the electron p-like levels of the extrapolated dot seems to prove that a realistic experimental structure can reproduce the right symmetry and a correct splitting usually given by atomistic calculations even within the multiband \\vec{k}\\;\\cdot \\;\\vec{p} approach. Moreover, the energy levels and the symmetry of the holes are strongly dependent on the shape of the dot. In particular, as far as we know, their wave function symmetries do not seem to resemble to any results previously obtained with simulations of zincblende ideal structures, such as lenses or truncated pyramids. The magnitude of the oscillator strengths is also strongly dependent on the shape of the dot, showing a lower intensity for the extrapolated dot, especially for the transition between the electrons and holes ground state, as a result of a relevant reduction of the wave functions overlap. We also compare an experimental photoluminescence spectrum measured on an homogeneous sample containing about 60 dots with a numerical ensemble average derived from single dot calculations. The broader energy range of the numerical spectrum motivated us to perform further
Jellium model potentials for the C60 molecule and the photoionization of endohedral atoms, A@C60
NASA Astrophysics Data System (ADS)
Baltenkov, A. S.; Manson, S. T.; Msezane, A. Z.
2015-09-01
Approximating the C60 shell as a collection of carbon atoms, the potential experienced by a confined atom has been calculated within the framework of the self-consistent spherical jellium model. It has been found that the potential well in this model has a cusp-shaped Lorentz-like profile. The parameters of the model Lorentz-bubble potential (depth and thickness) have been selected so that in the potential well there would be an electronic level corresponding to the experimental electron affinity of the C60 molecule. The spatial distribution of the positive charge of the C-atomic nuclei and the negative charge of the electron clouds forming the electrostatic potential of C60, as a whole, has been analyzed using the Poisson equation. It is demonstrated that the often used radial square-well potential to approximate the C60 corresponds to a non-physical charge density for the C60 molecule. This analysis demonstrates that the phenomenological potentials simulating the C60 shell potential should belong to a family of potentials with a non-flat bottom and non-parallel potential walls similar to the Lorentz-bubble potential. The photoionization cross-sections of a hydrogen atom localized at the center of the C60 shell have been calculated as well. It is found that confinement oscillations in the cross-sections are exhibited within the framework of the cusp-shaped potential model and these oscillations are essentially the same as those in the case of the potential wells with well-defined borders (parallel walls), thereby demonstrating that the inherent characteristic distances of the potential, e.g., radii of the potential walls, or the distances between potential walls, are not necessary to produce confinement resonances; this should be a general result for atoms or molecules confined in near-spherical fullerenes.
Dooher, J.
1996-10-01
Atomization tests on simulated fluids are being performed. For each sample tested, {Delta}P{sub c} is being determined as described in the last quarterly report. The results will be reported when the coal slurry testing is completed for comparative purposes. The viscoelastic properties on the simulated fluids and coal water slurries are being determined using the Adelphi Stresstech Viscometer. A discussion of viscoelastic properties and their relationship to atomization is presented.
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. PMID:19653995
Miccio, Luis A. Colmenero, Juan; Kummali, Mohammed M.; Alegría, Ángel; Schwartz, Gustavo A.
2014-05-14
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
Foerster, 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.
Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.
Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos
2012-11-21
We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging. PMID:23181323
NASA Astrophysics Data System (ADS)
Cui, Qizhi; Smith, Vedene H.
2000-12-01
An all-atom molecular model and optimized site-site pair potential parameters are employed for methane solute. By use of the reference interaction site model theory, the methane hydration structure is analyzed at the atomic level and its hydration free energies, energies, enthalpies, and entropies for four different thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3 are calculated. Our calculated thermodynamic properties are in rather good agreement with experiments.
The atomic approach to the Anderson model for the finite U case: application to a quantum dot.
Lobo, T; Figueira, M S; Foglio, M E
2010-07-01
In the present work we apply the atomic approach to the single-impurity Anderson model (SIAM). A general formulation of this approach, that can be applied both to the impurity and to the lattice Anderson Hamiltonian, was developed in a previous work (Foglio et al 2009 arxiv: 0903.0139v2 [cond-mat.str-el]). The method starts from the cumulant expansion of the periodic Anderson model, employing the hybridization as a perturbation. The atomic Anderson limit is analytically solved and its sixteen eigenenergies and eigenstates are obtained. This atomic Anderson solution, which we call the AAS, has all the fundamental excitations that generate the Kondo effect, and in the atomic approach is employed as a 'seed' to generate the approximate solutions for finite U. The width of the conduction band is reduced to zero in the AAS, and we choose its position such that the Friedel sum rule is satisfied, close to the chemical potential mu. We perform a complete study of the density of states of the SIAM over the whole relevant range of parameters: the empty dot, intermediate valence, Kondo and magnetic regimes. In the Kondo regime we obtain a density of states that characterizes well the structure of the Kondo peak. To show the usefulness of the method we have calculated the conductance of a quantum dot, side-coupled to a conduction band. PMID:20571194
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
Reznik, Alexander N.
2014-08-25
An electrodynamic model is proposed for the tunneling microwave microscope with subnanometer space resolution as developed by Lee et al. [Appl. Phys. Lett. 97, 183111 (2010)]. Tip-sample impedance Z{sub a} was introduced and studied in the tunneling and non-tunneling regimes. At tunneling breakdown, the microwave current between probe and sample flows along two parallel channels characterized by impedances Z{sub p} and Z{sub t} that add up to form overall impedance Z{sub a}. Quantity Z{sub p} is the capacitive impedance determined by the near field of the probe and Z{sub t} is the impedance of the tunnel junction. By taking into account the distance dependences of effective tip radius r{sub 0}(z) and tunnel resistance R{sub t}(z) = Re[Z{sub t}(z)], we were able to explain the experimentally observed dependences of resonance frequency f{sub r}(z) and quality factor Q{sub L}(z) of the microscope. The obtained microwave resistance R{sub t}(z) and direct current tunnel resistance R{sub t}{sup dc}(z) exhibit qualitatively similar behavior, although being largely different in both magnitude and the characteristic scale of height dependence. Interpretation of the microwave images of the atomic structure of test samples proved possible by taking into account the inductive component of tunnel impedance ImZ{sub t} = ωL{sub t}. Relation ωL{sub t}/R{sub t} ≈ 0.235 was obtained.
Amyloid-β aggregation on model lipid membranes: an atomic force microscopy study.
Hane, Francis; Drolle, Elizabeth; Gaikwad, Ravi; Faught, Erin; Leonenko, Zoya
2011-01-01
Amyloid fibril formation is generally associated with many neurodegenerative disorders, including Alzheimer's disease (AD). Although fibril plaque formation is associated with biological membranes in vivo, the role of the cell surfaces in amyloid fibril formation and the molecular mechanism of amyloid toxicity are not well understood. Understanding the details of amyloid interaction with lipid membrane may shed light on the mechanism of amyloid toxicity. Using atomic force microscopy, we investigated aggregation of amyloid-β1-42 (Aβ1-42) on model phospholipid membranes as a function of time and membrane composition. Neutral, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), anionic - 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt) (DOPG), and cationic - 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), were used to study the effect of lipid type on amyloid binding. We showed that both the charge on the lipid head group and lipid phase affect the interaction of amyloid oligomers with the membrane surface changing the rate of adsorption and causing changes in membrane structure and structure of amyloid deposits. We observed that amyloid aggregates progressively accumulate in a similar manner on the surface of neutral DPPC gel phase membrane and on the surface of fluid phase negatively charged DOPG membrane. In contrast to DPPC and DOPG, positively charged fluid DOTAP membrane and neutral fluid phase DOPC membrane contain amyloid deposits with reduced height, which suggests fusing of Aβ1-42 into the lipid membrane surface. PMID:21694459
DiMaio, Frank; Song, Yifan; Li, Xueming; Brunner, Matthias J; Xu, Chunfu; Conticello, Vincent; Egelman, Edward; Marlovits, Thomas C; Cheng, Yifan; Baker, David
2015-04-01
We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems. PMID:25707030
NASA Astrophysics Data System (ADS)
Fournier, R.; Andzelm, J.; Goursot, A.; Russo, N.; Salahub, D. R.
1990-08-01
Both spin-polarized and unpolarized linear combinations of Gaussian-type orbitals-model core potential-local spin density (LCGTO-MCP-LSD) calculations have been performed for clusters representing the three possible high symmetry chemisorption sites for carbon on the (100) surface of nickel. We found that the most stable chemisorption site is the fourfold hollow, in agreement with the experimental evidence. For this site, the computed equilibrium NiC distances are 1.79 and 1.77 Å at the spin-polarized and unpolarized levels, very close to the most recent experimental measurements. The calculated spin-polarized vibrational frequency perpendicular to the surface is found to be 407 cm-1 (410 cm-1 expt). The values of the binding energy are 11.5 and 11.8 eV at polarized and unpolarized levels, respectively (˜7 eV, expt); the carbon atom is strongly bound, essentially by a triple bond formed by interaction of the px, py, and pz orbitals of carbon with, primarily, the d orbitals of the four nearby surface nickel atoms. The effect of carbon chemisorption on the nickel magnetism has also been studied. The addition of the carbon atom reduces the spin magnetic moment of pure nickel by 2 or 4 μB depending on which of the two nearly degenerate nickel cluster states is taken as reference. The reduction of atomic spin magnetic moments is clearly larger on the 4 nickel atoms nearest to the carbon. The global and local (atomic) reduction in spin magnetic moments originate from some up-spin d density of states being pushed above EF, through antibonding interactions with the carbon 2p orbitals, and hence emptied.
NASA Astrophysics Data System (ADS)
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.
NASA Technical Reports Server (NTRS)
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.
Yamamoto, T; Shibata, T; Ohta, M; Yasumoto, M; Nishida, K; Hatayama, A; Mattei, S; Lettry, J; Sawada, K; Fantz, U
2014-02-01
To control the H(0) atom production profile in the H(-) ion sources is one of the important issues for the efficient and uniform surface H(-) production. The purpose of this study is to construct a collisional radiative (CR) model to calculate the effective production rate of H(0) atoms from H2 molecules in the model geometry of the radio-frequency (RF) H(-) ion source for Linac4 accelerator. In order to validate the CR model by comparison with the experimental results from the optical emission spectroscopy, it is also necessary for the model to calculate Balmer photon emission rate in the source. As a basic test of the model, the time evolutions of H(0) production and the Balmer Hα photon emission rate are calculated for given electron energy distribution functions in the Linac4 RF H(-) ion source. Reasonable test results are obtained and basis for the detailed comparisons with experimental results have been established. PMID:24593558
NASA Technical Reports Server (NTRS)
Yakshinskiy, B. V.; Madey, T. E.
2003-01-01
We report recent results on an investigation of source mechanisms for the origin of alkali atoms in the tenuous planetary atmospheres, with focus on non-thermal processes (photon stimulated desorption (PSD), electron stimulated desorption (ESD), and ion sputtering). Whereas alkaline earth oxides (MgO, CaO) are far more abundant in lunar samples than alkali oxides (Na2O, K2O), the atmosphere of the Moon contains easily measurable concentrations of Na and K, while Ca and Mg are undetected there; traces of Ca have recently been seen in the Moon's atmosphere (10-3 of Na). The experiments have included ESD, PSD and ion sputtering of alkali atoms from model mineral surface (amorphous SiO2) and from a lunar basalt sample obtained from NASA. The comparison is made between ESD and PSD efficiency of monovalent alkalis (Na, K) and divalent alkaline earths (Ba, Ca).The ultrahigh vacuum measurement scheme for ESD and PSD of Na atoms includes a highly sensitive alkali metal detector based on surface ionization, and a time-of-flight technique. For PSD measurements, a mercury arc light source (filtered and chopped) is used. We find that bombardment of the alkali covered surfaces by ultraviolet photons or by low energy electrons (E>4 eV) causes desorption of hot alkali atoms. This results are consistent with the model developed to explain our previous measurements of sodium desorption from a silica surface and from water ice: electron- or photon-induced charge transfer from the substrate to the ionic adsorbate causes formation of a neutral alkali atom in a repulsive configuration, from which desorption occurs. The two-electron charge transfer to cause desorption of divalent alkaline eath ions is a less likely process.The data support the suggestion that PSD by UV solar photons is a dominant source process for alkalis in the tenuous lunar atmosphere.
NASA Astrophysics Data System (ADS)
Cui, Qizhi; Smith, Vedene H.
2001-08-01
Following our previous paper on methane [Cui and Smith, J. Chem. Phys. 113, 10240 (2000)], we study the solvation structures and thermodynamics of ethane and propane in water at the infinite dilution limit by using the hypernetted chain closure reference interaction site model (HNC-RISM) theory with all-atom representations for solute molecules. At four thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3, all the atomic solute-solvent radial distribution functions are obtained, and the corresponding running coordination numbers and the hydration free energies, energies, enthalpies, and entropies are calculated with the radial distribution functions as input. The hydration structures of ethane and propane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes [Yin and Mackerell, J. Comput. Chem. 19, 334 (1998)], the ethane and propane hydration thermodynamic properties predicted by the HNC-RISM theory are improved in the specified temperature range (10-55 °C).
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
2013-11-13
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 (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered. PMID:24140935
The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Schultz, D. R.; Ovchinnikov, S. Yu; Stancil, P. C.; Zaman, T.
2016-04-01
Updating and extending previous work (Krstić and Schultz 1999 J. Phys. B: At. Mol. Opt. Phys. 32 3458 and other references) comprehensive calculations were performed for elastic scattering and charge transfer in proton—atomic hydrogen collisions. The results, obtained for 1301 collision energies in the center-of-mass energy range of 10‑4–104 eV, are provided for integral and differential cross sections relevant to transport modeling in astrophysical and other plasma environments, and are made available through a website. Use of the data is demonstrated through a Monte Carlo transport simulation of solar wind proton propagation through atomic hydrogen gas representing a simple model of the solar wind interaction with heliospheric neutrals.
Agirrezabala, Xabier; Velázquez-Muriel, Javier A; Gómez-Puertas, Paulino; Scheres, Sjors H W; Carazo, José M; Carrascosa, José L
2007-04-01
The existence of similar folds among major structural subunits of viral capsids has shown unexpected evolutionary relationships suggesting common origins irrespective of the capsids' host life domain. Tailed bacteriophages are emerging as one such family, and we have studied the possible existence of the HK97-like fold in bacteriophage T7. The procapsid structure at approximately 10 A resolution was used to obtain a quasi-atomic model by fitting a homology model of the T7 capsid protein gp10 that was based on the atomic structure of the HK97 capsid protein. A number of fold similarities, such as the fitting of domains A and P into the L-shaped procapsid subunit, are evident between both viral systems. A different feature is related to the presence of the amino-terminal domain of gp10 found at the inner surface of the capsid that might play an important role in the interaction of capsid and scaffolding proteins. PMID:17437718
Floquet Engineering of Correlated Tunneling in the Bose-Hubbard Model with Ultracold Atoms
NASA Astrophysics Data System (ADS)
Meinert, F.; Mark, M. J.; Lauber, K.; Daley, A. J.; Nägerl, H.-C.
2016-05-01
We report on the experimental implementation of tunable occupation-dependent tunneling in a Bose-Hubbard system of ultracold atoms via time-periodic modulation of the on-site interaction energy. The tunneling rate is inferred from a time-resolved measurement of the lattice site occupation after a quantum quench. We demonstrate coherent control of the tunneling dynamics in the correlated many-body system, including full suppression of tunneling as predicted within the framework of Floquet theory. We find that the tunneling rate explicitly depends on the atom number difference in neighboring lattice sites. Our results may open up ways to realize artificial gauge fields that feature density dependence with ultracold atoms.
Assessment of ion-atom collision data for magnetic fusion plasma edge modelling
NASA Astrophysics Data System (ADS)
Phaneuf, R. A.
Cross-section data for ion-atom collision processes which play important roles in the edge plasma of magnetically-confined fusion devices are surveyed and reviewed. The species considered include H, He, Li, Be, C, O, Ne, Al, Si, Ar, Ti, Cr, Fe, Ni, Cu, Mo, W and their ions. The most important ion-atom collision processes occurring in the edge plasma are charge-exchange reactions. Excitation and ionization processes are also considered. The scope is limited to atomic species and to collision velocities corresponding to plasma ion temperatures in the 2 to 200 eV range. Sources of evaluated or recommended data are presented where possible, and deficiencies in the data base are indicated.
ERIC Educational Resources Information Center
Holden, Alan
This monograph was written for the purpose of presenting physics to college students who are not preparing for careers in physics. It deals with the nature of atoms, and treats the following topics: (1) the atomic hypothesis, (2) the chemical elements, (3) models of an atom, (4) a particle in a one-dimensional well, (5) a particle in a central…
NASA Astrophysics Data System (ADS)
dSouza, A. D.; Cardoso, W. B.; Avelar, A. T.; Baseia, B.
2009-04-01
We consider recent schemes [J.M. Liu, B. Weng, Physica A 367 (2006) 215] to teleport unknown atomic states and superposition of zero- and two-photon states using the two-photon Jaynes-Cummings model. Here we do the same using the “full two-photon Jaynes-Cumming”, valid for arbitrary average number of photons. The success probability and fidelity of this teleportation are also considered.
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Santangelo, Paolo E.
2012-12-01
Pressure-swirl atomizers are often employed to generate a water-mist spray, typically employed in fire suppression. In the present study, an experimental characterization of dispersion (velocity and cone angle) and atomization (drop-size axial evolution) was carried out following a previously developed methodology, with specific reference to the initial region of the spray. Laser-based techniques were used to quantitatively evaluate the considered phenomena: velocity field was reconstructed through a Particle Image Velocimetry analysis; drop-size distribution was measured by a Malvern Spraytec device, highlighting secondary atomization and subsequent coalescence along the spray axis. Moreover, a comprehensive set of relations was validated as predictive of the involved parameters, following an inviscid-fluid approach. The proposed model pertains to early studies on pressure-swirl atomizers and primarily yields to determine both initial velocity and cone angle. The spray thickness is also predicted and a classic correlation for Sauter Mean Diameter is shown to provide good agreement with experimental results. The analysis was carried out at the operative pressure of 80 bar; two injectors were employed featuring different orifice diameters and flow numbers, as a sort of parametric approach to this spray typology.
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Klahr, Benjamin M.
An increasing global demand for energy, combined with an awareness of anthropogenic climate change, has recently fueled the search for abundant, carbon neutral energy sources. The sun offers an enormous amount of energy that is practically inexhaustible and well distributed across Earth. Thus, it is an ideal source for meeting our future energy needs in a carbon neutral fashion. This work focuses on using hematite and sunlight to oxidize water, which is the rate limiting step of splitting water into the energy dense fuel, hydrogen, and the byproduct, oxygen. Hematite is abundant, absorbs a large fraction of the solar spectrum and has an appropriately placed valence band for water oxidation. However, the often cited poor bulk properties, and slow charge transfer kinetics require large applied potentials to oxidize water. Atomic layer deposition (ALD) was utilized to deposit uniform thin films of hematite on transparent conductive substrates as model electrodes to better understand the nature of the limitations in the bulk and at the surface. Comparison of the oxidation of water to the oxidation of fast redox shuttles allowed for the separation of bulk and surface processes. A combination of electrochemical impedance spectroscopy, photoelectrochemical and electrochemical measurements were employed to determine the cause of the large required applied potential. It was found that photogenerated holes initially oxidize the electrode surface under water oxidation conditions, which is attributed to the first step in water oxidation. A critical number of these surface intermediates need to be generated in order for subsequent hole-transfer steps to proceed. At low applied potentials, these intermediates are subject to recombination from the large concentration of electrons in the conduction band due to low band bending. At higher applied potentials, high band bending eliminates surface recombination and the charge collection efficiency of the electrolyte reaches unity. A
A Computer-Controlled Classroom Model of an Atomic Force Microscope
ERIC Educational Resources Information Center
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…
The Multiphoton Interaction of Lambda Model Atom and Two-Mode Fields
NASA Technical Reports Server (NTRS)
Liu, Tang-Kun
1996-01-01
The system of two-mode fields interacting with atom by means of multiphotons is addressed, and the non-classical statistic quality of two-mode fields with interaction is discussed. Through mathematical calculation, some new rules of non-classical effects of two-mode fields which evolue with time, are established.
Entanglement and the Jaynes-Cummings model with Rydberg-dressed atoms
NASA Astrophysics Data System (ADS)
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.
Cau, M; Dorval, N; Cao, B; Attal-Trétout, B; Cochon, J L; Loiseau, A; Farhat, S; Scott, C D
2006-05-01
Spatial investigations of nickel and cobalt atoms and of C2 and C3 radicals are performed by laser induced fluorescence (LIF) in a continuous CO2 laser-vaporization reactor during the synthesis of single-walled carbon nanotubes. The chemical composition of the gas vaporized from bimetallic Ni/Co catalysts-carbon targets is determined using a chemical kinetic model. In this model, the evolution of Ni and Co atoms is driven by kinetics of condensation/evaporation process of pure metal clusters. Metal-carbon clusters are assumed to form from soot particles (C80) and 128-atom metal clusters. Spatial profiles of Ni and Co atoms obtained by LIF are compared with the calculations to validate the modeling and to adjust the input data. The value of the initial molar fraction of carbon-metal mixture diluted in helium is determined through a parametric study. Good agreement is found between the measured and the calculated evolution of Ni for a molar fraction of the helium diluent ranging from 10 to 15%. To fit the spatial profile of Co, the activation energy is adjusted in the evaporation rate, changing the cobalt dimer bond energy. The latter is found to be largely uncertain; and three values are tested: 167, 208, and 230 kJ x mol(-1). From comparison, the activation energy is found to be 208 kJ x mol(-1). However, the C2 LIF profiles show that the depletion of C2 is accelerated when cobalt is present. The observed Co evolutions suggest that small Co-C clusters are easier and/or faster to form compared to Ni-C clusters. PMID:16792356
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
NASA Astrophysics Data System (ADS)
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.
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. PMID:27367366
Biscay, F; Ghoufi, A; Goujon, F; Lachet, V; Malfreyt, P
2008-11-01
The anisotropic united atoms (AUA4) model has been used for linear and branched alkanes to predict the surface tension as a function of temperature by Monte Carlo simulations. Simulations are carried out for n-alkanes ( n-C5, n-C6, n-C7, and n-C10) and for two branched C7 isomers (2,3-dimethylpentane and 2,4-dimethylpentane). Different operational expressions of the surface tension using both the thermodynamic and the mechanical definitions have been applied. The simulated surface tensions with the AUA4 model are found to be consistent within both definitions and in good agreement with experiments. PMID:18847235
NASA Astrophysics Data System (ADS)
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.
Precisely detecting atomic position of atomic intensity images.
Wang, Zhijun; Guo, Yaolin; Tang, Sai; Li, Junjie; Wang, Jincheng; Zhou, Yaohe
2015-03-01
We proposed a quantitative method to detect atomic position in atomic intensity images from experiments such as high-resolution transmission electron microscopy, atomic force microscopy, and simulation such as phase field crystal modeling. The evaluation of detection accuracy proves the excellent performance of the method. This method provides a chance to precisely determine atomic interactions based on the detected atomic positions from the atomic intensity image, and hence to investigate the related physical, chemical and electrical properties. PMID:25544105
EXAFS Measurements and Reverse Monte Carlo Modeling of Atomic Structure in Amorphous Ni80P20 Alloys
Luo,W.; Ma, E.
2008-01-01
This paper presents a full account of the EXAFS measurements and reverse Monte Carlo (RMC) modeling of the atomic arrangements and short-to-medium range structure in an amorphous Ni-P alloy, expanding on the description included in our recent publication. The atomic packing is analyzed from the standpoint of solute atoms. The short-to-medium range structure is discussed based on single-solute-centered quasi-equivalent clusters that form due to strong chemical short-range ordering, and the topological order is described in terms of both intra-cluster and inter-cluster dense packing for efficient filling of space. This analysis is also conducted for amorphous Ni80P20 prepared via different processing routes, to observe if the polyamorphism suggested in literature for amorphous Ni-P can be confirmed from the local structure perspective. The structural differences between the proposed polymorphs are apparently subtle and a full resolution of this issue is found to be beyond the capabilities of our EXAFS/RMC modeling approach. The amorphous structural features uncovered are also compared briefly with those observed before in amorphous alloy systems with positive heat of mixing.
ERIC Educational Resources Information Center
Pine, Julian M.; Rowland, Caroline F.; Lieven, Elena V. M.; Theakston, Anna L.
2005-01-01
One of the most influential recent accounts of pronoun case-marking errors in young children's speech is Schutze & Wexler's (1996) Agreement/Tense Omission Model (ATOM). The ATOM predicts that the rate of agreeing verbs with non-nominative subjects will be so low that such errors can be reasonably disregarded as noise in the data. The present…
NASA Astrophysics Data System (ADS)
Pakniat, R.; Tavassoly, M. K.; Zandi, M. H.
2016-03-01
In this paper we have studied the dynamical evolution of Shannon information entropies in position and momentum spaces for two classes of (nonstationary) atom-field entangled states, which are obtained via the Jaynes–Cummings model and its generalization. We have focused on the interaction between two- and Ξ-type three-level atoms with the single-mode quantized field. The three-dimensional plots of entropy densities in position and momentum spaces are presented versus corresponding coordinates and time, numerically. It is observed that for particular values of the parameters of the systems, the entropy squeezing in position space occurs. Finally, we have shown that the well-known BBM (Beckner, Bialynicki-Birola and Mycielsky) inequality, which is a stronger statement of the Heisenberg uncertainty relation, is properly satisfied.
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Raju, Subramanian; Saibaba, Saroja
2016-07-01
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.
NASA Technical Reports Server (NTRS)
Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Przekwas, A. J.; Gross, Klaus
1992-01-01
This paper describes a novel method of coupling the atomization and spray combustion processes encountered in coaxial injection elements of liquid rocket engine thrust chambers. This method is based on the Jet-Embedding technique in which the liquid jet core equations and the gas phase equations are solved separately. The liquid and gas phase solutions, however, are coupled through the boundary conditions at the interface between the phases. The computational grid for the gas phase calculations are adapted to the shape of the liquid jet core. The axial variation of droplet sizes are calculated using a stability analysis appropriate for the atomization regime of liquid jet breakup. The predictions of this method have been validated with experimental data on low speed water jets. Using this method, calculations are performed for the SSME fuel preburner single injector flow field. The results obtained are in good agreement with the predictions of the volume-of-fluid method.
Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*
NASA Technical Reports Server (NTRS)
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.
Proton scattering by a hydrogen atom in an effectively two-body model
Pupyshev, V. V.
2013-02-15
It is assumed that the total potential of proton interaction with a hydrogen atom is the sum of the short-range nuclear soft-core Reid potential and the long-range Thomas-Fermi potential. A quantum mechanical analysis of low-energy features of the phase shift and cross section for elastic proton scattering on a hydrogen atom is given for the case of zero total angular momentum. The calculations performed in the present study within a nonlinear version of the variable-phase approach ultimately revealed that, because of a long-range character of the asymptotic behavior of the Thomas-Fermi potential, the respective cross section at low energies oscillates but has a finite number of zeros.
Atomic Fisher information versus atomic number
NASA Astrophysics Data System (ADS)
Nagy, Á.; Sen, K. D.
2006-12-01
It is shown that the Thomas Fermi Fisher information is negative. A slightly more sophisticated model proposed by Gáspár provides a qualitatively correct expression for the Fisher information: Gáspár's Fisher information is proportional to the two-third power of the atomic number. Accurate numerical calculations show an almost linear dependence on the atomic number.
Dynamic response of chlorine atoms on a RuO(2)(110) model catalyst surface.
Hofmann, Jan Philipp; Zweidinger, Stefan; Seitsonen, Ari Paavo; Farkas, Attila; Knapp, Marcus; Balmes, Olivier; Lundgren, Edvin; Andersen, Jesper N; Over, Herbert
2010-12-21
The dynamic behavior of surface accommodated chlorine atoms on RuO(2)(110) was studied by a variety of experimental methods including high resolution core level shift, thermal desorption-, and in situ infrared spectroscopy as well as in situ surface X-ray diffraction in combination with state-of-the-art density functional theory calculations. On the chlorinated RuO(2)(110) surface the undercoordinated oxygen atoms have been selectively replaced by chlorine. These strongly bound surface chlorine atoms shift from bridging to on-top sites when the sample is annealed in oxygen, while the reverse shift of Cl from on-top into bridge positions is observed during CO exposure; the vacant bridge position is then occupied by either chlorine or CO. For the CO oxidation reaction over chlorinated RuO(2)(110), the reactant induced site switching of chlorine causes a site-blocking of the catalytically active one-fold coordinatively unsaturated (1f-cus) Ru sites. This site blocking reduces the number of active sites and, even more important, on-top Cl blocks the free migration of the adsorbed reactants along the one-dimensional 1f-cus Ru rows, thus leading to a loss of catalytic activity. PMID:20967353
NASA Astrophysics Data System (ADS)
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.
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. PMID:26957166
Xu, Zhijie; Li, Dongsheng; Xu, Wei; Devaraj, Arun; Colby, Robert J.; Thevuthasan, Suntharampillai; Geiser, B. P.; Larson, David J.
2015-04-01
In atom probe tomography (APT), accurate reconstruction of the spatial positions of field evaporated ions from measured detector patterns depends upon a correct understanding of the dynamic tip shape evolution and evaporation laws of component atoms. Artifacts in APT reconstructions of heterogeneous materials can be attributed to the assumption of homogeneous evaporation of all the elements in the material in addition to the assumption of a steady state hemispherical dynamic tip shape evolution. A level set method based specimen shape evolution model is developed in this study to simulate the evaporation of synthetic layered-structured APT tips. The simulation results of the shape evolution by the level set model qualitatively agree with the finite element method and the literature data using the finite difference method. The asymmetric evolving shape predicted by the level set model demonstrates the complex evaporation behavior of heterogeneous tip and the interface curvature can potentially lead to the artifacts in the APT reconstruction of such materials. Compared with other APT simulation methods, the new method provides smoother interface representation with the aid of the intrinsic sub-grid accuracy. Two evaporation models (linear and exponential evaporation laws) are implemented in the level set simulations and the effect of evaporation laws on the tip shape evolution is also presented.
Atom-atom inelastic collisions and three-body atomic recombination in weakly ionized argon plasmas
NASA Technical Reports Server (NTRS)
Braun, C. G.; Kunc, J. A.
1989-01-01
A stationary collisional-radiative model including both inelastic electron-atom and atom-atom collisions is used to examine nonequilibrium weakly ionized argon plasmas with atomic densities 10 to the 16th to 10 to the 20th/cu cm, temperatures below 6000 K, and with different degrees of radiation trapping. It is shown that three-body atomic recombination becomes important at high particle densities. Comparison is made between the present approach and Thomson's theory for atomic recombination.
NASA Astrophysics Data System (ADS)
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.
Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang
2015-04-01
The phase behavior of multi-component metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamic aspects of such a model ternary metallic liquid Cu40Zr51Al9 using molecular dynamics simulation with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (diffusion coefficient, relaxation times, and shear viscosity) bordered at Tx ~1300K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs in the equilibrium liquid state well above the melting temperature of the system (Tm ~ 900K), and the crossover temperature ismore » roughly twice of the glass-transition temperature (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 non-parametric, 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 and the four-point correlation function.« less
Leite, Fabio L.; Bueno, Carolina C.; Da Róz, Alessandra L.; Ziemath, Ervino C.; Oliveira, Osvaldo N.
2012-01-01
The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of AFS, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution. PMID:23202925
NASA Astrophysics Data System (ADS)
Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.
2013-04-01
Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.
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
Mauche, C W; Liedahl, D A; Akiyama, S; Plewa, T
2008-02-08
We describe the results of an effort, funded by the Lawrence Livermore National Laboratory Directed Research and Development Program, to model, using FLASH time-dependent adaptive-mesh hydrodynamic simulations, XSTAR photoionization calculations, HULLAC atomic data, and Monte Carlo radiation transport, the radiatively-driven photoionized wind and accretion flow of high-mass X-ray binaries (HMXBs). In this final report, we describe the purpose, approach, and technical accomplishments of this effort, including maps of the density, temperature, velocity, ionization parameter, and emissivity distributions of the X-ray emission lines of the well-studied HMXB Vela X-1.
The Boson peak of model glass systems and its relation to atomic structure
NASA Astrophysics Data System (ADS)
Derlet, P. M.; Maaß, R.; Löffler, J. F.
2012-05-01
Bulk metallic glasses (BMGs) exhibit a rich variety of vibrational properties resulting from significant atomic scale disorder. The Boson peak, which reflects an enhancement of states in the low frequency regime of the vibrational density of states (VDOS), is one such experimental signature of amorphous materials that has gained much interest in recent times. However, the precise nature of these low frequency modes and how they are influenced by local atomic structure remains unclear. Past simulation work has demonstrated that such modes consist of a mixture of propagating and localized components, and have been referred to as quasi-localized modes. Using standard harmonic analysis, the present work investigates the structural origin of such modes by diagonalising the Hessian of atomistic BMG structures derived from molecular dynamics simulations using a binary Lennard Jones pair potential. It is found that the quasi-localized vibrational modes responsible for the low frequency enhancement of the VDOS exist in a structural environment characterized primarily by low elastic shear moduli, but also increased free volume, a hydrostatic pressure that is tensile, and low bulk moduli. These findings are found to arise from the long-range attractive nature of the pair-wise interaction potential, which manifests itself in the corresponding Hessian as long-range off-diagonal disorder characterized by a distribution of negative effective spring constants.
2015-01-01
Summary This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments. PMID:26734515
Solares, Santiago D.
2015-11-26
This study introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretationmore » of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tappingmode imaging, for both of which the force curves exhibit the expected features. Lastly, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.« less
Solares, Santiago D.
2015-11-26
This study introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tappingmode imaging, for both of which the force curves exhibit the expected features. Lastly, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.
NASA Astrophysics Data System (ADS)
Bayvel, L.; Orzechowski, Z.
The present text defines the physical processes of liquid atomization, the primary types of atomizers and their design, and ways of measuring spray characteristics; it also presents experimental investigation results on atomizers and illustrative applications for them. Attention is given to the macrostructural and microstructural parameters of atomized liquids; swirl, pneumatic, and rotary atomizers; and optical drop sizing methods, with emphasis on nonintrusive optical methods.
Brigatti, M.F.; Malferrari, D.; Poppi, M.; Mottana, A.; Cibin, G.; Marcelli, A.; Cinque, G.
2009-05-12
A detailed description of the interlayer site in trioctahedral true micas is presented based on a statistical appraisal of crystal-chemical, structural, and spectroscopic data determined on two sets of trioctahedral micas extensively studied by both X-ray diffraction refinement on single crystals (SC-XRD) and X-ray absorption fine spectroscopy (XAFS) at the potassium K-edge. Spectroscopy was carried out on both random powders and oriented cleavage flakes, the latter setting taking advantage of the polarized character of synchrotron radiation. Such an approach (AXANES) is shown to be complementary to crystal-chemical investigation based on SC-XRD refinement. However, the results are not definitive as they focus on few samples having extreme features only (e.g., end-members, unusual compositions, and samples with extreme and well-identified substitution mechanisms). The experimental absorption K-edge (XANES) for potassium was decomposed by calculation and extrapolated into a full in-plane absorption component ({sigma}{parallel}) and a full out-of-plane absorption component ({sigma}{perpendicular}). These two patterns reflect different structural features: {sigma}{parallel}represents the arrangement of the atoms located in the mica interlayer space and facing tetrahedral sheets; {sigma}{perpendicular} is associated with multiple-scattering interactions entering deep into the mica structure, thus also reflecting interactions with the heavy atoms (essentially Fe) located in the octahedral sheet. The out-of-plane patterns also provide insights into the electronic properties of the octahedral cations, such as their oxidation states (e.g., Fe{sup 2+} and Fe{sup 3+}) and their ordering (e.g., trans- vs. cis-setting). It is also possible to distinguish between F- and OH-rich micas due to peculiar absorption features originating from the F vs. OH occupancy of the O4 octahedral site. Thus, combining crystal-chemical, structural, and spectroscopic information is shown to be a
NASA Astrophysics Data System (ADS)
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.
Huang, Jen-Ching; Weng, Yung-Jin
2014-01-01
This study focused on the nanomachining property and cutting model of single-crystal sapphire during nanomachining. The coated diamond probe is used to as a tool, and the atomic force microscopy (AFM) is as an experimental platform for nanomachining. To understand the effect of normal force on single-crystal sapphire machining, this study tested nano-line machining and nano-rectangular pattern machining at different normal force. In nano-line machining test, the experimental results showed that the normal force increased, the groove depth from nano-line machining also increased. And the trend is logarithmic type. In nano-rectangular pattern machining test, it is found when the normal force increases, the groove depth also increased, but rather the accumulation of small chips. This paper combined the blew by air blower, the cleaning by ultrasonic cleaning machine and using contact mode probe to scan the surface topology after nanomaching, and proposed the "criterion of nanomachining cutting model," in order to determine the cutting model of single-crystal sapphire in the nanomachining is ductile regime cutting model or brittle regime cutting model. After analysis, the single-crystal sapphire substrate is processed in small normal force during nano-linear machining; its cutting modes are ductile regime cutting model. In the nano-rectangular pattern machining, due to the impact of machined zones overlap, the cutting mode is converted into a brittle regime cutting model. PMID:25241676
Atomic Scale Modeling of High Strain Rate Deformation and Failure of HCP Metals
NASA Astrophysics Data System (ADS)
Mackenchery, Karoon; Agarwal, Garvit; Dongare, Avinash
2015-06-01
A fundamental understanding of the microstructure effects on the defect evolution at the atomic resolution and the related contribution to plasticity at the macro-scales is needed to obtain a reliable performance of metallic materials in extreme environments. Large-scale molecular dynamics simulations are carried out to characterize the dynamic evolution of defect/damage structures during the deformation and failure behavior of HCP (Mg, Ti) metallic systems (single crystal and nanocrystalline at high strain rates as well as under shock loading conditions. The evolution of various types of dislocations, twins, faults, etc. and the related deformation and failure response (nucleation and growth of voids/cracks) will be discussed. The effects of strain rates on relationships between the microstructure and the strength of these materials at high strain rates and the underlying micromechanisms related to deformation and failure will be discussed.
Energetic Neutral Atom Emissions From Venus: VEX Observations and Theoretical Modeling
NASA Technical Reports Server (NTRS)
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.
Nurbawono, Argo; Liu, Shuanglong; Zhang, Chun
2015-04-21
Time dependent density functional tight binding (TDDFTB) method is implemented with sparse matrix techniques and improved parallelization algorithms. The method is employed to calculate the optical properties of various Si nanocrystals (NCs). The calculated light absorption spectra of small Si NCs from TDDFTB were found to be comparable with many body perturbation methods utilizing planewave basis sets. For large Si NCs (more than a thousand atoms) that are beyond the reach of conventional approaches, the TDDFTB method is able to produce reasonable results that are consistent with prior experiments. We also employed the method to study the effects of surface chemistry on the optical properties of large Si NCs. We learned that the optical properties of Si NCs can be manipulated with small molecule passivations such as methyl, hydroxyl, amino, and fluorine. In general, the shifts and profiles in the absorption spectra can be tuned with suitably chosen passivants.
Atomically detailed models of gas mixture diffusion through CuBTC membranes
Keskin S; Liu JC; Johnson JK.
2009-10-01
Metal–organic frameworks are intriguing crystalline nanoporous materials that have potential applications in adsorption-based and membrane-based gas separations. We describe atomically detailed simulations of gas adsorption and diffusion in CuBTC that have been used to predict the performance of CuBTC membranes for separation of H2/CH4, CO2/CH4 and CO2/H2 mixtures. CuBTC membranes are predicted to have higher selectivities for all three mixtures than MOF-5 membranes, the only other metal–organic framework material for which detailed predictions of membrane selectivities have been made. Our results give insight into the physical properties that will be desirable in tuning the pore structure of MOFs for specific membrane-based separations
An atomic model of the nitrous-oxide-nitrided SiO2/Si interface
NASA Astrophysics Data System (ADS)
Kushida-Abdelghafar, Keiko; Watanabe, Kikuo; Kikawa, Takeshi; Kamigaki, Yoshiaki; Ushio, Jiro
2002-09-01
The interfacial structure of nitrous-oxide- (NO-)nitrided SiO2/Si is determined on the basis of the configuration of the Pb centers and the results of physical analysis. We used electron spin-resonance analysis to observe a decrease in the number of Pb centers after NO annealing, which corresponds to the decrease in the density of interface traps. The nitrogen bonds at the interface were analyzed by x-ray photoelectron spectroscopy. An asymmetric N 1s peak at around 398 eV was detected; the peak may be decomposed into two peaks with a binding-energy difference of 0.6 eV. This core-level shift originates in the difference between the numbers of oxygen atoms that are second-nearest neighbors of the nitrogen which terminates the Pb0 and Pb1 centers.
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. PMID:26930454
Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling
NASA Astrophysics Data System (ADS)
Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro
2012-10-01
Grain boundaries influence many physical and chemical properties of crystalline materials. Here, we perform molecular dynamics simulations to study the structure of a series of [100] symmetric tilt grain boundaries in Mg2SiO4 forsterite. The present results show that grain boundary energies depend significantly on misorientation angle. For small misorientation angles (up to 22°), grain boundary structures consist of an array of partial edge dislocations with Burgers vector 1/2[001] associated with stacking faults and their energies can be readily fit with a model which adds the Peach-Koehler equation to the Read-Shockley dislocation model for grain boundaries. The core radius of partial dislocations and the spacing between the partials derived from grain boundary energies show that the transition from low- to high-angle grain boundaries occurs for a misorientation angle between 22° and 32°. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Finally, we use a low energy atomic configuration obtained by molecular dynamics for the misorientation of 12.18° as input to simulate a high-resolution transmission electron microscopy (HRTEM) image. The simulated image is in good agreement with an observed HRTEM image, which indicates the power of the present approach to predict realistic atomic structures of grain boundaries in complex silicates.
Improving Atomic Force Microscopy Imaging by a Direct Inverse Asymmetric PI Hysteresis Model
Wang, Dong; Yu, Peng; Wang, Feifei; Chan, Ho-Yin; Zhou, Lei; Dong, Zaili; Liu, Lianqing; Li, Wen Jung
2015-01-01
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. PMID:25654719
NASA Astrophysics Data System (ADS)
Monti, J. M.; Fojón, O. A.; Hanssen, J.; Rivarola, R. D.
2013-07-01
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.
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
A new computational model for protein folding based on atomic solvation.
Wang, Y.; Zhang, H.; Scott, R. A.
1995-01-01
A new model for calculating the solvation energy of proteins is developed and tested for its ability to identify the native conformation as the global energy minimum among a group of thousands of computationally generated compact non-native conformations for a series of globular proteins. In the model (called the WZS model), solvation preferences for a set of 17 chemically derived molecular fragments of the 20 amino acids are learned by a training algorithm based on maximizing the solvation energy difference between native and non-native conformations for a training set of proteins. The performance of the WZS model confirms the success of this learning approach; the WZS model misrecognizes (as more stable than native) only 7 of 8,200 non-native structures. Possible applications of this model to the prediction of protein structure from sequence are discussed. PMID:7670381
Jaiswal, Abhishek; Egami, Takeshi; Zhang, Yang
2015-04-01
The phase behavior of multi-component metallic liquids is exceedingly complex because of the convoluted many-body and many-elemental interactions. Herein, we present systematic studies of the dynamic aspects of such a model ternary metallic liquid Cu_{40}Zr_{51}Al_{9} using molecular dynamics simulation with embedded atom method. We observed a dynamical crossover from Arrhenius to super-Arrhenius behavior in the transport properties (diffusion coefficient, relaxation times, and shear viscosity) bordered at T_{x} ~1300K. Unlike in many molecular and macromolecular liquids, this crossover phenomenon occurs in the equilibrium liquid state well above the melting temperature of the system (T_{m} ~ 900K), and the crossover temperature is roughly twice of the glass-transition temperature (T_{g}). Below T_{x}, 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 non-parametric, 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 T_{x} 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 and the four-point correlation function.
Socol, Yehoshua; Dobrzyński, Ludwik
2015-01-01
The atomic bomb survivors life-span study (LSS) is often claimed to support the linear no-threshold hypothesis (LNTH) of radiation carcinogenesis. This paper shows that this claim is baseless. The LSS data are equally or better described by an s-shaped dependence on radiation exposure with a threshold of about 0.3 Sievert (Sv) and saturation level at about 1.5 Sv. A Monte-Carlo simulation of possible LSS outcomes demonstrates that, given the weak statistical power, LSS cannot provide support for LNTH. Even if the LNTH is used at low dose and dose rates, its estimation of excess cancer mortality should be communicated as 2.5% per Sv, i.e., an increase of cancer mortality from about 20% spontaneous mortality to about 22.5% per Sv, which is about half of the usually cited value. The impact of the "neutron discrepancy problem" - the apparent difference between the calculated and measured values of neutron flux in Hiroshima - was studied and found to be marginal. Major revision of the radiation risk assessment paradigm is required. PMID:26673526
A Comprehensive Opacities/Atomic Database for the Analysis of Astrophysical Spectra and Modeling
NASA Technical Reports Server (NTRS)
Pradhan, Anil K. (Principal Investigator)
1997-01-01
The main goals of this ADP award have been accomplished. The electronic database TOPBASE, consisting of the large volume of atomic data from the Opacity Project, has been installed and is operative at a NASA site at the Laboratory for High Energy Astrophysics Science Research Center (HEASRC) at the Goddard Space Flight Center. The database will be continually maintained and updated by the PI and collaborators. TOPBASE is publicly accessible from IP: topbase.gsfc.nasa.gov. During the last six months (since the previous progress report), considerable work has been carried out to: (1) put in the new data for low ionization stages of iron: Fe I - V, beginning with Fe II, (2) high-energy photoionization cross sections computed by Dr. Hong Lin Zhang (consultant on the Project) were 'merged' with the current Opacity Project data and input into TOPbase; (3) plans laid out for a further extension of TOPbase to include TIPbase, the database for collisional data to complement the radiative data in TOPbase.
Theoretical study of heavy-atom molecules to search for physics beyond the Standard model
NASA Astrophysics Data System (ADS)
Petrov, A. N.; Skripnikov, L. V.; Kudashov, A. D.; Mosyagin, N. S.; Titov, A. V.
2015-05-01
The goal of the report is to review our latest studies for heavy-atom diatomics - ThO, RaO, RaF, PbF - which are of practical interest to search the T, P-odd effects. Particular attention is devoted to the H3Δ1 state of ThO. Combination of the spin precession measurement of ThO with the calculated Eeff (ThO) leads to the most rigid limit on eEDM:, |de|<8.7 × 10-29e .cm. This is more than one order of magnitude better than other limits obtained. The knowledge of the g-factor dependence on electric fields is important for understanding possible systematic effects. Our study of the g-factors for H3Δ1 has shown that the J = 2 rotational state should be even more robust against a number of systematic errors compared to J = 1. This work is supported by the SPbU Fundamental Science Research grant from Federal Budget No. 0.38.652.2013, RFBR Grant No. 13-02-01406. L.S. is also grateful to the President of RF grant no MK-5877.2014.2.
Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach
NASA Astrophysics Data System (ADS)
Yakubovich, Alexander V.; Surdutovich, Eugene; Solov'yov, Andrey V.
2011-05-01
We present a brief overview of the multiscale approach towards understanding of the processes responsible for the radiation damage caused by energetic ions. This knowledge is very important, because it can be utilized in the ion-beam cancer therapy, which is one of the most advanced modern techniques to cure certain type of cancer. The central element of the multiscale approach is the theoretical evaluation and quantification of the DNA damage within cell environment. To achieve this goal one needs a significant amount of data on various atomic and molecular processes involved into the cascade of events starting with the ion entering and propagation in the biological medium and resulting in the DNA damage. The discussion of the follow up biological processes are beyond the scope of this brief overview. We consider different paths of the DNA damage and focus on the the illustration of the thermo-mechanical effects caused by the propagation of ions through the biological environment and in particular on the possibility of the creation of the shock waves in the vicinity of the ion tracks. We demonstrate that at the initial stages after ion's passage the shock wave is so strong that it can contribute to the DNA damage due to large pressure gradients developed at the distances of a few nanometers from the ionic tracks. This novel mechanism of the DNA damage provides an important contribution to the cumulative biodamage caused by low-energy secondary electrons, holes and free radicals.
Three-body scattering hypervolume for ultracold atoms with a model two-body potential
NASA Astrophysics Data System (ADS)
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.
Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach
Yakubovich, Alexander V.; Solov'yov, Andrey V.; Surdutovich, Eugene
2011-05-11
We present a brief overview of the multiscale approach towards understanding of the processes responsible for the radiation damage caused by energetic ions. This knowledge is very important, because it can be utilized in the ion-beam cancer therapy, which is one of the most advanced modern techniques to cure certain type of cancer. The central element of the multiscale approach is the theoretical evaluation and quantification of the DNA damage within cell environment. To achieve this goal one needs a significant amount of data on various atomic and molecular processes involved into the cascade of events starting with the ion entering and propagation in the biological medium and resulting in the DNA damage. The discussion of the follow up biological processes are beyond the scope of this brief overview. We consider different paths of the DNA damage and focus on the the illustration of the thermo-mechanical effects caused by the propagation of ions through the biological environment and in particular on the possibility of the creation of the shock waves in the vicinity of the ion tracks. We demonstrate that at the initial stages after ion's passage the shock wave is so strong that it can contribute to the DNA damage due to large pressure gradients developed at the distances of a few nanometers from the ionic tracks. This novel mechanism of the DNA damage provides an important contribution to the cumulative biodamage caused by low-energy secondary electrons, holes and free radicals.
History and Philosophy of Science through Models: Some Challenges in the Case of "The Atom".
ERIC Educational Resources Information Center
Justi, Rosaria; Gilbert, John
2000-01-01
Suggests that the contribution of history and philosophy of science (HPS) to science education can be enhanced through a consideration of scientific models. Analyzes the curriculum and textbooks for 14-16 year olds in Brazil and the United Kingdom and identifies the use of hybrid models. (Contains 35 references.) (Author/YDS)
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
NASA Astrophysics Data System (ADS)
Pineiro Orioli, Asier; Berges, Juergen; Signoles, Adrien; Schempp, Hanna; Whitlock, Shannon; Weidemueller, Matthias; Safavi-Naini, Arghavan; Wall, Michael; Schachenmayer, Johannes; Rey, Ana Maria
2016-05-01
Accurate description of the dynamics of quantum spin models is a theoretically challenging problem with widespread applications ranging from condensed matter to high-energy physics. Furthermore recent experimental progress in AMO experiments allows for the physical realization of these models in a variety of setups, such as Rydberg systems and trapped ion experiments, with an unprecedented degree of control and flexibility. Therefore, it is vital to develop efficient theoretical methods capable of simulating the many-body dynamics of such systems. In this work, we employ and extend the recently developed discrete Truncated Wigner Approximation (dTWA), an approximation based on the phase space description of quantum mechanics, to compute the dynamics of two types of spin models: the long-range XY model, which can be realized with Rydberg atoms, and a coupled spin-boson model, which is relevant to trapped ion experiments. Comparisons to experimental results and to available exact solutions to benchmark the method show that the dTWA is capable of capturing important features of the spin evolution and can also help uncovering some underlying non-equilibrium processes.
NASA Astrophysics Data System (ADS)
Buchachenko, A. A.; Kroupnov, A. A.; Kovalev, V. L.
2014-07-01
Atomic oxygen and nitrogen adsorption on the Si site of the (1 1 1) face of ideal β-cristobalite is studied within the cluster model using the density functional approach. The M06 and B3LYP functionals are found to be the most appropriate for studying atomic adsorption on silica. The calculations show significant difference in adsorption properties with respect to previously studied (1 0 0) β-cristobalite face, but do not reveal remarkable effect of the surface relaxation.
All-atom polarizable force field for DNA based on the classical Drude oscillator model.
Savelyev, Alexey; MacKerell, Alexander D
2014-06-15
Presented is a first generation atomistic force field (FF) for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages, and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting quantum mechanical (QM) data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude FF yields stable DNA duplexes on the 100-ns time scale and satisfactorily reproduce (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII substates of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive FF, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978
All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
Savelyev, Alexey; MacKerell, Alexander D.
2014-01-01
Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978
Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.
2015-06-03
We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascade production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.
NASA Astrophysics Data System (ADS)
Samolyuk, G. D.; Osetsky, Y. N.; Stoller, R. E.
2015-10-01
We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascade production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (∼0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential. The Gao-Weber potential appears to give a more realistic description of cascade dynamics in SiC, but still has some shortcomings when the defect migration barriers are compared to the ab initio results.
Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.
2015-06-03
We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascademore » production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.« less
NASA Astrophysics Data System (ADS)
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
Producing high-accuracy lattice models from protein atomic coordinates including side chains.
Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M
2012-01-01
Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models. PMID:22934109
Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains
Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M.
2012-01-01
Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models. PMID:22934109
Dooher, J.
1995-10-01
In the quarterly report of January 1995, atomization was described in terms of fragmentation of ligaments and subsequent breakup of drops into a fine spray. In this way, atomization can be considered a form of comminution. In this report, an analysis is presented which applies probability theory to atomization. In future work, the predictions of this analysis will be examined experimentally.
NASA Astrophysics Data System (ADS)
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
Safronova, M. S.; Mitroy, J.; Clark, Charles W.; Kozlov, M. G.
2015-01-22
The atomic dipole polarizability governs the first-order response of an atom to an applied electric field. Atomic polarization phenomena impinge upon a number of areas and processes in physics and have been the subject of considerable interest and heightened importance in recent years. In this paper, we will summarize some of the recent applications of atomic polarizability studies. A summary of results for polarizabilities of noble gases, monovalent, and divalent atoms is given. The development of the CI+all-order method that combines configuration interaction and linearized coupled-cluster approaches is discussed.
NASA Astrophysics Data System (ADS)
Tonks, Michael R.; Millett, Paul C.; Nerikar, Pankaj; Du, Shiyu; Andersson, David; Stanek, Christopher R.; Gaston, Derek; Andrs, David; Williamson, Richard
2013-09-01
Fission gas production and evolution significantly impact the fuel performance, causing swelling, a reduction in the thermal conductivity and fission gas release. However, typical empirical models of fuel properties treat each of these effects separately and uncoupled. Here, we couple a fission gas release model to a model of the impact of fission gas on the fuel thermal conductivity. To quantify the specific impact of grain boundary (GB) bubbles on the thermal conductivity, we use atomistic and mesoscale simulations. Atomistic molecular dynamic simulations were employed to determine the GB thermal resistance. These values were then used in mesoscale heat conduction simulations to develop a mechanistic expression for the effective GB thermal resistance of a GB containing gas bubbles, as a function of the percentage of the GB covered by fission gas. The coupled fission gas release and thermal conductivity model was implemented in Idaho National Laboratory's BISON fuel performance code to model the behavior of a 10-pellet LWR fuel rodlet, showing how the fission gas impacts the UO2 thermal conductivity. Furthermore, additional BISON simulations were conducted to demonstrate the impact of average grain size on both the fuel thermal conductivity and the fission gas release.
Visualization of atom's orbits.
Kim, Byungwhan
2014-02-01
High-resolution imaging techniques have been used to obtain views of internal shapes of single atoms or columns of atoms. This review article focuses on the visualization of internal atomic structures such as the configurations of electron orbits confined to atoms. This is accomplished by applying visualization techniques to the reported images of atoms or molecules as well as static and dynamic ions in a plasma. It was found that the photon and electron energies provide macroscopic and microscopic views of the orbit structures of atoms, respectively. The laser-imaged atoms showed a rugged orbit structure, containing alternating dark and bright orbits believed to be the pathways for an externally supplied laser energy and internally excited electron energy, respectively. By contrast, the atoms taken by the electron microscopy provided a structure of fine electron orbits, systematically formed in increasing order of grayscale representing the energy state of an orbit. This structure was identical to those of the plasma ions. The visualized electronic structures played a critical role in clarifying vague postulates made in the Bohr model. Main features proposed in the atomic model are the dynamic orbits absorbing an externally supplied electromagnetic energy, electron emission from them while accompanying light radiation, and frequency of electron waves not light. The light-accompanying electrons and ionic speckles induced by laser light signify that light is composed of electrons and ions. PMID:24749452
Wesolowski, David J.; Wang, Hsiu -Wen; Page, Katharine L.; Naguib, Michael; Gogotsi, Yury
2015-12-08
MXenes are a recently discovered family of two-dimensional (2D) early transition metal carbides and carbonitrides, which have already shown many attractive properties and a great promise in energy storage and many other applications. However, a complex surface chemistry and small coherence length has been an obstacle in some applications of MXenes, also limiting accuracy of predictions of their properties. In this study, we describe and benchmark a novel way of modeling layered materials with real interfaces (diverse surface functional groups and stacking order between the adjacent monolayers) against experimental data. The structures of three kinds of Ti3C2Tx MXenes (T standsmore » for surface terminating species, including O, OH, and F) produced under different synthesis conditions were resolved for the first time using atomic pair distribution function obtained by high-quality neutron total scattering. The true nature of the material can be easily captured with the sensitivity of neutron scattering to the surface species of interest and the detailed third-generation structure model we present. The modeling approach leads to new understanding of MXene structural properties and can replace the currently used idealized models in predictions of a variety of physical, chemical and functional properties of Ti3C2-based MXenes. Furthermore, the developed models can be employed to guide the design of new MXene materials with selected surface termination and controlled contact angle, catalytic, optical, electrochemical and other properties. We suggest that the multi-level structural modeling should form the basis for a generalized methodology on modeling diffraction and pair distribution function data for 2D and layered materials.« less
Po, Hoi Chun; Zhou, Qi
2015-01-01
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. PMID:26268154
NASA Astrophysics Data System (ADS)
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.
Application of cluster-plus-glue-atom model to barrierless Cu–Ni–Ti and Cu–Ni–Ta films
Li, Xiaona Ding, Jianxin; Wang, Miao; Dong, Chuang; Chu, Jinn P.
2014-11-01
To improve the thermal stability of copper and avoid its diffusion into surrounding dielectrics or interfacial reactions with them, the authors applied the cluster-plus-glue-atom model to investigate barrierless Cu–Ni–M (M = Ti or Ta) seed layers. The dissolution of the third element (Ti or Ta) in the Cu lattice with the aid of Ni significantly improved the thermal stability of the Cu seed layer. The appropriate M/Ni (M = Ti or Ta) ratio was selected to obtain a low resistivity: the resistivity was as low as 2.5 μΩ cm for the (Ti{sub 1.5/13.5}Ni{sub 12/13.5}){sub 0.3}Cu{sub 99.7} film and 2.8 μΩ cm for the (Ta{sub 1.1/13.1}Ni{sub 12/13.1}){sub 0.4}Cu{sub 99.6} film after annealing at 500 °C for 1 h. After annealing at 500 °C for 40 h, the two films remained stable without forming a Cu{sub 3}Si compound. The authors confirmed that the range of applications of the cluster-plus-glue-atom model could be extended. Therefore, a third element M with negative enthalpies of mixing with both Cu and Ni could be selected, under the premise that the mixing enthalpy of M–Ni is more negative than that of M–Cu.
A.V.G. Chizmeshya; M.J. McKelvy; J.B. Adams
2001-11-01
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
NASA Astrophysics Data System (ADS)
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
NASA Technical Reports Server (NTRS)
Mcdonough, T. R.
1974-01-01
The trapping of Titan's escaping atmosphere in the Saturnian system by a toroidal ring is discussed. The radius of the toroid is comparable to Titan's orbit, or about ten times larger than the visible rings. Theoretical atmospheric models are formulated that consider Saturn's gravitational attraction and magnetospheric properties in forming this toroid and in protecting toroid particles from direct ionization by solar wind particles.
Bridging scales: from atoms to coarse-grained models for soft matter systems
NASA Astrophysics Data System (ADS)
Peter, Christine
2015-03-01
Molecular simulation has extended to increasingly complex soft matter systems, and time-scale and system-size requirements have instigated the use of simulation models on multiple levels of resolution. On the classical particle-based level, a large variety of methods to develop coarse grained (CG) simulation models has emerged, an important subgroup being those scale-bridging methods where the CG model is derived from and systematically linked to an underlying atomistic description. In my talk, I will introduce a few of these methods, address the underlying concepts as well as some of the ongoing challenges that are inherent to coarse graining. A natural consequence of reducing the level of resolution in a simulation model is a loss of transferability, i.e. a decreasing ability to correctly describe a system at several thermodynamic state points. Intimately linked to this is a loss of the ability to correctly represent all structural, thermodynamic and dynamic properties of the system. Examples for these limitations are easily found in all CG simulations of multicomponent or multiphase soft matter systems - ranging from liquid crystals, biomolecular aggregates, biomaterials to hard/soft nanocomposites. A correct representation of phase transitions, phase coexistence, environment-induced conformational transitions, or effects due to surfaces and interfaces is a severe challenge for bottom-up CG models. Addressing this challenge requires both a method of generating CG potentials as well as finding and rationalizing an appropriate reference state point to start out from. I will illustrate several of these aspects using examples from the biomolecular and (biomimetic-) materials world.
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
Carrez, P.; Cordier, P.; Ferre, D.; Mainprice, D.; Tommasi, A.
2007-12-01
The D" layer that extends up to several hundred kilometers at the transition between the silicate mantle and the metallic core is an essential feature of the mantle's convecting system. This layer is known to display a strong and heterogeneous seismic anisotropy. At the same time, seismic velocities change laterally, indicating large thermal and chemical variation. It is generally accepted that D" is essentially composed of (Mg,Fe)SiO3, which can be found in the Perovskite (Pv) structure or in the post perovskite (PPv) structure depending on the temperature of the region of interest. The interpretation of the origin of the anisotropy of D" is still in debate. Essentially, two propositions appear: strain-induced Crystal Preferred Orientation (CPO) of mineral (MgSiO3 PPv or (Mg,Fe)O2) and/or shape preferred orientation (SPO) of inclusions. With the last assumption, to produce azimuthal anisotropy, inclusions have to be inclined or strain-induced CPO has to be invoked. To explore the contribution of CPO due to plastic flow of PPv to seismic anisotropy in the D" layer, we use a multi- scale modeling approach that couple atomistic/continuum models of dislocations at D" pressures to polycrystal plasticity simulations (using a viscoplastic self-consistent (VPSC) model). Indeed to model the development of CPO, we need to determine a fundamental parameter that controls the activity of a dislocation glide system: the critical resolved shear stress (CRSS). Nowadays, dislocation core properties can be calculated from first principles calculation through the Peierls- Nabarro model using the generalized stacking faults approach. Dislocation properties such as planar core spreading and Peierls stresses are thus modeled under a pressure of 120 GPa for 10 potential glide systems of the PPv structure. As lattice friction is commonly considered as the major factor in plastic deformation of minerals, we have then chosen to take the CRSS proportional to the Peierls stresses for
NASA Astrophysics Data System (ADS)
Takeuchi, Wataru; Matsuda, Naoki
2008-03-01
The interaction potential between an incident ion and a target atom in impact-collision ion scattering spectroscopy (ICISS), which is a specialization of low energy ion scattering (LEIS) and its variants, i.e. ICISS with detection of neutrals (NICISS), coaxial ICISS (CAICISS) and impact-collision atom scattering spectroscopy with detection of neutrals (NICASS), has been evaluated by the new method using the dependence of the total scattering angle on the impact parameter for the first collision in the numerical calculations based on the two-atom scattering model (TWASM). From the comparison of determined values of scaling factor for the Firsov screening length by three-dimensional computer simulations with calculated ones by TWASM, it became obviously that the interatomic potentials for the various combinations of an incident ion and a target atom in LEIS are suitably given by the Moliere potential with the reduced Firsov screening length employing the scaling factor obtained in TWASM calculations.
Atomic data for a five-configuration model of Fe XIV
NASA Technical Reports Server (NTRS)
Bhatia, A. K.; Kastner, S. O.
1993-01-01
Collision strengths calculated in the distorted wave approximation are presented for electron excitation of Fe XIV at incident energies of 10, 20 and 30 Rydbergs. Configurations 3s(2)3p, 3s3p(2), 3s(2)3d, 3p(3), and 3s3p3d are included, comprising 40 levels, and wave function mixing coefficients are tabulated. Radiative transition rates are given for the same model using the Superstructure program.
NASA Astrophysics Data System (ADS)
Kushner, Mark; Cooley, James; Xue, Jun; Urdhal, Randall
2011-10-01
Low pressure plasmas sustained in rare gases and rare gas mixtures can be efficient sources of VUV light from resonant optical transitions. Many applications would benefit from having small, inexpensive sources of plasma produced VUV light. To address this need, microwave wave excited microplasma sources in rare gases operating at pressures of <10 Torr are being developed. The microplasmas are sustained in ceramic cavities having cross sectional dimensions of <=1 mm, excited by a split-ring resonator antenna operated at 2.45 GHz. Power deposition is a few W. Hybrid computer modeling of microplasmas sustained in Ar has been performed to develop scaling laws for increasing the efficiency of VUV light production. The model includes a Monte Carlo simulation for the electron energy distribution and for radiation transport. Results from those studies will be discussed for plasma densities, electron energy distributions, VUV light production and excited state densities as a function of power, pressure and aspect ratio of the microplasma cavities. Modeling results will be compared to laser absorption spectroscopy of Ar excited state densities. Work supported by Agilent Technologies.
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
Xu, Xiaojun; Yan, Chunli; Wohlhueter, Robert; Ivanov, Ivaylo
2015-01-01
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. PMID:26557958
NASA Astrophysics Data System (ADS)
Gorokhovski, M. A.; Saveliev, V. L.
2003-01-01
This paper considers the breakup of liquid drops at the large Weber number within the framework of Kolmogorov's scenario of breakup. The population balances equation for droplet radius distribution is written to be an invariant under the group of scaling transformations. It is shown that due to this symmetry, the long-time limit solution of this equation is a power function. When the standard deviation of droplet radius strongly increases and, consequently, the characteristic length scale disappears, the power asymptotic solution can be viewed as a further evolution of Kolmogorov's log-normal distribution. This new universality appears to be consistent with the experimental observation of fractal properties of droplets produced by air-blast breakup. The scaling properties of Kolmogorov's model at later times are also demonstrated in the case where the breakup frequency is a power function of instantaneous radius. The model completes the Liouville equation for distribution function of liquid particles in the phase space of droplet position, velocity, and radius. The numerical scheme is proposed for stochastic modeling of droplets production. Lagrangian simulation of the spray under air-blast atomization is performed using KIVA II code, which is a frequently used code for computation of turbulent flows with sprays. The qualitative agreement of simulation with measurements is demonstrated.
Feature Modeling of HfO2 Atomic Layer Deposition Using HfCl4/H2O
NASA Astrophysics Data System (ADS)
Stout, Phillip J.; Adams, Vance; Ventzek, Peter L. G.
2003-03-01
A Monte Carlo based feature scale model (Papaya) has been applied to atomic layer deposition (ALD) of HfO2 using HfCl_4/H_20. The model includes physical effects of transport to surface, specular and diffusive reflection within feature, adsorption, surface diffusion, deposition and etching. Discussed will be the 3D feature modeling of HfO2 deposition in assorted features (vias and trenches). The effect of feature aspect ratios, pulse times, cycle number, and temperature on film thickness, feature coverage, and film Cl fraction (surface/bulk) will be discussed. Differences between HfO2 ALD on blanket wafers and in features will be highlighted. For instance, the minimum pulse times sufficient for surface reaction saturation on blanket wafers needs to be increased when depositing on features. Also, HCl products created during the HfCl4 and H_20 pulses are more likely to react within a feature than at the field, reducing OH coverage within the feature (vs blanket wafer) thus limiting the maximum coverage attainable for a pulse over a feature.
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
ERIC Educational Resources Information Center
Cummo, Evelyn; Matthews, Catherine E.
2002-01-01
Presents an activity designed to provide students with opportunities to practice drawing atomic models and discover the logical pairings of whole families on the periodic table. Follows the format of a television game show. (DDR)
Hybrid-PIC Modeling of the Transport of Atomic Boron in a Hall Thruster
NASA Technical Reports Server (NTRS)
Smith, Brandon D.; Boyd, Iaian D.; Kamhawi, Hani
2015-01-01
Computational analysis of the transport of boron eroded from the walls of a Hall thruster is performed by implementing sputter yields of hexagonal boron nitride and velocity distribution functions of boron within the hybrid-PIC model HPHall. The model is applied to simulate NASA's HiVHAc Hall thruster at a discharge voltage of 500V and discharge powers of 1-3 kW. The number densities of ground- and 4P-state boron are computed. The density of ground-state boron is shown to be a factor of about 30 less than the plasma density. The density of the excited state is shown to be about three orders of magnitude less than that of the ground state, indicating that electron impact excitation does not significantly affect the density of ground-state boron in the discharge channel or near-field plume of a Hall thruster. Comparing the rates of excitation and ionization suggests that ionization has a greater influence on the density of ground-state boron, but is still negligible. The ground-state boron density is then integrated and compared to cavity ring-down spectroscopy (CRDS) measurements for each operating point. The simulation results show good agreement with the measurements for all operating points and provide evidence in support of CRDS as a tool for measuring Hall thruster erosion in situ.
Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.
2014-01-01
We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing native-like substructures or "foldons". Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R.O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that native-like propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the MD study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo. PMID:23889448
NASA Astrophysics Data System (ADS)
López, Xavier; Rohmer, Marie-Madeleine; Bénard, Marc
2008-11-01
Following the recent findings on heterometallic string complexes, we extend the recently published work on NiPdNi(dpa) 4Cl 2 to discuss the Ni-Pd-Ni and Pd 3 chains with equatorial ligands (L) being dipyridylamide (dpa), 2,6-bis(phenylamido)pyridine (BPAP) and N, N'-bis-( p-toluenesulfonyl)-pyridyldiamide (Lpts), using the DFT formalism. The analysis of such a hypothetical series of linear trimetallics anticipates that, for NiPdNi(dpa) 4Cl 2, the extended valence shell of palladium strengthens the antiferromagnetic coupling between high-spin terminal nickel atoms. For L = BPAP the system, as expected, becomes diamagnetic, and antiferromagnetism reappears for L = Lpts. The theoretical modelling of the coupling following the Heisenberg Hamiltonian applied to two magnetic centres (H^=-2JS·S) gives -2 J = 320 and 497 cm -1 for L = dpa and Lpts, respectively. Pd 3 chains display an enhanced tendency to be diamagnetic with various ligands. More specifically with dpa, Pd 3(dpa) 4Cl 2—should it be synthesized—could be magnetically inactive since the strongly antiferromagnetic state generated by the coupling of two terminal, high-spin Pd atoms (-2 J = 1393 cm -1) is computed to be in close competition with the diamagnetic, closed-shell state. For L = Lpts as for BPAP, the hypothetic [Pd 3] 6+ chain is predicted to be diamagnetic, resulting from the high energy of the antibonding d(Pd)-p(N) orbital. The shift toward diamagnetism induced by the replacement of Ni by Pd in terminal position is therefore assigned to a stronger N → M donation interaction with M = Pd.
Atomic and molecular supernovae
Liu, W.
1997-12-01
Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.
Atomic and molecular supernovae
NASA Technical Reports Server (NTRS)
Liu, Weihong
1997-01-01
Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.
NASA Astrophysics Data System (ADS)
Mančev, Ivan
2007-05-01
The four-body continuum-distorted-wave model is formulated and used to investigate single electron capture in fast collisions of hydrogenlike projectiles with one- and multi-electron targets. The presented method of an analytical calculation of scattering integrals yields the total cross sections in terms of four-dimensional numerical quadratures. As an illustration, total cross sections are computed for electron capture processes in He+-H , He+-He , and Li2+-He collisions at intermediate and high impact energies. The contribution from the interelectron interaction during the collision is evaluated. The prior and post total cross sections are found to be in good agreement with the available experimental data.
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
An extended soft-cube model for the thermal accommodation of gas atoms on solid surfaces
NASA Technical Reports Server (NTRS)
Burke, J. R.; Hollenbach, D. J.
1980-01-01
A numerical soft cube model was developed for calculating thermal accommodation coefficients alpha and trapping fractions f sub t for the interaction of gases incident upon solid surfaces. A semiempirical correction factor c which allows the calculation of alpha and f sub t when the collision times are long compared to the surface oscillator period were introduced. The processes of trapping, evaporation, and detailed balancing were discussed. The numerical method was designed to treat economically and with moderate (+ or - 20 percent) accuracy the dependence of alpha and f sub t on finite and different surface and gas temperatures for a large number of gas/surface combinations. Comparison was made with experiments of rare gases on tungsten and on alkalis, as well as one astrophysical case of H2 on graphite. The dependence of alpha on the soft cube dimensionless parameters is presented graphically.
Atomic kinetic Monte Carlo modeling of multi-component Fe dilute alloys under irradiation
NASA Astrophysics Data System (ADS)
Domain, C.; Becquart, C. S.
2014-06-01
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 multiscale 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 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.
Wallace, Rodrick
2015-08-01
The stabilization of human cognition via feedback from embedding social and cultural contexts is a dynamic process deeply intertwined with it, constituting, in a sense, the riverbanks directing the flow of a stream of generalized consciousness at different scales: Cultural norms and social interaction are synergistic with individual and group cognition and their disorders. A canonical failure mode in atomistic cultures is found to be a 'ground state' collapse well represented by atomistic models of economic interaction that are increasingly characterized as divorced from reality by heterodox economists. That is, high rates of psychopathic and antisocial personality disorder and obsessive compulsive disorder emerge as culture-bound syndromes particular to Western or Westernizing societies, or to those undergoing social disintegration. PMID:26003470
Mass predictions of atomic nuclei in the infinite nuclear matter model
NASA Astrophysics Data System (ADS)
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.
Mass predictions of atomic nuclei in the infinite nuclear matter model
Nayak, R.C.; Satpathy, L.
2012-07-15
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{<=}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 {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 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 {sup 31}Na and {sup 62}Ti. 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.
NASA Astrophysics Data System (ADS)
Merten, D.; Heitland, P.; Broekaert, J. A. C.
1997-11-01
This paper is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta, Part B (SAB). This hardcopy text, comprising the main body and an appendix, is accompanied by a disk with programs, data files and a brief manual. The main body discusses purpose, design principle and usage of the computer software for modelling the evaporation behaviour of particles in inductively coupled plasma atomic emission spectrometry (ICP-AES). Computer software has been developed in FORTRAN 77 language in order to simulate the evaporation behaviour of particles of refractory materials such as encountered in the analysis of advanced ceramic powders by slurry nebulization inductively coupled argon plasma atomic spectrometry. The program simulates the evaporation of single particles in the inductively coupled plasma and also enable it to calculate on the base of a given particle size distribution the evaporation behaviour of all the particles contained in a sample. In a so-called "intensity concept", the intensity is calculated as a function of the observation height in order to determine recovery rates for slurries compared with aqueous solutions. This yields a quick insight whether a calibration with aqueous solutions can be used for analysis of slurries of a given powder by slurry nebulization ICP-AES and also is a help in determining the optimal parameters for analyses of powders by means of slurry nebulization ICP-AES. Applications for the evaporation of Al 2O 3 and SiC powders document the usefulness of the model for the case of a 1.5 kW argon ICP of which the temperature at 8 mm above the load coil has been determined to be 6100 K. The model predicts the maximum particle size for SiC and Al 2O 3 that can be transported (10-15 μm) and evaporated for a given efficiency under given experimental conditions. For both Al 2O 3 and SiC, two ceramic powders of different grain size were investigated. The median particle sizes cover
Chaloosi, Marzieh; Asadollahi, Seyed Azadeh; Khanchi, Ali Reza; FirozZare, Mahmoud; Mahani, Mohamad Khayatzadeh
2009-01-01
A partial least-squares (PLS) calibration model was developed for simultaneous multicomponent elemental analysis with inductively coupled plasma-atomic emission spectrometry (ICP-AES) in the presence of spectral interference. The best calibration model was obtained using a PLS2 algorithm. Validation was performed with an artificial test set. Multivariate calibration models were constructed using 2 series of synthetic mixtures (Zn, Cu, Fe, and U, V). Accuracy of the method was evaluated with unknown synthetic and real samples. PMID:19382589
NASA Astrophysics Data System (ADS)
Cail, Tracy L.; Hochella, Michael F.
2005-06-01
Atomic force microscopy (AFM) and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory in combination with the interaction force boundary layer (IFBL) model have been used to empirically and theoretically calculate sticking efficiencies (α) of Enterococcus faecalis cells against a silica glass surface. Sticking efficiencies were calculated in solutions of varying pH and ionic strength and related to maximum distances of transport through a hypothetical soil block using colloid filtration theory. AFM measurements show that the repulsive and attractive forces between E. faecalis cells and a glass surface are a function of ionic strength but are less sensitive to changes in solution pH. Zeta (ζ)-potential measurements of the cells and glass surfaces correlate with these trends. Calculated DLVO energy profiles predict much greater sensitivity to changing solution chemistry. Sticking efficiencies derived from AFM measurements range from 9.6 × 10 -17 to 1 in solutions of low ionic strength (IS) and from 2.6 × 10 -33 to 1 at higher IS. Corresponding α values determined from DLVO theory are essentially zero in all tested solutions. Sticking efficiencies calculated in this study are smaller than values determined from column and field studies in similar systems; however, α derived from AFM data and the IFBL model more closely represent field data than do values calculated from DLVO energy values. A comparison with different methods of calculating α suggests that reversible adhesion may be significant in column-scale transport studies.
NASA Astrophysics Data System (ADS)
Ramos, E.; Silva-Valencia, J.; Franco, R.; Siqueira, E. C.; Figueira, M. S.
2015-11-01
We study the spin-current Seebeck effect through an immersed gate defined quantum dot, employing the U-finite atomic method for the single impurity Anderson model. Our description qualitatively confirms some of the results obtained by an earlier Hartree-Fock work, but as our calculation includes the Kondo effect, some new features will appear in the spin-current Seebeck effect S, which as a function of the gate voltage present an oscillatory shape. At intermediate temperatures, our results show a three zero structure and at low temperatures, our results are governed by the emergence of the Kondo peak in the transmittance, which defines the behavior of the shape of the S coefficient as a function of the parameters of the model. The oscillatory behavior obtained by the Hartree-Fock approximation reproduces the shape obtained by us in a non-interacting system (U=0). The S sign is sensitive to different polarization of the quantum dot, and as a consequence the device could be employed to experimentally detect the polarization states of the system. Our results also confirm that the large increase of S upon increasing U, obtained by the mean field approximation, is correct only for low temperatures. We also discuss the role of the Kondo peak in defining the behavior of the spin thermopower at low temperatures.
NASA Astrophysics Data System (ADS)
Zatsarinny, Oleg; Bartschat, Klaus; Babaeva, Natalia; Kushner, Mark
2014-10-01
The B-spline R-matrix (BSR) with pseudostates method was employed to describe electron collisions with cesium atoms. Over 300 states were kept in the close-coupling expansion, including a large number of pseudostates to model the effect of the Rydberg spectrum and the ionization continuum on the results for transitions between the discrete physical states of interest. Predictions for elastic scattering, excitation, and ionization for incident energies up to 200 eV are presented and compared to previous results [2,3] and experimental data. Our data were used to model plasma formation in the excimer-pumped alkali laser, XPAL, operating on the Cs (62P3 / 2 , 1 / 2 --> (62S1 / 2) (852nm and 894nm) transitions. At sufficiently high operating temperature, pump power, and repetition rate, plasma formation in excess of 1014--1015cm-3 occurs. This may reduce laser output power by electron collisional mixing of the upper and lower laser levels. Work supported by the NSF under PHY-1068140, PHY-1212450, and the XSEDE allocation PHY-090031 (OZ, KB), and by the DoD High Energy Laser Multidisciplinary Research Initiative (NYB, MJK).
Yuqin, Li; Guirong, You; Zhen, Yang; Caihong, Liu; Baoxiu, Jia; Jiao, Chen; Yurong, Guo
2014-01-01
The interaction of patulin with human serum albumin (HSA) was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis), circular dichroism (CD), atomic force microscopy (AFM), and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K) were 2.60 × 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. PMID:25110690
Nguyen, Hung T.; Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois; Case, David A.
2014-12-14
A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb{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.
NASA Astrophysics Data System (ADS)
Nguyen, Hung T.; Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois; Case, David A.
2014-12-01
A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb+ and Sr2+) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein-Zernike equations, with results from the Kovalenko-Hirata closure being closest to experiment for the cases studied here.
NASA Astrophysics Data System (ADS)
March, N. H.; Angilella, G. G. N.; Pucci, R.
2013-10-01
The review begins with a consideration of three forms of quantum information entropy associated with Shannon and Jaynes. For model two-electron spin compensated systems, some analytic progress is first reported. The Jaynes entropy is clearly related to correlation kinetic energy. A way of testing the usefulness of a known uncertainty principle inequality is proposed for a whole class of model two-electron atoms with harmonic confinement but variable electron-electron interaction. Emerging properties are then studied by reference to bcc Na at ambient pressure and its modeling by "jellium". Jellium itself has collective behavior with changes of the density, especially noteworthy being the discontinuity of the momentum distribution at the Fermi surface. This has almost reduced to zero at rs = 100 a.u., the neighborhood in which the quantal Wigner electron solid transition is known to occur. However, various workers have studied crystalline Na under pressure and their results are compared and contrasted. Work by DFT on K, Rb and Cs is discussed, but now with reduced density from the ambient pressure value. The crystalline results for the cohesive energy of these metals as a function of lattice parameters and local coordination number are shown to be closely reproduced by means of ground and excited states for dimer potential energy curves. Then, pair potentials for liquid Na and Be are reviewed, and compared with the results of computer simulations from the experimental structure factor for Na. Finally, magnetic field effects are discussed. First a phenomenological model of the metal-to-insulator transition is presented with an order parameter which is the discontinuity in the Fermi momentum distribution. Lastly, experiments on a two-dimensional electron assembly in a GaAs/AlGaAs heterojunction in a perpendicular magnetic field are briefly reviewed and then interpreted.