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…
Tsekov, R
2014-01-01
The finite size effect of electron and nucleus is accounted for in the model of atom. Due to their hard sphere repulsion the energy of the 1s orbital decreases and the corrections amount up to 8 % in Uranium. Several models for boundary conditions on the atomic nucleus surface are discussed as well.
Stochastic models for atomic clocks
Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.
1983-01-01
For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.
A Quantum Model of Atoms (the Energy Levels of Atoms).
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.
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Outlines an alternative atomic model to the probability model, the descriptive quantum atomic model Electronium. Discusses the way in which it is intended to support students in learning quantum-mechanical concepts. (Author/MM)
Can atom-surface potential measurements test atomic structure models?
Lonij, Vincent P A; Klauss, Catherine E; Holmgren, William F; Cronin, Alexander D
2011-06-30
van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C₃(K)/C₃(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C₃ ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C₃ ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C₃ values that depends more strongly on the permittivity of the surface.
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.
Students' Mental Models of Atomic Spectra
Körhasan, Nilüfer Didis; Wang, Lu
2016-01-01
Mental modeling, which is a theory about knowledge organization, has been recently studied by science educators to examine students' understanding of scientific concepts. This qualitative study investigates undergraduate students' mental models of atomic spectra. Nine second-year physics students, who have already taken the basic chemistry and…
Atomic model of liquid pure Fe
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Using a θ-θX-ray diffractometer, the liquid structure of pure Fewas investigated and the diffraction intensity, structure factor, pair distribution function as well as the coordination number and atomic distance were obtained. The experimental results showed that there was also a pre-peak on the curve of the structure factor of liquid pure Fe. The pre-peak is a mark of medium-range order in melts. According to the characteristics of pre-peak, an atomic model of liquid pure Fe is constructed, namely, the structure of liquid pure Fe is a combination of clusters consisting of bcc cells with shared vertexes and other atoms with random dense atom distribution.
Contemporary models of the atomic nucleus
Nemirovskii, P E
2013-01-01
Contemporary Models of the Atomic Nucleus discusses nuclear structure and properties, expounding contemporary theoretical concepts of the low-energy nuclear processes underlying in nuclear models. This book focuses on subjects such as the optical nuclear model, unified or collective model, and deuteron stripping reaction. Other topics discussed include the basic nuclear properties; shell model; theoretical analysis of the shell model; and radiative transitions and alpha-decay. The deuteron theory and the liquid drop nuclear model with its application to fission theory are also mentioned, but o
Jaynes-Cummings model with a collective atomic mode
Zheng, Shi-Biao
2012-01-01
We study the dynamics of a single control atom and an atomic sample interacting with a nonresonant cavity mode. The control atom is driven by an auxiliary classical field. Under certain conditions, the coherent energy exchange between the control atom and the atomic sample induced by the cavity mode is described by the Jaynes-Cummings model. The idea provides a possibility for quantum-state engineering and reconstruction for collective atomic modes.
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.
Atom-Role-Based Access Control Model
Cai, Weihong; Huang, Richeng; Hou, Xiaoli; Wei, Gang; Xiao, Shui; Chen, Yindong
Role-based access control (RBAC) model has been widely recognized as an efficient access control model and becomes a hot research topic of information security at present. However, in the large-scale enterprise application environments, the traditional RBAC model based on the role hierarchy has the following deficiencies: Firstly, it is unable to reflect the role relationships in complicated cases effectively, which does not accord with practical applications. Secondly, the senior role unconditionally inherits all permissions of the junior role, thus if a user is under the supervisor role, he may accumulate all permissions, and this easily causes the abuse of permission and violates the least privilege principle, which is one of the main security principles. To deal with these problems, we, after analyzing permission types and role relationships, proposed the concept of atom role and built an atom-role-based access control model, called ATRBAC, by dividing the permission set of each regular role based on inheritance path relationships. Through the application-specific analysis, this model can well meet the access control requirements.
Making It Visual: Creating a Model of the Atom
Pringle, Rose M.
2004-01-01
This article describes a lesson in which students construct Bohr's planetary model of the atom. Niels Bohr's atomic model provides a framework for discussing with middle and high school students the historical development of our understanding of the structure of the atom. The model constructed in this activity will enable students to visualize the…
Cipolla, Laura; Ferrari, Lia A.
2016-01-01
A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).
Computer Model Of Fragmentation Of Atomic Nuclei
Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.
1995-01-01
High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.
Calculation of Al-Zn diagram from central atoms model
Institute of Scientific and Technical Information of China (English)
无
1999-01-01
A slightly modified central atoms model was proposed. The probabilities of various clusters with the central atoms and their nearest neighboring shells can be calculated neglecting the assumption of the param eter of energy in the central atoms model in proportion to the number of other atoms i (referred with the central atom). A parameter Pα is proposed in this model, which equals to reciprocal of activity coefficient of a component, therefore, the new model can be understood easily. By this model, the Al-Zn phase diagram and its thermodynamic properties were calculated, the results coincide with the experimental data.
The two-atom Jaynes-Cummings model's dynamic properties
Institute of Scientific and Technical Information of China (English)
无
2003-01-01
The model of two two-level atoms interact with a single-mode cavity was investigated. The formulation of the time evolution operator for the two-atom Jaynes-Cummings model is pressented by the bare-states approach. Besides, the time evolution of the two-atom common population probabilities is studied, and some novel features are obtained.
Harmonic oscillator model for the helium atom
Carlsen, Martin
2015-01-01
A harmonic oscillator model in four dimensions is presented for the helium atom to estimate the distance to the inner and outer electron from the nucleus, the angle between electrons and the energy levels. The method is algebraic and is not based on the choice of correct trial wave function. Three harmonic oscillators and thus three quantum numbers are sufficient to describe the two-electron system. We derive a simple formula for the energy in the general case and in the special case of the Wannier Ridge. For a set of quantum numbers the distance to the electrons and the angle between the electrons are uniquely determined as the intersection between three surfaces. We show that the excited states converge either towards ionization thresholds or towards extreme parallel or antiparallel states and provide an estimate of the ground state energy.
Atomic force microscopy of model lipid membranes.
Morandat, Sandrine; Azouzi, Slim; Beauvais, Estelle; Mastouri, Amira; El Kirat, Karim
2013-02-01
Supported lipid bilayers (SLBs) are biomimetic model systems that are now widely used to address the biophysical and biochemical properties of biological membranes. Two main methods are usually employed to form SLBs: the transfer of two successive monolayers by Langmuir-Blodgett or Langmuir-Schaefer techniques, and the fusion of preformed lipid vesicles. The transfer of lipid films on flat solid substrates offers the possibility to apply a wide range of surface analytical techniques that are very sensitive. Among them, atomic force microscopy (AFM) has opened new opportunities for determining the nanoscale organization of SLBs under physiological conditions. In this review, we first focus on the different protocols generally employed to prepare SLBs. Then, we describe AFM studies on the nanoscale lateral organization and mechanical properties of SLBs. Lastly, we survey recent developments in the AFM monitoring of bilayer alteration, remodeling, or digestion, by incubation with exogenous agents such as drugs, proteins, peptides, and nanoparticles.
Operation of the computer model for microenvironment atomic oxygen exposure
Bourassa, R. J.; Gillis, J. R.; Gruenbaum, P. E.
1995-01-01
A computer model for microenvironment atomic oxygen exposure has been developed to extend atomic oxygen modeling capability to include shadowing and reflections. The model uses average exposure conditions established by the direct exposure model and extends the application of these conditions to treat surfaces of arbitrary shape and orientation.
An atomic model for neutral and singly ionized uranium
Maceda, E. L.; Miley, G. H.
1979-01-01
A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.
Effect of energetic oxygen atoms on neutral density models.
Rohrbaugh, R. P.; Nisbet, J. S.
1973-01-01
The dissociative recombination of O2(+) and NO(+) in the F region results in the production of atomic oxygen and atomic nitrogen with substantially greater kinetic energy than the ambient atoms. In the exosphere these energetic atoms have long free paths. They can ascend to altitudes of several thousand kilometers and can travel horizontally to distances of the order of the earth's radius. The distribution of energetic oxygen atoms is derived by means of models of the ion and neutral densities for quiet and disturbed solar conditions. A distribution technique is used to study the motion of the atoms in the collision-dominated region. Ballistic trajectories are calculated in the spherical gravitational field of the earth. The present calculations show that the number densities of energetic oxygen atoms predominate over the ambient atomic oxygen densities above 1000 km under quiet solar conditions and above 1600 km under disturbed solar conditions.
Institute of Scientific and Technical Information of China (English)
刘洪毓
2007-01-01
Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what
INFERNO - A better model of atoms in dense plasmas
Liberman, D. A.
1982-03-01
A self-consistent field model of atoms in dense plasmas has been devised and incorporated in a computer program. In the model there is a uniform positive charge distribution with a hole in it and at the center of the hole an atomic nucleus. There are electrons, in both bound and continuum states, in sufficient number to form an electrically neutral system. The Dirac equation is used so that high Z atoms can be dealt with. A finite temperature is assumed, and a mean field (average atom) approximation is used in statistical averages. Applications have been made to equations of states and to photoabsorption.
The Quantum Atomic Model "Electronium": A Successful Teaching Tool.
Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John
2002-01-01
Focuses on the quantum atomic model Electronium. Outlines the Bremen teaching approach in which this model is used, and analyzes the learning of two students as they progress through the teaching unit. (Author/MM)
Project Physics Tests 5, Models of the Atom.
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,…
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter
2004-01-01
framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....
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.
Analytic Solutions of Three-Level Dressed-Atom Model
Institute of Scientific and Technical Information of China (English)
WANG Zheng-Ling; YIN Jian-Ping
2004-01-01
On the basis of the dressed-atom model, the general analytic expressions for the eigenenergies, eigenstates and their optical potentials of the A-configuration three-level atom system are derived and analysed. From the calculation of dipole matrix element of different dressed states, we obtain the spontaneous-emission rates in the dressed-atom picture. We find that our general expressions of optical potentials for the three-level dressed atom can be reduced to the same as ones in previous references under the approximation of a small saturation parameter. We also analyse the dependences of the optical potentials of a three-level 85Rb atom on the laser detuning and the dependences of spontaneous-emission rates on the radial position in the dark hollow beam, and discuss the probability (population) evolutions of dressed-atomic eigenstates in three levels in the hollow beam.
Woo Kim, Hyun; Rhee, Young Min
2012-07-30
Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability.
A liquid drop model for embedded atom method cluster energies
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.
Muller, Christophe; Marcou, Gilles; Horvath, Dragos; Aires-de-Sousa, João; Varnek, Alexandre
2012-12-21
Machine learning (SVM and JRip rule learner) methods have been used in conjunction with the Condensed Graph of Reaction (CGR) approach to identify errors in the atom-to-atom mapping of chemical reactions produced by an automated mapping tool by ChemAxon. The modeling has been performed on the three first enzymatic classes of metabolic reactions from the KEGG database. Each reaction has been converted into a CGR representing a pseudomolecule with conventional (single, double, aromatic, etc.) bonds and dynamic bonds characterizing chemical transformations. The ChemAxon tool was used to automatically detect the matching atom pairs in reagents and products. These automated mappings were analyzed by the human expert and classified as "correct" or "wrong". ISIDA fragment descriptors generated for CGRs for both correct and wrong mappings were used as attributes in machine learning. The learned models have been validated in n-fold cross-validation on the training set followed by a challenge to detect correct and wrong mappings within an external test set of reactions, never used for learning. Results show that both SVM and JRip models detect most of the wrongly mapped reactions. We believe that this approach could be used to identify erroneous atom-to-atom mapping performed by any automated algorithm.
Toward an anisotropic atom-atom model for the crystalline phases of the molecular S8 compound
Pastorino, C.; Gamba, Z.
2000-01-01
We analize two anisotropic atom-atom models used to describe the crystalline alpha,beta and gamma phases of S8 crystals, the most stable compound of elemental sulfur in solid phases, at ambient pressure and T
Alpha-cluster model of atomic nuclei
Energy Technology Data Exchange (ETDEWEB)
Sosin, Zbigniew; Kallunkathariyil, Jinesh [Jagiellonian University, M. Smoluchowski Institute of Physics, Krakow (Poland); Blocki, Jan [NCBJ, Theoretical Physics Division (BP2), Swierk (Poland); Lukasik, Jerzy; Pawlowski, Piotr [IFJ PAN, Krakow (Poland)
2016-05-15
The description of a nuclear system in its ground state and at low excitations based on the equation of state (EoS) around normal density is presented. In the expansion of the EoS around the saturation point, additional spin polarization terms are taken into account. These terms, together with the standard symmetry term, are responsible for the appearance of the α-like clusters in the ground-state configurations of the N=Z even-even nuclei. At the nuclear surface these clusters can be identified as alpha particles. A correction for the surface effects is introduced for atomic nuclei. Taking into account an additional interaction between clusters the binding energies and sizes of the considered nuclei are very accurately described. The limits of the EoS parameters are established from the properties of the α, {sup 3}He and t particles. (orig.)
An extension of dynamic droplet deformation models to secondary atomization
Bartz, F.O.; Schmehl, R.; Koch, R.; Bauer, H.J.
2010-01-01
A detailed model for secondary atomization of liquid droplets by aerodynamic forces is presented. As an empirical extension of dynamic droplet deformation models, it accounts for temporal variations of the relative velocity between droplet and gas phase during the deformation and breakup process and
Hirshfeld atom refinement for modelling strong hydrogen bonds.
Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon
2014-09-01
High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.
Physically representative atomistic modeling of atomic-scale friction
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
Modeling noncontact atomic force microscopy resolution on corrugated surfaces
Directory of Open Access Journals (Sweden)
Kristen M. Burson
2012-03-01
Full Text Available Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid. The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.
Gas Atomization of Aluminium Melts: Comparison of Analytical Models
Directory of Open Access Journals (Sweden)
Georgios Antipas
2012-06-01
Full Text Available A number of analytical models predicting the size distribution of particles during atomization of Al-based alloys by N2, He and Ar gases were compared. Simulations of liquid break up in a close coupled atomizer revealed that the finer particles are located near the center of the spray cone. Increasing gas injection pressures led to an overall reduction of particle diameters and caused a migration of the larger powder particles towards the outer boundary of the flow. At sufficiently high gas pressures the spray became monodisperse. The models also indicated that there is a minimum achievable mean diameter for any melt/gas system.
Modeling sympathetic cooling of molecules by ultracold atoms
Lim, Jongseok; Hutson, Jeremy M; Tarbutt, M R
2015-01-01
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 are less sensitive to the exact value of the s-wave scattering length when Rb is used. Using realistic experimental parameters, we find th...
Atomic-scale modeling of cellulose nanocrystals
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
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.
Model based control of dynamic atomic force microscope
Energy Technology Data Exchange (ETDEWEB)
Lee, Chibum [Department of Mechanical System Design Engineering, Seoul National University of Science and Technology, Seoul 139-743 (Korea, Republic of); Salapaka, Srinivasa M., E-mail: salapaka@illinois.edu [Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)
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.
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
Energy Technology Data Exchange (ETDEWEB)
Quan, Wei; Lv, Lin, E-mail: lvlinlch1990@163.com; Liu, Baiqi [School of Instrument Science and Opto-Electronics Engineering, Beihang University, Beijing 100191 (China)
2014-11-15
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Quan, Wei; Lv, Lin; Liu, Baiqi
2014-11-01
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
Quan, Wei; Lv, Lin; Liu, Baiqi
2014-11-01
In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.
Chen, Chunxia; Depa, Praveen; Sakai, Victoria García; Maranas, Janna K; Lynn, Jeffrey W; Peral, Inmaculada; Copley, John R D
2006-06-21
We compare static and dynamic properties obtained from three levels of modeling for molecular dynamics simulation of poly(ethylene oxide) (PEO). Neutron scattering data are used as a test of each model's accuracy. The three simulation models are an explicit atom (EA) model (all the hydrogens are taken into account explicitly), a united atom (UA) model (CH(2) and CH(3) groups are considered as a single unit), and a coarse-grained (CG) model (six united atoms are taken as one bead). All three models accurately describe the PEO static structure factor as measured by neutron diffraction. Dynamics are assessed by comparison to neutron time of flight data, which follow self-motion of protons. Hydrogen atom motion from the EA model and carbon/oxygen atom motion from the UA model closely follow the experimental hydrogen motion, while hydrogen atoms reinserted in the UA model are too fast. The EA and UA models provide a good description of the orientation properties of C-H vectors measured by nuclear magnetic resonance experiments. Although dynamic observables in the CG model are in excellent agreement with their united atom counterparts, they cannot be compared to neutron data because the time after which the CG model is valid is greater than the neutron decay times.
Application of the model of delocalized atoms to metallic glasses
Sanditov, D. S.; Darmaev, M. V.; Sanditov, B. D.
2017-01-01
The parameters of the model of delocalized atoms applied to metallic glasses have been calculated using the data on empirical constants of the Vogel-Fulcher-Tammann equation (for the temperature dependence of viscosity). It has been shown that these materials obey the same glass-formation criterion as amorphous organic polymers and inorganic glasses. This fact qualitatively confirms the universality of the main regularities of the liquid-glass transition process for all amorphous materials regardless of their origin. The energy of the delocalization of an atom in metallic glasses, Δɛ e ≈ 20-25 kJ/mol, coincides with the results obtained for oxide inorganic glasses. It is substantially lower than the activation energies for a viscous flow and for ion diffusion. The delocalization of an atom (its displacement from the equilibrium position) for amorphous metallic alloys is a low-energy small-scale process similar to that for other glass-like systems.
Theory and modelling of diamond fracture from an atomic perspective.
Brenner, Donald W; Shenderova, Olga A
2015-03-28
Discussed in this paper are several theoretical and computational approaches that have been used to better understand the fracture of both single-crystal and polycrystalline diamond at the atomic level. The studies, which include first principles calculations, analytic models and molecular simulations, have been chosen to illustrate the different ways in which this problem has been approached, the conclusions and their reliability that have been reached by these methods, and how these theory and modelling methods can be effectively used together.
A constructive model potential method for atomic interactions
Bottcher, C.; Dalgarno, A.
1974-01-01
A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.
AtomDB and PyAtomDB: Atomic Data and Modelling Tools for High Energy and Non-Maxwellian Plasmas
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.
CHARMM36 united atom chain model for lipids and surfactants.
Lee, Sarah; Tran, Alan; Allsopp, Matthew; Lim, Joseph B; Hénin, Jérôme; Klauda, Jeffery B
2014-01-16
Molecular simulations of lipids and surfactants require accurate parameters to reproduce and predict experimental properties. Previously, a united atom (UA) chain model was developed for the CHARMM27/27r lipids (Hénin, J., et al. J. Phys. Chem. B. 2008, 112, 7008-7015) but suffers from the flaw that bilayer simulations using the model require an imposed surface area ensemble, which limits its use to pure bilayer systems. A UA-chain model has been developed based on the CHARMM36 (C36) all-atom lipid parameters, termed C36-UA, and agreed well with bulk, lipid membrane, and micelle formation of a surfactant. Molecular dynamics (MD) simulations of alkanes (heptane and pentadecane) were used to test the validity of C36-UA on density, heat of vaporization, and liquid self-diffusion constants. Then, simulations using C36-UA resulted in accurate properties (surface area per lipid, X-ray and neutron form factors, and chain order parameters) of various saturated- and unsaturated-chain bilayers. When mixed with the all-atom cholesterol model and tested with a series of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/cholesterol mixtures, the C36-UA model performed well. Simulations of self-assembly of a surfactant (dodecylphosphocholine, DPC) using C36-UA suggest an aggregation number of 53 ± 11 DPC molecules at 0.45 M of DPC, which agrees well with experimental estimates. Therefore, the C36-UA force field offers a useful alternative to the all-atom C36 lipid force field by requiring less computational cost while still maintaining the same level of accuracy, which may prove useful for large systems with proteins.
Empirical model of atomic nitrogen in the upper thermosphere
Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.
1977-01-01
Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.
Extended Hubbard models for ultracold atoms in optical lattices
Energy Technology Data Exchange (ETDEWEB)
Juergensen, Ole
2015-06-05
In this thesis, the phase diagrams and dynamics of various extended Hubbard models for ultracold atoms in optical lattices are studied. Hubbard models are the primary description for many interacting particles in periodic potentials with the paramount example of the electrons in solids. The very same models describe the behavior of ultracold quantum gases trapped in the periodic potentials generated by interfering beams of laser light. These optical lattices provide an unprecedented access to the fundamentals of the many-particle physics that govern the properties of solid-state materials. They can be used to simulate solid-state systems and validate the approximations and simplifications made in theoretical models. This thesis revisits the numerous approximations underlying the standard Hubbard models with special regard to optical lattice experiments. The incorporation of the interaction between particles on adjacent lattice sites leads to extended Hubbard models. Offsite interactions have a strong influence on the phase boundaries and can give rise to novel correlated quantum phases. The extended models are studied with the numerical methods of exact diagonalization and time evolution, a cluster Gutzwiller approximation, as well as with the strong-coupling expansion approach. In total, this thesis demonstrates the high relevance of beyond-Hubbard processes for ultracold atoms in optical lattices. Extended Hubbard models can be employed to tackle unexplained problems of solid-state physics as well as enter previously inaccessible regimes.
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…
A Comprehensive X-Ray Absorption Model for Atomic Oxygen
Gorczyca, T. W.; Bautista, M. A.; Hasoglu, M. F.; Garcia, J.; Gatuzz, E.; Kaastra, J. S.; Kallman, T. R.; Manson, S. T.; Mendoza, C.; Raassen, A. J. J.; de Vries, C. P.; Zatsarinny, O.
2013-01-01
An analytical formula is developed to accurately represent the photoabsorption cross section of atomic Oxygen for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects, that accurately predict the absorption oscillator strengths below threshold and merge consistently and continuously to the above-threshold cross section. Further, minor adjustments are made to the threshold energies in order to reliably align the atomic Rydberg resonances after consideration of both experimental and observed line positions. At energies far below or above the K-edge region, the formulation is based on both outer- and inner-shell direct photoionization, including significant shake-up and shake-off processes that result in photoionization-excitation and double-photoionization contributions to the total cross section. The ultimate purpose for developing a definitive model for oxygen absorption is to resolve standing discrepancies between the astronomically observed and laboratory-measured line positions, and between the inferred atomic and molecular oxygen abundances in the interstellar medium from XSTAR and SPEX spectral models.
Four-component united-atom model of bitumen
DEFF Research Database (Denmark)
Hansen, Jesper Schmidt; Lemarchand, Claire; Nielsen, Erik
2013-01-01
We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based...... software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation...... the stress autocorrelation function, the shear viscosity and shear modulus are evaluated, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin...
Chemical domain of QSAR models from atom-centered fragments.
Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit
2009-12-01
A methodology to characterize the chemical domain of qualitative and quantitative structure-activity relationship (QSAR) models based on the atom-centered fragment (ACF) approach is introduced. ACFs decompose the molecule into structural pieces, with each non-hydrogen atom of the molecule acting as an ACF center. ACFs vary with respect to their size in terms of the path length covered in each bonding direction starting from a given central atom and how comprehensively the neighbor atoms (including hydrogen) are described in terms of element type and bonding environment. In addition to these different levels of ACF definitions, the ACF match mode as degree of strictness of the ACF comparison between a test compound and a given ACF pool (such as from a training set) has to be specified. Analyses of the prediction statistics of three QSAR models with their training sets as well as with external test sets and associated subsets demonstrate a clear relationship between the prediction performance and the levels of ACF definition and match mode. The findings suggest that second-order ACFs combined with a borderline match mode may serve as a generic and at the same time a mechanistically sound tool to define and evaluate the chemical domain of QSAR models. Moreover, four standard categories of the ACF-based membership to a given chemical domain (outside, borderline outside, borderline inside, inside) are introduced that provide more specific information about the expected QSAR prediction performance. As such, the ACF-based characterization of the chemical domain appears to be particularly useful for QSAR applications in the context of REACH and other regulatory schemes addressing the safety evaluation of chemical compounds.
Atomic collision processes for modelling cool star spectra
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.
Model study in chemisorption: atomic hydrogen on beryllium clusters
Energy Technology Data Exchange (ETDEWEB)
Bauschlicher, C.W. Jr.
1976-08-01
The interaction between atomic hydrogen and the (0001) surface of Be metal has been studied by ab initio electronic structure theory. Self-consistent-field (SCF) calculations have been performed using minimum, optimized minimum, double zeta and mixed basis sets for clusters as large as 22 Be atoms. The binding energy and equilibrium geometry (the distance to the surface) were determined for 4 sites. Both spatially restricted (the wavefunction was constrained to transform as one of the irreducible representations of the molecular point group) and unrestricted SCF calculations were performed. Using only the optimized minimum basis set, clusters containing as many as 22 beryllium atoms have been investigated. From a variety of considerations, this cluster is seen to be nearly converged within the model used, providing the most reliable results for chemisorption. The site dependence of the frequency is shown to be a geometrical effect depending on the number and angle of the bonds. The diffusion of atomic hydrogen through a perfect beryllium crystal is predicted to be energetically unfavorable. The cohesive energy, the ionization energy and the singlet-triplet separation were computed for the clusters without hydrogen. These quantities can be seen as a measure of the total amount of edge effects. The chemisorptive properties are not related to the total amount of edge effects, but rather the edge effects felt by the adsorbate bonding berylliums. This lack of correlation with the total edge effects illustrates the local nature of the bonding, further strengthening the cluster model for chemisorption. A detailed discussion of the bonding and electronic structure is included. The remaining edge effects for the Be/sub 22/ cluster are discussed.
Sudden birth of entanglement between two atoms in a double JC model
Institute of Scientific and Technical Information of China (English)
Mingdi Du; Maofa Fang; Xiang Liu
2009-01-01
Sudden birth of entanglement between two initially separate atoms interacting with two entangled photons in a double JC model is investigated,arid the influences of different atomic initial states on entanglement among atoms are discussed.The results show that sudden birth of entanglement can occur when the two atoms are initially in excited states.
Lattice location of dopant atoms: An -body model calculation
Indian Academy of Sciences (India)
N K Deepak
2010-03-01
The channelling and scattering yields of 1 MeV -particles in the $\\langle 1 0 0 \\rangle$, $\\langle 1 1 0 \\rangle and $\\langle 1 1 1 \\rangle$ directions of silicon implanted with bismuth and ytterbium have been simulated using -body model. The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and Fontenille method. All previous works reported in literature so far have been done with computer programmes using a statistical analytical expression or by a binary collision model or a continuum model. These results at the best gave only the transverse displacement of the lattice site from the concerned channelling direction. Here we applied the superior -body model to study the yield from bismuth in silicon. The finding that bismuth atom occupies a position close to the silicon substitutional site is new. The transverse displacement of the suggested lattice site from the channelling direction is consistent with the experimental results. The above model is also applied to determine the location of ytterbium in silicon. The present values show good agreement with the experimental results.
Atom-field entanglement in two-atom Jaynes-Cummings model with intensity-dependent coupling
Bashkirov, E. K.
2014-01-01
An exact solution of the problem of two-atom one- and two-mode Jaynes-Cummings model with intensity-dependent coupling is presented. Asymptotic solutions for system state vectors are obtained in the approximation of large initial coherent fields. The atom-field entanglement is investigated on the basis of the reduced atomic entropy dynamics. The possibility of the system being initially in a pure disentangled state to revive into this state during the evolution process for both models is show...
Quantum Rabi model in the Brillouin zone with ultracold atoms
Felicetti, Simone; Rico, Enrique; Sabin, Carlos; Ockenfels, Till; Koch, Johannes; Leder, Martin; Grossert, Christopher; Weitz, Martin; Solano, Enrique
2017-01-01
The quantum Rabi model describes the interaction between a two-level quantum system and a single bosonic mode. We propose a method to perform a quantum simulation of the quantum Rabi model, introducing an implementation of the two-level system provided by the occupation of Bloch bands in the first Brillouin zone by ultracold atoms in tailored optical lattices. The effective qubit interacts with a quantum harmonic oscillator implemented in an optical dipole trap. Our realistic proposal allows one to experimentally investigate the quantum Rabi model for extreme parameter regimes, which are not achievable with natural light-matter interactions. When the simulated wave function exceeds the validity region of the simulation, we identify a generalized version of the quantum Rabi model in a periodic phase space.
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.
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.
Fully variational average atom model with ion-ion correlations.
Starrett, C E; Saumon, D
2012-02-01
An average atom model for dense ionized fluids that includes ion correlations is presented. The model assumes spherical symmetry and is based on density functional theory, the integral equations for uniform fluids, and a variational principle applied to the grand potential. Starting from density functional theory for a mixture of classical ions and quantum mechanical electrons, an approximate grand potential is developed, with an external field being created by a central nucleus fixed at the origin. Minimization of this grand potential with respect to electron and ion densities is carried out, resulting in equations for effective interaction potentials. A third condition resulting from minimizing the grand potential with respect to the average ion charge determines the noninteracting electron chemical potential. This system is coupled to a system of point ions and electrons with an ion fixed at the origin, and a closed set of equations is obtained. Solution of these equations results in a self-consistent electronic and ionic structure for the plasma as well as the average ionization, which is continuous as a function of temperature and density. Other average atom models are recovered by application of simplifying assumptions.
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.
Analysis and application of the scale effect of flood discharge atomization model
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
The phenomenon of discharge atomization occurs as hydraulic structures discharging,which influences the safety of power station,electrical equipment and produces environmental pollution.A series of physical model tests and feedback analysis are adapted to preliminarily study the scale effect of discharge atomization model by use of the field observation data of discharge atomization.The effect of Re and We numbers of flow on the atomization intensity is analyzed.A conversion relationship of atomization intensity between prototype and model results and the similarity criteria of the atomization range are developed. The conclusion is that the surface tension of discharge atomization model could be ignored when the Weber number is larger than 500.Some case studies are given by use of the similitude criteria of the atomization model.
Development of a Kohn-Sham like potential in the Self-Consistent Atomic Deformation Model
Mehl, M. J.; Boyer, L. L.; Stokes, H. T.
1996-01-01
This is a brief description of how to derive the local ``atomic'' potentials from the Self-Consistent Atomic Deformation (SCAD) model density function. Particular attention is paid to the spherically averaged case.
Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF
Banks, Bruce A.; Degroh, Kim K.; Auer, Bruce M.; Gebauer, Linda; Edwards, Jonathan L.
1993-01-01
Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) assists in understanding of the mechanisms involved. Thus the reliability of predicting in-space durability of materials based on ground laboratory testing should be improved. A computational model which simulates atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of an assumed mechanistic behavior of atomic oxygen interaction based on in-space atomic oxygen erosion of unprotected polymers and ground laboratory atomic oxygen interaction with protected polymers, prediction of atomic oxygen interaction with protected polymers on LDEF was accomplished. However, the results of these predictions are not consistent with the observed LDEF results at defect sites in protected polymers. Improved agreement between observed LDEF results and predicted Monte Carlo modeling can be achieved by modifying of the atomic oxygen interactive assumptions used in the model. LDEF atomic oxygen undercutting results, modeling assumptions, and implications are presented.
Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity
DEFF Research Database (Denmark)
Gammelmark, S.; Molmer, K.; Alt, W.
2014-01-01
We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic state...... manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory...
Model of spacecraft atomic oxygen and solar exposure microenvironments
Bourassa, R. J.; Pippin, H. G.
1993-01-01
Computer models of environmental conditions in Earth orbit are needed for the following reasons: (1) derivation of material performance parameters from orbital test data, (2) evaluation of spacecraft hardware designs, (3) prediction of material service life, and (4) scheduling spacecraft maintenance. To meet these needs, Boeing has developed programs for modeling atomic oxygen (AO) and solar radiation exposures. The model allows determination of AO and solar ultraviolet (UV) radiation exposures for spacecraft surfaces (1) in arbitrary orientations with respect to the direction of spacecraft motion, (2) overall ranges of solar conditions, and (3) for any mission duration. The models have been successfully applied to prediction of experiment environments on the Long Duration Exposure Facility (LDEF) and for analysis of selected hardware designs for deployment on other spacecraft. The work on these models has been reported at previous LDEF conferences. Since publication of these reports, a revision has been made to the AO calculation for LDEF, and further work has been done on the microenvironments model for solar exposure.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Directory of Open Access Journals (Sweden)
Peter C Lai
2012-05-01
Full Text Available Olfactory receptors (ORs are a type of GTP-binding protein-coupled receptor (GPCR. These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can validate experimental functional studies as well as generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level. Here we have shown the specific advantages of simulating the dynamic environment that is associated with OR-odorant interactions. We present a rigorous methodology that ranges from the creation of a computationally-derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.
Penetration of alkali atoms throughout a graphene membrane: theoretical modeling.
Boukhvalov, D W; Virojanadara, C
2012-03-07
Theoretical studies of penetration of various alkali atoms (Li, Na, Rb, Cs) throughout a graphene membrane grown on a silicon carbide substrate are reported and compared with recent experimental results. Results of first principles modeling demonstrate a rather low (about 0.8 eV) energy barrier for the formation of temporary defects in the carbon layer required for the penetration of Li at a high concentration of adatoms, a higher (about 2 eV) barrier for Na, and barriers above 4 eV for Rb and Cs. Experiments prove migration of lithium adatoms from the graphene surface to the buffer layer and SiC substrate at room temperature, sodium at 100 °C and impenetrability of the graphene membrane for Rb and Cs. Differences between epitaxial and free-standing graphene for the penetration of alkali ions are also discussed.
Independent-particle models for light negative atomic ions
Ganas, P. S.; Talman, J. D.; Green, A. E. S.
1980-01-01
For the purposes of astrophysical, aeronomical, and laboratory application, a precise independent-particle model for electrons in negative atomic ions of the second and third period is discussed. The optimum-potential model (OPM) of Talman et al. (1979) is first used to generate numerical potentials for eight of these ions. Results for total energies and electron affinities are found to be very close to Hartree-Fock solutions. However, the OPM and HF electron affinities both depart significantly from experimental affinities. For this reason, two analytic potentials are developed whose inner energy levels are very close to the OPM and HF levels but whose last electron eigenvalues are adjusted precisely with the magnitudes of experimental affinities. These models are: (1) a four-parameter analytic characterization of the OPM potential and (2) a two-parameter potential model of the Green, Sellin, Zachor type. The system O(-) or e-O, which is important in upper atmospheric physics is examined in some detail.
Modelling laser-atom interactions in the strong field regime
Galstyan, A; Mota-Furtado, F; O'Mahony, P F; Janssens, N; Jenkins, S D; Chuluunbaatar, O; Piraux, B
2016-01-01
We consider the ionisation of atomic hydrogen by a strong infrared field. We extend and study in more depth an existing semi-analytical model. Starting from the time-dependent Schroedinger equation in momentum space and in the velocity gauge we substitute the kernel of the non-local Coulomb potential by a sum of N separable potentials, each of them supporting one hydrogen bound state. This leads to a set of N coupled one-dimensional linear Volterra integral equations to solve. We analyze the gauge problem for the model, the different ways of generating the separable potentials and establish a clear link with the strong field approximation which turns out to be a limiting case of the present model. We calculate electron energy spectra as well as the time evolution of electron wave packets in momentum space. We compare and discuss the results obtained with the model and with the strong field approximation and examine in this context, the role of excited states.
Entanglement in Three-Atom Tavis-Cummings Model Induced by a Thermal Field
Institute of Scientific and Technical Information of China (English)
CAI Jin-Fang; LIU Hui-Ping
2005-01-01
The explicit form of the evolution operator for the three-atom Tavis-Cummings model is given. The atoms can be entangled through their interaction with a thermal field. The degree of entanglement depends on the mean photon number of the thermal field and the initial state of the atoms.
Löbling, L.
2017-03-01
Aluminum (Al) nucleosynthesis takes place during the asymptotic-giant-branch (AGB) phase of stellar evolution. Al abundance determinations in hot white dwarf stars provide constraints to understand this process. Precise abundance measurements require advanced non-local thermodynamic stellar-atmosphere models and reliable atomic data. In the framework of the German Astrophysical Virtual Observatory (GAVO), the Tübingen Model-Atom Database (TMAD) contains ready-to- use model atoms for elements from hydrogen to barium. A revised, elaborated Al model atom has recently been added. We present preliminary stellar-atmosphere models and emergent Al line spectra for the hot white dwarfs G191–B2B and RE 0503–289.
Global atmospheric model for mercury including oxidation by bromine atoms
Directory of Open Access Journals (Sweden)
C. D. Holmes
2010-12-01
Full Text Available Global models of atmospheric mercury generally assume that gas-phase OH and ozone are the main oxidants converting Hg^{0} to Hg^{II} and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg^{0} oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming gas-phase Br to be the sole Hg^{0} oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O_{3} model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O_{3} models, we add an aqueous photochemical reduction of Hg^{II} in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O_{3} models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of Hg^{II} deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux to the Arctic of 60 Mg a^{−1}. Summertime events of depleted Hg^{0} at Antarctic sites due to subsidence are much better simulated by
Global atmospheric model for mercury including oxidation by bromine atoms
Directory of Open Access Journals (Sweden)
C. D. Holmes
2010-08-01
Full Text Available Global models of atmospheric mercury generally assume that OH and ozone are the main oxidants converting Hg^{0} to Hg^{II} and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg^{0} oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming Br to be the sole Hg^{0} oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O_{3} model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O_{3} models, we add an aqueous photochemical reduction of Hg^{II} in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O_{3} models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of Hg^{II} deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux of 60 Mg a^{−1}. Summertime events of depleted Hg^{0} at Antarctic sites due to subsidence are much better simulated by the Hg + Br model. Model
Secondary Students' Mental Models of Atoms and Molecules: Implications for Teaching Chemistry.
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
Energy Technology Data Exchange (ETDEWEB)
Dooher, J.P. [Adelphi Univ., Garden City, NY (United States)
1995-11-01
Highly concentrated suspensions of coal particles in water or alternate fluids appear to have a wide range of applications for energy production. For enhanced implementation of coal slurry fuel technology, an understanding of coal slurry atomization as a function coal and slurry properties for specific mechanical configurations of nozzle atomizers should be developed.
Derouich, M.
2017-02-01
Simulations of the generation of the atomic polarization is necessary for interpreting the second solar spectrum. For this purpose, it is important to rigorously determine the effects of the isotropic collisions with neutral hydrogen on the atomic polarization of the neutral atoms, ionized atoms and molecules. Our aim is to treat in generality the problem of depolarizing isotropic collisions between singly ionized atoms and neutral hydrogen in its ground state. Using our numerical code, we computed the collisional depolarization rates of the p-levels of ions for large number of values of the effective principal quantum number n* and the Unsöld energy Ep. Then, genetic programming has been utilized to fit the available depolarization rates. As a result, strongly non-linear relationships between the collisional depolarization rates, n* and Ep are obtained, and are shown to reproduce the original data with accuracy clearly better than 10%. These relationships allow quick calculations of the depolarizing collisional rates of any simple ion which is very useful for the solar physics community. In addition, the depolarization rates associated to the complex ions and to the hyperfine levels can be easily derived from our results. In this work we have shown that by using powerful numerical approach and our collisional method, general model giving the depolarization of the ions can be obtained to be exploited for solar applications.
Operation of the computer model for direct atomic oxygen exposure of Earth satellites
Bourassa, R. J.; Gruenbaum, P. E.; Gillis, J. R.; Hargraves, C. R.
1995-01-01
One of the primary causes of material degradation in low Earth orbit (LEO) is exposure to atomic oxygen. When atomic oxygen molecules collide with an orbiting spacecraft, the relative velocity is 7 to 8 km/sec and the collision energy is 4 to 5 eV per atom. Under these conditions, atomic oxygen may initiate a number of chemical and physical reactions with exposed materials. These reactions contribute to material degradation, surface erosion, and contamination. Interpretation of these effects on materials and the design of space hardware to withstand on-orbit conditions requires quantitative knowledge of the atomic oxygen exposure environment. Atomic oxygen flux is a function of orbit altitude, the orientation of the orbit plan to the Sun, solar and geomagnetic activity, and the angle between exposed surfaces and the spacecraft heading. We have developed a computer model to predict the atomic oxygen exposure of spacecraft in low Earth orbit. The application of this computer model is discussed.
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.
1993-01-01
The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.
Improving the Ni I atomic model for solar and stellar atmospheric models
Vieytes, Mariela C
2013-01-01
Neutral nickel (Ni I) is abundant in the solar atmosphere and is one of the important elements that contribute to the emission and absorption of radiation in the spectral range between 1900 and 3900 A. Previously, the Solar Radiation Physical Modeling (SRPM) models of the solar atmosphere considered only few levels of this species. Here we improve the Ni I atomic model by taking into account 61 levels and 490 spectral lines. We compute the populations of these levels in full NLTE using the SRPM code and compare the resulting emerging spectrum with observations. The present atomic model improves significantly the calculation of the solar spectral irradiance at near-UV wavelengths that are important for Earth atmo spheric studies, and particularly for ozone chemistry.
Institute of Scientific and Technical Information of China (English)
王忠纯; 王琪; 张永生; 郭光灿
2005-01-01
We study the properties of atoms and cavity field in the two-atom Tavis-Cummings model where the two atoms interact with each other and are also driven by an external classical field. We consider the special case that the cavity is initially in a coherent state. The atomic inversion, the average photons number and the Mandel parameter in the driven Tavis-Cummings model are given and analysed numerically. We pay special attention to the dynamical behaviour of the atoms and the cavity field modified by the external field.
Squeezing effect of the cavity field in the two-atom Jay nes-Cummings model
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Authors investigate the model that two two-level atoms in terac t with a single-mode cavity. The formulation of the time evolution operator for the two-atom Jaynes-Cummings model is presented by the bare-states approach. Besides, squeezing effect of the cavity field is studied and some novel feature s are obtained.
Photon statistical properties of the cavity field in the two-atom Jaynes-Cummings model
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
The model that two two-level atoms interact with a singel-mode cavity is studied. The exact solution of the time evolution operator for the two-atom Jaynes-Cummings model is presented by the bare-states approach. Furthermore, we investigate the dynamical properties of the photon statistics of the cavity field, and obtain a number of novel features.
APPROXIMATE MODEL OF INTENSE FIELD STABILIZATION FOR.HYDlROGEN ATOM
Institute of Scientific and Technical Information of China (English)
XIE BAI-SONG
2000-01-01
An approximate model is proposed to study the stabilization problem of hydrogen atoms under monochromatic intense laser field.The stabilization regime for system parameters such as laser field strength,laser field frequency and atomic magnetic quantum number are obtained by stability analysis of fixed points of the model.The results are consistent with those obtained by other methods.
Modeling Strongly Correlated Fermi Systems Using Ultra-Cold Atoms
2008-06-28
exceeds the optical scattering rate Γsc). For the lattice described above, the Lamb Dicke parameter ER/hν = 0.12 and the festina lente criterion Γsc...zero entropy ). Initialization of the quantum register for quantum computations requires a gas of neutral atoms in a near-zero- entropy state...zero- entropy state is prepared by selectively removing atoms in the second band from the lattice potential. optical lattice experiments have
Classical-field model of the hydrogen atom
Rashkovskiy, Sergey A.
2017-02-01
It is shown that all of the basic properties of the hydrogen atom can be consistently described in terms of classical electrodynamics if instead of considering the electron to be a particle, we consider an electrically charged classical wave field—an "electron wave"—which is held by the electrostatic field of the proton. It is shown that quantum mechanics must be considered not as a theory of particles but as a classical field theory in the spirit of classical electrodynamics. In this case, we are not faced with difficulties in interpreting the results of the theory. In the framework of classical electrodynamics, all of the well-known regularities of the spontaneous emission of the hydrogen atom are obtained, which is usually derived in the framework of quantum electrodynamics. It is shown that there are no discrete states and discrete energy levels of the atom: the energy of the atom and its states change continuously. An explanation of the conventional corpuscular-statistical interpretation of atomic phenomena is given. It is shown that this explanation is only a misinterpretation of continuous deterministic processes. In the framework of classical electrodynamics, the nonlinear Schrödinger equation is obtained, which accounts for the inverse action of self-electromagnetic radiation of the electron wave and completely describes the spontaneous emissions of an atom.
Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning
Rupp, Matthias; Müller, Klaus-Robert; von Lilienfeld, O Anatole
2011-01-01
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\\"odinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross-validation over more than seven thousand small organic molecules yields a mean absolute error of ~10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.
Modeling and understanding of effects of randomness in arrays of resonant meta-atoms
DEFF Research Database (Denmark)
Tretyakov, Sergei A.; Albooyeh, Mohammad; Alitalo, Pekka;
2013-01-01
In this review presentation we will discuss approaches to modeling and understanding electromagnetic properties of 2D and 3D lattices of small resonant particles (meta-atoms) in transition from regular (periodic) to random (amorphous) states. Nanostructured metasurfaces (2D) and metamaterials (3D......) are arrangements of optically small but resonant particles (meta-atoms). We will present our results on analytical modeling of metasurfaces with periodical and random arrangements of electrically and magnetically resonant meta-atoms with identical or random sizes, both for the normal and oblique-angle excitations......) of the arrangements of meta-atoms....
Mapping trapped atomic gas with spin-orbit coupling to quantum Rabi-like model
Hu, Haiping; Chen, Shu
2013-01-01
We construct a connection of the ultracold atomic system in a harmonic trap with Raman-induced spin-orbit coupling to the quantum Rabi-like model. By mapping the trapped atomic system to a Rabi-like model, we can get the exact solution of the Rabi-like model following the methods to solve the quantum Rabi model. The existence of such a mapping implies that we can study the basic model in quantum optics by using trapped atomic gases with spin-orbit coupling.
Modeling molecular crystals formed by spin-active metal complexes by atom-atom potentials
Sinitskiy, Anton V; Tokmachev, Andrei M; Dronskowski, Richard
2009-01-01
We apply the atom-atom potentials to molecular crystals of iron (II) complexes with bulky organic ligands. The crystals under study are formed by low-spin or high-spin molecules of Fe(phen)$_{2}$(NCS)$_{2}$ (phen = 1,10-phenanthroline), Fe(btz)$_{2}$(NCS)$_{2}$ (btz = 5,5$^{\\prime }$,6,6$^{\\prime}$-tetrahydro-4\\textit{H},4$^{\\prime}$\\textit{H}-2,2$^{\\prime }$-bi-1,3-thiazine), and Fe(bpz)$_{2}$(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2$^{\\prime}$-bipyridine). All molecular geometries are taken from the X-ray experimental data and assumed to be frozen. The unit cell dimensions and angles, positions of the centers of masses of molecules, and the orientations of molecules corresponding to the minimum energy at 1 atm and 1 GPa are calculated. The optimized crystal structures are in a good agreement with the experimental data. Sources of the residual discrepancies between the calculated and experimental structures are discussed. The intermolecular contributions to the enthalpy of the spin transiti...
'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
Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I.
Bautista, M. A.; Fivet, V.; Quinet, P.; Dunn, J.; Gull, T. R.; Kallman, T. R.; Mendoza, C.
2013-01-01
We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data.We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of Oiii and Fe ii and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe ii]. Key words: atomic data - atomic processes - line: formation - methods: data analysis - molecular data - molecular processes - techniques: spectroscopic
Jin, Lin; Auerbach, Scott M; Monson, Peter A
2011-04-07
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 SiO(4) 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 Q(n) 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.
Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.
Shen, Lin; Hu, Hao
2014-06-10
We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.
Atomic charges for modeling metal–organic frameworks: Why and how
Energy Technology Data Exchange (ETDEWEB)
Hamad, Said, E-mail: said@upo.es; Balestra, Salvador R.G.; Bueno-Perez, Rocio; Calero, Sofia; Ruiz-Salvador, A. Rabdel
2015-03-15
Atomic partial charges are parameters of key importance in the simulation of Metal–Organic Frameworks (MOFs), since Coulombic interactions decrease with the distance more slowly than van der Waals interactions. But despite its relevance, there is no method to unambiguously assign charges to each atom, since atomic charges are not quantum observables. There are several methods that allow the calculation of atomic charges, most of them starting from the electronic wavefunction or the electronic density or the system, as obtained with quantum mechanics calculations. In this work, we describe the most common methods employed to calculate atomic charges in MOFs. In order to show the influence that even small variations of structure have on atomic charges, we present the results that we obtained for DMOF-1. We also discuss the effect that small variations of atomic charges have on the predicted structural properties of IRMOF-1. - Graphical abstract: We review the different method with which to calculate atomic partial charges that can be used in force field-based calculations. We also present two examples that illustrate the influence of the geometry on the calculated charges and the influence of the charges on structural properties. - Highlights: • The choice of atomic charges is crucial in modeling adsorption and diffusion in MOFs. • Methods for calculating atomic charges in MOFs are reviewed. • We discuss the influence of the framework geometry on the calculated charges. • We discuss the influence of the framework charges on structural the properties.
Nonclassical Effects of a Four-Level Excited-Doublet Atom Model
Institute of Scientific and Technical Information of China (English)
ZHANG Jian-Song; XU Jing-Bo
2006-01-01
We adopt a dynamical algebraic method to study a four-level excited-doublet atom model and obtain the explicit expressions of the time-evolution operator and the density operator for the system. The nonclassical effects of the system, such as collapses and revivals of the atomic inversion and squeezing of the radiation field, are also discussed.
Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness
Park, Eun Jung; Light, Gregory
2009-01-01
Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…
Analytical model for relativistic corrections to the nuclear magnetic shielding constant in atoms
Energy Technology Data Exchange (ETDEWEB)
Romero, Rodolfo H. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)]. E-mail: rhromero@exa.unne.edu.ar; Gomez, Sergio S. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)
2006-04-24
We present a simple analytical model for calculating and rationalizing the main relativistic corrections to the nuclear magnetic shielding constant in atoms. It provides good estimates for those corrections and their trends, in reasonable agreement with accurate four-component calculations and perturbation methods. The origin of the effects in deep core atomic orbitals is manifestly shown.
Mg I as a probe of the solar chromosphere - The atomic model
Mauas, Pablo J.; Avrett, Eugene H.; Loeser, Rudolf
1988-01-01
This paper presents a complete atomic model for Mg I line synthesis, where all the atomic parameters are based on recent experimental and theoretical data. It is shown how the computed profiles at 4571 A and 5173 A are influenced by the choice of these parameters and the number of levels included in the model atom. In addition, observed profiles of the 5173 A b2 line and theoretical profiles for comparison (based on a recent atmospheric model for the average quiet sun) are presented.
Santhanam, K S V; Chen, Xu; Gupta, S
2014-04-01
Ab initio studies of ferromagnetic atom interacting with carbon nanotubes have been reported in the literature that predict when the interaction is strong, a higher hybridization with confinement effect will result in spin polarization in the ferromagnetic atom. The spin polarization effect on the thermal oxidation to form its oxide is modeled here for the ferromagnetic atom and its alloy, as the above studies predict the 4s electrons are polarized in the atom. The four models developed here provide a pathway for distinguishing the type of interaction that exists in the real system. The extent of spin polarization in the ferromagnetic atom has been examined by varying the amount of carbon nanotubes in the composites in the thermogravimetric experiments. In this study we report the experimental results on the CoNi alloy which appears to show selective spin polarization. The products of the thermal oxidation has been analyzed by Fourier Transform Infrared Spectroscopy.
UNIFIED MODEL FOR SPLASH DROPLETS AND SUSPENDED MIST OF ATOMIZED FLOW
Institute of Scientific and Technical Information of China (English)
LIU Shi-he; SUN Xiao-fei; LUO Jing
2008-01-01
In this article, the unified mathematical model for splash droplets and suspended mist of atomized flow was established, which classifies the atomized sources into the splash source and the suspended source. For the splash source, the Lagrangian method was used to simulate the random motion of splash water droplets, and for the suspended source the theory of air-water two-phase flow was used to simulate the mist flow moving in particle clouds. The rainfall intensity of the atomized flow was obtained by summarizing the rainfall intensities relative to the above two types of atomized sources. Both experimental data and prototype observation data were used for the verification of the mathematical model. For both the distribution of rainfall intensity, and the outer edge of the atomized flow, the simulation results are in agreement with the experimental data or prototype observation data.
Roy, Kunal; Ghosh, Gopinath
2008-11-01
In this communication, we have developed quantitative predictive models using human lethal concentration values of 26 organic compounds including some pharmaceuticals with extended topochemical atom (ETA) indices applying different chemometric tools and compared the extended topochemical atom models with the models developed from non-extended topochemical atom ones. Extended topochemical atom descriptors were also tried in combination with non-extended topochemical atom descriptors to develop better predictive models. The use of extended topochemical atom descriptors along with non-extended topochemical atom ones improved equation statistics and cross-validation quality. The best model with sound statistical quality was developed from partial least squares regression using extended topochemical atom descriptors in combination non-extended topochemical atom ones. Finally, to check true predictability of the ETA parameters, the data set was divided into training (n = 19) and test (n = 7) sets. Partial least squares and genetic partial least squares models were developed from the training set using extended topochemical atom indices and the models were validated using the test set. The extended topochemical atom models developed from different statistical tools suggest that the toxicity increases with bulk, chloro functionality, presence of electronegative atoms within a chain or ring and unsaturation, and decreases with hydroxy functionality and branching. The results suggest that the extended topochemical atom descriptors are sufficiently rich in chemical information to encode the structural features for QSAR/QSPR/QSTR modeling.
An Analytical Model for Adsorption and Diffusion of Atoms/Ions on Graphene Surface
Directory of Open Access Journals (Sweden)
Yan-Zi Yu
2015-01-01
Full Text Available Theoretical investigations are made on adsorption and diffusion of atoms/ions on graphene surface based on an analytical continuous model. An atom/ion interacts with every carbon atom of graphene through a pairwise potential which can be approximated by the Lennard-Jones (L-J potential. Using the Fourier expansion of the interaction potential, the total interaction energy between the adsorption atom/ion and a monolayer graphene is derived. The energy-distance relationships in the normal and lateral directions for varied atoms/ions, including gold atom (Au, platinum atom (Pt, manganese ion (Mn2+, sodium ion (Na1+, and lithium-ion (Li1+, on monolayer graphene surface are analyzed. The equilibrium position and binding energy of the atoms/ions at three particular adsorption sites (hollow, bridge, and top are calculated, and the adsorption stability is discussed. The results show that H-site is the most stable adsorption site, which is in agreement with the results of other literatures. What is more, the periodic interaction energy and interaction forces of lithium-ion diffusing along specific paths on graphene surface are also obtained and analyzed. The minimum energy barrier for diffusion is calculated. The possible applications of present study include drug delivery system (DDS, atomic scale friction, rechargeable lithium-ion graphene battery, and energy storage in carbon materials.
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.
Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling
Energy Technology Data Exchange (ETDEWEB)
Tawara, H. [ed.
1997-01-01
This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)
Jung, Hyunseung; In, Chihun; Choi, Hyunyong; Lee, Hojin
2014-06-09
Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems.
Urzhumtsev, Alexandre; Afonine, Pavel V; Van Benschoten, Andrew H; Fraser, James S; Adams, Paul D
2016-09-01
Researcher feedback has indicated that in Urzhumtsev et al. [(2015) Acta Cryst. D71, 1668-1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. These issues are addressed in this article.
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 radiat...
Kinetic modeling of primary and secondary oxygen atom fluxes at 1 AU
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.
Classical trajectory perspective of atomic ionization in strong laser fields semiclassical modeling
Liu, Jie
2014-01-01
The ionization of atoms and molecules in strong laser fields is an active field in modern physics and has versatile applications in such as attosecond physics, X-ray generation, inertial confined fusion (ICF), medical science and so on. Classical Trajectory Perspective of Atomic Ionization in Strong Laser Fields covers the basic concepts in this field and discusses many interesting topics using the semiclassical model of classical trajectory ensemble simulation, which is one of the most successful ionization models and has the advantages of a clear picture, feasible computing and accounting for many exquisite experiments quantitatively. The book also presents many applications of the model in such topics as the single ionization, double ionization, neutral atom acceleration and other timely issues in strong field physics, and delivers useful messages to readers with presenting the classical trajectory perspective on the strong field atomic ionization. The book is intended for graduate students and researchers...
Sound speed and oscillation frequencies for solar models evolved with Los Alamos ATOMIC opacities
Guzik, Joyce A; Walczak, P; Wood, S R; Mussack, K; Farag, E
2016-01-01
Los Alamos National Laboratory has calculated a new generation of radiative opacities (OPLIB data using the ATOMIC code) for elements with atomic number Z=1-30 with improved physics input, updated atomic data, and finer temperature grid to replace the Los Alamos LEDCOP opacities released in the year 2000. We calculate the evolution of standard solar models including these new opacities, and compare with models evolved using the Lawrence Livermore National Laboratory OPAL (Iglesias and Rogers 1996) opacities. We use the solar abundance mixture of Asplund et al. (2009). The new Los Alamos ATOMIC opacities have steeper opacity derivatives than those of OPAL for temperatures and densities of the solar interior radiative zone. We compare the calculated nonadiabatic solar oscillation frequencies and solar interior sound speed to observed frequencies and helioseismic inferences. The calculated sound-speed profiles are similar for models evolved using either the updated Iben evolution code (see \\cite{Guzik2010}), or ...
Does God Play Dice with Universe The Hydrogen Atomic Model of Bohr and de Broglie
Kamenov, P S
1999-01-01
In this paper it is shown that if one accept assumption of de Broglie that "unitary wave-particle" exists simultaneously and this coexistence is real, then one can find the mean life time of the hydrogen atom of Bohr (intensities). Something more, the acceptance of de Broglie's ideas show that a single excited hydrogen atom decays at exactly predictable moment (after excitation). The natural width of excited hydrogen atoms are found using the Bohr's model of this atom and de Broglie's ideas. The mean life time of the excited states is a characteristic only of a statistical ensemble of many atoms and coincide exactly with experimental data and can be used for analytical applications. It is shown also that resonant Mossbauer absorption in time domain provides a qualitative evidence of the existence of "own lifetime" for first excited states of the nuclei.
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.
Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom
Lorente, M.
2004-01-01
The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.
Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom
Lorente, M
2001-01-01
The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.
Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom
Lorente, Miguel
2001-07-01
The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.
Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.
Orben, Claudia M; Dittrich, Birger
2014-06-01
For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å(-1). The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å(-1), but requires good low-order data.
Engineering the Dynamics of Effective Spin-Chain Models for Strongly Interacting Atomic Gases
DEFF Research Database (Denmark)
Volosniev, A. G.; Petrosyan, D.; Valiente, M.
2015-01-01
We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We...... find that bosonic atoms offer more flexibility for tuning independently the parameters of the spin Hamiltonian through interatomic (intra-species) interaction which is absent for fermions due to the Pauli exclusion principle. Our formalism can have important implications for control and manipulation...
Parity violation in atomic cesium and alternatives to the standard model of electroweak interactions
Energy Technology Data Exchange (ETDEWEB)
Bouchiat, C.; Piketty, C.A. (Ecole Normale Superieure, 75 - Paris (France). Lab. de Physique Theorique)
1983-08-18
We study the implications of the recent observation of a parity violation in atomic cesium. After a discussion of the uncertainties associated with the atomic physics calculations we derive conservative bounds for the weak charge Qsub(W). These bounds are used to put constraints on alternatives to the standard electroweak model, involving an 'extra U(1)' gauge group. We analyze the possibility that the extra gauge boson might be very light and give, as a by-product, the typical range of momentum transfer explored in atomic parity violation experiments.
Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I
Bautista, Manuel A; Quinet, Pascal; Dunn, Jay; Kallman, Theodore R Gull Timothy R; Mendoza, Claudio
2013-01-01
We present a method for computing uncertainties in spectral models, i.e. level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data. We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of O III and Fe II and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe II].
Atomic scale simulations for improved CRUD and fuel performance modeling
Energy Technology Data Exchange (ETDEWEB)
Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cooper, Michael William Donald [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2017-01-06
A more mechanistic description of fuel performance codes can be achieved by deriving models and parameters from atomistic scale simulations rather than fitting models empirically to experimental data. The same argument applies to modeling deposition of corrosion products on fuel rods (CRUD). Here are some results from publications in 2016 carried out using the CASL allocation at LANL.
A Model for Nitrogen Atom Recombination on a Silicon Dioxide Surface
1987-12-01
developed according to @ 8 kinetic theory arguments (81). The rate equations for atomic nitrogen bonded via the Langmuir-Rideal model consisted of the...Aeronautics and Space Administracion (NASA) published a report (55) which detailed the Space Shuttle and the design of its Thermal Protection System (TPS...surface atoms. According to Schwab (68:230), chemdsorption can be defined as adsorption via 1. Complete transition of electrons and the formation of polar
Atomic and field dynamics in the time-dependent Jaynes-Cummings model with arbitrary detuning
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
We propose a general numerical method for solving the time -dependent Jaynes-Cummings model with arbitrary detuning by integrating relate d groups of coupled equations using Runge-Kutta numerical technique. The atomic and field dynamics such as evolution of atomic population inversion and second -order correlation function of photons are studied in case of different detunin g. The results show that the field tends to exhibit bunching effect due to the I ncreasing of detuning.
Size distribution of islands according to 2D growth model with 2 kinds of diffusion atoms
Yamauchi, R; Koyama, M; Sasakura, H; Nakata, Y; Muto, S
2015-01-01
We simulated the growth of 2D islands with 2 kinds of diffusion atoms using the kinetic Monte- Carlo (kMC) method. As a result, we found that the slow atoms tend to create nuclei and determine the island volume distribution, along with additional properties such as island density. We also conducted a theoretical analysis using the rate equation of the point-island model to confirm these results.
Simulating Quantum Spin Models using Rydberg-Excited Atomic Ensembles in Magnetic Microtrap Arrays
Whitlock, Shannon; Hannaford, Peter
2016-01-01
We propose a scheme to simulate lattice spin models based on strong and long-range interacting Rydberg atoms stored in a large-spacing array of magnetic microtraps. Each spin is encoded in a collective spin state involving a single $nP$ Rydberg atom excited from an ensemble of ground-state alkali atoms prepared via Rydberg blockade. After the excitation laser is switched off the Rydberg spin states on neighbouring lattice sites interact via general isotropic or anisotropic spin-spin interactions. To read out the collective spin states we propose a single Rydberg atom triggered avalanche scheme in which the presence of a single Rydberg atom conditionally transfers a large number of ground-state atoms in the trap to an untrapped state which can be readily detected by site-resolved absorption imaging. Such a quantum simulator should allow the study of quantum spin systems in almost arbitrary two-dimensional configurations. This paves the way towards engineering exotic spin models, such as spin models based on tr...
Mapping the Two-Component Atomic Fermi Gas to the Nuclear Shell-Model
DEFF Research Database (Denmark)
Özen, C.; Zinner, Nikolaj Thomas
2014-01-01
of the external potential becomes important. A system of two-species fermionic cold atoms with an attractive zero-range interaction is analogous to a simple model of nucleus in which neutrons and protons interact only through a residual pairing interaction. In this article, we discuss how the problem of a two......-component atomic fermi gas in a tight external trap can be mapped to the nuclear shell model so that readily available many-body techniques in nuclear physics, such as the Shell Model Monte Carlo (SMMC) method, can be directly applied to the study of these systems. We demonstrate an application of the SMMC method...
Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".
Belnap, D M; Kumar, A; Folk, J T; Smith, T J; Baker, T S
1999-01-01
Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.
Reasoning with Atomic-Scale Molecular Dynamic Models
Pallant, Amy; Tinker, Robert F.
2004-01-01
The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…
Everyone Wants to Be a Model Teacher: Part III: Extensions to Atomic Structures and Bonding.
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.…
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…
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)
Nano Goes to School: A Teaching Model of the Atomic Force Microscope
Planinsic, Gorazd; Kovac, Janez
2008-01-01
The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…
Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation
Willey, Ronald J.
1993-01-01
Five kinetic models are compared for their ability to predict recombination coefficients for oxygen and nitrogen atoms over high-temperature reusable surface insulation (HRSI). Four of the models are derived using Rideal-Eley or Langmuir-Hinshelwood catalytic mechanisms to describe the reaction sequence. The fifth model is an empirical expression that offers certain features unattainable through mechanistic description. The results showed that a four-parameter model, with temperature as the only variable, works best with data currently available. The model describes recombination coefficients for oxygen and nitrogen atoms for temperatures from 300 to 1800 K. Kinetic models, with atom concentrations, demonstrate the influence of atom concentration on recombination coefficients. These models can be used for the prediction of heating rates due to catalytic recombination during re-entry or aerobraking maneuvers. The work further demonstrates a requirement for more recombination experiments in the temperature ranges of 300-1000 K, and 1500-1850 K, with deliberate concentration variation to verify model requirements.
A comparison of two atomic models for the radiative properties of dense hot low Z plasmas
Energy Technology Data Exchange (ETDEWEB)
Minguez, E. E-mail: minguez@denim.upm.es; Sauvan, P.; Gil, J.M.; Rodriguez, R.; Rubiano, J.G.; Florido, R.; Martel, P.; Angelo, P.; Schott, R.; Philippe, F.; Leboucher-Dalimier, E.; Mancini, R
2003-11-01
In this work, two different atomic models (ANALOP based on parametric potentials and IDEFIX based on the dicenter model) are used to calculate the opacities for bound-bound transitions in hot dense, low Z plasmas, and the results are compared to each other. In addition, the ANALOP code has been used to compute free-bound cross sections for hydrogen-like ions.
Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen
Banks, Bruce A.; Miller, Sharon K.
2004-01-01
Atomic oxygen is one of the predominant constituents of Earth's upper atmosphere. It is created by the photodissociation of molecular oxygen (O2) into single O atoms by ultraviolet radiation. It is chemically very reactive because a single O atom readily combines with another O atom or with other atoms or molecules that can form a stable oxide. The effects of atomic oxygen on the external surfaces of spacecraft in low Earth orbit can have dire consequences for spacecraft life, and this is a well-known and much studied problem. Much less information is known about the effects of atomic oxygen on the internal surfaces of spacecraft. This degradation can occur when openings in components of the spacecraft exterior exist that allow the entry of atomic oxygen into regions that may not have direct atomic oxygen attack but rather scattered attack. Openings can exist because of spacecraft venting, microwave cavities, and apertures for Earth viewing, Sun sensors, or star trackers. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft were simulated at the NASA Glenn Research Center by using Monte Carlo computational techniques. A two-dimensional model was used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of the distance into a parallel-walled cavity. The model allows the atomic oxygen arrival direction, the Maxwell Boltzman temperature, and the ram energy to be varied along with the interaction parameters of the degree of recombination upon impact with polymer or nonreactive surfaces, the initial reaction probability, the reaction probability dependence upon energy and angle of attack, degree of specularity of scattering of reactive and nonreactive surfaces, and the degree of thermal accommodation upon impact with reactive and non-reactive surfaces to be varied to allow the model to produce atomic oxygen erosion geometries that replicate actual experimental results from space. The degree of
Institute of Scientific and Technical Information of China (English)
周玲; 宋鹤山; 李崇; 郭彦青
2003-01-01
The dissipation of the field in the two-photon Jaynes-Cummings model (JCM) with degenerate atomic levels was studied. The initial degenerate atomic state affects the field coherence loss. When the degenerate atom is initially in an equal probability superposition state, the field coherence loss is smallest. It is found that the degeneracy of the atomic level increases the period of entanglement between the atom and the field. When the degeneracy was considered, the coherence properties of the field could be affected by the reservoir qualitatively, if a nonlinear two-photon process is involved. This is different from the dissipation of one-photon JCM with degenerate atomic levels.
Relativistic Corrections to the Bohr Model of the Atom
Kraft, David W.
1974-01-01
Presents a simple means for extending the Bohr model to include relativistic corrections using a derivation similar to that for the non-relativistic case, except that the relativistic expressions for mass and kinetic energy are employed. (Author/GS)
Many-Body Quantum Optics with Decaying Atomic Spin States: ($\\gamma$, $\\kappa$) Dicke model
Gelhausen, Jan; Strack, Philipp
2016-01-01
We provide a theory for quantum-optical realizations of the open Dicke model with internal, atomic spin states subject to uncorrelated, single-site spontaneous emission with rate $\\gamma$. This introduces a second decay channel for excitations to irreversibly dissipate into the environment, in addition to the photon loss with rate $\\kappa$. We compute the mean-field non-equilibrium steady states for spin and photon observables in the long-time limit, $t\\rightarrow \\infty$. Although $\\gamma$ does not conserve the total angular momentum of the spin array, we argue that our solution is exact in the thermodynamic limit, for the number of atoms $N\\rightarrow \\infty$. In light of recent and upcoming experiments realizing superradiant phase transitions using internal atomic states with pinned atoms in optical lattices, our work lays the foundation for the pursuit of a new class of open quantum magnets coupled to quantum light.
Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.
Kukol, Andreas
2009-03-10
United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.
Cold-atom quantum simulation of U(1) lattice gauge-Higgs model
Kasamatsu, Kenichi; Kuno, Yoshihito; Takahashi, Yoshiro; Ichinose, Ikuo; Matsui, Tetsuo
2015-03-01
We discuss the possible methods to construct a quantum simulator of the U(1) lattice gauge-Higgs model using cold atoms in an optical lattice. These methods require no severe fine tunings of parameters of atomic-interactions in contrast with the other previous literature. We propose some realistic experimental setups to realize the atomic quantum simulator of the U(1) lattice gauge-Higgs model in a two-dimensional optical lattice. Our target gauge-Higgs model has a nontrivial phase structure, i.e., existence of the phase boundary between confinement and Higgs phases, and this phase boundary is to be observed by cold-atom experiments. As a reference to such experiments, we make numerical simulations of the time-dependent Gross-Pitaevskii equation and observe the real-time dynamics of the atomic simulators. Clarification of the dynamics of this gauge-Higgs model sheds some lights upon various unsolved problems including the inflation process of the early universe.
Four-component united-atom model of bitumen
Hansen, Jesper S; Nielsen, Erik; Dyre, Jeppe C; Schrøder, Thomas B
2013-01-01
We propose a four-component molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse-graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are being carried out using Graphic-Processor-Units based software in time spans in order of microseconds, and this enables the study of slow relaxation processes characterizing bitumen. This paper focuses on the high-temperature dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales as a result of the different constituents in the system. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From the stress autocorrelation function, the shear viscosity and shear ...
The contribution of atom accessibility to site of metabolism models for cytochromes P450.
Rydberg, Patrik; Rostkowski, Michal; Gloriam, David E; Olsen, Lars
2013-04-01
Three different types of atom accessibility descriptors are investigated in relation to site of metabolism predictions. To enable the integration of local accessibility we have constructed 2DSASA, a method for the calculation of the atomic solvent accessible surface area that is independent of 3D coordinates. The method was implemented in the SMARTCyp site of metabolism prediction models and improved the results by up to 4 percentage points for nine cytochrome P450 isoforms. The final models are made available at http://www.farma.ku.dk/smartcyp.
Popa, Alexandru
2013-01-01
Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamic Systems is intended for scientists and graduate students interested in the foundations of quantum mechanics and applied scientists interested in accurate atomic and molecular models. This is a reference to those working in the new field of relativistic optics, in topics related to relativistic interactions between very intense laser beams and particles, and is based on 30 years of research. The novelty of this work consists of accurate connections between the properties of quantum equations and correspon
Hybrid-structure atomic models for HED laboratory plasma diagnostics and simulations
Hansen, Stephanie
2010-03-01
While theoretical atomic physics calculations are well developed for isolated atoms and have been thoroughly benchmarked against low-density laboratory sources such as electron beam ion traps and tokamak plasmas, the high energy density (HED) regime offers significant challenges for atomic physics and spectroscopic modeling. High plasma densities lead to collective effects such as continuum lowering, line broadening, and significant populations in multiply excited atomic states. These effects change the plasma equation of state and the character of emission and absorption spectra and must be accounted for in order to accurately simulate radiative transfer in and apply spectroscopic diagnostics to HED plasmas. Modeling complex mid- and high-Z ions in the HED regime is a particular challenge because exponential growth in accessible configuration space overwhelms the reduction of the Rydberg levels through continuum lowering. This talk will discuss one approach to generating a tractable spectroscopic-quality atomic kinetics model and describe its application to HED laboratory plasmas produced on Sandia's Z facility. [4pt] Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
An atomic model of brome mosaic virus using direct electron detection and real-space optimization.
Wang, Zhao; Hryc, Corey F; Bammes, Benjamin; Afonine, Pavel V; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F; Adams, Paul D; Chiu, Wah
2014-09-04
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.
Galilean invariance in the exponential model of atomic collisions
Energy Technology Data Exchange (ETDEWEB)
del Pozo, A.; Riera, A.; Yaez, M.
1986-11-01
Using the X/sup n//sup +/(1s/sup 2/)+He/sup 2+/ colliding systems as specific examples, we study the origin dependence of results in the application of the two-state exponential model, and we show the relevance of polarization effects in that study. Our analysis shows that polarization effects of the He/sup +/(1s) orbital due to interaction with X/sup (//sup n//sup +1)+/ ion in the exit channel yield a very small contribution to the energy difference and render the dynamical coupling so strongly origin dependent that it invalidates the basic premises of the model. Further study, incorporating translation factors in the formalism, is needed.
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.
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.
Derouich, Moncef
2016-01-01
Simulations of the generation of the atomic polarization is necessary for interpreting the second solar spectrum. For this purpose, it is important to rigorously determine the effects of the isotropic collisions with neutral hydrogen on the atomic polarization of the neutral atoms, ionized atoms and molecules. Our aim is to treat in generality the problem of depolarizing isotropic collisions between singly ionized atoms and neutral hydrogen in its ground state. Using our numerical code, we computed the collisional depolarization rates of the $p$-levels of ions for large number of values of the effective principal quantum number $n^{*}$ and the Uns\\"old energy $E_p$. Then, genetic programming has been utilized to fit the available depolarization rates. As a result, strongly non-linear relationships between the collisional depolarization rates, $n^{*}$ and $E_p$ are obtained, and are shown to reproduce the original data with accuracy clearly better than 10\\%. These relationships allow quick calculations of the ...
Atomic Data and Spectral Models for FeII
Bautista, Manuel A; Ballance, Connor; Quinet, Pascal; Ferland, Gary; Mendoza, Claudio; Kallman, Timothy R
2015-01-01
We present extensive calculations of radiative transition rates and electron impact collision strengths for Fe II. The data sets involve 52 levels from the $3d\\,^7$, $3d\\,^64s$, and $3d\\,^54s^2$ configurations. Computations of $A$-values are carried out with a combination of state-of-the-art multiconfiguration approaches, namely the relativistic Hartree--Fock, Thomas--Fermi--Dirac potential, and Dirac--Fock methods; while the $R$-matrix plus intermediate coupling frame transformation, Breit--Pauli $R$-matrix and Dirac $R$-matrix packages are used to obtain collision strengths. We examine the advantages and shortcomings of each of these methods, and estimate rate uncertainties from the resulting data dispersion. We proceed to construct excitation balance spectral models, and compare the predictions from each data set with observed spectra from various astronomical objects. We are thus able to establish benchmarks in the spectral modeling of [Fe II] emission in the IR and optical regions as well as in the UV Fe...
Explicit all-atom modeling of realistically sized ligand-capped nanocrystals.
Kaushik, Ananth P; Clancy, Paulette
2012-03-21
We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), "capped" with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes.
Explicit all-atom modeling of realistically sized ligand-capped nanocrystals
Kaushik, Ananth P.
2012-01-01
We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.
Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former.
Kim, Jeongmin; Sung, Bong June
2015-06-17
The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.
Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former
Kim, Jeongmin; Sung, Bong June
2015-06-01
The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.
Modelling of liquid flow after a hydraulic jump on a rotating disk prior to centrifugal atomization
Zhao, Y. Y.; Dowson, A. L.; Jacobs, M. H.
2000-01-01
This paper describes a simplified numerical model which is used to calculate the height distribution, and the radial and tangential velocities of a liquid on a rotating disk after a hydraulic jump and prior to centrifugal atomization. The results obtained from this numerical model are compared with predictions made using previously derived `hydraulic jump' and `analytical' models. Calculations, in conjunction with experimental measurements relating to the trajectory of liquid flow on the atomizing disk, have shown that the numerical model can not only give a reasonable prediction of the hydraulic jump location, but also yields more accurate information regarding the variations in liquid height, and radial and tangential velocities. The model is ideally suited for engineering applications.
De Backer, A; Martinez, G T; Rosenauer, A; Van Aert, S
2013-11-01
In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration.
Atomic Model and Micelle Dynamics of QS-21 Saponin
Directory of Open Access Journals (Sweden)
Conrado Pedebos
2014-03-01
Full Text Available QS-21 is a saponin extracted from Quillaja saponaria, widely investigated as a vaccine immunoadjuvant. However, QS-21 use is mainly limited by its chemical instability, significant variety in molecular composition and low tolerance dose in mammals. Also, this compound tends to form micelles in a concentration-dependent manner. Here, we aimed to characterize its conformation and the process of micelle formation, both experimentally and computationally. Therefore, molecular dynamics (MD simulations were performed in systems containing different numbers of QS-21 molecules in aqueous solution, in order to evaluate the spontaneous micelle formation. The applied methodology allowed the generation of micelles whose sizes were shown to be in high agreement with small-angle X-ray scattering (SAXS. Furthermore, the ester linkage between fucose and acyl chain was less solvated in the micellar form, suggesting a reduction in hydrolysis. This is the first atomistic interpretation of previous experimental data, the first micellar characterization of saponin micelles by SAXS and first tridimensional model of a micelle constituted of saponins, contributing to the understanding of the molecular basis of these compounds.
Atomic Dipole Squeezing in the Correlated Two-Mode Two-Photon Jaynes-Cummings Model
Dong, Zhengchao; Zhao, Yonglin
1996-01-01
In this paper, we study the atomic dipole squeezing in the correlated two-mode two-photon JC model with the field initially in the correlated two-mode SU(1,1) coherent state. The effects of detuning, field intensity and number difference between the two field modes are investigated through numerical calculation.
Construction of an E. Coli genome-scale atom mapping model for MFA calculations.
Ravikirthi, Prabhasa; Suthers, Patrick F; Maranas, Costas D
2011-06-01
Metabolic flux analysis (MFA) has so far been restricted to lumped networks lacking many important pathways, partly due to the difficulty in automatically generating isotope mapping matrices for genome-scale metabolic networks. Here we introduce a procedure that uses a compound matching algorithm based on the graph theoretical concept of pattern recognition along with relevant reaction information to automatically generate genome-scale atom mappings which trace the path of atoms from reactants to products for every reaction. The procedure is applied to the iAF1260 metabolic reconstruction of Escherichia coli yielding the genome-scale isotope mapping model imPR90068. This model maps 90,068 non-hydrogen atoms that span all 2,077 reactions present in iAF1260 (previous largest mapping model included 238 reactions). The expanded scope of the isotope mapping model allows the complete tracking of labeled atoms through pathways such as cofactor and prosthetic group biosynthesis and histidine metabolism. An EMU representation of imPR90068 is also constructed and made available.
New phases in an extended Hubbard model explicitly including atomic polarizabilities
Brink, van de J.; Meinders, M.B.J.; Lorenzana, J.; Eder, R.; Sawatzky, G.A.
1996-01-01
We consider the influence of a nearest-neighbor Coulomb interaction in an extended Hubbard model and introduce a new interaction term which simulates atomic polarizabilities. This has the effect of screening the on-site Coulomb interaction for charged excitations, unlike a neighbor Coulomb interacti
Plasma-statistical models of the atom in the theory of some collisional and radiative processes
Astapenko, VA
2002-01-01
A plasma-statistical model was used to describe collisional and radiative processes involving target ionization, namely, collisional ionization of atoms and incoherent polarization bremsstrahlung. The cross sections of these processes were expressed through the Compton profile of X-ray scattering, f
Kinetic model of II-VI(001) semiconductor surfaces : Growth rates in atomic layer epitaxy
Volkmann, T; Ahr, M; Biehl, M
2004-01-01
We present a zinc-blende lattice gas model of II-VI(001) surfaces, which is investigated by means of kinetic Monte Carlo simulations. Anisotropic effective interactions between surface metal atoms allow for the description of, e.g., the sublimation of CdTe(001), including the reconstruction of Cd-te
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.
Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep
2015-02-02
Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.
Popa, Alexandru
2013-01-01
Applications of Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamical Systems is a reference on the new field of relativistic optics, examining topics related to relativistic interactions between very intense laser beams and particles. Based on 30 years of research, this unique book connects the properties of quantum equations to corresponding classical equations used to calculate the energetic values and the symmetry properties of atomic, molecular and electrodynamical systems. In addition, it examines applications for these methods, and for the calculation of
Kozlov, Alex; Quiney, Harry
2016-01-01
We describe a method for the calculation of photoionization cross-sections using square-integrable amplitudes obtained from the diagonalization of finite-basis set representations of the electronic Hamiltonian. Three examples are considered: a model example in which the final state is a free particle, the hydrogen atom and neutral atomic sodium. The method exploits the Whittaker-Shannon-Kotel'nikov sampling theorem, which is widely used in digital signal sampling and reconstruction. The approach reproduces known data with very good accuracy and converges to the exact solution with increase of the basis set size.
Modeling inelastic phonon scattering in atomic- and molecular-wire junctions
DEFF Research Database (Denmark)
Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads
2005-01-01
Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between...... the full nonequilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including nonequilibrium heating and provide...... a convenient way of parameterizing the physics. This is exemplified by fitting the expressions to the experimentally observed conductances through both an atomic gold wire and a hydrogen molecule....
Dynamics for a two-atom two-mode intensity-dependent Raman coupled model
Singh, S.; Gilhare, K.
2016-06-01
We study the quantum dynamics of a two-atom Raman coupled model interacting with a quantized bimodal field with intensity-dependent coupling terms in a lossless cavity. The unitary transformation method used to solve the time-dependent problem also gives the eigensolutions of the interaction Hamiltonian. We study the atomic-population dynamics and dynamics of the photon statistics in the two cavity modes, and present evidence of cooperative effects in the production of antibunching and anticorrelations between the modes. We also investigate the effect of detuning on the evolution of second-order correlation functions and observe that the oscillations become more rapid for large detuning.
Model for Interaction Between Photon and Cold Atom in QED Cavity
Institute of Scientific and Technical Information of China (English)
ZHANG Li; WANG Cheng; LI Yan-Min; RUAN Sheng-Ping; XUAN Li
2004-01-01
A model has been established for the interaction between a single-mode optical field and a 2-energy-level cold atom with exact analytic solutions given. The processes of momentum and energy exchanges between the optical field and the cold atom due to the interaction between them are discussed in detail, and a formula has been given for the variation of momentum and energy exchange volumes with time t in dress state while both the effects of photon recoil and Doppler effect are taken into consideration.
Kozlov, A.; Saha, S.; Quiney, H. M.
2017-01-01
We describe a method for the calculation of photoionization cross-sections using square-integrable amplitudes obtained from the diagonalization of finite-basis set representations of the electronic Hamiltonian. Three examples are considered: a model example in which the final state is a free particle, the hydrogen atom and neutral atomic sodium. The method exploits the Whittaker-Shannon-Kotel’nikov sampling theorem, which is widely used in digital signal sampling and reconstruction. The approach reproduces known data with very good accuracy and converges to the exact solution with increase of the basis set size.
Simulations of Edge Effect in 1D Spin Crossover Compounds by Atom-Phonon Coupling Model
Linares, J.; Chiruta, D.; Jureschi, C. M.; Alayli, Y.; Turcu, C. O.; Dahoo, P. R.
2016-08-01
We used the atom-phonon coupling model to explain and illustrate the behaviour of a linear nano-chain of molecules. The analysis of the system's behaviour was performed using Free Energy method, and by applying Monte Carlo Metropolis (MCM) method which take into account the phonon contribution. In particular we tested both the MCM algorithm and the dynamic-matrix method and we expose how the thermal behaviour of a 1D spin crossover system varies as a function of different factors. Furthermore we blocked the edge atoms of the chain in its high spin state to study the effect on the system's behaviour.
Institute of Scientific and Technical Information of China (English)
LIU Zong-Liang; LI Shao-Hua; CHEN Chang-Yong
2008-01-01
We propose a scheme for approximately and conditionally teleporting an unknown atomic-entangled state in dissipative cavity QED.It is the further development of the scheme of [Phys.Rev.A 69 (2004) 064302],where the cavity mode decay has not been considered and the state teleportated is an unknown atomic state.In this paper,we investigate the influence of the decay on the approximate and conditional teleportation of the unknown atomic-entangled state,which is different from that teleportated in [Phys.Rev.A 69 (2004) 064302] and then give the fidelity of the teleportation,which depends on the cavity mode decay.The scheme may be generalized to not only the teleportation of the cavity-mode-entangled-state by means of a single atom but also the teleportation of the unknown trapped-ion-entangled-state in a linear ion trap.
Ma, Qianli; Dagdigian, Paul J
2011-07-01
A kinetic model previously developed to predict the relative intensities of atomic emission lines in laser-induced breakdown spectroscopy has been extended to include processes related to CN and C(2) molecular emissions. Simulations with this model were performed to predict the relative excited-state populations. The results from the simulations are compared with experimentally determined excited-state populations from 1,064 nm laser irradiation of organic residues on aluminum foil. The model reasonably predicts the relative intensity of the molecular emissions. Significantly, the model reproduces the vastly different temporal profiles of the atomic and molecular emissions. The latter are found to extend to much longer times after the laser pulse, and this appears to be due to the increasing concentration of the molecules versus time. From the simulations, the important processes affecting the CN and C(2) concentrations are identified.
Berry phase in a two-atom Jaynes-Cummings model with Kerr medium
Bu, Shen-Ping; Zhang, Guo-Feng; Liu, Jia; Chen, Zi-Yu
2008-12-01
The Jaynes-Cummings model (JCM) is an very important model for describing interaction between quantized electromagnetic fields and atoms in cavity quantum electrodynamics (QED). This model is generalized in many different directions since it predicts many novel quantum effects that can be verified by modern physics experimental technologies. In this paper, the Berry phase and entropy of the ground state for arbitrary photon number n of a two-atom Jaynes-Cummings model with Kerr-like medium are investigated. It is found that there is some correspondence between their images, especially the existence of a curve in the Δ-ɛ plane along which the energy, Berry phase and entropy all reach their special values. So it is available for detecting entanglement by applying Berry phase.
Model operator approach to the Lamb shift calculations in relativistic many-electron atoms
Shabaev, V M; Yerokhin, V A
2013-01-01
A model operator approach to calculations of the QED corrections to energy levels in relativistic many-electron atomic systems is developed. The model Lamb shift operator is represented by a sum of local and nonlocal potentials which are defined using the results of ab initio calculations of the diagonal and nondiagonal matrix elements of the one-loop QED operator with H-like wave functions. The model operator can be easily included in any calculations based on the Dirac-Coulomb-Breit Hamiltonian. Efficiency of the method is demonstrated by comparison of the model QED operator results for the Lamb shifts in many-electron atoms and ions with exact QED calculations.
Institute of Scientific and Technical Information of China (English)
ZHOU Yu-Rong; CHEN Chang-Yong; PAN Hui-Mei; GUO Feng; PANG Xiao-Feng
2008-01-01
A scheme for approximately and conditionally teleporting an unknown atomic state in dissipative cavity QED is proposed. It is the extension of the scheme of [Phys. Rev. A 69 (2004) 064302], where the cavity mode decay has not been considered and only a time point of system evolution and the corresponding fidelity implementing the teleportation are given. In fact, the cavity mode decay exists really and must be delt with. In this paper, we investigate the influence from the cavity mode decay on the implementation of the approximate and conditional teleportation by means of the dissipative Jaynes Cummings model and then show the analytical expression of the fidelity of realization of the teleportation, Alternatively, our scheme does not involve an additional atom, only requiring two atoms and one single-mode cavity.
Finite Bias Calculations to Model Interface Dipoles in Electrochemical Cells at the Atomic Scale
DEFF Research Database (Denmark)
Hansen, Martin Hangaard; Jin, Chengjun; Thygesen, Kristian Sommer
2016-01-01
The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure t...... to satisfy the thermodynamic constraints imposed by the environment. This is captured by the generalized computational hydrogen electrode model, which enables us to make efficient first-principles calculations of atomic scale properties of the electrochemical interface.......The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure...
Parity violation in atomic cesium and alternatives to the standard model of electroweak interactions
Bouchiat, C.; Piketty, C. A.
1983-08-01
We study the implications of the recent observation of a parity violation in atomic cesium. After a discussion of the uncertainties associated with the atomic physics calculations we derive conservative bounds for the weak charge QW. These bounds are used to put constraints on alternatives to the standard electroweak model, involving an ``extra U(1)'' gauge group. We analyze the possibility that the extra gauge boson might be very and give, as a by-product, the typical range of momentum transfer explored in atomic parity violation experiments. Laboratoire Propre du Centre National de la Recherche Scientifique associée à l'Ecole Normale Supérieure et à l'Université de Paris Sud.
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
Energy Technology Data Exchange (ETDEWEB)
Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Jackson, Bret [Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom); Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main (Germany); Martinazzo, Rocco, E-mail: rocco.martinazzo@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Richerche, v. Golgi 19, 20133 Milano (Italy)
2015-09-28
An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.
Accurate model annotation of a near-atomic resolution cryo-EM map.
Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah
2017-03-21
Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.
Polat-Yaseen, Zeynep
2012-01-01
This study was designed for two major goals, which are to describe students' mental models about atom concept from 6th to 8th grade and to compare students' mental models with visual representations of atom in textbooks. Qualitative and quantitative data were collected with 4 open-ended questions including drawings which were quantified using the…
Modeling the heating and atomic kinetics of a photoionized neon plasma experiment
Lockard, Tom E.
Motivated by gas cell photoionized plasma experiments performed by our group at the Z facility of Sandia National Laboratories, we discuss in this dissertation a modeling study of the heating and ionization of the plasma for conditions characteristic of these experiments. Photoionized plasmas are non-equilibrium systems driven by a broadband x-ray radiation flux. They are commonly found in astrophysics but rarely seen in the laboratory. Several modeling tools have been employed: (1) a view-factor computer code constrained with side x-ray power and gated monochromatic image measurements of the z-pinch radiation, to model the time-history of the photon-energy resolved x-ray flux driving the photoionized plasma, (2) a Boltzmann self-consistent electron and atomic kinetics model to simulate the electron distribution function and configuration-averaged atomic kinetics, (3) a radiation-hydrodynamics code with inline non-equilibrium atomic kinetics to perform a comprehensive numerical simulation of the experiment and plasma heating, and (4) steady-state and time-dependent collisional-radiative atomic kinetics calculations with fine-structure energy level description to assess transient effects in the ionization and charge state distribution of the plasma. The results indicate that the photon-energy resolved x-ray flux impinging on the front window of the gas cell is very well approximated by a linear combination of three geometrically-diluted Planckian distributions. Knowledge of the spectral details of the x-ray drive turned out to be important for the heating and ionization of the plasma. The free electrons in the plasma thermalize quickly relative to the timescales associated with the time-history of the x-ray drive and the plasma atomic kinetics. Hence, electrons are well described by a Maxwellian energy distribution of a single temperature. This finding is important to support the application of a radiation-hydrodynamic model to simulate the experiment. It is found
Liu, Guisen; Cheng, Xi; Wang, Jian; Chen, Kaiguo; Shen, Yao
2017-03-02
Prediction of Peierls stress associated with dislocation glide is of fundamental concern in understanding and designing the plasticity and mechanical properties of crystalline materials. Here, we develop a nonlocal semi-discrete variational Peierls-Nabarro (SVPN) model by incorporating the nonlocal atomic interactions into the semi-discrete variational Peierls framework. The nonlocal kernel is simplified by limiting the nonlocal atomic interaction in the nearest neighbor region, and the nonlocal coefficient is directly computed from the dislocation core structure. Our model is capable of accurately predicting the displacement profile, and the Peierls stress, of planar-extended core dislocations in face-centered cubic structures. Our model could be extended to study more complicated planar-extended core dislocations, such as {111} dislocations in Al-based and Ti-based intermetallic compounds.
Protein Nano-Object Integrator (ProNOI for generating atomic style objects for molecular modeling
Directory of Open Access Journals (Sweden)
Smith Nicholas
2012-12-01
Full Text Available Abstract Background With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results Here we report the Protein Nano-Object Integrator (ProNOI which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions The Protein Nano-Object Integrator (ProNOI is a convenient tool for
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.
Klocke, Michael; Wolf, Dietrich E
2016-01-01
A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.
Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy
Directory of Open Access Journals (Sweden)
Michael Klocke
2016-05-01
Full Text Available 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.
Rognlien, Thomas; Rensink, Marvin
2016-10-01
Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.
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.
Institute of Scientific and Technical Information of China (English)
王忠纯
2004-01-01
@@ We study the properties of the atoms and cavity field in the Tavis-Cummings Model where the two atoms interact each other and also are driven by an external classical field.We consider the special case that the cavity is initially in a coherent state.After work out the atomic inversion, the average photons number and the Mandel parameter in the driven Tavis-Cummings Model, we do numerical analysis of them, and pay special attention to the dynamical behavior of the atoms and the cavity field modified by the external field.
Why has the bohr-sommerfeld model of the atom been ignoredby general chemistry textbooks?
Niaz, Mansoor; Cardellini, Liberato
2011-12-01
Bohr's model of the atom is considered to be important by general chemistry textbooks. A major shortcoming of this model was that it could not explain the spectra of atoms containing more than one electron. In order to increase the explanatory power of the model, Sommerfeld hypothesized the existence of elliptical orbits. This study has the following objectives: 1) Formulation of criteria based on a history and philosophy of science framework; and 2) Evaluation of university-level general chemistry textbooks based on the criteria, published in Italy and U.S.A. Presentation of a textbook was considered to be "satisfactory" if it included a description of the Bohr-Sommerfeld model along with diagrams of the elliptical orbits. Of the 28 textbooks published in Italy that were analyzed, only five were classified as "satisfactory". Of the 46 textbooks published in U.S.A., only three were classified as "satisfactory". This study has the following educational implications: a) Sommerfeld's innovation (auxiliary hypothesis) by introducing elliptical orbits, helped to restore the viability of Bohr's model; b) Bohr-Sommerfeld's model went no further than the alkali metals, which led scientists to look for other models; c) This clearly shows that scientific models are tentative in nature; d) Textbook authors and chemistry teachers do not consider the tentative nature of scientific knowledge to be important; e) Inclusion of the Bohr-Sommerfeld model in textbooks can help our students to understand how science progresses.
Building a pseudo-atomic model of the anaphase-promoting complex.
Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; da Fonseca, Paula C A; Barford, David
2013-11-01
The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14-15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.
Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle.
Sener, Melih K; Olsen, John D; Hunter, C Neil; Schulten, Klaus
2007-10-02
The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.
Atomic density functional and diagram of structures in the phase field crystal model
Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.
2016-02-01
The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindrical tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.
Energy Technology Data Exchange (ETDEWEB)
Balleza D, E
2004-07-01
In the first chapter of this work we will show a detailed analysis of the one cooling Doppler phenomenon that appears when a laser induces a dipolar moment to the atoms in such a way that these may interact with him to transfer moment to the field with the subsequent decrease of kinetic energy that macroscopically it is translated in cooling of the atomic cloud. When the experiments of atomic cooling were carried out it was observed that the temperature was smaller to the one than it predicted the cooling Doppler, this originates the creation of a theory but it dies in which the over simplification is eliminated that the alone atom consists of two energy levels and levels are introduced of it structures fine that are able to explain the extra cooling. To this phenomenon it is called Sisifo effect and it is studied detailedly in the chapter two. The first two chapters talk each other about the atomic cooling, but it stops that the atomic cloud can be manipulated, before being confined, problem that we will expose in the chapter three with experimental solutions that at the moment they are implemented in the laboratories around the world. In particular we will concentrate on the traps FORT (Far Off Resonance Trap, trap very outside of resonance) that confine to the atoms in optic nets. The lasers gaussianos originate a potential sinusoidal along the propagation address and gaussiano in the perpendicular plane to this. In the I surrender four he/she intends a three-dimensional model that substitutes To the variation sinusoidal for a function crenel and he/she makes an approach To first order in the radial dependence to obtain an oscillator potential Harmonic instead of the gaussiano that you taenia. The pattern is solved in a similar way To the pattern unidimensional of bands: they are the functions of wave solution For every period and they are coupled among if so that they satisfy conditions of rhythm, When making this you arrives to a womb that couples the
Atom-field entanglement in the Jaynes Cummings model without rotating wave approximation
Institute of Scientific and Technical Information of China (English)
M. Mirzaee; M. Batavani
2015-01-01
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.
Directory of Open Access Journals (Sweden)
Tcheou Michel P
2007-01-01
Full Text Available The number of waveforms monitored in power systems is increasing rapidly. This creates a demand for computational tools that aid in the analysis of the phenomena and also that allow efficient transmission and storage of the information acquired. In this context, signal processing techniques play a fundamental role. This work is a tutorial reviewing the principles and applications of atomic signal modeling of electric disturbance signals. The disturbance signal is modeled using a linear combination of damped sinusoidal components which are closely related to the phenomena typically observed in power systems. The signal model obtained is then employed for disturbance signal denoising, filtering of "DC components," and compression.
Institute of Scientific and Technical Information of China (English)
王金照; 陈民; 过增元
2002-01-01
Pair distribution functions and constant-volume heat capacities of liquid copper, silver and nickel have been calculated by molecular dynamics simulations with four different versions of the embedded-atom method (EAM) model, namely, the versions of Johnson, Mei, Cai and Pohlong. The simulated structural properties with the four potential models show reasonable agreement with experiments and have little difference with each other, while the calculated heat capacities with the different EAM versions show remarkable discrepancies. Detailed analyses of the energy of the liquid metallic system show that, to predict successfully the heat capacity, an EAM model should match the state equation first proposed by Rose.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej
2013-01-01
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Modeling of inelastic transport in one-dimensional metallic atomic wires
DEFF Research Database (Denmark)
Frederiksen, Thomas; Brandbyge, Mads; Lorente, N
2004-01-01
devices. A full description of the transport properties of atomic-size conductors therefore requires a quantum mechanical treatment of both the electronic and mechanical degrees of freedom. In this paper, we study a one-dimensional tight-binding model of the conducting electrons combined with a balls......Atomic-size conductors represent the ultimate limit of miniaturization, and understanding their properties is an important problem in the fields of nanoelectronics and molecular electronics. Quantum effects become important which leads to a physical behavior fundamentally different from macroscopic......-and-springs model for the mechanical motion of the nuclei comprising the wire. We determine the vibrational modes and frequencies for the wires. The electronic Hamiltonian is expanded to lowest order in these normal modes....
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.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Directory of Open Access Journals (Sweden)
Andrzej Koliński
2013-05-01
Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.
Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej
2013-05-10
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
COUPLED ATOMIZATION AND SPRAY MODELLING IN THE SPRAY FORMING PROCESS USING OPENFOAM
DEFF Research Database (Denmark)
Gjesing, Rasmus; Hattel, Jesper Henri; Fritsching, Udo
2009-01-01
model for droplet cooling and solidification. The model is tested and validated against results from literature and experiments. Subsequently, the model is used to simulate the complex flow fields in the spray forming process and the results are discussed. The presented model of the spray forming......The paper presents a numerical model capable of simulating the atomization, break-up and in-flight spray phenomena in the spray forming process. The model is developed and implemented in the freeware code openFOAM. The focus is on studying the coupling effect of the melt break-up phenomena...... by describing the thermal state of the particles in the spray. Therefore, the model includes a full thermal solver for the droplets, which also takes the rapid solidification of different drop sizes into account....
Classical and quantum dynamics of a model for atomic-molecular Bose--Einstein condensates
Santos Filho, Gilberto Nascimento; Tonel, Arlei Prestes; Foerster, Angela; Links, Jon(Centre for Mathematical Physics, School of Mathematics and Physics, The University of Queensland, 4072, Australia)
2005-01-01
We study a model for a two-mode atomic-molecular Bose--Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the coupling parameter space into four regions. The different regions give rise to qualitatively different dynamics. We then show that this classification holds true for the quantum dynamics.
Error sources in atomic force microscopy for dimensional measurements: Taxonomy and modeling
DEFF Research Database (Denmark)
Marinello, F.; Voltan, A.; Savio, E.
2010-01-01
This paper aimed at identifying the error sources that occur in dimensional measurements performed using atomic force microscopy. In particular, a set of characterization techniques for errors quantification is presented. The discussion on error sources is organized in four main categories......: scanning system, tip-surface interaction, environment, and data processing. The discussed errors include scaling effects, squareness errors, hysteresis, creep, tip convolution, and thermal drift. A mathematical model of the measurement system is eventually described, as a reference basis for errors...
DALGIÇ, Seyfettin; ÇOLAKOĞULLARI, Mutlu
2006-01-01
We present the dynamical properties of liquid Ag at different temperatures, using the Mishin and Doyoma-Kagure version of the Embedded Atom Model (EAM) potentials. They have been evaluated within the framework of the mode-coupling theory, using a self-consistent scheme that uses as input data only the static structure functions and the interatomic pair potentials of the liquid Ag. We have computed single-particle and collective time dependent properties of liquid Ag, and thereby calc...
Institute of Scientific and Technical Information of China (English)
HU ZHENG-FA; ZHOU SHI-KANG; GONG SHUN-SHENG; ZHAN MING-SHENG
2000-01-01
The potential model method for computation of Stark structure of Cs Rydberg states atoms and oscillator strength is described,for external electric fields varying from 0 to 600V/cm.Anticrossing,l-mixing and n-mixing phenomena are observed clearly from the map of Stark.Corresponding experiment is performed under the same condition,and the two results are in good agreement with each other within the experimental uncertainty.
On model materials designed by atomic layer deposition for catalysis purposes
Diskus, Madeleine
2011-01-01
The aim of this work was to investigate the potential of model materials designed by atomic layer deposition toward applications in catalysis research. Molybdenum based catalysts promoted with cobalt were selected as target materials, considering their important roles in various industrial processes. Particular attention was paid to understand the growth dynamics of the ALD processes involved and further to characterize the obtained materials carefully. It was of main concern to verify the fe...
Model for Atomic Oxygen Visible Line Emissions in Comet C/1995 O1 Hale-Bopp
Raghuram, Susarla
2012-01-01
We have recently developed a coupled chemistry-emission model for the green and red-doublet emissions of atomic oxygen on comet Hyakutake. In the present work we applied our model to comet Hale-Bopp, which had an order of magnitude higher H2O production rate than comet Hyakutake, to evaluate the photochemistry associated with the production and loss of O(1S) and O(1D) atoms and emission processes of green and red-doublet lines. We present the wavelength-dependent photo-attenuation rates for different photodissociation processes forming O(1S) and O(1D). The calculated radiative efficiency profiles of O(1S) and O(1D) atoms show that in comet Hale-Bopp the green and red-doublet emissions are emitted mostly above radial distances of 10^3 and 10^4 km, respectively. The model calculated [OI] 6300 A emission surface brightness and average intensity over the Fabry-P{\\'e}rot spectrometer field of view are consistent with the observation of Morgenthaler et al. (2001), while the intensity ratio of green to red-doublet e...
Directory of Open Access Journals (Sweden)
Hyuntae Na
2015-10-01
Full Text Available Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.
Na, Hyuntae; Jernigan, Robert L; Song, Guang
2015-10-01
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.
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.
Institute of Scientific and Technical Information of China (English)
李春先; 方卯发
2003-01-01
We study the squeezing for a two-level atom in the Jaynes-Cummings model with intensity-dependent coupling using quantum information entropy, and examine the influences of the initial state of the system on the squeezed component number and direction of the information entropy squeezing. Our results show that, the squeezed component number depends on the atomic initial distribution angle, while the squeezed direction is determined by both the phases of the atom and the field for the information entropy squeezing. Quantum information entropy is shown to be a remarkable precision measure for atomic squeezing.
Institute of Scientific and Technical Information of China (English)
李春先; 方卯发; 等
2003-01-01
We study the squeezing for a two-level atom in the Jaynes-Cumings model with intensity-dependent coupling using quantum information entropy,and examine the influences of the initial state of the system on the squeezed component number and direction of the information entropy squeezing.Our results show that,the squeezed component number depends on the atomic initial distribution angle,while the squeezed direction is determined by both the phases of the atom and the field for the information entropy squeezing.Quantum information entropy is shown to be a remarkable precision measure for atomic squeezing.
Directory of Open Access Journals (Sweden)
Vinícius Catão de Assis Souza
2006-03-01
Full Text Available Assuming (i the importance of using analogies in science teaching, (ii the learning difficulties related to the atomic models both discussed in the literature and observed in our previous research, and (iii the gap found in the literature concerning studies that probe how students really understand analogies presented to them in science teaching, we investigate, in this study, how students from the Medium Level understand the atomic models from analogies used to present and explain them. In order to limit the study, we chose only the atomic models proposed by J.J.Thomson and Niels Bohr. This was because the analogies of “the plum pudding” and “the solar system” are very often used in their teaching. This study aims at discussing the contributions and limitations of using such analogies in the teaching of the correspondent atomic models. Data were gathered from a written questionnaire answered by 99 1st year students (from one public and one private school. Data analysis made it evident that most students do not understand the analogies, as well as the atomic models to which they are associated. Moreover, there is no meaning for them in using two different analogies for the atom. From data analysis we discuss some teaching implications. We also propose new research questions that may contribute to foster the discussion and the improvement in the teaching of the atomic models.
Error analysis for momentum conservation in Atomic-Continuum Coupled Model
Yang, Yantao; Cui, Junzhi; Han, Tiansi
2016-08-01
Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.
Self-consistent tight-binding atomic-relaxation model of titanium dioxide
Energy Technology Data Exchange (ETDEWEB)
Schelling, P.K.; Yu, N.; Halley, J.W. [School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455 (United States)
1998-07-01
We report a self-consistent tight-binding atomic-relaxation model for titanium dioxide. We fit the parameters of the model to first-principles electronic structure calculations of the band structure and energy as a function of lattice parameters in bulk rutile. We report the method and results for the surface structures and energies of relaxed (110), (100), and (001) surfaces of rutile TiO{sub 2} as well as work functions for these surfaces. Good agreement with first-principles calculations and experiments, where available, is found for these surfaces. We find significant charge transfer (increased covalency) at the surfaces. {copyright} {ital 1998} {ital The American Physical Society}
A quasi-stationary numerical model of atomized metal droplets, II: Prediction and assessment
DEFF Research Database (Denmark)
Pryds, Nini H.; Hattel, Jesper Henri; Thorborg, Jesper
1999-01-01
by comparing experimental and calculated results for the powder particles of 12Cr-Mo-V steel. The study is also focusing on some aspects of the process which are not available experimentally, e.g. the effect of undercooling and gas/metal ratio on the solidification. The important effect of these parameters has......A new model which extends previous studies and includes the interaction between enveloping gas and an array of droplets has been developed and presented in a previous paper. The model incorporates the probability density function of atomized metallic droplets into the heat transfer equations...
Atomically thin spherical shell-shaped superscatterers based on a Bohr model.
Li, Rujiang; Lin, Xiao; Lin, Shisheng; Liu, Xu; Chen, Hongsheng
2015-12-18
Graphene monolayers can be used for atomically thin three-dimensional shell-shaped superscatterer designs. Due to the excitation of the first-order resonance of transverse magnetic (TM) graphene plasmons, the scattering cross section of the bare subwavelength dielectric particle is enhanced significantly by five orders of magnitude. The superscattering phenomenon can be intuitively understood and interpreted with a Bohr model. In addition, based on the analysis of the Bohr model, it is shown that contrary to the TM case, superscattering is hard to achieve by exciting the resonance of transverse electric (TE) graphene plasmons due to their poor field confinements.
Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model
Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2016-12-01
In this paper, we study theoretically atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice by using an extended Bose-Hubbard model with intersite repulsions on a 3D optical lattice. Here, the phase and density fluctuations of the boson variable on each site of the optical lattice describe the vector potential and the electric field on each link of the gauge-model lattice, respectively. The target gauge model is different from the standard Wilson-type U(1) gauge-Higgs model because it has plaquette and Higgs interactions with asymmetric couplings in the space-time directions. Nevertheless, the corresponding quantum simulation is still important as it provides us with a platform to study unexplored time-dependent phenomena characteristic of each phase in the general gauge-Higgs models. To determine the phase diagram of the gauge-Higgs model at zero temperature, we perform Monte Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the confinement and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time evolution of an electric flux that initially is put on a straight line connecting two external point charges. We also calculate the potential energy between this pair of charges and obtain the string tension in the confinement phase. Finally, we propose a feasible experimental setup for the atomic simulations of this quantum gauge-Higgs model on the 3D optical lattice. These results may serve as theoretical guides for future experiments.
Stauffer, D; Dragneva, N; Floriano, W B; Mawhinney, R C; Fanchini, G; French, S; Rubel, O
2014-07-28
Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.
Testing the validity of the International Atomic Energy Agency (IAEA) safety culture model.
López de Castro, Borja; Gracia, Francisco J; Peiró, José M; Pietrantoni, Luca; Hernández, Ana
2013-11-01
This paper takes the first steps to empirically validate the widely used model of safety culture of the International Atomic Energy Agency (IAEA), composed of five dimensions, further specified by 37 attributes. To do so, three independent and complementary studies are presented. First, 290 students serve to collect evidence about the face validity of the model. Second, 48 experts in organizational behavior judge its content validity. And third, 468 workers in a Spanish nuclear power plant help to reveal how closely the theoretical five-dimensional model can be replicated. Our findings suggest that several attributes of the model may not be related to their corresponding dimensions. According to our results, a one-dimensional structure fits the data better than the five dimensions proposed by the IAEA. Moreover, the IAEA model, as it stands, seems to have rather moderate content validity and low face validity. Practical implications for researchers and practitioners are included.
DEFF Research Database (Denmark)
Valentin, Jan B.; Andreetta, Christian; Boomsma, Wouter
2014-01-01
We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length...... scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy...... terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive...
Sound speed and oscillation frequencies for a solar model evolved with Los Alamos ATOMIC opacities
Guzik, Joyce Ann; Fontes, Christopher; Walczak, Przemyslaw; Wood, Suzannah R.; Mussack, Katie
2015-08-01
Los Alamos has calculated a new generation of radiative opacities for elements with atomic number Z=1-30 with improved physics input, updated atomic data, and finer temperature grid to replace the Los Alamos LEDCOP opacities released in the year 2000. We calculate the evolution of a standard solar model including these new opacities, and compare with a model evolved using the Lawrence Livermore National Laboratory OPAL opacities released about 1996. We use the solar abundance mixture of Asplund, Grevesse, Sauval, and Scott (2009), including 2015 updates. The Los Alamos ATOMIC opacities (Colgan et al. 2013a,b) are somewhat higher than those of OPAL for temperatures and densities near the base of the solar convection zone. We compare the calculated nonadiabatic solar oscillation frequencies and solar interior sound speed to observed frequencies and helioseismic inferences. We discuss the potential for increased opacities to partially mitigate the ‘solar abundance problem’.References:J. Colgan, D.P. Kilcrease, N.H. Magee, Jr., G.S.J. Armstrong, J. Abdallah, Jr., M.E. Sherrill, C.J. Fontes, H.L. Zhang and P. Hakel, Eighth International Conference on Atomic and Molecular Data and their Applications: ICAMDATA, Gaithersburg, MD 2012, AIP Conf. Proc. No. 1545, (AIP, New York, 2013a), pp. 17-26.J. Colgan, D.P. Kilcrease, N.H. Magee, Jr, G.S.J. Armstrong, J. Abdallah, Jr., M.E. Sherrill, C.J. Fontes, H.L. Zhang and P. Hakel, High Energy Density Physics 9, 369 (2013b).
What is the "best" atomic charge model to describe through-space charge-transfer excitations?
Jacquemin, Denis; Le Bahers, Tangui; Adamo, Carlo; Ciofini, Ilaria
2012-04-28
We investigate the efficiency of several partial atomic charge models (Mulliken, Hirshfeld, Bader, Natural, Merz-Kollman and ChelpG) for investigating the through-space charge-transfer in push-pull organic compounds with Time-Dependent Density Functional Theory approaches. The results of these models are compared to benchmark values obtained by determining the difference of total densities between the ground and excited states. Both model push-pull oligomers and two classes of "real-life" organic dyes (indoline and diketopyrrolopyrrole) used as sensitisers in solar cell applications have been considered. Though the difference of dipole moments between the ground and excited states is reproduced by most approaches, no atomic charge model is fully satisfactory for reproducing the distance and amount of charge transferred that are provided by the density picture. Overall, the partitioning schemes fitting the electrostatic potential (e.g. Merz-Kollman) stand as the most consistent compromises in the framework of simulating through-space charge-transfer, whereas the other models tend to yield qualitatively inconsistent values.
Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.
Ni, Boris; Baumketner, Andrij
2013-02-14
Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.
Institute of Scientific and Technical Information of China (English)
LI Shichun
2004-01-01
Based on the Thomas-Fermi-Dirac-Cheng model, atomic phase diagram or electron density versus atomic radius diagram describing the interaction properties of atoms of different kinds in equilibrium state is developed. Atomic phase diagram is established based on the two-atoms model. Besides atomic radius, electron density and continuity condition for electron density on interfaces between atoms, the lever law of atomic phase diagram involving other physical parameters is taken into account, such as the binding energy, for the sake of simplicity.
From deep TLS validation to ensembles of atomic models built from elemental motions
Energy Technology Data Exchange (ETDEWEB)
Urzhumtsev, Alexandre, E-mail: sacha@igbmc.fr [Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Université de Lorraine, BP 239, 54506 Vandoeuvre-les-Nancy (France); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); Van Benschoten, Andrew H.; Fraser, James S. [University of California, San Francisco, San Francisco, CA 94158 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); University of California Berkeley, Berkeley, CA 94720 (United States); Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France)
2015-07-28
Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.
Energy Technology Data Exchange (ETDEWEB)
Deng, Zhang; He, Wenjie; Duan, Chenlong [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Chen, Rong, E-mail: rongchen@mail.hust.edu.cn [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Shan, Bin [State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)
2016-01-15
Spatial atomic layer deposition (SALD) is a promising technology with the aim of combining the advantages of excellent uniformity and conformity of temporal atomic layer deposition (ALD), and an industrial scalable and continuous process. In this manuscript, an experimental and numerical combined model of atmospheric SALD system is presented. To establish the connection between the process parameters and the growth efficiency, a quantitative model on reactant isolation, throughput, and precursor utilization is performed based on the separation gas flow rate, carrier gas flow rate, and precursor mass fraction. The simulation results based on this model show an inverse relation between the precursor usage and the carrier gas flow rate. With the constant carrier gas flow, the relationship of precursor usage and precursor mass fraction follows monotonic function. The precursor concentration, regardless of gas velocity, is the determinant factor of the minimal residual time. The narrow gap between precursor injecting heads and the substrate surface in general SALD system leads to a low Péclet number. In this situation, the gas diffusion act as a leading role in the precursor transport in the small gap rather than the convection. Fluid kinetics from the numerical model is independent of the specific structure, which is instructive for the SALD geometry design as well as its process optimization.
Mg line formation in late-type stellar atmospheres: I. The model atom
Osorio, Y; Lind, K; Belyaev, A K; Spielfiedel, A; Guitou, M; Feautrier, N
2015-01-01
Mg is often traced in late-type stars using lines of neutral magnesium, which is expected to be subject to departures from LTE. The astrophysical importance of Mg as well as its relative simplicity from an atomic physics point of view, makes it a prime target and test bed for detailed ab initio non-LTE modelling in stellar atmospheres. For the low-lying states of Mg i, electron collision data were calculated using the R-matrix method. Calculations for collisional broadening by neutral hydrogen were also performed where data were missing. These calculations, together with data from the literature, were used to build a model atom. First, the modelling was tested by comparisons with observed spectra of benchmark stars with well-known parameters. Second, the spectral line behaviour and uncertainties were explored by extensive experiments in which sets of collisional data were changed or removed. The modelled spectra agree well with observed spectra. The line-to-line scatter in the derived abundances shows improve...
Pairwise energies for polypeptide coarse-grained models derived from atomic force fields
Betancourt, Marcos R.; Omovie, Sheyore J.
2009-05-01
The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.
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.
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.
Charge-state-dependent energy loss of slow ions. II. Statistical atom model
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.
A computer code for calculations in the algebraic collective model of the atomic nucleus
Welsh, T A
2016-01-01
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1,1) x SO(5) dynamical group. This, in particular, obviates the use of coefficients of fractional parentage. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [pi x q x pi]_0 and [pi x pi]_{LM}, where q_M are the model's quadrupole moments, and pi_N are corresponding conjugate momenta (-2>=M,N<=2). The code also provides ready access to SO(3)-reduced SO(5) Clebsch-Gordan coefficients through data files provided with the code.
Quantum simulation of the Hubbard model with dopant atoms in silicon.
Salfi, J; Mol, J A; Rahman, R; Klimeck, G; Simmons, M Y; Hollenberg, L C L; Rogge, S
2016-04-20
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.
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.
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.
Coqblin-Schrieffer model for an ultracold gas of ytterbium atoms with metastable state
Kuzmenko, Igor; Kuzmenko, Tetyana; Avishai, Yshai; Jo, Gyu-Boong
2016-03-01
Motivated by the impressive recent advance in manipulating cold ytterbium atoms, we explore and substantiate the feasibility of realizing the Coqblin-Schrieffer model in a gas of cold fermionic 173Yb atoms. Making use of different AC polarizabillity of the electronic ground state (electronic configuration S10) and the long lived metastable state (electronic configuration P30), it is substantiated that the latter can be localized and serve as a magnetic impurity while the former remains itinerant. The exchange mechanism between the itinerant S10 and the localized P30 atoms is analyzed and shown to be antiferromagnetic. The ensuing SU(6) symmetric Coqblin-Schrieffer Hamiltonian is constructed, and, using the calculated exchange constant J , perturbative renormalization group (RG) analysis yields the Kondo temperature TK that is experimentally accessible. A number of thermodynamic measurable observables are calculated in the weak-coupling regime T >TK (using perturbative RG analysis) and in the strong-coupling regime T
Atomic spin-chain realization of a model for quantum criticality
Toskovic, R.; van den Berg, R.; Spinelli, A.; Eliens, I. S.; van den Toorn, B.; Bryant, B.; Caux, J.-S.; Otte, A. F.
2016-07-01
The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum computing and spintronic devices; on the other hand, they can be used as fundamental building blocks for the realization of textbook many-body quantum models, illustrating key concepts such as quantum phase transitions, topological order or frustration as a function of system size. Here, we use low-temperature scanning tunnelling microscopy to construct arrays of magnetic atoms on a surface, designed to behave like spin-1/2 XXZ Heisenberg chains in a transverse field, for which a quantum phase transition from an antiferromagnetic to a paramagnetic phase is predicted in the thermodynamic limit. Site-resolved measurements on these finite-size realizations reveal a number of sudden ground state changes when the field approaches the critical value, each corresponding to a new domain wall entering the chains. We observe that these state crossings become closer for longer chains, suggesting the onset of critical behaviour. Our results present opportunities for further studies on quantum behaviour of many-body systems, as a function of their size and structural complexity.
Why Do We Believe that an Atom Is Colourless? Reflections about the Teaching of the Particle Model.
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…
Euston, Stephen R
2010-10-11
The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.
Misquitta, Alston J; Stone, Anthony J
2016-09-13
Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models.
Chen, Jianhan
2010-09-14
The generalized Born (GB) theory is a prime choice for implicit treatment of solvent that provides a favorable balance between efficiency and accuracy for reliable simulation of protein conformational equilibria. In GB, the dielectric boundary is a key physical property that needs to be properly described. While it is widely accepted that the molecular surface (MS) should provide the most physical description, most existing GB models are based on van der Waals (vdW)-like surfaces for computational simplicity and efficiency. A simple and effective approximation to molecular volume is explored here using atom-centered dielectric functions within the context of a generalized Born model with simple switching (GBSW). The new model, termed GBSW/MS2, is as efficient as the original vdW-like-surface-based GBSW model, but is able to reproduce the Born radii calculated from the "exact" Poisson-Boltzmann theory with a correlation of 0.95. More importantly, examination of the potentials of mean force of hydrogen-bonding and charge-charge interactions demonstrates that GBSW/MS2 correctly captures the first desolvation peaks, a key signature of true MS. Physical parameters including atomic input radii and peptide backbone torsion were subsequently optimized on the basis of solvation free energies of model compounds, potentials of mean force of their interactions, and conformational equilibria of a set of helical and β-hairpin model peptides. The resulting GBSW/MS2 protein force field reasonably recapitulates the structures and stabilities of these model peptides. Several remaining limitations and possible future developments are also discussed.
State-to-state modeling of non equilibrium low-temperature atomic plasmas
Bultel, Arnaud; Morel, Vincent; Annaloro, Julien; Druguet, Marie-Claude
2017-03-01
The most relevant approach leading to a thorough understanding of the behavior of non equilibrium atomic plasmas is to elaborate state-to-state models in which the mass conservation equation is applied directly to atoms or ions on their excited states. The present communication reports the elaboration of such models and the results obtained. Two situations close to each other are considered. First, the plasmas produced behind shock fronts obtained in ground test facilities (shock tubes) or during planetary atmospheric entries of spacecrafts are discussed. We focused our attention on the nitrogen case for which a complete implementation of the CoRaM-N2 collisional-radiative model has been performed in a steady one-dimensional computation code based on the Rankine-Hugoniot assumptions. Second, the plasmas produced by the interaction between an ultra short laser pulse and a tungsten sample are discussed in the framework of the elaboration of the Laser-Induced Breakdown Spectroscopy (LIBS) technique. In the present case, tungsten has been chosen in the purpose of validating an in situ experimental method able to provide the elemental composition of the divertor wall of a tokamak like WEST or ITER undergoing high energetic deuterium and tritium nuclei fluxes.
Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.
Jorge, Miguel; Garrido, Nuno M; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M
2017-03-05
We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.
Valentin, Jan B; Andreetta, Christian; Boomsma, Wouter; Bottaro, Sandro; Ferkinghoff-Borg, Jesper; Frellsen, Jes; Mardia, Kanti V; Tian, Pengfei; Hamelryck, Thomas
2014-02-01
We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications.
Silva, Arnaldo F; Richter, Wagner E; Meneses, Helen G C; Bruns, Roy E
2014-11-14
Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.
Topological phases of the kicked Harper-Kitaev model with ultracold atoms
Chen, M. N.; Mei, Feng; Su, W.; Wang, Huai-Qiang; Zhu, Shi-Liang; Sheng, L.; Xing, D. Y.
2017-01-01
We propose using ultracold atoms trapped in a one-dimensional periodically driven optical lattice to realize the Harper-Kitaev model, where the on-site energies are periodically kicked. Such a system provides a natural platform to study both Chern insulators and Majorana fermions. Based on calculating the quasienergy spectra, we find that both Floquet Majorana modes and Hall chiral edge modes could appear at the sample boundary in the gaps between the quasienergy bands. We also study the competition of topological superconductor and Chern insulator states in the model. We calculate the {{{Z}}2}× {{{Z}}2} index and Floquet Chern number to characterize the above two different topological states, including the topological phase transitions in the kicked Harper-Kitaev model with the increase in the strength of the kick.
Directory of Open Access Journals (Sweden)
Marco A. M. Rodrigues
2007-01-01
Full Text Available The number of waveforms monitored in power systems is increasing rapidly. This creates a demand for computational tools that aid in the analysis of the phenomena and also that allow efficient transmission and storage of the information acquired. In this context, signal processing techniques play a fundamental role. This work is a tutorial reviewing the principles and applications of atomic signal modeling of electric disturbance signals. The disturbance signal is modeled using a linear combination of damped sinusoidal components which are closely related to the phenomena typically observed in power systems. The signal model obtained is then employed for disturbance signal denoising, filtering of “DC components,” and compression.
Model for fast, nonadiabatic collisions between alkali atoms and diatomic molecules
Hickman, A. P.
1980-11-01
Equations for collisions involving two potential surfaces are presented in the impact parameter approximation. In this approximation, a rectilinear classical trajectory is assumed for the translational motion, leading to a time-dependent Schroedinger's equation for the remaining degrees of freedom. Model potentials are considered for collisions of alkali atoms with diatomic molecules that lead to a particularly simple form of the final equations. Using the Magnus approximation, these equations are solved for parameters chosen to model the process Cs+O2→Cs++O2-, and total cross sections for ion-pair formation are obtained as a function of energy. The results exhibit oscillations that correspond qualitatively to those seen in recent measurements. In addition, the model predicts that the oscillations will become less pronounced as the initial vibrational level of O2 is increased.
Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains
Glaessgen, E. H.; Saether, E.; Yamakov, V.
2008-01-01
Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.
Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2013-09-13
Recently, the possibility of quantum simulation of dynamical gauge fields was pointed out by using a system of cold atoms trapped on each link in an optical lattice. However, to implement exact local gauge invariance, fine-tuning the interaction parameters among atoms is necessary. In the present Letter, we study the effect of violation of the U(1) local gauge invariance by relaxing the fine-tuning of the parameters and showing that a wide variety of cold atoms is still a faithful quantum simulator for a U(1) gauge-Higgs model containing a Higgs field sitting on sites. The clarification of the dynamics of this gauge-Higgs model sheds some light upon various unsolved problems, including the inflation process of the early Universe. We study the phase structure of this model by Monte Carlo simulation and also discuss the atomic characteristics of the Higgs phase in each simulator.
Application of atomic force microscopy to the study of natural and model soil particles.
Cheng, S; Bryant, R; Doerr, S H; Rhodri Williams, P; Wright, C J
2008-09-01
The structure and surface chemistry of soil particles has extensive impact on many bulk scale properties and processes of soil systems and consequently the environments that they support. There are a number of physiochemical mechanisms that operate at the nanoscale which affect the soil's capability to maintain native vegetation and crops; this includes soil hydrophobicity and the soil's capacity to hold water and nutrients. The present study used atomic force microscopy in a novel approach to provide unique insight into the nanoscale properties of natural soil particles that control the physiochemical interaction of material within the soil column. There have been few atomic force microscopy studies of soil, perhaps a reflection of the heterogeneous nature of the system. The present study adopted an imaging and force measurement research strategy that accounted for the heterogeneity and used model systems to aid interpretation. The surface roughness of natural soil particles increased with depth in the soil column a consequence of the attachment of organic material within the crevices of the soil particles. The roughness root mean square calculated from ten 25 microm(2) images for five different soil particles from a Netherlands soil was 53.0 nm, 68.0 nm, 92.2 nm and 106.4 nm for the respective soil depths of 0-10 cm, 10-20 cm, 20-30 cm and 30-40 cm. A novel analysis method of atomic force microscopy phase images based on phase angle distribution across a surface was used to interpret the nanoscale distribution of organic material attached to natural and model soil particles. Phase angle distributions obtained from phase images of model surfaces were found to be bimodal, indicating multiple layers of material, which changed with the concentration of adsorbed humic acid. Phase angle distributions obtained from phase images of natural soil particles indicated a trend of decreasing surface coverage with increasing depth in the soil column. This was consistent with
Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model
Kuno, Yoshihito; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2016-01-01
In this paper, we study atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice. We start from an extended 3D Bose-Hubbard model with nearest-neighbor repulsions and show that it can simulate a U(1) gauge-Higgs model with next nearest-neighbor Higgs couplings. Here the phase of the boson variable on each site of the optical lattice describes the vector potential on each link of the gauge-model lattice. To determine the phase diagram of the gauge-Higgs model at a zero temperature, we perform Monte-Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the three phases, i.e., the confinement, Coulomb and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time-evolution of an electric flux initially put on a straight line connecting two external point charges. We also calculate the potential energy between this pair ...
Scrape-off layer modeling with kinetic or diffusion description of charge-exchange atoms
Tokar, M. Z.
2016-12-01
Hydrogen isotope atoms, generated by charge-exchange (c-x) of neutral particles recycling from the first wall of a fusion reactor, are described either kinetically or in a diffusion approximation. In a one-dimensional (1-D) geometry, kinetic calculations are accelerated enormously by applying an approximate pass method for the assessment of integrals in the velocity space. This permits to perform an exhaustive comparison of calculations done with both approaches. The diffusion approximation is deduced directly from the velocity distribution function of c-x atoms in the limit of charge-exchanges with ions occurring much more frequently than ionization by electrons. The profiles across the flux surfaces of the plasma parameters averaged along the main part of the scrape-off layer (SOL), beyond the X-point and divertor regions, are calculated from the one-dimensional equations where parallel flows of charged particles and energy towards the divertor are taken into account as additional loss terms. It is demonstrated that the heat losses can be firmly estimated from the SOL averaged parameters only; for the particle loss the conditions in the divertor are of importance and the sensitivity of the results to the so-called "divertor impact factor" is investigated. The coupled 1-D models for neutral and charged species, with c-x atoms described either kinetically or in the diffusion approximation, are applied to assess the SOL conditions in a fusion reactor, with the input parameters from the European DEMO project. It is shown that the diffusion approximation provides practically the same profiles across the flux surfaces for the plasma density, electron, and ion temperatures, as those obtained with the kinetic description for c-x atoms. The main difference between the two approaches is observed in the characteristics of these species themselves. In particular, their energy flux onto the wall is underestimated in calculations with the diffusion approximation by 20 %-30
Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji
2016-12-13
Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.
Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.
Mazhab-Jafari, Mohammad T; Rohou, Alexis; Schmidt, Carla; Bueler, Stephanie A; Benlekbir, Samir; Robinson, Carol V; Rubinstein, John L
2016-11-03
Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V1 region drives proton translocation through the membrane-embedded VO region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V1 and VO regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the VO complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits ac8c'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.
Non-equilibrium dynamical phases of the two-atom Dicke model
Energy Technology Data Exchange (ETDEWEB)
Bhattacherjee, Aranya B.
2014-09-12
In this paper, we investigate the non-equilibrium dynamical phases of the two-atom Dicke model, which can be realized in a two species Bose–Einstein condensate interacting with a single light mode in an optical cavity. Apart from the usual non-equilibrium normal and inverted phases, a non-equilibrium mixed phase is possible which is a combination of normal and inverted phase. A new kind of dynamical phase transition is predicted from non-superradiant mixed phase to the superradiant phase which can be achieved by tuning the two different atom–photon couplings. We also show that a dynamical phase transition from the non-superradiant mixed phase to the superradiant phase is forbidden for certain values of the two atom–photon coupling strengths. - Highlights: • We investigate the non-equilibrium dynamical phases of the two-atom Dicke model. • The dynamical phase diagram reveals a new kind of non-equilibrium mixed phase. • A new kind of dynamical phase transition is predicted from mixed phase to the superradiant phase. • In the dynamical phase diagram of the mixed phase, there are regions where the superradiant phase cannot exist.
Electric dipole moments of nucleons, nuclei, and atoms: The Standard Model and beyond
Engel, Jonathan; Ramsey-Musolf, Michael J.; van Kolck, U.
2013-07-01
Searches for the permanent electric dipole moments (EDMs) of molecules, atoms, nucleons and nuclei provide powerful probes of CP violation both within the Standard Model and beyond the Standard Model (BSM). The interpretation of experimental EDM limits requires careful delineation of physics at a wide range of scales, from the long-range atomic and molecular scales to the short-distance dynamics of physics at or beyond the Fermi scale. In this review, we provide a framework for disentangling contributions from physics at these disparate scales, building out from the set of dimension four and six effective operators that embody CP violation at the Fermi scale. We survey computations of hadronic and nuclear matrix elements associated with Fermi-scale CP violation in systems of experimental interest and quantify the present level of theoretical uncertainty in these calculations. Using representative BSM scenarios of current interest, we discuss ways in which the interplay of physics at various scales can generate EDMs at a potentially observable level.
Energy Technology Data Exchange (ETDEWEB)
Bertolus, Marjorie, E-mail: marjorie.bertolus@cea.fr [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Freyss, Michel; Dorado, Boris; Martin, Guillaume; Hoang, Kiet; Maillard, Serge; Skorek, Richard; Garcia, Philippe; Valot, Carole [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Chartier, Alain; Van Brutzel, Laurent; Fossati, Paul [CEA, DEN, DPC/SCCME, 91191 Gif-sur-Yvette (France); Grimes, Robin W.; Parfitt, David C.; Bishop, Clare L.; Murphy, Samuel T.; Rushton, Michael J.D. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Staicu, Dragos; Yakub, Eugen; Nichenko, Sergii [European Commission, Joint Research Centre, Institute for Transuranium Elements, 76125 Karlsruhe (Germany); and others
2015-07-15
This article presents a synthesis of the investigations at the atomic scale of the transport properties of defects and fission gases in uranium dioxide, as well as of the transfer of results from the atomic scale to models at the mesoscopic scale, performed during the F-BRIDGE European project (2008–2012). We first present the mesoscale models used to investigate uranium oxide fuel under irradiation, and in particular the cluster dynamics and kinetic Monte Carlo methods employed to model the behaviour of defects and fission gases in UO{sub 2}, as well as the parameters of these models. Second, we describe briefly the atomic scale methods employed, i.e. electronic structure calculations and empirical potential methods. Then, we show the results of the calculation of the data necessary for the mesoscale models using these atomic scale methods. Finally, we summarise the links built between the atomic and mesoscopic scale by listing the data calculated at the atomic scale which are to be used as input in mesoscale modelling. Despite specific difficulties in the description of fuel materials, the results obtained in F-BRIDGE show that atomic scale modelling methods are now mature enough to obtain precise data to feed higher scale models and help interpret experiments on nuclear fuels. These methods bring valuable insight, in particular the formation, binding and migration energies of point and extended defects, fission product localization, incorporation energies and migration pathways, elementary mechanisms of irradiation induced processes. These studies open the way for the investigation of other significant phenomena involved in fuel behaviour, in particular the thermochemical and thermomechanical properties and their evolution in-pile, complex microstructures, as well as of more complex fuels.
A cluster expansion model for predicting activation barrier of atomic processes
Energy Technology Data Exchange (ETDEWEB)
Rehman, Tafizur; Jaipal, M. [Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208 016 (India); Chatterjee, Abhijit, E-mail: achatter@iitk.ac.in [Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208 016 (India); Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400 076 (India)
2013-06-15
We introduce a procedure based on cluster expansion models for predicting the activation barrier of atomic processes encountered while studying the dynamics of a material system using the kinetic Monte Carlo (KMC) method. Starting with an interatomic potential description, a mathematical derivation is presented to show that the local environment dependence of the activation barrier can be captured using cluster interaction models. Next, we develop a systematic procedure for training the cluster interaction model on-the-fly, which involves: (i) obtaining activation barriers for handful local environments using nudged elastic band (NEB) calculations, (ii) identifying the local environment by analyzing the NEB results, and (iii) estimating the cluster interaction model parameters from the activation barrier data. Once a cluster expansion model has been trained, it is used to predict activation barriers without requiring any additional NEB calculations. Numerical studies are performed to validate the cluster expansion model by studying hop processes in Ag/Ag(100). We show that the use of cluster expansion model with KMC enables efficient generation of an accurate process rate catalog.
Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.
Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E
2012-08-01
Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.
Song, Young-Sun; Kim, Jeongwoo; Jhi, Seung-Hoon
2017-03-01
We study the nature of atomic rearrangement during the phase-change processes in the superlattice of GeTe and Sb2Te3 by developing a new approach combining the first-principles calculations and a pair-potential model. We investigate the phase-change process in terms of energy changes from individual pairs or atoms by applying the pair (atom)-projection analysis to the intermediate structures between the initial and final states obtained from the climbing-image nudged elastic band method. Among the prototypical steps that can lead to the atomic layer rearrangement, we find that the required energy for the phase change is dominated by specific atoms responsible for the intrinsic energy barrier and the response to external pressure. Our approach of combining the first-principles methods and pair potential model with the projecting analysis can be a very efficient method in revealing the detailed atomic motions and the mechanism of fast atomic transition of the phase-change materials.
Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei
2015-12-28
Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.
Directory of Open Access Journals (Sweden)
Nuri Yazdani
2014-03-01
Full Text Available Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD. Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.
Johns, H. M.; Lanier, N. E.; Kline, J. L.; Fontes, C. J.; Perry, T. S.; Fryer, C. L.; Brown, C. R. D.; Morton, J. W.; Hager, J. D.; Sherrill, M. E.
2016-11-01
We present synthetic transmission spectra generated with PrismSPECT utilizing both the ATBASE model and the Los Alamos opacity library (OPLIB) to evaluate whether an alternative choice in atomic data will impact modeling of experimental data from radiation transport experiments using Sc-doped aerogel foams (ScSi6O12 at 75 mg/cm3 density). We have determined that in the 50-200 eV Te range there is a significant difference in the 1s-3p spectra, especially below 100 eV, and for Te = 200 eV above 5000 eV in photon energy. Examining synthetic spectra generated using OPLIB with 300 resolving power reveals spectral sensitivity to Te changes of ˜3 eV.
An analytic technique for statistically modeling random atomic clock errors in estimation
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.
Dynamic Modeling for the Design and Cyclic Operation of an Atomic Layer Deposition (ALD Reactor
Directory of Open Access Journals (Sweden)
Curtisha D. Travis
2013-08-01
Full Text Available A laboratory-scale atomic layer deposition (ALD reactor system model is derived for alumina deposition using trimethylaluminum and water as precursors. Model components describing the precursor thermophysical properties, reactor-scale gas-phase dynamics and surface reaction kinetics derived from absolute reaction rate theory are integrated to simulate the complete reactor system. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm based on collocation discretization in time, resulting in an unambiguous definition of film growth-per-cycle (gpc. A key finding of this study is that unintended chemical vapor deposition conditions can mask regions of operation that would otherwise correspond to ideal saturating ALD operation. The use of the simulator for assisting in process design decisions is presented.
Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa; Park, Hyung Gyu; Utke, Ivo
2014-01-01
Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT) arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD). Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.
An atomic model of the tropomyosin cable on F-actin.
Orzechowski, Marek; Li, Xiaochuan Edward; Fischer, Stefan; Lehman, William
2014-08-05
Tropomyosin regulates a wide variety of actin filament functions and is best known for the role that it plays together with troponin in controlling muscle activity. For effective performance on actin filaments, adjacent 42-nm-long tropomyosin molecules are joined together by a 9- to 10-residue head-to-tail overlapping domain to form a continuous cable that wraps around the F-actin helix. Yet, despite the apparent simplicity of tropomyosin's coiled-coil structure and its well-known periodic association with successive actin subunits along F-actin, the structure of the tropomyosin cable on actin is uncertain. This is because the conformation of the overlap region that joins neighboring molecules is poorly understood, thus leaving a significant gap in our understanding of thin-filament structure and regulation. However, recent molecular-dynamics simulations of overlap segments defined their overall shape and provided unique and sufficient cues to model the whole actin-tropomyosin filament assembly in atomic detail. In this study, we show that these MD structures merge seamlessly onto the ends of tropomyosin coiled-coils. Adjacent tropomyosin molecules can then be joined together to provide a comprehensive model of the tropomyosin cable running continuously on F-actin. The resulting complete model presented here describes for the first time (to our knowledge) an atomic-level structure of αα-striated muscle tropomyosin bound to an actin filament that includes the critical overlap domain. Thus, the model provides a structural correlate to evaluate thin-filament mechanics, self-assembly mechanisms, and the effect of disease-causing mutations.
Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo
2016-01-01
In this paper, we study atomic quantum simulations of $(1+1)$-dimensional($(1+1)$D) U(1) gauge-Higgs models (GHMs) defined on a lattice. We explain how U(1) lattice GHMs appear from an extended Bose-Hubbard model (EBHM) describing ultra-cold atoms with a nearest neighbor repulsion in a 1D optical lattice. We first study a phase diagram of the 1D EBHM at low fillings by means of a quantum Monte-Carlo(MC) simulation. Next, we study the EBHM at large fillings and also GHMs by the MC simulations in the path-integral formalism and show that there are four phases, i.e., the Higgs phase(superfluid), the confinement phase (Mott insulator), and phases corresponding to the density wave and the supersolid. With the obtained phase diagrams, we investigate the relationship between the two models. Finally, we study real-time dynamic of an electric flux in the GHMs by the Gross-Pitaevskii equations and the truncated Wigner approximation.
Malinska, Maura; Dauter, Zbigniew
2016-06-01
In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.
Energy Technology Data Exchange (ETDEWEB)
MacFarlane, Joseph J [Prism Computational Sciences
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
The Pre-Service Science Teachers' Mental Models for Concept of Atoms and Learning Difficulties
Kiray, Seyit Ahmet
2016-01-01
The purpose of this study is to reveal the pre-service science teachers' difficulties about the concept of atoms. The data was collected from two different sources: The Draw an Atom Test (DAAT) and face-to-face interviews. Draw an atom test (DAAT) were administered to the 142 science teacher candidates. To elaborate the results, the researcher…
How Sommerfeld extended Bohr's model of the atom (1913-1916)
Eckert, Michael
2014-04-01
Sommerfeld's extension of Bohr's atomic model was motivated by the quest for a theory of the Zeeman and Stark effects. The crucial idea was that a spectral line is made up of coinciding frequencies which are decomposed in an applied field. In October 1914 Johannes Stark had published the results of his experimental investigation on the splitting of spectral lines in hydrogen (Balmer lines) in electric fields, which showed that the frequency of each Balmer line becomes decomposed into a multiplet of frequencies. The number of lines in such a decomposition grows with the index of the line in the Balmer series. Sommerfeld concluded from this observation that the quantization in Bohr's model had to be altered in order to allow for such decompositions. He outlined this idea in a lecture in winter 1914/15, but did not publish it. The First World War further delayed its elaboration. When Bohr published new results in autumn 1915, Sommerfeld finally developed his theory in a provisional form in two memoirs which he presented in December 1915 and January 1916 to the Bavarian Academy of Science. In July 1916 he published the refined version in the Annalen der Physik. The focus here is on the preliminary Academy memoirs whose rudimentary form is better suited for a historical approach to Sommerfeld's atomic theory than the finished Annalen-paper. This introductory essay reconstructs the historical context (mainly based on Sommerfeld's correspondence). It will become clear that the extension of Bohr's model did not emerge in a singular stroke of genius but resulted from an evolving process.
DiMaio, F; Chiu, W
2016-01-01
Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F
2007-02-19
Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.
A computer code for calculations in the algebraic collective model of the atomic nucleus
Welsh, T. A.; Rowe, D. J.
2016-03-01
A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1 , 1) × SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functions of the model's quadrupole moments qˆM and are at most quadratic in the corresponding conjugate momenta πˆN (- 2 ≤ M , N ≤ 2). The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [ π ˆ ⊗ q ˆ ⊗ π ˆ ] 0 and [ π ˆ ⊗ π ˆ ] LM. The code is made efficient by use of an analytical expression for the needed SO(5)-reduced matrix elements, and use of SO(5) ⊃ SO(3) Clebsch-Gordan coefficients obtained from precomputed data files provided with the code.
Akaygun, Sevil
2016-01-01
Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…
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.
Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation.
Zhang, Qiang; Zhang, Ruiting; Zhao, Ying; Li, HuanHuan; Gao, Yi Qin; Zhuang, Wei
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.
Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA.
Fojan, Peter; Gurevich, Leonid
2017-01-01
The cell membrane is the first barrier and quite often the primary target that antimicrobial peptides (AMPs) have to destroy or penetrate to fulfill their mission. Upon penetrating through the membrane, the peptides can further attack intracellular targets, in particular DNA. Studying the interaction of an antimicrobial peptide with a cell membrane and DNA holds keys to understanding its killing mechanisms. Commonly, these interactions are studied by using optical or scanning electron microscopy and appropriately labeled peptides. However, labeling can significantly affect the hydrophobicity, conformation, and size of the peptide, hence altering the interaction significantly. Here, we describe the use of atomic force microscopy (AFM) for a label-free study of the interactions of peptides with model membranes under physiological conditions and DNA as a possible intracellular target.
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.
Fast low-rank approximations of multidimensional integrals in ion-atomic collisions modelling
Litsarev, M S
2015-01-01
An efficient technique based on low-rank separated approximations is proposed for computation of three-dimensional integrals arising in the energy deposition model that describes ion-atomic collisions. Direct tensor-product quadrature requires grids of size $4000^3$ which is unacceptable. Moreover, several of such integrals have to be computed simultaneously for different values of parameters. To reduce the complexity, we use the structure of the integrand and apply numerical linear algebra techniques for the construction of low-rank approximation. The resulting algorithm is $10^3$ faster than spectral quadratures in spherical coordinates used in the original DEPOSIT code. The approach can be generalized to other multidimensional problems in physics.
Atomic Force Microscopy Based Nanorobotics Modelling, Simulation, Setup Building and Experiments
Xie, Hui; Régnier, Stéphane; Sitti, Metin
2012-01-01
The atomic force microscope (AFM) has been successfully used to perform nanorobotic manipulation operations on nanoscale entities such as particles, nanotubes, nanowires, nanocrystals, and DNA since 1990s. There have been many progress on modeling, imaging, teleoperated or automated control, human-machine interfacing, instrumentation, and applications of AFM based nanorobotic manipulation systems in literature. This book aims to include all of such state-of-the-art progress in an organized, structured, and detailed manner as a reference book and also potentially a textbook in nanorobotics and any other nanoscale dynamics, systems and controls related research and education. Clearly written and well-organized, this text introduces designs and prototypes of the nanorobotic systems in detail with innovative principles of three-dimensional manipulation force microscopy and parallel imaging/manipulation force microscopy.
Suzuki, C.; Murakami, I.; Koike, F.; Tamura, N.; Sakaue, H. A.; Morita, S.; Goto, M.; Kato, D.; Ohashi, H.; Higashiguchi, T.; Sudo, S.; O'Sullivan, G.
2017-01-01
We report recent results of extreme ultraviolet (EUV) spectroscopy of highly charged heavy ions in plasmas produced in the Large Helical Device (LHD). The LHD is an ideal source of experimental databases of EUV spectra because of high brightness and low opacity, combined with the availability of pellet injection systems and reliable diagnostic tools. The measured heavy elements include tungsten, tin, lanthanides and bismuth, which are motivated by ITER as well as a variety of plasma applications such as EUV lithography and biological microscopy. The observed spectral features drastically change between quasicontinuum and discrete depending on the plasma temperature, which leads to some new experimental identifications of spectral lines. We have developed collisional-radiative models for some of these ions based on the measurements. The atomic number dependence of the spectral feature is also discussed.
Kubo-Greenwood approach to conductivity in dense plasmas with average atom models
Starrett, C E
2016-01-01
A new formulation of the Kubo-Greenwood conductivity for average atom models is given. The new formulation improves upon previous by explicitly including the ionic-structure factor. Calculations based on this new expression lead to much improved agreement with ab initio results for DC conductivity of warm dense hydrogen and beryllium, and for thermal conductivity of hydrogen. We also give and test a slightly modified Ziman-Evans formula for the resistivity that includes a non-free electron density of states, thus removing an ambiguity in the original Ziman-Evans formula. Again results based on this expression are in good agreement with ab initio simulations for warm dense beryllium and hydrogen. However, for both these expressions, calculations of the electrical conductivity of warm dense aluminum lead to poor agreement at low temperatures compared to ab initio simulations.
Levashov, Valentin A
2015-01-01
It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a model 3D binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. Thus correlations relevant to the Green-Kubo expression for viscosity are interpreted in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonst...
Atomic resolution model of the antibody Fc interaction with the complement C1q component.
Schneider, Sebastian; Zacharias, Martin
2012-05-01
The globular C1q heterotrimer is a subunit of the C1 complement factor. Binding of the C1q subunit to the constant (Fc) part of antibody molecules is a first step and key event of complement activation. Although three-dimensional structures of C1q and antibody Fc subunits have been determined experimentally no atomic resolution structure of the C1q-Fc complex is known so far. Based on systematic protein-protein docking searches and Molecular Dynamics simulations a structural model of the C1q-IgG1-Fc-binding geometry has been obtained. The structural model is compatible with available experimental data on the interaction between the two partner proteins. It predicts a binding geometry that involves mainly the B-subunit of the C1q-trimer and both subunits of the IgG1-Fc-dimer with small conformational adjustments with respect to the unbound partners to achieve high surface complementarity. In addition to several charge-charge and polar contacts in the rim region of the interface it also involves nonpolar contacts between the two proteins and is compatible with the carbohydrate moiety of the Fc subunit. The model for the complex structure provides a working model for rationalizing available biochemical data on this important interaction and can form the basis for the design of Fc variants with a greater capacity to activate the complement system for example on binding to cancer cells or other target structures.
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.
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.
A quasi-stationary numerical model of atomized metal droplets, I: Model formulation
DEFF Research Database (Denmark)
Hattel, Jesper Henri; Pryds, Nini H; Thorborg, Jesper
1999-01-01
A mathematical model for accelerating powder particles by a gas and for their thermal behavior during flight has been developed. Usually, dealing with the solidification of metal droplets, the interaction between an array of droplets and the surrounding gas is not integrated into the modeling...
Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.
Wang, Xue; Xu, Fengting; Liu, Jiasen; Gao, Bingquan; Liu, Yanxin; Zhai, Yujia; Ma, Jun; Zhang, Kai; Baker, Timothy S; Schulten, Klaus; Zheng, Dong; Pang, Hai; Sun, Fei
2013-01-01
Rabbit hemorrhagic disease, first described in China in 1984, causes hemorrhagic necrosis of the liver. Its etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus in the family Caliciviridae. The detailed molecular structure of any lagovirus capsid has yet to be determined. Here, we report a cryo-electron microscopic (cryoEM) reconstruction of wild-type RHDV at 6.5 Å resolution and the crystal structures of the shell (S) and protruding (P) domains of its major capsid protein, VP60, each at 2.0 Å resolution. From these data we built a complete atomic model of the RHDV capsid. VP60 has a conserved S domain and a specific P2 sub-domain that differs from those found in other caliciviruses. As seen in the shell portion of the RHDV cryoEM map, which was resolved to ~5.5 Å, the N-terminal arm domain of VP60 folds back onto its cognate S domain. Sequence alignments of VP60 from six groups of RHDV isolates revealed seven regions of high variation that could be mapped onto the surface of the P2 sub-domain and suggested three putative pockets might be responsible for binding to histo-blood group antigens. A flexible loop in one of these regions was shown to interact with rabbit tissue cells and contains an important epitope for anti-RHDV antibody production. Our study provides a reliable, pseudo-atomic model of a Lagovirus and suggests a new candidate for an efficient vaccine that can be used to protect rabbits from RHDV infection.
Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang
2015-10-29
Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.
Caffau, Elisabetta; Steffen, Matthias; Ayres, Thomas R; Bonifacio, Piercarlo; Cayrel, Roger; Freytag, Bernd; Plez, Bertrand
2008-01-01
The solar oxygen abundance has undergone a major downward revision in the last decade, the most noticeable one being the update including 3D hydrodynamical simulations to model the solar photosphere. Up to now, such an analysis has been carried out only by one group using one radiation-hydrodynamics code. We investigate the photospheric oxygen abundance considering lines from atomic transitions. We also consider the relationship between the solar model used and the resulting solar oxygen abundance, to understand whether the downward abundance revision is specifically related to 3D hydrodynamical effects. We perform a new determination of the solar photospheric oxygen abundance by analysing different high-resolution high signal-to-noise ratio atlases of the solar flux and disc-centre intensity making use of the latest generation of CO5BOLD 3D solar model atmospheres. We find 8.73 < logNoxygen/Nhydrogen +12 < 8.79. The lower and upper value represent extreme assumptions on the role of collisional excitati...
Rovibrationally Inelastic Atom-Molecule Collision Cross Sections from a Hard Sphere Model
Lashner, Jacob; Stewart, Brian
2016-05-01
Hard-shell models have long been used to elucidate the principal features of molecular energy transfer and exchange reaction in the A + BC system. Nevertheless, no three-dimensional hard-shell calculation of inelastic collision cross sections has been reported. This work aims to fill that void. A particular motivation comes from our experimental results, which show the importance of equatorial impacts in the vibrational excitation process. Working with the simple hard-sphere model, we incorporated secondary impacts, defined as those in which A strikes C after striking B. Such collisions are important in systems such as Li2 - X, in which vibrational energy transfer occurs principally through side impacts. We discuss the complexity this adds to the model and present fully three-dimensional cross sections for rovibrational excitation of an initially stationary molecule in the homonuclear A + B2 system, examining the cross section as a function of the masses and radii of the atoms. We show how the features in the cross section evolve as these parameters are varied and calculate the contribution of secondary (near-equatorial) impacts to the dynamics. We compare with recent measurements in our laboratory and with the results of quasiclassical trajectories.
Energy Technology Data Exchange (ETDEWEB)
Babilas, Rafał, E-mail: rafal.babilas@polsl.pl
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.
Gleadall, Andrew; Pan, Jingzhe; Ding, Lifeng; Kruft, Marc-Anton; Curcó, David
2015-11-01
Molecular dynamics (MD) simulations are widely used to analyse materials at the atomic scale. However, MD has high computational demands, which may inhibit its use for simulations of structures involving large numbers of atoms such as amorphous polymer structures. An atomic-scale finite element method (AFEM) is presented in this study with significantly lower computational demands than MD. Due to the reduced computational demands, AFEM is suitable for the analysis of Young's modulus of amorphous polymer structures. This is of particular interest when studying the degradation of bioresorbable polymers, which is the topic of an accompanying paper. AFEM is derived from the inter-atomic potential energy functions of an MD force field. The nonlinear MD functions were adapted to enable static linear analysis. Finite element formulations were derived to represent interatomic potential energy functions between two, three and four atoms. Validation of the AFEM was conducted through its application to atomic structures for crystalline and amorphous poly(lactide).
Van der Waals interactions and the limits of isolated atom models at interfaces.
Kawai, Shigeki; Foster, Adam S; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H; Jung, Thomas A; Meyer, Ernst
2016-05-13
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.
Modeling non local thermodynamic equilibrium plasma using the Flexible Atomic Code data
Han, Bo; Salzmann, David; Zhao, Gang
2015-01-01
We present a new code, RCF("Radiative-Collisional code based on FAC"), which is used to simulate steady-state plasmas under non local thermodynamic equilibrium condition, especially photoinization dominated plasmas. RCF takes almost all of the radiative and collisional atomic processes into rate equation to interpret the plasmas systematically. The Flexible Atomic Code (FAC) supplies all the atomic data RCF needed, which insures calculating completeness and consistency of atomic data. With four input parameters relating to the radiation source and target plasma, RCF calculates the population of levels and charge states, as well as potentially emission spectrum. In preliminary application, RCF successfully reproduces the results of a photoionization experiment with reliable atomic data. The effects of the most important atomic processes on the charge state distribution are also discussed.
Modeling of adhesion in tablet compression - I. atomic force microscopy and molecular simulation.
Energy Technology Data Exchange (ETDEWEB)
Wang, J. J.; Li, T.; Bateman, S. D.; Erck, R.; Morris, K. R.; Energy Technology; Purdue Univ.; Novartis Pharmaceutical Corp.
2003-04-01
Adhesion problems during tablet manufacturing have been observed to be dependent on many formulation and process factors including the run time on the tablet press. Consequently, problems due to sticking may only become apparent towards the end of the development process when a prolonged run on the tablet press is attempted for the first time. It would be beneficial to predict in a relative sense if a formulation or new chemical entity has the potential for adhesion problems early in the development process. It was hypothesized that favorable intermolecular interaction between the drug molecules and the punch face is the first step or criterion in the adhesion process. Therefore, the rank order of adhesion during tablet compression should follow the rank order of these energies of interaction. The adhesion phenomenon was investigated using molecular simulations and contact mode atomic force microscopy (AFM). Three model compounds were chosen from a family of profen compounds. Silicon nitride AFM tips were modified by coating a 20-nm iron layer on the surfaces by sputter coating. Profen flat surfaces were made by melting and recrystallization. The modified AFM probe and each profen surface were immersed in the corresponding profen saturated water during force measurements using AFM. The work of adhesion between iron and ibuprofen, ketoprofen, and flurbiprofen in vacuum were determined to be -184.1, -2469.3, -17.3 mJ {center_dot} m-2, respectively. The rank order of the work of adhesion between iron and profen compounds decreased in the order: ketoprofen > ibuprofen > flurbiprofen. The rank order of interaction between the drug molecules and the iron superlattice as predicted by molecular simulation using Cerius2 is in agreement with the AFM measurements. It has been demonstrated that Atomic Force Microscopy is a powerful tool in studying the adhesion phenomena between organic drug compounds and metal surface. The study has provided insight into the adhesion problems
HYBRID ORBITALS OF CARBON ATOMS IN THE D6hC36 MOLECULE UNDER THE ROTATING ELLIPSOID MODEL
Institute of Scientific and Technical Information of China (English)
Tong Guo-ping
2000-01-01
The hybrid orbitals of carbon atoms in the D6h C36 molecule arestudied using two rotating ellipsoid models. The model 1 is 1.66R for theshort semi-axis and 2.34R for the long semi-axis, and the model 2 is 1.78R and 2.26R respectively, where R is the C-C bond length. By comparison,we think the model 2 to be more proper in revealing the electronic properties of the D6h C36 molecule. The component of s orbitals in the states hybridized for each of the atoms is much larger than C60, in which the sorbit component is 0.0380 and the porbit is 0.9620. The most component is 0.2098and the least is 0.0482 for model 1; the most is 0.1764 and the least is0.0656 for model 2.
Aerosol cluster impact and break-up : II. Atomic and Cluster Scale Models.
Energy Technology Data Exchange (ETDEWEB)
Lechman, Jeremy B.; Takato, Yoichi (State University of New York at Buffalo, Buffalo, NY)
2010-09-01
Understanding the interaction of aerosol particle clusters/flocs with surfaces is an area of interest for a number of processes in chemical, pharmaceutical, and powder manufacturing as well as in steam-tube rupture in nuclear power plants. Developing predictive capabilities for these applications involves coupled phenomena on multiple length and timescales from the process macroscopic scale ({approx}1m) to the multi-cluster interaction scale (1mm-0.1m) to the single cluster scale ({approx}1000 - 10000 particles) to the particle scale (10nm-10{micro}m) interactions, and on down to the sub-particle, atomic scale interactions. The focus of this report is on the single cluster scale; although work directed toward developing better models of particle-particle interactions by considering sub-particle scale interactions and phenomena is also described. In particular, results of mesoscale (i.e., particle to single cluster scale) discrete element method (DEM) simulations for aerosol cluster impact with rigid walls are presented. The particle-particle interaction model is based on JKR adhesion theory and is implemented as an enhancement to the granular package in the LAMMPS code. The theory behind the model is outlined and preliminary results are shown. Additionally, as mentioned, results from atomistic classical molecular dynamics simulations are also described as a means of developing higher fidelity models of particle-particle interactions. Ultimately, the results from these and other studies at various scales must be collated to provide systems level models with accurate 'sub-grid' information for design, analysis and control of the underlying systems processes.
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.
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.
Adsorption of metal atoms at a buckled graphene grain boundary using model potentials
Energy Technology Data Exchange (ETDEWEB)
Helgee, Edit E.; Isacsson, Andreas [Department of Applied Physics, Chalmers University of Technology, SE-412 96, Göteborg (Sweden)
2016-01-15
Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable.
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.
Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing
2017-03-20
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.
The atom-surface interaction potential for He-NaCl: A model based on pairwise additivity
Hutson, Jeremy M.; Fowler, P. W.
1986-08-01
The recently developed semi-empirical model of Fowler and Hutson is applied to the He-NaCl atom-surface interaction potential. Ab initio self-consistent field calculations of the repulsive interactions between He atoms and in-crystal Cl - and Na + ions are performed. Dispersion coefficients involving in-crystal ions are also calculated. The atom-surface potential is constructed using a model based on pairwise additivity of atom-ion forces. With a small adjustment of the repulsive part, this potential gives good agreement with the experimental bound state energies obtained from selective adsorption resonances in low-energy atom scattering experiments. Close-coupling calculations of the resonant scattering are performed, and good agreement with the experimental peak positions and intensity patterns is obtained. It is concluded that there are no bound states deeper than those observed in the selective adsorption experiments, and that the well depth of the He-NaCl potential is 6.0 ± 0.2 meV.
Savall-Alemany, Francisco; Domènech-Blanco, Josep Lluís; Guisasola, Jenaro; Martínez-Torregrosa, Joaquín
2016-06-01
Our study sets out to identify the difficulties that high school students, teachers, and university students encounter when trying to explain atomic spectra. To do so, we identify the key concepts that any quantum model for the emission and absorption of electromagnetic radiation must include to account for the gas spectra and we then design two questionnaires, one for teachers and the other for students. By analyzing the responses, we conclude that (i) teachers lack a quantum model for the emission and absorption of electromagnetic radiation capable of explaining the spectra, (ii) teachers and students share the same difficulties, and (iii) these difficulties concern the model of the atom, the model of radiation, and the model of the interaction between them.
The contribution of atom accessibility to site of metabolism models for cytochromes P450
DEFF Research Database (Denmark)
Rydberg, Patrik; Rostkowski, M.; Gloriam, D.E.
2013-01-01
Three different types of atom accessibility descriptors are investigated in relation to site of metabolism predictions. To enable the integration of local accessibility we have constructed 2DSASA, a method for the calculation of the atomic solvent accessible surface area that is independent of 3D...
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.
Aguiar, Joana G.; Correia, Paulo R. M.
2016-01-01
In this paper, we explore the use of concept maps (Cmaps) as instructional materials prepared by teachers, to foster the understanding of chemistry. We choose fireworks as a macroscopic event to teach basic chemical principles related to the Bohr atomic model and matter-energy interaction. During teachers' Cmap navigation, students can experience…
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…
Institute of Scientific and Technical Information of China (English)
CHEN LaiWen; WANG JingHua; LEE Chun-Hian
2009-01-01
When hyperthermal atomic oxygen collides with a silicon surface, an ultrathin oxidation regime characterized by fractional atomic-oxygen anions having low diffusive and reactive barriers, along with their enhanced diffusion due to both the electric field and image potential, will form on the surface. In accordance with these properties, an attempt was made in the present study to modify the AlmeidaGoncalves-Baumvol (AGB) model by setting the diffusivity and reaction rate constant to be diffusion-length dependence. According to the modified model, numerical parametric studies for oxidation thin growth were performed. The dependencies of the diffusion coefficient, the reaction rate constant,the attenuation length, and the adjustable parameter upon the translational kinetic energy, flux, temperature, and tangential flux of atomic oxygen were analyzed briefly via the fitting of the experimental data given by Tagawa et al. The numerical results confirmed the rationality of the modified diffusion-reaction model. The model together with the computer code developed in this study would be a useful tool for thickness evaluation of the protective film against the oxidation of atomic oxygen toward spacecraft surface materials in LEO environment.
Institute of Scientific and Technical Information of China (English)
LEE; Chun-Hian
2009-01-01
When hyperthermal atomic oxygen collides with a silicon surface, an ultrathin oxidation regime characterized by fractional atomic-oxygen anions having low diffusive and reactive barriers, along with their enhanced diffusion due to both the electric field and image potential, will form on the surface. In ac- cordance with these properties, an attempt was made in the present study to modify the Almeida- Goncalves-Baumvol (AGB) model by setting the diffusivity and reaction rate constant to be diffu- sion-length dependence. According to the modified model, numerical parametric studies for oxidation thin growth were performed. The dependencies of the diffusion coefficient, the reaction rate constant, the attenuation length, and the adjustable parameter upon the translational kinetic energy, flux, tem- perature, and tangential flux of atomic oxygen were analyzed briefly via the fitting of the experimental data given by Tagawa et al. The numerical results confirmed the rationality of the modified diffu- sion-reaction model. The model together with the computer code developed in this study would be a useful tool for thickness evaluation of the protective film against the oxidation of atomic oxygen toward spacecraft surface materials in LEO environment.
Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom
Clark, Ted M.; Chamberlain, Julia M.
2014-01-01
An activity supporting the PhET interactive simulation, Models of the Hydrogen Atom, has been designed and used in the laboratory portion of a general chemistry course. This article describes the framework used to successfully accomplish implementation on a large scale. The activity guides students through a comparison and analysis of the six…
Energy Technology Data Exchange (ETDEWEB)
A.V.G. Chizmeshya; M.J. McKelvy; G.H. Wolf; R.W. Carpenter; D.A. Gormley; J.R. Diefenbacher; R. Marzke
2006-03-01
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 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
Energy Technology Data Exchange (ETDEWEB)
A.V.G. Chizmeshya
2003-12-19
DOE/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
Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models
Energy Technology Data Exchange (ETDEWEB)
Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl; Kolinski, Andrzej [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw (Poland); Co, Nguyen Truong [Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City (Viet Nam); Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City (Viet Nam); Nguyen, Phuong H. [Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan, E-mail: masli@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)
2015-04-14
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in
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
Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A
2016-06-24
A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.
Offner, Stella S R; Viti, Serena; Bell, Thomas A
2013-01-01
We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C+, C, H2 and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric probl...
Energy Technology Data Exchange (ETDEWEB)
Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: stella.offner@yale.edu [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)
2013-06-10
We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.
Modeling of an atomizer for two fluids; Modelacion de un atomizador de dos fluidos
Energy Technology Data Exchange (ETDEWEB)
Tapia Ramirez, Zoili [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)
1998-09-01
The work reported in this article presents the results of the effort to improve the basic understanding of the flow structure that is formed in a two fluid sprayer before and after the interaction between the sprayed fluid and the spraying fluid. The images in the interior of the mixing chamber of the atomizer are shown, which were taken with a high velocity video camera. Also the results of the numerical simulation of the internal flow obtained by means of a package of commercial modeling are shown. [Espanol] El trabajo reportado en este articulo presenta los resultados del esfuerzo por mejorar el entendimiento basico de la estructura del flujo que se forma en un atomizador de dos fluidos antes y despues de la interaccion entre el fluido atomizado y el fluido atomizante. Se muestran imagenes del flujo en el interior de la camara de mezclado del atomizador, las cuales fueron tomadas con una camara de video de alta velocidad. Tambien se incluyen los resultados de la simulacion numerica del flujo interno obtenidas por medio de un paquete de modelacion comercial.
Optimized Model Surfaces for Advanced Atomic Force Microscopy Studies of Surface Nanobubbles.
Song, Bo; Zhou, Yi; Schönherr, Holger
2016-11-01
The formation of self-assembled monolayers (SAMs) of binary mixtures of 16-mercaptohexadecanoic acid (MHDA) and 1-octadecanethiol (ODT) on ultraflat template-stripped gold (TSG) surfaces was systematically investigated to clarify the assembly behavior, composition, and degree of possible phase segregation in light of atomic force microscopy (AFM) studies of surface nanobubbles on these substrates. The data for SAMs on TSG were compared to those obtained by adsorption on rough evaporated gold, as reported in a previous study. Quartz crystal microbalance and surface plasmon resonance data acquired in situ on TSG indicate that similar to SAM formation on conventional evaporated gold substrates ODT and MHDA form monolayers and bilayers, respectively. The second layer on MHDA, whose formation is attributed to hydrogen bonding, can be easily removed by adequate rinsing with water. The favorable agreement of the grazing incidence reflection Fourier transform infrared (GIR FTIR) spectroscopy and contact angle data analyzed with the Israelachvili-Gee model suggests that the binary SAMs do not segregate laterally. This conclusion is fully validated by high-resolution friction force AFM observations down to a length scale of 8-10 nm, which is much smaller than the typical observed surface nanobubble radii. Finally, correspondingly functionalized TSG substrates are shown to be valuable supports for studying surface nanobubbles by AFM in water and for addressing the relation between surface functionality and nanobubble formation and properties.
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.
Near-atomic resolution structural model of the yeast 26S proteasome.
Beck, Florian; Unverdorben, Pia; Bohn, Stefan; Schweitzer, Andreas; Pfeifer, Günter; Sakata, Eri; Nickell, Stephan; Plitzko, Jürgen M; Villa, Elizabeth; Baumeister, Wolfgang; Förster, Friedrich
2012-09-11
The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.
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.
Beswick, Benjamin T; Gardiner, Simon A; Hughes, Ifan G; Andersen, Mikkel F; Daszuta, Boris
2016-01-01
Atom interferometers are a useful tool for precision measurements of fundamental physical phenomena, ranging from local gravitational field strength to the atomic fine structure constant. In such experiments, it is desirable to implement a high momentum transfer "beam-splitter," which may be achieved by inducing quantum resonance in a finite-temperature laser-driven atomic gas. We use Monte Carlo simulations to investigate these quantum resonances in the regime where the gas receives laser pulses of finite duration, and demonstrate that an $\\epsilon$-classical model for the dynamics of the gas atoms is capable of reproducing quantum resonant behavior for both zero-temperature and finite-temperature non-interacting gases. We show that this model agrees well with the fully quantum treatment of the system over a time-scale set by the choice of experimental parameters. We also show that this model is capable of correctly treating the time-reversal mechanism necessary for implementing an interferometer with this p...
Institute of Scientific and Technical Information of China (English)
Jiuzhou ZHAO; Dongming LIU; Hengqiang YE
2003-01-01
In order to understand the solidification process of an atomized droplet and predict the fraction solidification ofdroplets with flight distance during spray forming, a numerical model based on the population dynamics approach isdeveloped to describe the microstructure evolution under the common action of the nucleation and growth of grains.The model is coupled with droplets heat transfer controlling equations and solved for Al-4.5 wt pct Cu alloy. It isdemonstrated that the numerical results describe the solidification process well.
A simple nonbinary scattering model applicable to atomic collisions is crystals at 1ow energies
DEFF Research Database (Denmark)
Andersen, Hans Henrik; Sigmund, Peter
1966-01-01
Presents the solution of a special scattering problem which may be important in the theory of slowing-down of atomic particles in crystals. A projectile moves along the centre axis of a regular ring of n equal atoms which are free and do not interact with each other. The interaction between...... the projectile and each ring atom is described by a Born-Mayer potential, and the scattering is assumed to be elastic and governed by the classical equations of motion. Because of symmetry, the problem can be reduced to plane motion of a particle in a potential of elliptic symmetry. The elliptic force field...... the asymptotic velocities of the ring atoms as well as the energy loss of the projectile. Furthermore, it can be decided whether the projectile is reflected by the ring. Both the feasibility of assumptions specifying the problem and the validity of different approximations made in the transformation from...
Zhou, Chong-Wen; Simmie, John M; Somers, Kieran P; Goldsmith, C Franklin; Curran, Henry J
2017-03-09
Hydrogen atom abstraction from allylic C-H bonds by molecular oxygen plays a very important role in determining the reactivity of fuel molecules having allylic hydrogen atoms. Rate constants for hydrogen atom abstraction by molecular oxygen from molecules with allylic sites have been calculated. A series of molecules with primary, secondary, tertiary, and super secondary allylic hydrogen atoms of alkene, furan, and alkylbenzene families are taken into consideration. Those molecules include propene, 2-butene, isobutene, 2-methylfuran, and toluene containing the primary allylic hydrogen atom; 1-butene, 1-pentene, 2-ethylfuran, ethylbenzene, and n-propylbenzene containing the secondary allylic hydrogen atom; 3-methyl-1-butene, 2-isopropylfuran, and isopropylbenzene containing tertiary allylic hydrogen atom; and 1-4-pentadiene containing super allylic secondary hydrogen atoms. The M06-2X/6-311++G(d,p) level of theory was used to optimize the geometries of all of the reactants, transition states, products and also the hinder rotation treatments for lower frequency modes. The G4 level of theory was used to calculate the electronic single point energies for those species to determine the 0 K barriers to reaction. Conventional transition state theory with Eckart tunnelling corrections was used to calculate the rate constants. The comparison between our calculated rate constants with the available experimental results from the literature shows good agreement for the reactions of propene and isobutene with molecular oxygen. The rate constant for toluene with O2 is about an order magnitude slower than that experimentally derived from a comprehensive model proposed by Oehlschlaeger and coauthors. The results clearly indicate the need for a more detailed investigation of the combustion kinetics of toluene oxidation and its key pyrolysis and oxidation intermediates. Despite this, our computed barriers and rate constants retain an important internal consistency. Rate constants
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
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.
An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome
Energy Technology Data Exchange (ETDEWEB)
Foerster, Friedrich [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany); Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Lasker, Keren [Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv (Israel); Beck, Florian; Nickell, Stephan [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany); Sali, Andrej [Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, San Francisco (United States); Baumeister, Wolfgang, E-mail: baumeist@biochem.mpg.de [Department of Structural Biology, Max-Planck-Institute of Biochemistry, D-82152 Martinsried (Germany)
2009-10-16
The 26S proteasome is the most downstream element of the ubiquitin-proteasome pathway of protein degradation. It is composed of the 20S core particle (CP) and the 19S regulatory particle (RP). The RP consists of 6 AAA-ATPases and at least 13 non-ATPase subunits. Based on a cryo-EM map of the 26S proteasome, structures of homologs, and physical protein-protein interactions we derive an atomic model of the AAA-ATPase-CP sub-complex. The ATPase order in our model (Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5) is in excellent agreement with the recently identified base-precursor complexes formed during the assembly of the RP. Furthermore, the atomic CP-AAA-ATPase model suggests that the assembly chaperone Nas6 facilitates CP-RP association by enhancing the shape complementarity between Rpt3 and its binding CP alpha subunits partners.
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.
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
2010-07-09
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.
Energy Technology Data Exchange (ETDEWEB)
Roy, Kunal, E-mail: kunalroy_in@yahoo.com [Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700 032 (India); Das, Rudra Narayan [Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700 032 (India)
2010-11-15
Aldehydes are a toxic class of chemicals causing severe health hazards. In this background, quantitative structure-toxicity relationship (QSTR) models have been developed in the present study using Extended Topochemical Atom (ETA) indices for a large group of 77 aromatic aldehydes for their acute toxicity against the protozoan ciliate Tetrahymena pyriformis. The ETA models have been compared with those developed using various non-ETA topological indices. Attempt was also made to include the n-octanol/water partition coefficient (log K{sub o/w}) as an additional descriptor considering the importance of hydrophobicity in toxicity prediction. Thirty different models were developed using different chemometric tools. All the models have been validated using internal validation and external validation techniques. The statistical quality of the ETA models was found to be comparable to that of the non-ETA models. The ETA models have shown the important effects of steric bulk, lipophilicity, presence of electronegative atom containing substituents and functionality of the aldehydic oxygen to the toxicity of the aldehydes. The best ETA model (without using log K{sub o/w}) shows encouraging statistical quality (Q{sub int}{sup 2}=0.709,Q{sub ext}{sup 2}=0.744). It is interesting to note that some of the topological models reported here are better in statistical quality than previously reported models using quantum chemical descriptors.
Pan, Jianjun; Khadka, Nawal K
2016-05-26
Quantitative characterization of membrane defects (pores) is important for elucidating the molecular basis of many membrane-active peptides. We study kinetic defects induced by melittin in vesicular and planar lipid bilayers. Fluorescence spectroscopy measurements indicate that melittin induces time-dependent calcein leakage. Solution atomic force microscopy (AFM) is used to visualize melittin-induced membrane defects. After initial equilibration, the most probable defect radius is ∼3.8 nm in 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) bilayers. Unexpectedly, defects become larger with longer incubation, accompanied by substantial shape transformation. The initial defect radius is ∼4.7 nm in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. Addition of 30 mol % cholesterol to DOPC bilayers suppresses defect kinetics, although the inhibitory impact is negated by longer incubation. Overall, the kinetic rate of defect development follows DLPC > DOPC > DOPC/cholesterol. Kinetic defects are also observed when anionic lipids are present. Based on the observation that defects can occupy as large as 40% of the bilayer surface, we propose a kinetic defect growth model. We also study the effect of melittin on the phase behavior of DOPC/egg-sphingomyelin/cholesterol bilayers. We find that melittin initially suppresses or eliminates liquid-ordered (Lo) domains; Lo domains gradually emerge and become the dominant species with longer incubation; and defects in phase-coexisting bilayers have a most probable radius of ∼5 nm and are exclusively localized in the liquid-disordered (Ld) phase. Our experimental data highlight that melittin-induced membrane defects are not static; conversely, spontaneous defect growth is intrinsically associated with membrane permeabilization exerted by melittin.
Arafat, A Syed Yasir; Arun, A; Ilamathi, M; Asha, J; Sivashankari, P R; D'Souza, Cletus J M; Sivaramakrishnan, V; Dhananjaya, B L
2014-03-01
5' Nucleotidase (5' NUC) is a ubiquitously distributed enzyme known to be present in snake venoms (SV) that is responsible primarily for causing dysregulation of physiological homeostasis in humans by inducing anticoagulant effects and by inhibiting platelet aggregation. It is also known to act synergistically with other toxins to exert a more pronounced anti-coagulant effect during envenomation. Its structural and functional role is not yet ascertained clearly. The 3D structure of snake venom 5' nucleotidase (SV-5' NUC) is not yet known and was predicted by us for the first time using a comparative homology modeling approach using Demansia vestigiata protein sequence. The accuracy and stability of the predicted SV-5' NUC structure were validated using several computational approaches. Key interactions of SV-5' NUC were studied using experimental studies/molecular docking analysis of the inhibitors vanillin, vanillic acid and maltol. All these inhibitors were found to dock favorably following pharmacologically relevant absorption, distribution, metabolism and excretion (ADME) profiles. Further, atomic level docking interaction studies using inhibitors of the SV-5' NUC active site revealed amino acid residues Y65 and T72 as important for inhibitor-(SV-5' NUC) interactions. Our in silico analysis is in good agreement with experimental inhibition results of SV-5' NUC with vanillin, vanillic acid and maltol. The present study should therefore play a guiding role in the experimental design of new SV-5' NUC inhibitors for snake bite management. We also identified a few pharmacophoric features essential for SV-5' NUC inhibitory activity that can be utilized further for the discovery of putative anti-venom agents of therapeutic value for snake bite management.
Modeling and Estimation of Stationary and Non-stationary Noises of Rubidium Atomic Clock
Directory of Open Access Journals (Sweden)
Deepak Mishra,
2014-07-01
Full Text Available Noise estimation of atomic clock is one of the important research areas in the field of atomic clock development and application. Most of the atomic clocks are having random-stochastic noises and periodic noises due to temperature variation. Random-stochastic noises have a well identified signature in time domain but periodic noises are difficult to analyze in time domain. However, in this paper, an effort is made to identify and analyze the deterministic trends of both random-stochastic noises and periodic noises due to variation in temperature using an alternate approach of least-squares normalized-error (LSNE regression algorithm. A MATLAB based application with graphical user interface (GUI is developed to estimate and analyze random-stochastic noises and periodic noises and re-estimate the stability of rubidium atomic clock after removing these noises from the raw phase data. The estimation of stationary noises are done using Allan variance from time domain data and noise profile is calculated using curve fit method. The estimation of periodic noises due to temperature variation is carried in frequency domain through spurious analysis of the frequency data of atomic clock.
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.
Institute of Scientific and Technical Information of China (English)
2007-01-01
Using the numerical solution of the time-dependent Schr(o)dinger equation of a one-dimensional model atom in a two-colour laser field, we have investigated the effects of the potential models on coherent control of atomic multiphoton ionization. It is found that the photoelectron spectra are obviously different for the long-range (Coulomb-like) and short-range (with no excited bound states) potential model atoms, which are produced by two-colour coherent control of atomic multiphoton ionization in a few laser cycles. Our results indicate that two-colour coherent control of atomic multiphoton ionization can be observed in simulations, depending on the choice of the model potentials.
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.
Quantum-Shell Corrections to the Finite-Temperature Thomas-Fermi-Dirac Statistical Model of the Atom
Energy Technology Data Exchange (ETDEWEB)
Ritchie, A B
2003-07-22
Quantum-shell corrections are made directly to the finite-temperature Thomas-Fermi-Dirac statistical model of the atom by a partition of the electronic density into bound and free components. The bound component is calculated using analytic basis functions whose parameters are chosen to minimize the energy. Poisson's equation is solved for the modified density, thereby avoiding the need to solve Schroedinger's equation for a self-consistent field. The shock Hugoniot is calculated for aluminum: shell effects characteristic of quantum self-consistent field models are fully captures by the present model.
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.
Effect of Squeezing on the Atomic and the Entanglement Dynamics in the Jaynes-Cummings Model
Subeesh, T; Ahmed, A B M; Satyanarayana, M Venkata
2012-01-01
The dynamics of the Jaynes-Cummings interaction of a two-level atom interacting with a single mode of the radiation field is investigated, as the state of the field is gradually changed from a coherent state to a squeezed coherent state. The effect of mild squeezing on the coherent light is shown to be striking: the photon number distribution gets localized and it peaks maximally for a particular value of squeezing. The atomic inversion retains its structure for a longer time. The mean linear entropy shows that the atom has a tendency to get disentangled from field within the collapse region and also in the revival region, for mild squeezing. These properties are absent for the case of a coherent state or for an excessively squeezed coherent state. We also elucidate a connection between these properties and the photon statistics of the mildly squeezed coherent state; these states have the minimum variance and are also maximally sub-Poissonian.
Sattonnay, G; Tétot, R
2014-02-05
Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd2Ti2O7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd2Zr2O7. Therefore, the defect stability in A2B2O7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd2Ti2O7 amorphization induced by irradiation.
Luan, P.; Knoll, A. J.; Wang, H.; Kondeti, V. S. S. K.; Bruggeman, P. J.; Oehrlein, G. S.
2017-01-01
The surface interaction of a well-characterized time modulated radio frequency (RF) plasma jet with polystyrene, poly(methyl methacrylate) and poly(vinyl alcohol) as model polymers is investigated. The RF plasma jet shows fast polymer etching but mild chemical modification with a characteristic carbonate ester and NO formation on the etched surface. By varying the plasma treatment conditions including feed gas composition, environment gaseous composition, and treatment distance, we find that short lived species, especially atomic O for Ar/1% O2 and 1% air plasma and OH for Ar/1% H2O plasma, play an essential role for polymer etching. For O2 containing plasma, we find that atomic O initiates polymer etching and the etching depth mirrors the measured decay of O atoms in the gas phase as the nozzle-surface distance increases. The etching reaction probability of an O atom ranging from 10-4 to 10-3 is consistent with low pressure plasma research. We also find that adding O2 and H2O simultaneously into Ar feed gas quenches polymer etching compared to adding them separately which suggests the reduction of O and OH density in Ar/O2/H2O plasma.
The atomic parameter model for the fifth and sixth transition metal quasicrystal alloys(Mc=0.5)
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
The forming ability of quasicrystal phase has a relationship with the atomic bond factors based on differences in atom size and electron factors.Usually,those factors or their combination are used to describe the forming ability,stability of alloys,etc.In this paper,the quasicrystal alloy forming abilities for the fifth and sixth transition metals(Y,Zr,Nb,Mo,Ru,Rh,Pd and La,Hf,Ta,W,Re,Os,Ir,Pt) based alloys have been studied by the size factor and the atomic parametric function.It has been found that an ellipse curve can be used to separate the quasicrystal formed area from the informed area in the size factor and atomic parameters functional graph.The ellipse curve can be defined by an equation(x-m)2/c2+(y?n)2/d2=1.The overall reliabilities for the model are up to 97.4% and 95.5% for the fifth and the sixth transition metals based quasicrystal alloys,respectively.Also,the ellipse parameters m,n,c and d can be paraphrased by some appropriate parameters for each host metal.
The atomic parameter model for the fifth and sixth transition metal quasicrystal alloys (Mc=0.5)
Institute of Scientific and Technical Information of China (English)
LIAO ShuZhi; GUI XuChun; ZHANG Chun; PENG HaoJun; XIE HaoWen; OUYANG YiFang; ZHANG BangWei
2009-01-01
The forming ability of quasicrystal phase has a relationship with the atomic bond factors based on differences in atom size and electron factors.Usually,those factors or their combination are used to describe the forming ability,stability of alloys,etc.In this paper,the quasicrystal alloy forming abilities for the fifth and sixth transition metals (Y,Zr,Nb,Mo,Ru,Rh,Pd and La,Hf,Ta,W,Re,Os,Ir,Pt) based alloys have been studied by the size factor and the atomic parametric function.It has been found that an ellipse curve can be used to separate the quasicrystal formed area from the informed area in the size factor and atomic parameters functional graph.The ellipse curve can be defined by an equation(x-m)2/c2+(y-n)2/d2=1.The overall reliabilities for the model are up to 97.4% and 95.5% for the fifth and the sixth transition metals based quasicrystal alloys,respectively.Also,the ellipse parameters m,n,c and d can be paraphrased by some appropriate parameters for each host metal.
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.
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.
The Holographic Nature of Bohr Atomic Model%波尔原子模型及其全息性
Institute of Scientific and Technical Information of China (English)
赵丽特; 王喜建; 周党培
2016-01-01
This paper shows the holographic nature of the micro world and the macro world in physics by comparing the Bohr atomic model and the movement of the planets in the solar system.%文章通过波尔原子模型和太阳系中行星运动的对比，展现物理学中微观世界和宏观世界的全息性。
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
A scheme is proposed to simulate the Ising model and preserve the maximum entangled states (Bell states) in cavity quantum electrodynamics (QED) driven by a classical field with large detuning. In the strong driving and large-detuning regime, the effective Hamiltonian of the system is the same as the standard Ising model, and the scheme can also make the initial four Bell states of two atoms at the maximum entanglement all the time. So it is a simple memory for the maximal entangled states. The system is insensitive to the cavity decay and the thermal field and more immune to decoherence. These advantages can warrant the experimental feasibility of the current scheme. Furthermore, the genuine four-atom entanglement may be acquired via two Bell states through one-step implementation on four two-level atoms in the strong-driven model, and when two Greenberger-Horne-Zeilinger (GHZ) states are prepared in our scheme, the entangled cluster state may be acquired easily. The success probability for the scheme is 1.
Atomic model of anti-phase boundaries in a face-centred icosahedral Zn-Mg-Dy quasicrystal
Wang Jian Bo; Wang Ren Hui
2003-01-01
An atomic model in the physical space for an anti-phase boundary (APB) in the ordered face-centred icosahedral Zn-Mg-Dy quasicrystal phase is presented, based on a six-dimensional model suggested by Ishimasa and Shimizu (2000 Mater. Sci. Eng. A 294-296 232, Ishimasa 2001 private communication). The physical space atomic positions of the defected structure were used for the calculation of the corresponding exit-plane wavefunction and high-resolution transmission electron microscopy images. The analysis of the defect by inverse Fourier transformation reveals that when superstructure reflection spots are used for back-transformation, then at the APB, bright lattice fringes are found to turn into dark ones, and vice versa. When fundamental reflections are used, the APB is not visible. This phenomenon is the same as the corresponding experimental study recently published by Heggen et al(2001a Phys. Rev. B 64 014202). Based on this atomic model it is found that the APB perpendicular to a fivefold axis A5 (APB-A5) i...
Khuseynov, Dmitry; Blackstone, Christopher C; Culberson, Lori M; Sanov, Andrei
2014-09-28
We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO(-) photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions.
Institute of Scientific and Technical Information of China (English)
Lu Daoming
2012-01-01
Using multipohton Tavis-Cummings model, the entanglement evolution of two coupling two-level atoms in Bell states interacting with a single-mode vacuum field is investigated by using negativity. The influences of coupling constants between atoms, the atomic initial states and the photon number of transition on the entanglement evolution of two coupling two-level atoms are discussed. The results obtained using the numerical method show that the entanglement of two atoms is related with coupling constants between atoms, the atomic initial states and the photon number of transition. The two-atom entanglement state will forever stay in the maximum entanglement state when the initial state is ｜β11 〉 . When the initial state of two atoms is ｜β 01 〉, the entanglement of two atoms displays periodic oscillation behavior. And its oscillation period decreases with increasing of coupling constant between atoms or the photon number of transition. On the other hand, when the initial state is ｜β 00 〉 or ｜β10 ）, the entanglement of two atoms displays quasiperiodic oscillation behavior and its oscillation period decreases with increasing of coupling constant between atoms or the photon number of transition.
Point defect absorption by grain boundaries in α -iron by atomic density function modeling
Kapikranian, O.; Zapolsky, H.; Patte, R.; Pareige, C.; Radiguet, B.; Pareige, P.
2015-12-01
Using the atomic density function theory (ADFT), we examine the point defect absorption at [110] symmetrical tilt grain boundaries in body-centered cubic iron. It is found that the sink strength strongly depends on misorientation angle. We also show that the ADFT is able to reproduce reasonably well the elastic properties and the point defect formation volume in α -iron.
Some entanglement features of three-atoms Tavis-Cummings model: Cooperative case
Youssef, M; Metwally, N
2009-01-01
In this paper we consider a system of identical three two-level atoms interacting at resonance with a single-mode of the quantized field in a lossless cavity. The initial cavity field is prepared in the coherent state while the atoms are taken initially to be either in the uppermost excited state "$|eee>$" or The $\\textmd{GHZ}$-state or the $\\textmd{W}$-state. For this system we investigate different kinds of atomic inversion and entanglement, which arise between the different parts of the system due to the interaction. Also the relationship, between entanglement and some other nonclassical effects in the statistical properties, such as collapses and revivals in the atomic inversion where superharmonic effects appear, is discussed. The $Q$-functions for different cases are discussed. Most remarkably it is found that the $\\textmd{GHZ}$-state is more robust against energy losses, showing almost coherent trapping and Schr\\"odinger-cat states can not be produced from such state. Also the entanglement of $\\textmd{...
The Multiphoton Interaction of Lambda Model Atom and Two-Mode Fields
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.
A Computer-Controlled Classroom Model of an Atomic Force Microscope
Engstrom, Tyler A.; Johnson, Matthew M.; Eklund, Peter C.; Russin, Timothy J.
2015-01-01
The concept of "seeing by feeling" as a way to circumvent limitations on sight is universal on the macroscopic scale--reading Braille, feeling one's way around a dark room, etc. The development of the atomic force microscope (AFM) in 1986 extended this concept to imaging in the nanoscale. While there are classroom demonstrations that use…
Characterization and modeling of atomic layer deposited high-density trench capacitors in silicon
Matters-Kammerer, M.K.; Jinesh, K.B.; Rijks, T.G.S.M.; Roozeboom, F.; Klootwijk, J.H.
2012-01-01
A detailed electrical analysis of multiple layer trench capacitors fabricated in silicon with atomic-layer-deposited Al 2O 3 and TiN is presented. It is shown that in situ ozone annealing of the Al 2O 3 layers prior to the TiN electrode deposition significantly improves the electric properties of th
Atomic-Scale Modeling of Particle Size Effects for the Oxygen Reduction Reaction of Pt
DEFF Research Database (Denmark)
Tritsaris, Georgios; Greeley, Jeffrey Philip; Rossmeisl, Jan;
2011-01-01
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...
Martinez, G T; Rosenauer, A; De Backer, A; Verbeeck, J; Van Aert, S
2014-02-01
High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed.
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.
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…
De Backer, A; van den Bos, K H W; Van den Broek, W; Sijbers, J; Van Aert, S
2016-12-01
An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.
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.
Three-body recombination of two-component cold atomic gases into deep dimers in an optical model
DEFF Research Database (Denmark)
Mikkelsen, Mathias; Jensen, A. S.; Fedorov, D. V.
2015-01-01
We consider three-body recombination into deep dimers in a mass-imbalanced two-component atomic gas. We use an optical model where a phenomenological imaginary potential is added to the lowest adiabatic hyper-spherical potential. The consequent imaginary part of the energy eigenvalue corresponds...... to the decay rate or recombination probability of the three-body system. The method is formulated in details and the relevant qualitative features are discussed as functions of scattering lengths and masses. We use zero-range model in analyses of recent recombination data. The dominating scattering length...
Levashov, V A
2016-03-07
It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.
Garrido, Nephtali
2012-01-01
We put to the test an effective three-dimensional electrostatic potential, obtained effectively by considering an electrostatic source inside a (5+$p$)-dimensional braneworld scenario with $p$ compact and one infinite spacial extra dimensions in the RS II-$p$ model, for $p=1$ and $p=2$. This potential is regular at the source and matches the standard Coulomb potential outside a neighborhood. We use variational and perturbative approximation methods to calculate corrections to the ground energy of the Helium atom modified by this potential, by making use of a 6 and 39-parameter trial wave function of Hylleraas type for the ground state. These corrections to the ground-state energy are compared with experimental data for Helium atom in order to set bounds for the extra dimensions length scale. We find that these bounds are less restrictive than the ones obtained by Morales et. al. through a calculation using the Lamb shift in Hydrogen.
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
Chu, Manh-Hung; Tian, Liang; Chaker, Ahmad; Skopin, Evgenii; Cantelli, Valentina; Ouled, Toufik; Boichot, Raphaël; Crisci, Alexandre; Lay, Sabine; Richard, Marie-Ingrid; Thomas, Olivier; Deschanvres, Jean-Luc; Renevier, Hubert; Fong, Dillon; Ciatto, Gianluca
2017-03-01
ZnO thin films are interesting for applications in several technological fields, including optoelectronics and renewable energies. Nanodevice applications require controlled synthesis of ZnO structures at nanometer scale, which can be achieved via atomic layer deposition (ALD). However, the mechanisms governing the initial stages of ALD had not been addressed until very recently. Investigations into the initial nucleation and growth as well as the atomic structure of the heterointerface are crucial to optimize the ALD process and understand the structure-property relationships for ZnO. We have used a complementary suite of in situ synchrotron x-ray techniques to investigate both the structural and chemical evolution during ZnO growth by ALD on two different substrates, i.e., SiO2 and Al2O3, which led us to formulate an atomistic model of the incipient growth of ZnO. The model relies on the formation of nanoscale islands of different size and aspect ratio and consequent disorder induced in the Zn neighbors' distribution. However, endorsement of our model requires testing and discussion of possible alternative models which could account for the experimental results. In this work, we review, test, and rule out several alternative models; the results confirm our view of the atomistic mechanisms at play, which influence the overall microstructure and resulting properties of the final thin film.
Derouich, M; Barklem, P S
2015-01-01
Interpretation of solar polarization spectra accounting for partial or complete frequency redistribution requires data on various collisional processes. Data for depolarization and polarization transfer are needed but often missing, while data for collisional broadening are usually more readily available. Recent work by Sahal-Br\\'echot and Bommier concluded that despite underlying similarities in the physics of collisional broadening and depolarization processes, relationships between them are not possible to derive purely analytically. We aim to derive accurate numerical relationships between the collisional broadening rates and the collisional depolarization and polarization transfer rates due to hydrogen atom collisions. Such relationships would enable accurate and efficient estimation of collisional data for solar applications. Using earlier results for broadening and depolarization processes based on general (i.e. not specific to a given atom), semi-classical calculations employing interaction potentials...
Fast and accurate conversion of atomic models into electron density maps
Directory of Open Access Journals (Sweden)
Carlos O.S. Sorzano
2015-03-01
Full Text Available New image processing methodologies and algorithms have greatly contributed to the signi cant progress in three-dimensional electron microscopy (3DEM of biological complexes we have seen over the last decades. Naturally, the availability of accurate procedures for the objective testing of new algorithms is a crucial requirement for the further advancement of the eld. A good and accepted testing work ow involves the generation of realistic 3DEM-like maps of biological macromolecules from which some measure of ground truth can be derived, ideally because their 3D atomic structure is already known. In this work we propose a very accurate generation of maps using atomic form factors for electron scattering. We thoroughly review current approaches in the eld, quantitatively demonstrating the bene ts of the new methodology. Additionally, we study a concrete example of the use of this approach for hypothesis testing in 3D Electron Microscopy.
Domagała, Sławomir; Fournier, Bertrand; Liebschner, Dorothee; Guillot, Benoît; Jelsch, Christian
2012-05-01
ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMAM2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations.
Quantum Simulation of the Hubbard Model Using Ultra-Cold Atoms
2008-11-01
gas of atoms. We also report on our observation of resonances in the three-body recombination rate in this gas which indicate the formation of Efimov ...recombination can also be used to test universal predictions for the quantum three-body problem such as the Efimov effect. We have already observed...two resonant features which indicate the formation of Efimov trimer states and are currently testing predictions of Efimov ¿s theory when the scattering
Determination of a high spatial resolution geopotential model using atomic clock comparisons
Lion, Guillaume; Panet, Isabelle; Wolf, Peter; Guerlin, Christine; Bize, Sébastien; Delva, Pacôme
2016-01-01
Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging ...
Jin, Lin; Auerbach, Scott M; Monson, Peter A
2012-03-15
The potential of tailored nanopores to transform technologies such as drug delivery, biofuel production, and optical-electronic devices depends on fundamental knowledge of the self-assembly of ordered nanoporous solids. Atomic-level geometries of critical nuclei that lead to such solids have remained hidden in the nanoscale blind spot between local (5 nm) probes of structure. Heroic efforts at molecular simulation of nanopore formation have provided massive libraries of hypothetical structures; (1-5) however, to date no statistical simulation has generated a crystallization pathway from random initial condition to ordered nanoporous solid, until now. In this work, we show that a recently developed atomic lattice model of silica and related materials can form ordered nanoporous solids with a rich variety of structures including known chalcogenides, zeolite analogs, and layered materials. We find that whereas canonical Monte Carlo simulations of the model consistently produce the amorphous solids studied in our previous work, parallel tempering Monte Carlo gives rise to ordered nanoporous solids. The utility of parallel tempering highlights the existence of barriers between amorphous and crystalline phases of our model. Moreover, the self-assembly or nanoporous crystalline phases in the model open the door to detailed understanding of nanopore nucleation.
Jorge, Miguel
2017-03-05
Existing united-atom models for non-polar hydrocarbons lead to systematic deviations in predicted solvation free energies in hydrophobic solvents. In this article, an improved set of parameters is proposed for alkane molecules that corrects this systematic deviation and accurately predicts solvation free energies in hydrophobic media, while simultaneously providing a very good description of pure liquid densities. The model is then extended to alkenes and alkynes, again yielding very accurate predictions of solvation free energies and densities for these classes of compounds. For alkynes in particular, this work represents the first attempt at a systematic parameterization using the united-atom approach. Averaging over all 95 solute/solvent pairs tested, the mean signed deviation from experimental data is very close to zero, indicating no systematic error in the predictions. The fact that predictions are robust even for relatively large molecules suggests that the new model may be applicable to solvation of non-polar macromolecules without accumulation of errors. The root mean squared deviation of the simulations is only 0.6 kJ/mol, which is lower than the estimated uncertainty in the experimental measurements. This excellent performance constitutes a solid basis on which a more general model can be parameterized to describe solvation in both polar and non-polar environments. © 2016 Wiley Periodicals, Inc.
Anisimov, Victor M; Cavasotto, Claudio N
2011-06-23
To build the foundation for accurate quantum mechanical (QM) simulation of biomacromolecules in an aqueous environment, we undertook the optimization of the COnductor-like Screening MOdel (COSMO) atomic radii and atomic surface tension coefficients for different semiempirical Hamiltonians adhering to the same computational conditions recently followed in the simulation of biomolecular systems. This optimization was achieved by reproducing experimental hydration free energies of a set consisting of 507 neutral and 99 ionic molecules. The calculated hydration free energies were significantly improved by introducing a multiple atomic-type scheme that reflects different chemical environments. The nonpolar contribution was treated according to the scaled particle Claverie-Pierotti formalism. Separate radii and surface tension coefficient sets have been developed for AM1, PM3, PM5, and RM1 semiempirical Hamiltonians, with an average unsigned error for neutral molecules of 0.64, 0.66, 0.73, and 0.71 kcal/mol, respectively. Free energy calculation of each molecule took on average 0.5 s on a single processor. The new sets of parameters will enhance the quality of semiempirical QM calculations using COSMO in biomolecular systems. Overall, these results further extend the utility of QM methods to chemical and biological systems in the condensed phase.
Universal bosonic tetramers of dimer-atom-atom structure
Deltuva, A.
2012-01-01
Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.
Directory of Open Access Journals (Sweden)
Osvaldo N. Oliveira
2012-10-01
Full Text Available The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS, it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of afs, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution.
Leite, Fabio L; Bueno, Carolina C; Da Róz, Alessandra L; Ziemath, Ervino C; Oliveira, Osvaldo N
2012-10-08
The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of afs, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution.
Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan.
Schanda, Paul; Triboulet, Sébastien; Laguri, Cédric; Bougault, Catherine M; Ayala, Isabel; Callon, Morgane; Arthur, Michel; Simorre, Jean-Pierre
2014-12-24
The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains-the catalytic domain as well as the proposed peptidoglycan recognition domain-are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein-peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.
Directory of Open Access Journals (Sweden)
Peter Grgač
2012-10-01
Full Text Available The paper deals with the analysis of microstructure formation in the tool steel of ledeburite type Ch12MF4 with the chemical composition of 2.37% C, 12.06% Cr, 1.2% Mo and 4.0 % V [wt. (%] in the process of nitrogen gas atomization. Three main types of solidification microstructures were observed in rapidly solidified powder particles: dendritic, compound and cellular. Based on the morphological features of microstructures observed in rapidly solidified particles and mathematical modeling of the thermal history of solidifying spherical droplets, the semi-quantitative model of the microstructure development in the Ch12MF4 steel during atomization was suggested. According to this model, it is supposed that the transition from dendritic to partially dendritic (compound and nondendritic microstructures results from the thermally induced fragmentation of dendrites by the mechanism of their remelting, morphological changes of dendrite fragments and following spheroidization. The intensity of dendrite fragmentation in solidifying particles of different diameters is controlled mainly by the recalescence temperature and duration of quasi-isothermal period of solidification.
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.
A Computer-Controlled Classroom Model of an Atomic Force Microscope
Engstrom, Tyler A.; Johnson, Matthew M.; Eklund, Peter C.; Russin, Timothy J.
2015-12-01
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 a tactile probe to map the topography or some other property of a sample, the rastering of the probe over the sample is manually controlled, which is both tedious and potentially inaccurate. Other groups have used simulation or tele-operation of an AFM probe. In this paper we describe a teaching AFM with complete computer control to map out topographic and magnetic properties of a "crystal" consisting of two-dimensional arrays of spherical marble "atoms." Our AFM is well suited for lessons on the "Big Ideas of Nanoscale" such as tools and instrumentation, as well as a pre-teaching activity for groups with remote access AFM or mobile AFM. The principle of operation of our classroom AFM is the same as that of a real AFM, excepting the nature of the force between sample and probe.
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.
Reichel, Jakob
2010-01-01
This book provides a stimulating and multifaceted picture of a rapidly developing field. The first part reviews fundamentals of atom chip research in tutorial style, while subsequent parts focus on the topics of atom-surface interaction, coherence on atom chips, and possible future directions of atom chip research. The articles are written by leading researchers in the field in their characteristic and individual styles.
1996-01-01
Interviews following the 1991 co-operation Agreement between the Department of Atomic Energy (DAE) of the Government of India and the European Organization for Nuclear Research (CERN) concerning the participation in the Large Hadron Collider Project (LHC) . With Chidambaram, R, Chairman, Atomic Energy Commission and Secretary, Department of Atomic Energy, Department of Atomic Energy (DAE) of the Government of India and Professor Llewellyn-Smith, Christopher H, Director-General, CERN.
Energy Technology Data Exchange (ETDEWEB)
Bencs, László, E-mail: bencs.laszlo@wigner.mta.hu [Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Laczai, Nikoletta [Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Ajtony, Zsolt [Institute of Food Science, University of West Hungary, H-9200 Mosonmagyaróvár, Lucsony utca 15–17 (Hungary)
2015-07-01
A combination of former convective–diffusive vapor-transport models is described to extend the calculation scheme for sensitivity (characteristic mass — m{sub 0}) in graphite furnace atomic absorption spectrometry (GFAAS). This approach encompasses the influence of forced convection of the internal furnace gas (mini-flow) combined with concentration diffusion of the analyte atoms on the residence time in a spatially isothermal furnace, i.e., the standard design of the transversely heated graphite atomizer (THGA). A couple of relationships for the diffusional and convectional residence times were studied and compared, including in factors accounting for the effects of the sample/platform dimension and the dosing hole. These model approaches were subsequently applied for the particular cases of Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sn, V and Zn analytes. For the verification of the accuracy of the calculations, the experimental m{sub 0} values were determined with the application of a standard THGA furnace, operating either under stopped, or mini-flow (50 cm{sup 3} min{sup −1}) of the internal sheath gas during atomization. The theoretical and experimental ratios of m{sub 0}(mini-flow)-to-m{sub 0}(stop-flow) were closely similar for each study analyte. Likewise, the calculated m{sub 0} data gave a fairly good agreement with the corresponding experimental m{sub 0} values for stopped and mini-flow conditions, i.e., it ranged between 0.62 and 1.8 with an average of 1.05 ± 0.27. This indicates the usability of the current model calculations for checking the operation of a given GFAAS instrument and the applied methodology. - Highlights: • A calculation scheme for convective–diffusive vapor loss in GFAAS is described. • Residence time (τ) formulas were compared for sensitivity (m{sub 0}) in a THGA furnace. • Effects of the sample/platform dimension and dosing hole on τ were assessed. • Theoretical m{sub 0} of 18 analytes were
Solares, Santiago D
2015-01-01
This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.
Shen, Lin; Yang, Weitao
2016-04-12
We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.
Scientific models red atoms, white lies and black boxes in a yellow book
Gerlee, Philip
2016-01-01
A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches a...
Energetic Neutral Atom Emissions From Venus: VEX Observations and Theoretical Modeling
Fok, M.-C.; Galli, A.; Tanaka, T.; Moore, T. E.; Wurz, P.; Holmstrom, M.
2007-01-01
Venus has almost no intrinsic magnetic field to shield itself from its surrounding environment. The solar wind thus directly interacts with the planetary ionosphere and atmosphere. One of the by-products of this close encounter is the production of energetic neutral atom (ENA) emissions. Theoretical studies have shown that significant amount of ENAs are emanated from the planet. The launch of the Venus Express (VEX) in 2005 provided the first light ever of the Venus ENA emissions. The observed ENA flux level and structure are in pretty good agreement with the theoretical studies. In this paper, we present VEX ENA data and the comparison with numerical simulations. We seek to understand the solar wind interaction with the planet and the impacts on its atmospheres.
Time-dependent second Born calculations for model atoms and molecules in strong laser fields
Balzer, K; Bonitz, M
2010-01-01
Using the finite-element discrete variable representation of the nonequilibrium Green's function (NEGF) we extend previous work [K.~Balzer et al., Phys. Rev. A \\textbf{81}, 022510 (2010)] to nonequilibrium situations and compute---from the two-time Schwinger-Keldysh-Kadanoff-Baym equations---the response of the helium atom and the heteronuclear molecule lithium hydride to laser fields in the uv and xuv regime. In particular, by comparing the one-electron density and the dipole moment to time-dependent Hartree-Fock results on one hand and the full solution of the time-dependent Schr\\"odinger equation on the other hand, we demonstrate that the time-dependent second Born approximation carries valuable information about electron-electron correlation effects. Also, we outline an efficient distributed memory concept which enables a parallel and well scalable algorithm for computing the NEGF in the two-time domain.
Energy Technology Data Exchange (ETDEWEB)
Nurbawono, Argo; Liu, Shuanglong [Department of Physics and the Centre for Advanced 2D Materials, National University of Singapore, 2 Science Drive 3 (Singapore); Zhang, Chun, E-mail: phyzc@nus.edu.sg [Department of Physics and the Centre for Advanced 2D Materials, National University of Singapore, 2 Science Drive 3 (Singapore); Department of Chemistry, National University of Singapore, 3 Science Drive 3 (Singapore)
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.
Belotsky, K; Kouvaris, C; Laletin, M
2015-01-01
We study a two component dark matter candidate inspired by the Minimal Walking Technicolor model. Dark matter consists of a dominant SIMP-like dark atom component made of bound states between primordial helium nuclei and a doubly charged technilepton, and a small WIMP-like component made of another dark atom bound state between a doubly charged technibaryon and a technilepton. This scenario is consistent with direct search experimental findings because the dominant SIMP component interacts too strongly to reach the depths of current detectors with sufficient energy to recoil and the WIMP-like component is too small to cause significant amount of events. In this context a metastable technibaryon that decays to $e^+e^+$, $\\mu^+ \\mu^+$ and $\\tau^+ \\tau^+$ can in principle explain the observed positron excess by AMS-02 and PAMELA, while being consistent with the photon flux observed by FERMI/LAT. We scan the parameters of the model and we find the best possible fit to the latest experimental data. We find that th...
Pan, Lurong; Aller, Stephen G.
2015-01-01
P-glycoprotein (Pgp) is an ATP-binding cassette (ABC) transporter that alternates between inward- and outward-facing conformations to capture and force substrates out of cells like a peristaltic pump. The high degree of similarity in outward-facing structures across evolution of ABC transporters allowed construction of a high-confidence outward-facing Pgp atomic model based on crystal structures of outward-facing Sav1866 and inward-facing Pgp. The model adhered to previous experimentally determined secondary- and tertiary- configurations during all-atom molecular dynamics simulations in the presence or absence of MgATP. Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access. The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket. Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms. PMID:25600711
Energy Technology Data Exchange (ETDEWEB)
Apetrei, Alin Marian, E-mail: alin.apetrei@uaic.r [Department of Physics, Alexandru Ioan Cuza University of Iasi, 11 Blvd. Carol I, Iasi 700506 (Romania); Enachescu, Cristian; Tanasa, Radu; Stoleriu, Laurentiu; Stancu, Alexandru [Department of Physics, Alexandru Ioan Cuza University of Iasi, 11 Blvd. Carol I, Iasi 700506 (Romania)
2010-09-01
We apply here the Monte Carlo Metropolis method to a known atom-phonon coupling model for 1D spin transition compounds (STC). These inorganic molecular systems can switch under thermal or optical excitation, between two states in thermodynamical competition, i.e. high spin (HS) and low spin (LS). In the model, the ST units (molecules) are linked by springs, whose elastic constants depend on the spin states of the neighboring atoms, and can only have three possible values. Several previous analytical papers considered a unique average value for the elastic constants (mean-field approximation) and obtained phase diagrams and thermal hysteresis loops. Recently, Monte Carlo simulation papers, taking into account all three values of the elastic constants, obtained thermal hysteresis loops, but no phase diagrams. Employing Monte Carlo simulation, in this work we obtain the phase diagram at T=0 K, which is fully consistent with earlier analytical work; however it is more complex. The main difference is the existence of two supplementary critical curves that mark a hysteresis zone in the phase diagram. This explains the pressure hysteresis curves at low temperature observed experimentally and predicts a 'chemical' hysteresis in STC at very low temperatures. The formation and the dynamics of the domains are also discussed.
Genheden, Samuel; Eriksson, Leif A
2016-09-13
Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of mean force (PMFs) along a vector spanning the membrane. First, we provide an evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However, the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to what extent liposome simulations can fully reproduce experimental findings.
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.
Energy Technology Data Exchange (ETDEWEB)
Safronova, M. S. [Department of Physics and Astronomy, University of Delaware, Newark, DE 19716 (United States); Mitroy, J. [School of Engineering, Charles Darwin University, Darwin NT 0909 (Australia); Clark, Charles W. [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, Gaithersburg, Maryland 20899-8410 (United States); Kozlov, M. G. [Petersburg Nuclear Physics Institute, Gatchina 188300 (Russian Federation)
2015-01-22
The atomic dipole polarizability governs the first-order response of an atom to an applied electric field. Atomic polarization phenomena impinge upon a number of areas and processes in physics and have been the subject of considerable interest and heightened importance in recent years. In this paper, we will summarize some of the recent applications of atomic polarizability studies. A summary of results for polarizabilities of noble gases, monovalent, and divalent atoms is given. The development of the CI+all-order method that combines configuration interaction and linearized coupled-cluster approaches is discussed.
Directory of Open Access Journals (Sweden)
Settimi V.
2012-07-01
Full Text Available The nonlinear dynamical behavior of a single-mode model of noncontact AFM is analyzed in terms of attractors robustness and basin integrity. The model considered for the analyses, proposed by Hornstein and Gottlieb [7], consistently includes the nonlinear atomic interaction and the scan control, which appears as parametric excitation. Local bifurcation analyses are carried out to define the overall stability boundary in the excitation parameter space as the envelope of system local escapes, to be compared with the one obtained via numerical simulations. The dynamical integrity of the periodic bounded solutions is studied, and basin erosion is evaluated by means of IF and GIM integrity measures. The obtained erosion profiles allow us to dwell on the possible lack of homogeneous safeness of the stability boundary in terms of attractors robustness and to identify practical escape thresholds ensuring an a priori design safety target.
Energy Technology Data Exchange (ETDEWEB)
Mohammadi, M [Physics Department, Science and Research Campus Azad University of Tehran, Tehran (Iran, Islamic Republic of); Naderi, M H [Quantum Optics Group, University of Isfahan, Isfahan (Iran, Islamic Republic of); Soltanolkotabi, M [Quantum Optics Group, University of Isfahan, Isfahan (Iran, Islamic Republic of)
2006-09-01
We present a theoretical scheme based on an su(2) dynamical algebraic structure to investigate the influence of a homogeneous gravitational field on the quantum-nondemolition measurement of atomic momentum in the dispersive Jaynes-Cummings model. In the dispersive Jaynes-Cummings model, when detuning is large and the atomic motion is in a propagating light wave, we consider a two-level atom interacting with the quantized cavity field in the presence of a homogeneous gravitational field. We derive an effective Hamiltonian describing the dispersive atom-field interaction in the presence of the gravitational field. We investigate the influence of the gravitational field on both the momentum filter and momentum distribution. Particularly, we find that the gravitational field decreases both the tooth spacing of momentum and the tooth width of momentum.
Koskinen, T T; Yelle, R V; Lavvas, P
2012-01-01
The detections of atomic hydrogen, heavy atoms and ions surrounding the extrasolar giant planet (EGP) HD209458b constrain the composition, temperature and density profiles in its upper atmosphere. Thus the observations provide guidance for models that have so far predicted a range of possible conditions. We present the first hydrodynamic escape model for the upper atmosphere that includes all of the detected species in order to explain their presence at high altitudes, and to further constrain the temperature and velocity profiles. This model calculates the stellar heating rates based on recent estimates of photoelectron heating efficiencies, and includes the photochemistry of heavy atoms and ions in addition to hydrogen and helium. The composition at the lower boundary of the escape model is constrained by a full photochemical model of the lower atmosphere. We confirm that molecules dissociate near the 1 microbar level, and find that complex molecular chemistry does not need to be included above this level. ...
Enhancement of Squeezing in Two-Photon Jaynes-Cummings Model with Atomic Measurement
Institute of Scientific and Technical Information of China (English)
YE Sai-Yun
2006-01-01
We investigate the squeezing properties of the cavity field in the degenerate two-photon Jaynes-Cummings model. Compared with the one-photon Jaynes-Cummings model, the squeezing is more pronounced in the case of two-photon Jaynes-Cummings model under certain conditions.
Gleadall, Andrew; Pan, Jingzhe; Kruft, Marc-Anton
2015-11-01
Atomic simulations were undertaken to analyse the effect of polymer chain scission on amorphous poly(lactide) during degradation. Many experimental studies have analysed mechanical properties degradation but relatively few computation studies have been conducted. Such studies are valuable for supporting the design of bioresorbable medical devices. Hence in this paper, an Effective Cavity Theory for the degradation of Young's modulus was developed. Atomic simulations indicated that a volume of reduced-stiffness polymer may exist around chain scissions. In the Effective Cavity Theory, each chain scission is considered to instantiate an effective cavity. Finite Element Analysis simulations were conducted to model the effect of the cavities on Young's modulus. Since polymer crystallinity affects mechanical properties, the effect of increases in crystallinity during degradation on Young's modulus is also considered. To demonstrate the ability of the Effective Cavity Theory, it was fitted to several sets of experimental data for Young's modulus in the literature.
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.
Energy Technology Data Exchange (ETDEWEB)
Grau, A.; Arcos, J. M. los
1986-07-01
The present paper develops a three L-subshell a and K, M-a hells atomic model in order to obtain the counting efficiency in liquid scintillation counting. Mathematical expressions are given to calculate the probabilities of 264 different atomic rearrangement way so as the corresponding effective energies. This new model will permit to test the influence of the different atomic and nuclear parameters upon the counting efficiency nuclides of low and medium atomic number decaying by electron capture. (Author) 8 refs.
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.
Improving atomic force microscopy imaging by a direct inverse asymmetric PI hysteresis model.
Wang, Dong; Yu, Peng; Wang, Feifei; Chan, Ho-Yin; Zhou, Lei; Dong, Zaili; Liu, Lianqing; Li, Wen Jung
2015-02-03
A modified Prandtl-Ishlinskii (PI) model, referred to as a direct inverse asymmetric PI (DIAPI) model in this paper, was implemented to reduce the displacement error between a predicted model and the actual trajectory of a piezoelectric actuator which is commonly found in AFM systems. Due to the nonlinearity of the piezoelectric actuator, the standard symmetric PI model cannot precisely describe the asymmetric motion of the actuator. In order to improve the accuracy of AFM scans, two series of slope parameters were introduced in the PI model to describe both the voltage-increase-loop (trace) and voltage-decrease-loop (retrace). A feedforward controller based on the DIAPI model was implemented to compensate hysteresis. Performance of the DIAPI model and the feedforward controller were validated by scanning micro-lenses and standard silicon grating using a custom-built AFM.
Improving Atomic Force Microscopy Imaging by a Direct Inverse Asymmetric PI Hysteresis Model
Directory of Open Access Journals (Sweden)
Dong Wang
2015-02-01
Full Text Available A modified Prandtl–Ishlinskii (PI model, referred to as a direct inverse asymmetric PI (DIAPI model in this paper, was implemented to reduce the displacement error between a predicted model and the actual trajectory of a piezoelectric actuator which is commonly found in AFM systems. Due to the nonlinearity of the piezoelectric actuator, the standard symmetric PI model cannot precisely describe the asymmetric motion of the actuator. In order to improve the accuracy of AFM scans, two series of slope parameters were introduced in the PI model to describe both the voltage-increase-loop (trace and voltage-decrease-loop (retrace. A feedforward controller based on the DIAPI model was implemented to compensate hysteresis. Performance of the DIAPI model and the feedforward controller were validated by scanning micro-lenses and standard silicon grating using a custom-built AFM.
DeZutter, Christopher B; Horner, John H; Newcomb, Martin
2008-03-06
Rate constants for 1,5- and 1,6-hydrogen atom transfer reactions in models of polyunsaturated fatty acid radicals were measured via laser flash photolysis methods. Photolyses of PTOC (pyridine-2-thioneoxycarbonyl) ester derivatives of carboxylic acids gave primary alkyl radicals that reacted by 1,5-hydrogen transfer from mono-, di-, and tri-aryl-substituted positions or 1,6-hydrogen transfer from di- and tri-aryl-substituted positions to give UV-detectable products. Rate constants for reactions in acetonitrile at room temperature ranged from 1 x 10(4) to 4 x 10(6) s(-1). The activation energies for a matched pair of 1,5- and 1,6-hydrogen atom transfers giving tri-aryl-substituted radicals were approximately equal, as were the primary kinetic isotope effects, but the 1,5-hydrogen atom transfer reaction was 1 order of magnitude faster at room temperature than the 1,6-hydrogen atom transfer reaction due to a less favorable entropy of activation for the 1,6-transfer reaction. Solvent effects on the rate constants for the 1,5-hydrogen atom transfer reaction of the 2-[2-(diphenylmethyl)phenyl]ethyl radical at ambient temperature were as large as a factor of 2 with the reaction increasing in rate in lower polarity solvents. Hybrid density functional theory computations for the 1,5- and 1,6-hydrogen atom transfers of the tri-aryl-substituted donors were in qualitative agreement with the experimental results.
Michaud, Georges; Richer, Jacques
2015-01-01
This book gives an overview of atomic diffusion, a fundamental physical process, as applied to all types of stars, from the main sequence to neutron stars. The superficial abundances of stars as well as their evolution can be significantly affected. The authors show where atomic diffusion plays an essential role and how it can be implemented in modelling. In Part I, the authors describe the tools that are required to include atomic diffusion in models of stellar interiors and atmospheres. An important role is played by the gradient of partial radiative pressure, or radiative acceleration, which is usually neglected in stellar evolution. In Part II, the authors systematically review the contribution of atomic diffusion to each evolutionary step. The dominant effects of atomic diffusion are accompanied by more subtle effects on a large number of structural properties throughout evolution. One of the goals of this book is to provide the means for the astrophysicist or graduate student to evaluate the importanc...
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.
Edge-to-edge interfaces in Ti-Al modeled with the embedded atom method
Reynolds, W. T.; Farkas, D.
2006-03-01
The atomistic structure and energies of high-index interphase boundaries are explored using a combination of molecular statics and dynamics simulations with embedded atom potentials. We investigate planar boundaries between the α2 and γ phases in the Ti-Al system. The class of boundaries considered has a high-index boundary orientation; the orientation relationship between the α2 and γ phases also is high index, and a set of planes from each phase meet edge to edge at the boundary plane. For the particular case of a boundary that is commensurate in one direction and coincides with a moiré plane given by the so-called “Δ g” diffraction condition, the boundary is not structurally singular, but it is energetically stable and does not appear to dissociate into other low-energy configurations. Misfit compensating defects are not observed; misfit in directions other than the commensurate one appears to be distributed uniformly. The boundary energy is evaluated as a function of the orientation of the boundary plane, and the edge-to-edge (moiré) boundary is found to lie in an energy cusp.
Caffau, E; Bonifacio, P; Faraggiana, R; Steffen, M; Freytag, B; Kamp, I; Ayres, T R
2010-01-01
The use of hydrodynamical simulations, the selection of atomic data, and the computation of deviations from local thermodynamical equilibrium for the analysis of the solar spectra have implied a downward revision of the solar metallicity. We are in the process of using the latest simulations computed with the CO5BOLD code to reassess the solar chemical composition. We determine the solar photospheric carbon abundance by using a radiation-hydrodynamical CO5BOLD model, and compute the departures from local thermodynamical equilibrium by using the Kiel code. We measure equivalent widths of atomic CI lines on high resolution, high signal-to-noise ratio solar atlases. Deviations from local thermodynamic equilibrium are computed in 1D with the Kiel code. Our recommended value for the solar carbon abundance, relies on 98 independent measurements of observed lines and is A(C)=8.50+-0.06, the quoted error is the sum of statistical and systematic error. Combined with our recent results for the solar oxygen and nitrogen...
HERschel Observations of Edge-on Spirals (HEROES). II: Tilted-ring modelling of the atomic gas disks
Allaert, F; Baes, M; De Geyter, G; Hughes, T M; Lewis, F; Bianchi, S; De Looze, I; Fritz, J; Holwerda, B W; Verstappen, J; Viaene, S
2015-01-01
Context. Edge-on galaxies can offer important insights in galaxy evolution as they are the only systems where the distribution of the different components can be studied both radially and vertically. The HEROES project was designed to investigate the interplay between the gas, dust, stars and dark matter (DM) in a sample of 7 massive edge-on spiral galaxies. Aims. In this second HEROES paper we present an analysis of the atomic gas content of 6 out of 7 galaxies in our sample. The remaining galaxy was recently analysed according to the same strategy. The primary aim of this work is to constrain the surface density distribution, the rotation curve and the geometry of the gas disks in a homogeneous way. In addition we identify peculiar features and signs of recent interactions. Methods. We construct detailed tilted-ring models of the atomic gas disks based on new GMRT 21-cm observations of NGC 973 and UGC 4277 and re-reduced archival HI data of NGC 5907, NGC 5529, IC 2531 and NGC 4217. Potential degeneracies be...
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.
Xiao, Ke; Malvankar, Nikhil S; Shu, Chuanjun; Martz, Eric; Lovley, Derek R; Sun, Xiao
2016-03-22
The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.
Levashov, V A; Stepanov, M G
2016-01-01
Considerations of local atomic-level stresses associated with each atom represent a particular approach to address structures of disordered materials at the atomic level. We studied structural correlations in a two-dimensional model liquid using molecular dynamics simulations in the following way. We diagonalized the atomic-level stress tensor of every atom and investigated correlations between the eigenvalues and orientations of the eigenvectors of different atoms as a function of distance between them. It is demonstrated that the suggested approach can be used to characterize structural correlations in disordered materials. In particular, we found that changes in the stress correlation functions on decrease of temperature are the most pronounced for the pairs of atoms with separation distance that corresponds to the first minimum in the pair density function. We also show that the angular dependencies of the stress correlation functions previously reported by Wu et al. [Phys. Rev. E 91, 032301 (2015)10.1103/PhysRevE.91.032301] do not represent the anisotropic Eshelby's stress fields, as it is suggested, but originate in the rotational properties of the stress tensors.
History and Philosophy of Science through Models: Some Challenges in the Case of "The Atom".
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)
Determination of a high spatial resolution geopotential model using atomic clock comparisons
Lion, G.; Panet, I.; Wolf, P.; Guerlin, C.; Bize, S.; Delva, P.
2017-01-01
Recent technological advances in optical atomic clocks are opening new perspectives for the direct determination of geopotential differences between any two points at a centimeter-level accuracy in geoid height. However, so far detailed quantitative estimates of the possible improvement in geoid determination when adding such clock measurements to existing data are lacking. We present a first step in that direction with the aim and hope of triggering further work and efforts in this emerging field of chronometric geodesy and geophysics. We specifically focus on evaluating the contribution of this new kind of direct measurements in determining the geopotential at high spatial resolution (≈ 10 km). We studied two test areas, both located in France and corresponding to a middle (Massif Central) and high (Alps) mountainous terrain. These regions are interesting because the gravitational field strength varies greatly from place to place at high spatial resolution due to the complex topography. Our method consists in first generating a synthetic high-resolution geopotential map, then drawing synthetic measurement data (gravimetry and clock data) from it, and finally reconstructing the geopotential map from that data using least squares collocation. The quality of the reconstructed map is then assessed by comparing it to the original one used to generate the data. We show that adding only a few clock data points (less than 1% of the gravimetry data) reduces the bias significantly and improves the standard deviation by a factor 3. The effect of the data coverage and data quality on the results is investigated, and the trade-off between the measurement noise level and the number of data points is discussed.
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
Atomic and molecular supernovae
Energy Technology Data Exchange (ETDEWEB)
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.
EINSTEIN, SCHROEDINGER, AND ATOM
Directory of Open Access Journals (Sweden)
Trunev A. P.
2014-03-01
Full Text Available In this paper, we consider gravitation theory in multidimensional space. The model of the metric satisfying the basic requirements of quantum theory is proposed. It is shown that gravitational waves are described by the Liouville equation and the Schrodinger equation as well. The solutions of the Einstein equations describing the stationary states of arbitrary quantum and classical systems with central symmetry have been obtained. Einstein’s atom model has been developed, and proved that atoms and atomic nuclei can be represented as standing gravitational waves
Institute of Scientific and Technical Information of China (English)
LIU Shu-Shen; YIN Da-Qiang; CUI Shi-Hai; WANG Lian-Sheng
2005-01-01
The electrotopological state (E-state) index was employed to characterize the structures of 51 substituted benzenes. Eleven E-state indices of the compounds were calculated by the computer program developed in our laboratory. The method for variable selection and modeling based on prediction (VSMP) was used to select an optimal combination of the variables from 11 E-state descriptors. Then the optimal descriptors were employed to model the relationship between the relative biodegradability of the substituted benzenes and their molecular structures. A novel 5-descriptor linear model was developed and the model has a high quality with the correlation coefficient and the root mean square error in estimation step being 0.9378 and 0.35, respectively, and these in leave-one-out cross-validation procedure being 0.9210 and 0.39, respectively.
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.
Po, Hoi Chun; Zhou, Qi
2015-08-13
Bosons have a natural instinct to condense at zero temperature. It is a long-standing challenge to create a high-dimensional quantum liquid that does not exhibit long-range order at the ground state, as either extreme experimental parameters or sophisticated designs of microscopic Hamiltonians are required for suppressing the condensation. Here we show that synthetic gauge fields for ultracold atoms, using either the Raman scheme or shaken lattices, provide physicists a simple and practical scheme to produce a two-dimensional algebraic quantum liquid at the ground state. This quantum liquid arises at a critical Lifshitz point, where a two-dimensional quartic dispersion emerges in the momentum space, and many fundamental properties of two-dimensional bosons are changed in its proximity. Such an ideal simulator of the quantum Lifshitz model allows experimentalists to directly visualize and explore the deconfinement transition of topological excitations, an intriguing phenomenon that is difficult to access in other systems.
Quantum-kinetic modeling of electron release in low-energy surface collisions of atoms and molecules
Energy Technology Data Exchange (ETDEWEB)
Marbach, Johannes
2012-09-20
In this work we present a theoretical description of electron release in the collision of atomic and molecular projectiles with metallic and especially dielectric surfaces. The associated electron yield, the secondary electron emission coefficient, is an important input parameter for numerical simulations of dielectric barrier discharges and other bounded low-temperature gas discharges. The available reference data for emission coefficients is, however, very sparse and often uncertain, especially for molecular projectiles. With the present work we aim to contribute to the filling of these gaps by providing a flexible and easy-to-use model that allows for a convenient calculation of the emission coefficient and related quantities for a wide range of projectile-surface systems and the most dominant reaction channels.
Modeling of hydrogen atom diffusion and response behavior of hydrogen sensors in Pd–Y alloy nanofilm
Liu, Yi; Li, Yanli; Huang, Pengcheng; Song, Han; Zhang, Gang
2016-11-01
To detect hydrogen gas leakage rapidly, many types of hydrogen sensors containing palladium alloy film have been proposed and fabricated to date. However, the mechanisms and factors that determine the response rate of such hydrogen sensor have not been established theoretically. The manners in which response time is forecasted and sensitive film is designed are key issues in developing hydrogen sensors with nanometer film. In this paper, a unilateral diffusion model of hydrogen atoms in Pd alloy based on Fick’s second law is proposed to describe the Pd–H reaction process. Model simulation shows that the hydrogen sensor response time with Pd alloy film is dominated by two factors (film thickness and hydrogen diffusion coefficient). Finally, a series of response rate experiments with varying thicknesses of Pd–Y (yttrium) alloy film are implemented to verify model validity. Our proposed model can help researchers in the precise optimization of film thickness to realize a simultaneously speedy and sensitive hydrogen sensor. This study also aids in evaluating the influence of manufacturing errors on performances and comparing the performances of sensors with different thicknesses.
Liu, Yi; Li, Yanli; Huang, Pengcheng; Song, Han; Zhang, Gang
2016-11-15
To detect hydrogen gas leakage rapidly, many types of hydrogen sensors containing palladium alloy film have been proposed and fabricated to date. However, the mechanisms and factors that determine the response rate of such hydrogen sensor have not been established theoretically. The manners in which response time is forecasted and sensitive film is designed are key issues in developing hydrogen sensors with nanometer film. In this paper, a unilateral diffusion model of hydrogen atoms in Pd alloy based on Fick's second law is proposed to describe the Pd-H reaction process. Model simulation shows that the hydrogen sensor response time with Pd alloy film is dominated by two factors (film thickness and hydrogen diffusion coefficient). Finally, a series of response rate experiments with varying thicknesses of Pd-Y (yttrium) alloy film are implemented to verify model validity. Our proposed model can help researchers in the precise optimization of film thickness to realize a simultaneously speedy and sensitive hydrogen sensor. This study also aids in evaluating the influence of manufacturing errors on performances and comparing the performances of sensors with different thicknesses.
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
Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G
2009-05-07
We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous
Directory of Open Access Journals (Sweden)
B. J. Murray
2005-01-01
Full Text Available The formation, evolution and eventual sublimation of noctilucent clouds (NLC may have a significant effect on the odd oxygen and hydrogen chemistry of the high latitude summer mesosphere. Three mechanisms are considered here: the direct uptake of atomic oxygen on the surface of the ice particles; the redistribution of water vapour, which changes the photochemical source of odd hydrogen species; and the direct photolysis of the ice particles themselves to produce odd hydrogen species in the gas phase. A 1-D photochemical model is employed to investigate the potential importance of these mechanisms. This shows, using the recently measured uptake coefficients of O on ice, that the heterogeneous removal of O on the surface of the cloud particles is too slow by at least a factor of 5x103 to compete with gas-phase O chemistry. The second and third mechanisms involve the solar Lyman-α photolysis of H2O in the gas and solid phase, respectively. During twilight, Lyman-α radiation is severely attenuated and these mechanisms are insignificant. In contrast, when the upper mesosphere is fully illuminated there is a dramatic impact on the O profile, with depletion of O at the base of the cloud layer of close to an order of magnitude. A correspondingly large depletion in O3 is also predicted, while H, OH, HO2 and H2O2 are found to be enhanced by factors of 3-5. In fact, rocket-borne mass spectrometer measurements during summer have revealed local H2O2 enhancements in the region of the clouds. Rocket-borne measurements of atomic O and O3 profiles in the presence of mesospheric clouds in the daytime are highly desirable to test the predictions of this model and our understanding of the genesis of mesospheric clouds.
Krokhotin, Andrey; Dokholyan, Nikolay V
2015-01-01
Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.
How Modelling of Crystal Defects at the Atomic Scale can Provide Information on Seismic Anisotropy
Cordier, P.; Carrez, P.; Goryaeva, A.; Gouriet, K.; Hirel, P.; Kraych, A.; Ritterbex, S.
2014-12-01
Seismic anisotropy represents one of the few sources of information about flow in the mantle that takes place at timescales that are barely accessible at human timescales. Seismic waves travelling through rocks at the speed of sound can reveal flow lines frozen in rocks over hundreds of million years. The interpretation of seismic anisotropy also needs to bridge length-scales since crystal defects are responsible for the plastic anisotropy that align crystals in a deforming rock thus revealing elastic anisotropy at the macroscopic scale. Knowing the easiest slip systems for a given crystal structure is thus the fundamental information needed. To obtain it we propose the following approach based on multiscale numerical modeling. As a first approach, we calculate generalized stacking faults which inform us about the easiest shear paths imposed by the crystal chemistry. This leads to a short list of potential slip systems for which lattice friction will be calculated. A further selection will be done by modeling the core structures of screw dislocations. The tendency for core spreading of screw dislocations impose a selection on potential glide planes which is further validated by modeling corresponding edge dislocations and their respective mobilities. Finally, we model the mobility of these dislocations under the conjugate influence of stress and temperature using the kink-pair model which is based on the activation enthalpy of the critical configuration which allows a dislocation to glide from one stable position to the next. The output of this model is the so-called critical resolved shear stress which is the onset of plastic glide at a given temperature and strain rate. Comparison between slip systems provides constraints on the plastic anisotropy. Examples are presented among the major phases of the Earth's mantle.
Born, Max
1989-01-01
The Nobel Laureate's brilliant exposition of the kinetic theory of gases, elementary particles, the nuclear atom, wave-corpuscles, atomic structure and spectral lines, electron spin and Pauli's principle, quantum statistics, molecular structure and nuclear physics. Over 40 appendices, a bibliography, numerous figures and graphs.
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.
van Hooft, Paul A. M.; Höltje, Hans-Dieter
2000-11-01
A new method is described for generating all-atom protein structures from Cα-atom information. The method, which combines both local structural trace alignments and comparative side chain modeling with ab initio side chain modeling, makes use of both the virtual-bond and the dipole-path methods. Provided that 3D structures of structurally and functionally related proteins exist, the method presented here is highly suitable for generating all-atom coordinates of partly solved, low-resolution crystal structures. Particularly the active site region can be modeled accurately with this procedure, which enables investigation of the binding modes of different classes of ligands with molecular dynamics simulations. The method is applied to the trace of Streptococcus pneumoniae, in order to construct an all-atom structure of the transpeptidase domain. Since after generation of full coordinates of the transpeptidase domain the structure had been solved to 2.4 Å resolution, new X-ray coordinates for the worst modeled loop (residues T370 to M386; 17 out of a total number of 351 residues constituting the transpeptidase domain) were incorporated, as kindly provided by Dr. Dideberg. The structure was relaxed with molecular dynamics simulations and simulated annealing methods. The RMS deviation between the 144 aligned Cα-atoms and the corresponding ones in the originally solved 3.5 Å resolution crystal structure was 0.98. The 351 Cα-atoms of the whole transpeptidase domain of the final model showed an RMS deviation of 1.58. The Ramachandran plot showed that 79.3% of the residues are in the most favored regions, with only 1.0% occurring in disallowed regions. The model presented here can be used to investigate the three-dimensional influences of mutations around the active site of PBP2 x.
Energy Technology Data Exchange (ETDEWEB)
Pogorelov, Nikolai [Univ. of Alabama, Huntsville, AL (United States); Zhang, Ming [Florida Inst. of Technology, Melbourne, FL (United States)
2016-07-31
Interactions of flows of partially ionized, magnetized plasma are frequently accompanied by the presence of both thermal and non-thermal (pickup) ion components. Such interactions cannot be modeled using traditional MHD equations and require more advanced approaches to treat them. If a nonthermal component of ions is formed due to charge exchange and collisions between the thermal (core) ions and neutrals, it experiences the action of magnetic field, its distribution function is isotropized, and it soon acquires the velocity of the ambient plasma without being thermodynamically equilibrated. This situation, e. g., takes place in the outer heliosphere –- the part of interstellar space beyond the solar system whose properties are determined by the solar wind interaction with the local interstellar medium. This is also possible in laboratory, at million degrees and above, when plasma is conducting electricity far too well, which makes Ohmic heating ineffective. To attain the target temperatures one needs additional heating eventually playing a dominant role. Among such sources is a so-called neutral particle beam heating. This is a wide-spread technique (Joint European Torus and International Thermonuclear Experimental Reactor experiments) based on the injection of powerful beams of neutral atoms into ohmically preheated plasma. In this project we have investigated the energy and density separation between the thermal and nonthermal components in the solar wind and interstellar plasmas. A new model has been developed in which we solve the ideal MHD equations for mixture of all ions and the kinetic Boltzmann equation to describe the transport of neutral atoms. As a separate capability, we can treat the flow of neutral atoms in a multi-component fashion, where neutral atoms born in each thermodynamically distinct region are governed by the Euler gas dynamic equations. We also describe the behavior of pickup ions either kinetically, using the Fokker--Planck equation
Energy Technology Data Exchange (ETDEWEB)
Pogorelov, Nikolai [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and; Zhang, Ming [Florida Inst. of Technology, Melbourne, FL (United States). Physics and Space Sciences Dept.; Borovikov, Sergey [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and Aeronomic Research; Heerikhuisen, Jacob [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and Aeronomic Research; Zank, Gary [Univ. of Alabama, Huntsville, AL (United States). Dept. of Space Science. Center for Space Plasma and Aeronomic Research; Gamayunov, Konstantin [Florida Inst. of Technology, Melbourne, FL (United States). Physics and Space Sciences Dept.; Colella, Phillip [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
2016-07-31
Interactions of flows of partially ionized, magnetized plasma are frequently accompanied by the presence of both thermal and non-thermal (pickup) ion components. Such interactions cannot be modeled using traditional MHD equations and require more advanced approaches to treat them. If a nonthermal component of ions is formed due to charge exchange and collisions between the thermal (core) ions and neutrals, it experiences the action of magnetic field, its distribution function is isotropized, and it soon acquires the velocity of the ambient plasma without being thermodynamically equilibrated. This situation, e. g., takes place in the outer heliosphere - the part of interstellar space beyond the solar system whose properties are determined by the solar wind interaction with the local interstellar medium. This is also possible in laboratory, at million degrees and above, when plasma is conducting electricity far too well, which makes Ohmic heating ineffective. To attain the target temperatures one needs additional heating eventually playing a dominant role. Among such sources is a so-called neutral particle beam heating. This is a wide-spread technique (Joint European Torus and International Thermonuclear Experimental Reactor experiments) based on the injection of powerful beams of neutral atoms into ohmically preheated plasma. In this project we have investigated the energy and density separation between the thermal and nonthermal components in the solar wind and interstellar plasmas. A new model has been developed in which we solve the ideal MHD equations for mixture of all ions and the kinetic Boltzmann equation to describe the transport of neutral atoms. As a separate capability, we can treat the flow of neutral atoms in a multi-component fashion, where neutral atoms born in each thermodynamically distinct regions are governed by the Euler gas dynamic equations. We also describe the behavior of pickup ions either kinetically, using the Fokker–Planck equation, or
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.
The Muonium Atom as a Probe of Physics beyond the Standard Model
Willmann, L.; Jungmann, K.
1998-01-01
The observed interactions between particles are not fully explained in the successful theoretical description of the standard model to date. Due to the close confinement of the bound state muonium ($M = \\mu^+ e^-$) can be used as an ideal probe of quantum electrodynamics and weak interaction and als
Gaussian Schell Source as Model for Slit-Collimated Atomic and Molecular Beams
McMorran, Ben
2008-01-01
We show how to make a Gaussian Schell-model (GSM) beam. Then we compare the intensity profile, the transverse coherence width and the divergence angle of a GSM beam with those same properties of a beam that is collimated with two hard-edged slits. This work offers an intuitive way to understand various interferometer designs, and we compare our results with data.
Atomic data for a five-configuration model of Fe XIV
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.
The Muonium Atom as a Probe of Physics beyond the Standard Model
Willmann, L
1998-01-01
The observed interactions between particles are not fully explained in the successful theoretical description of the standard model to date. Due to the close confinement of the bound state muonium ($M = \\mu^+ e^-$) can be used as an ideal probe of quantum electrodynamics and weak interaction and also for a search for additional interactions between leptons. Of special interest is the lepton number violating process of sponteanous conversion of muonium to antimuonium.
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
Directory of Open Access Journals (Sweden)
Xiaojun Xu
2015-01-01
Full Text Available While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM and small angle X-ray scattering (SAXS have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair.
Energy Technology Data Exchange (ETDEWEB)
Elrawemi, Mohamed, E-mail: Mohamed.elrawemi@hud.ac.uk [EPSRC Centre for Innovative Manufacturing in Advanced Metrology, School of Computing and Engineering, University of Huddersfield, Huddersfield (United Kingdom); Blunt, Liam; Fleming, Leigh [EPSRC Centre for Innovative Manufacturing in Advanced Metrology, School of Computing and Engineering, University of Huddersfield, Huddersfield (United Kingdom); Bird, David, E-mail: David.Bird@uk-cpi.com [Centre for Process Innovation Limited, Sedgefield, County Durham (United Kingdom); Robbins, David [Centre for Process Innovation Limited, Sedgefield, County Durham (United Kingdom); Sweeney, Francis [EPSRC Centre for Innovative Manufacturing in Advanced Metrology, School of Computing and Engineering, University of Huddersfield, Huddersfield (United Kingdom)
2014-11-03
Transparent barrier films such as Al{sub 2}O{sub 3} used for prevention of oxygen and/or water vapour permeation are the subject of increasing research interest when used for the encapsulation of flexible photovoltaic modules. However, the existence of micro-scale defects in the barrier surface topography has been shown to have the potential to facilitate water vapour ingress, thereby reducing cell efficiency and causing internal electrical shorts. Previous work has shown that small defects (≤ 3 μm lateral dimension) were less significant in determining water vapour ingress. In contrast, larger defects (≥ 3 μm lateral dimension) seem to be more detrimental to the barrier functionality. Experimental results based on surface topography segmentation analysis and a model presented in this paper will be used to test the hypothesis that the major contributing defects to water vapour transmission rate are small numbers of large defects. The model highlighted in this study has the potential to be used for gaining a better understanding of photovoltaic module efficiency and performance. - Highlights: • A model of water vapour permeation through barrier defects is presented. • The effect of the defects on the water vapour permeability is investigated. • Defect density correlates with water vapour permeability. • Large defects may dominate the permeation properties of the barrier film.
Modeling Primary Atomization of Liquid Fuels using a Multiphase DNS/LES Approach
Energy Technology Data Exchange (ETDEWEB)
Arienti, Marco [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Oefelein, Joe [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Doisneau, Francois [Sandia National Lab. (SNL-CA), Livermore, CA (United States)
2016-08-01
As part of a Laboratory Directed Research and Development project, we are developing a modeling-and-simulation capability to study fuel direct injection in automotive engines. Predicting mixing and combustion at realistic conditions remains a challenging objective of energy science. And it is a research priority in Sandia’s mission-critical area of energy security, being also relevant to many flows in defense and climate. High-performance computing applied to this non-linear multi-scale problem is key to engine calculations with increased scientific reliability.
DEFF Research Database (Denmark)
Hukkerikar, Amol; Sarup, Bent; Sin, Gürkan
One of the most widely employed group contribution method for estimation of properties of pure components is the Marrero and Gani (MG) method. For the given component whose molecular structure is not completely described by any of the available groups, group contribution+ method (combined MG method...... and atomic connectivity index method) has been employed to create the missing groups and predict their contributions through the regressed contributions of connectivity indices. The objective of this work is to develop a systematic methodology to carry out uncertainty analysis of group contribution based...... and atom connectivity index based property prediction models. This includes: (i) parameter estimation using available MG based property prediction models and large training sets to determine improved group and atom contributions; and (ii) uncertainty analysis to establish statistical information...
Applying a one-dimensional PDR model to the Taurus molecular cloud and its atomic envelope
Heiner, J S
2012-01-01
In this contribution, we test our previously published one-dimensional PDR model for deriving total hydrogen volume densities from HI column density measurements in extragalactic regions by applying it to the Taurus molecular cloud, where its predictions can be compared to available data. Also, we make the first direct detailed comparison of our model to CO(1-0) and far-infrared emission. Using an incident UV flux G0 of 4.25 ({\\chi} = 5) throughout the main body of the cloud, we derive total hydrogen volume densities of \\approx 430 cm-3, consistent with the extensive literature available on Taurus. The distribution of the volume densities shows a log-normal shape with a hint of a power-law shape on the high density end. We convert our volume densities to H2 column densities assuming a cloud depth of 5 parsec and compare these column densities to observed CO emission. We find a slope equivalent to a CO conversion factor relation that is on the low end of reported values for this factor in the literature (0.9 x...
Sacchi, Mattia; Balleza, Daniel; Vena, Giulia; Puia, Giulia; Facci, Paolo; Alessandrini, Andrea
2015-05-01
Amphiphilic molecules which have a biological effect on specific membrane proteins, could also affect lipid bilayer properties possibly resulting in a modulation of the overall membrane behavior. In light of this consideration, it is important to study the possible effects of amphiphilic molecule of pharmacological interest on model systems which recapitulate some of the main properties of the biological plasma membranes. In this work we studied the effect of a neurosteroid, Allopregnanolone (3α,5α-tetrahydroprogesterone or Allo), on a model bilayer composed by the ternary lipid mixture DOPC/bSM/chol. We chose ternary mixtures which present, at room temperature, a phase coexistence of liquid ordered (Lo) and liquid disordered (Ld) domains and which reside near to a critical point. We found that Allo, which is able to strongly partition in the lipid bilayer, induces a marked increase in the bilayer area and modifies the relative proportion of the two phases favoring the Ld phase. We also found that the neurosteroid shifts the miscibility temperature to higher values in a way similarly to what happens when the cholesterol concentration is decreased. Interestingly, an isoform of Allo, isoAllopregnanolone (3β,5α-tetrahydroprogesterone or isoAllo), known to inhibit the effects of Allo on GABAA receptors, has an opposite effect on the bilayer properties.
Physicists' approach to studying socio-economic inequalities: Can humans be modelled as atoms?
Sharma, Kiran
2016-01-01
A brief overview of the models and data analyses of income, wealth, consumption distributions by the physicists, are presented here. It has been found empirically that the distributions of income and wealth possess fairly robust features, like the bulk of both the income and wealth distributions seem to reasonably fit both the log-normal and Gamma distributions, while the tail of the distribution fits well to a power law (as first observed by sociologist Pareto). We also present our recent studies of the unit-level expenditure on consumption across multiple countries and multiple years, where it was found that there exist invariant features of consumption distribution: the bulk is log-normally distributed, followed by a power law tail at the limit. The mechanisms leading to such inequalities and invariant features for the distributions of socio-economic variables are not well-understood. We also present some simple models from physics and demonstrate how they can be used to explain some of these findings and ...
Mass Predictions of Atomic Nuclei in the Infinite Nuclear Matter Model
Nayak, R C
2012-01-01
We present here the mass excesses, binding energies, one- and two- neutron, one and two- proton and \\alpha-particle separation energies of 6727 nuclei in the ranges 4 \\leq Z \\leq 120 and 8 \\leq A \\leq 303 calculated in the infinite nuclear matter model. Compared to our predictions of 1999 mass table, the present ones are obtained using larger data base of 2003 mass table of Wapstra and Audi and resorting to higher accuracy in the solutions of the \\eta-differential equations of the INM model. The local energy \\eta's supposed to carry signature of the characteristic properties of nuclei are found to possess the predictive capability. In fact \\eta-systematics reveal new magic numbers in the drip-line regions giving rise to new islands of stability supported by relativistic mean field theoretic calculations. This is a manifestation of a new phenomenon where shell-effect overcomes the instability due to repulsive components of the nucleon-nucleon force broadening the stability peninsula. The two-neutron separation...
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
Hybrid-PIC Modeling of the Transport of Atomic Boron in a Hall Thruster
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.
Ahmed, Maqsood; Nassour, Ayoub; Noureen, Sajida; Lecomte, Claude; Jelsch, Christian
2016-02-01
The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.
Directory of Open Access Journals (Sweden)
Graves N.
2013-01-01
Full Text Available A model is proposed for the hydrogen atom in which the electron is an objectively real particle orbiting at very near to light speed. The model is based on the postulate that certain velocity terms associated with orbiting bodies can be considered as being af- fected by relativity. This leads to a model for the atom in which the stable electron orbits are associated with orbital velocities where Gamma is n /α , leading to the idea that it is Gamma that is quantized and not angular momentum as in the Bohr and other models. The model provides a mechanism which leads to quantization of energy levels within the atom and also provides a simple mechanical explanation for the Fine Struc- ture Constant. The mechanism is closely associated with the Sampling theorem and the related phenomenon of aliasing developed in the mid-20th century by engineers at Bell labs.
Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.
2016-09-01
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an
Gumí-Audenis, Berta; Costa, Luca; Carlá, Francesco; Comin, Fabio; Sanz, Fausto; Giannotti, Marina I
2016-12-19
Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs) are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol) plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs). Atomic force microscope (AFM) is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS) has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR) techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information.
Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua
2013-04-01
The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments.
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.
Directory of Open Access Journals (Sweden)
Li Yuqin
2014-01-01
Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.
All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics.
Gangupomu, Vamshi K; Abrams, Cameron F
2010-11-17
The 27-residue membrane-spanning domain (MSD) of the HIV-1 glycoprotein gp41 bears conserved sequence elements crucial to the biological function of the virus, in particular a conserved GXXXG motif and a midspan arginine. However, structure-based explanations for the roles of these and other MSD features remain unclear. Using molecular dynamics and metadynamics calculations of an all-atom, explicit solvent, and membrane-anchored model, we study the conformational variability of the HIV-1 gp41 MSD. We find that the MSD peptide assumes a stable tilted α-helical conformation in the membrane. However, when the side chain of the midspan Arg (694) "snorkels" to the outer leaflet of the viral membrane, the MSD assumes a metastable conformation where the highly-conserved N-terminal core (between Lys(681) and Arg(694) and containing the GXXXG motif) unfolds. In contrast, when the Arg(694) side chain snorkels to the inner leaflet, the MSD peptide assumes a metastable conformation consistent with experimental observations where the peptide kinks at Phe(697) to facilitate Arg(694) snorkeling. Both of these models suggest specific ways that gp41 may destabilize viral membrane, priming the virus for fusion with a target cell.
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.
Gumí-Audenis, Berta; Costa, Luca; Carlá, Francesco; Comin, Fabio; Sanz, Fausto; Giannotti, Marina I.
2016-01-01
Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs) are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol) plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs). Atomic force microscope (AFM) is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS) has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR) techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information. PMID:27999368
Mass predictions of atomic nuclei in the infinite nuclear matter model
Nayak, R. C.; Satpathy, L.
2012-07-01
We present here the mass excesses, binding energies, one- and two-neutron, one- and two-proton and α-particle separation energies of 6727 nuclei in the ranges 4≤Z≤120 and 8≤A≤303 calculated in the infinite nuclear matter model. Compared to our predictions of 1999 mass table, the present ones are obtained using larger data base of 2003 mass table of Wapstra and Audi and resorting to higher accuracy in the solutions of the η-differential equations of the INM model. The local energy η's supposed to carry signature of the characteristic properties of nuclei are found to possess the predictive capability. In fact η-systematics reveal new magic numbers in the drip-line regions giving rise to new islands of stability supported by relativistic mean field theoretic calculations. This is a manifestation of a new phenomenon where shell-effect overcomes the instability due to repulsive components of the nucleon-nucleon force broadening the stability peninsula. The two-neutron separation energy-systematics derived from the present mass predictions reveal a general new feature for the existence of islands of inversion in the exotic neutron-rich regions of nuclear landscape, apart from supporting the presently known islands around 31Na and 62Ti. The five global parameters representing the properties of infinite nuclear matter, the surface, the Coulomb and the pairing terms are retained as per our 1999 mass table. The root-mean-square deviation of the present mass-fit to 2198 known masses is 342 keV, while the mean deviation is 1.3 keV, reminiscent of no left-over systematic effects. This is a substantive improvement over our 1999 mass table having rms deviation of 401 keV and mean deviation of 9 keV for 1884 data nuclei.
Liu, Jin; Weller, Gregory E R; Zern, Blaine; Ayyaswamy, Portonovo S; Eckmann, David M; Muzykantov, Vladimir R; Radhakrishnan, Ravi
2010-09-21
A computational methodology based on Metropolis Monte Carlo (MC) and the weighted histogram analysis method (WHAM) has been developed to calculate the absolute binding free energy between functionalized nanocarriers (NC) and endothelial cell (EC) surfaces. The calculated NC binding free energy landscapes yield binding affinities that agree quantitatively when directly compared against analogous measurements of specific antibody-coated NCs (100 nm in diameter) to intracellular adhesion molecule-1 (ICAM-1) expressing EC surface in in vitro cell-culture experiments. The effect of antibody surface coverage (σ(s)) of NC on binding simulations reveals a threshold σ(s) value below which the NC binding affinities reduce drastically and drop lower than that of single anti-ICAM-1 molecule to ICAM-1. The model suggests that the dominant effect of changing σ(s) around the threshold is through a change in multivalent interactions; however, the loss in translational and rotational entropies are also important. Consideration of shear flow and glycocalyx does not alter the computed threshold of antibody surface coverage. The computed trend describing the effect of σ(s) on NC binding agrees remarkably well with experimental results of in vivo targeting of the anti-ICAM-1 coated NCs to pulmonary endothelium in mice. Model results are further validated through close agreement between computed NC rupture-force distribution and measured values in atomic force microscopy (AFM) experiments. The three-way quantitative agreement with AFM, in vitro (cell-culture), and in vivo experiments establishes the mechanical, thermodynamic, and physiological consistency of our model. Hence, our computational protocol represents a quantitative and predictive approach for model-driven design and optimization of functionalized nanocarriers in targeted vascular drug delivery.
Energy Technology Data Exchange (ETDEWEB)
Nguyen, Hung T. [BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States); Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States); Case, David A., E-mail: case@biomaps.rutgers.edu [BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States); Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854 (United States)
2014-12-14
A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb{sup +} and Sr{sup 2+}) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein–Zernike equations, with results from the Kovalenko–Hirata closure being closest to experiment for the cases studied here.
Singh, Pragya; Nakatani, Eri; Goodlett, David R; Catalano, Carlos Enrique
2013-09-23
Bacteriophage lambda is one of the most exhaustively studied of the double-stranded DNA viruses. Its assembly pathway is highly conserved among the herpesviruses and many of the bacteriophages, making it an excellent model system. Despite extensive genetic and biophysical characterization of many of the lambda proteins and the assembly pathways in which they are implicated, there is a relative dearth of structural information on many of the most critical proteins involved in lambda assembly and maturation, including that of the lambda major capsid protein. Toward this end, we have utilized a combination of chemical cross-linking/mass spectrometry and computational modeling to construct a pseudo-atomic model of the lambda major capsid protein as a monomer, as well as in the context of the assembled procapsid shell. The approach described here is generalizable and can be used to provide structural models for any biological complex of interest. The procapsid structural model is in good agreement with published biochemical data indicating that procapsid expansion exposes hydrophobic surface area and that this serves to nucleate assembly of capsid decoration protein, gpD. The model further implicates additional molecular interactions that may be critical to the assembly of the capsid shell and for the stabilization of the structure by the gpD decoration protein.
Rider, Michael Eugene
1998-11-01
High temperature plasma emission sources have spatial characteristics. The Abel inversion calculates radial responses from lateral measurements of cylindrically symmetric emission sources. This dissertation presents three aspects of making spatial measurements: (1) Evaluation of an optical setup; (2) New numerically exact routine for improved spatial modeling; and (3) Radial and lateral measurements. Optical ray tracing software was been used for critical evaluation of the design of a unique imaging spectrometer. Position, area, and angles of view are calculated as a function of position of a translating lens and the optical properties of the quartz tube. The translating lens imaging spectrometer is compared to the more common alternative of moving the source or detector and found to perform comparatively well. A new Abel inversion technique, based on numerical improvements in a matrix-based algorithm, is described. The new approach (Mabel) combines exact computation of area terms for the Abel inversion with matrix calculation capabilities present in the MATLAB TM computational environment to generate radial profiles from lateral scans of the plasma with the best accuracy possible. Results of four 1000 ring Mabel inversions are presented. Comparisons between Mabel and two other numerical methods are made for test cases commonly cited in literature and for test cases having radial and lateral profiles with analytic solutions. The effects of noise propagation and of incomplete viewing of the plasma are also presented. Temperature is one of the most fundamental characteristic of high temperature plasmas. Lateral and radial temperatures measured from different views result in different values for a given plasma emission source. Four radial temperature profiles were used to generate radial intensities of five different wavelengths on the basis of a Boltzmann distribution of energies at each temperature. Forward Mabel transforms were performed on the radial intensities
Atomic-level description of protein-lipid interactions using an accelerated membrane model.
Baylon, Javier L; Vermaas, Josh V; Muller, Melanie P; Arcario, Mark J; Pogorelov, Taras V; Tajkhorshid, Emad
2016-07-01
Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein-membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics simulations offer a suitable approach to study protein-lipid interactions; however, the slow dynamics of the lipids often prevents sufficient sampling of specific membrane-protein interactions in atomistic simulations. To increase lipid dynamics while preserving the atomistic detail of protein-lipid interactions, in the highly mobile membrane-mimetic (HMMM) model the membrane core is replaced by an organic solvent, while short-tailed lipids provide a nearly complete representation of natural lipids at the organic solvent/water interface. Here, we present a brief introduction and a summary of recent applications of the HMMM to study different membrane proteins, complementing the experimental characterization of the presented systems, and we offer a perspective of future applications of the HMMM to study other classes of membrane proteins. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov.
Ground State and Charge Renormalization in a Nonlinear Model of Relativistic Atoms
Gravejat, Philippe; Sere, Eric
2007-01-01
We study the reduced Bogoliubov-Dirac-Fock (BDF) energy which allows to describe relativistic electrons interacting with the Dirac sea, in an external electrostatic potential. The model can be seen as a mean-field approximation of Quantum Electrodynamics (QED) where photons and the so-called exchange term are neglected. A state of the system is described by its one-body density matrix, an infinite rank self-adjoint operator which is a compact perturbation of the negative spectral projector of the free Dirac operator (the Dirac sea). We study the minimization of the reduced BDF energy under a charge constraint. We prove the existence of minimizers for a large range of values of the charge, and any positive value of the coupling constant $\\alpha$. Our result covers neutral and positively charged molecules, provided that the positive charge is not large enough to create electron-positron pairs. We also prove that the density of any minimizer is an $L^1$ function and compute the effective charge of the system, re...
Atomic scale modeling of defect production and microstructure evolution in irradiated metals
Energy Technology Data Exchange (ETDEWEB)
Diaz de la Rubia, T.; Soneda, N.; Shimomura, Y. [Lawrence Livermore National Lab., CA (United States)] [and others
1997-04-01
Irradiation effects in materials depend in a complex way on the form of the as-produced primary damage state and its spatial and temporal evolution. Thus, while collision cascades produce defects on a time scale of tens of picosecond, diffusion occurs over much longer time scales, of the order of seconds, and microstructure evolution over even longer time scales. In this report the authors present work aimed at describing damage production and evolution in metals across all the relevant time and length scales. They discuss results of molecular dynamics simulations of displacement cascades in Fe and V. They show that interstitial clusters are produced in cascades above 5 keV, but not vacancy clusters. Next, they discuss the development of a kinetic Monte Carlo model that enables calculations of damage evolution over much longer time scales (1000`s of s) than the picosecond lifetime of the cascade. They demonstrate the applicability of the method by presenting predictions on the fraction of freely migrating defects in {alpha}Fe during irradiation at 600 K.
Energy Technology Data Exchange (ETDEWEB)
Sommerfeld, Arnold
2013-07-01
In December 6th 1915 and January 8th 1916 Arnold Sommerfeld put the Bavarian Academy of Sciences two treatises in the amount of 75 printed pages before, by which he extended Bohr's atomic model from the year 1913 to the Bohr-Sommerfeld atom theory. In Sommerfeld's collected works only the publication submitted 1916 by Sommerfeld in the Annals of Physics about this is found.''My spectral lines are finally printed in the Academy to the impure. In the Annals they will appear in purer form'', so Sommerfeld has announced in this publication in February 10th 1916 to the editor of the Annals of Physics. From the science-historical view however for the extension of Bohr's atom theory just the Academy-treatises published before the purification process are of special interest. To the reproduction of these Academy-treatises an extensive physics-historical essay is prepended.
Directory of Open Access Journals (Sweden)
B. J. Murray
2004-11-01
Full Text Available The formation, evolution and eventual sublimation of noctilucent clouds (NLC could have a significant effect on the odd oxygen and hydrogen chemistry of the high latitude summer mesosphere. Three mechanisms are considered here: the direct uptake of atomic oxygen on the surface of the ice particles; the redistribution of water vapour, which changes the photochemical source of odd hydrogen species; and the direct photolysis of the ice particles themselves to produce odd hydrogen species in the gas phase. A 1-D photochemical model is employed to investigate the potential importance of these mechanisms. This shows, using the recently measured uptake coefficients of O on ice, that the heterogeneous removal of O on the surface of the cloud particles is too slow by at least a factor of 5×10^{3} to compete with gas-phase O chemistry. The second and third mechanisms involve the solar Lyman-α photolysis of H_{2}O in the gas and solid phase, respectively. During twilight, Lyman-α radiation is severely attenuated and these mechanisms are insignificant. In contrast, when the upper mesosphere is fully illuminated there is a dramatic impact on the O profile, with depletion of O at the base of the cloud layer of close to an order of magnitude. A correspondingly large depletion in O_{3} is also predicted, while H, OH, HO_{2} and H_{2}O_{2} are found to be enhanced by factors of 3–5. In fact, rocket-borne mass spectrometer measurements during summer have revealed local H_{2}O_{2} enhancements in the region of the clouds. Rocket-borne measurements of atomic O and O_{3} profiles in the presence of mesospheric clouds in the daytime are highly desirable to test the predictions of this model and our understanding of the genesis of mesospheric clouds.
Energy Technology Data Exchange (ETDEWEB)
Quemener, G.; Launay, J.M. [Rennes-1 Univ., Institut de Physique de Rennes, UMR CNRS 6251, 35 (France); Quemener, G. [Nevada Las Vegas niv., Dept. of Chemistry, NV (United States); Honvault, P. [University of Franche-Comte, Institut UTINAM, UMR CNRS 6213, 25 - Besancon (France)
2008-08-15
The role of the atom-atom scattering length and of the symmetrization in ultracold atom-diatom collisions in one dimension is presented. For an ultracold atom-diatom collision and for a diatomic molecule in its highest vibrational state, inelastic rate coefficients vanish for a system composed of fermionic atoms as the atom-atom scattering length increases whereas they do not for a system composed of bosonic atoms. The differences come from the symmetrization of the wavefunction of the systems. We explain these differences by comparing the shape of the effective potentials of the atom-diatom approach. For the fermionic system, we use a zero-range interaction to model the adiabatic energies and we give a lower estimate of the atom-diatom scattering length as a function of the atom-atom scattering length. (authors)
El-Orany, Faisal A A
2009-01-01
In this paper, we develop the notion of the linear atomic quantum coupler. This device consists of two modes propagating into two waveguides, each of them includes a localized and/or a trapped atom. These waveguides are placed close enough to allow exchanging energy between them via evanescent waves. Each mode interacts with the atom in the same waveguide in the standard way, i.e. as the Jaynes-Cummings model (JCM), and with the atom-mode in the second waveguide via evanescent wave. We present the Hamiltonian for the system and deduce the exact form for the wavefunction. We investigate the atomic inversions and the second-order correlation function. In contrast to the conventional linear coupler, the atomic quantum coupler is able to generate nonclassical effects. The atomic inversions can exhibit long revival-collapse phenomenon as well as subsidiary revivals based on the competition among the switching mechanisms in the system. Finally, under certain conditions, the system can yield the results of the two-m...
Effects of dark atom excitations
Cudell, Jean-René; Wallemacq, Quentin
2014-01-01
New stable quarks and charged leptons may exist and be hidden from detection, as they are bound by Coulomb interaction in neutral dark atoms of composite dark matter. This possibility leads to fundamentally new types of indirect effects related to the excitation of such dark atoms followed by their electromagnetic de-excitation. Stable -2 charged particles, bound to primordial helium in O-helium (OHe) atoms, represent the simplest model of dark atoms. Here we consider the structure of OHe atomic levels which is a necessary input for the indirect tests of such composite dark matter scenarios, and we give the spectrum of electromagnetic transitions from the levels excited in OHe collisions.
氢原子斯塔克效应的结构平衡模型仿真%Structural Equation Modeling Simulation of Hydrogen Atom Stark Effect
Institute of Scientific and Technical Information of China (English)
周志祥
2015-01-01
斯塔克效应常应用于原子分子结构的研究,对氢原子进行结构平衡模型数学建模和仿真,可以准确分析氢原子在外电场作用下能级和光谱特性.传统的氢原子斯塔克效应结构平衡采用双线间隔分离模型,对原始读数和测量值的等价分析具有随机性,不能有效实现结构平衡.提出一种基于固有电偶极矩外电场分析的氢原子斯塔克效应的结构平衡模型.首先分析氢原子的原子特性,进行斯塔克效应数学建模,分析氢原子的晶体反应谱线分裂特征模型,光谱的发射是由于价电子的跃迁形成,电场一定会改变原子内部电荷的分布,得出斯塔克效应下的结构平衡和模型的能级分裂,其裂距与电场强度成正比,采用固有电偶极矩外电场分析,实现数学模型构建,并通过Matlab进行仿真实现.实验结果表明,模型能有效反映氢原子斯塔库克效应下的光谱特征,基于固有电偶极矩外电场分析,外电场能耗降低,性能稳定.%The study of Stark effect applied to atomic and molecular structure, structural balance model for mathematical modeling and Simulation of the hydrogen atom, can accurate analysis of the hydrogen atom in the level in the external elec-tric field and spectral characteristics. The traditional hydrogen atomic Stark effect structure equilibrium separation model adopts double spaced, randomness is equivalent to the original reading and analysis of the measured value, can not effec-tively to achieve structural balance. Put forward a kind of intrinsic electric dipole moment equilibrium structure analysis of external electric field of the hydrogen atom Stark effect model based on. The first atomic properties analysis of atomic and hydrogen, Stark effect on mathematical modeling, analysis of crystal reaction of hydrogen atomic spectral line splitting fea-ture model, spectral emission is due to transition of the valence electron, electric field distribution will
Energy Technology Data Exchange (ETDEWEB)
Grau Malonda, A.; Fernandez Martinez, A.
1985-07-01
The present paper develops a four-shells atomic model in order to obtain the efficiency of detection in liquid scintillation courting, Mathematical expressions are given to calculate the probabilities of the 229 different atomic rearrangements so as the corresponding effective energies. This new model will permit the study of the influence of the different parameters upon the counting efficiency for nuclides of high atomic number. (Author) 7 refs.
Sarkadi, L
2015-01-01
The three-body dynamics of the ionization of the atomic hydrogen by 30 keV antiproton impact has been investigated by calculation of fully differential cross sections (FDCS) using the classical trajectory Monte Carlo (CTMC) method. The results of the calculations are compared with the predictions of quantum mechanical descriptions: The semi-classical time-dependent close-coupling theory, the fully quantal, time-independent close-coupling theory, and the continuum-distorted-wave-eikonal-initial-state model. In the analysis particular emphasis was put on the role of the nucleus-nucleus (NN) interaction played in the ionization process. For low-energy electron ejection CTMC predicts a large NN interaction effect on FDCS, in agreement with the quantum mechanical descriptions. By examining individual particle trajectories it was found that the relative motion between the electron and the nuclei is coupled very weakly with that between the nuclei, consequently the two motions can be treated independently. A simple ...
Lin, Zone-Ching; Chou, Ming-Ho
2010-07-01
This study proposes to construct a nano-scale simulative measuring model of Tapping Mode Atomic Force Microscopy (TM-AFM), compare with the edge effect of simulative and measurement results. It combines with the Morse potential and vibration theory to calculate the tip-sample atomic interaction force between probe and sample. Used Silicon atoms (Si) arrange the shape of the rectangular cantilever probe and the nano-scale ladder-shape standard sample atomic model. The simulative measurements are compared with the results for the simulative measurements and experimental measurement. It is found that the scan rate and the probe tip's bevel angle are the two reasons to cause the surface error and edge effect of measuring the nano-scale ladder-shape standard sample by TM-AFM. And the bevel angle is about equal to the probe tip's bevel angle from the results of simulated and experimented on the vertical section of the sample edge. To compare with the edge effect between the simulation and experimental measurement, its error is small. It could be verified that the constructed simulative measuring model for TM-AFM in this article is reasonable.
Beswick, Benjamin T.; Hughes, Ifan G.; Gardiner, Simon A.; Astier, Hippolyte P. A. G.; Andersen, Mikkel F.; Daszuta, Boris
2016-12-01
Atom interferometers are a useful tool for precision measurements of fundamental physical phenomena, ranging from the local gravitational-field strength to the atomic fine-structure constant. In such experiments, it is desirable to implement a high-momentum-transfer "beam splitter," which may be achieved by inducing quantum resonance in a finite-temperature laser-driven atomic gas. We use Monte Carlo simulations to investigate these quantum resonances in the regime where the gas receives laser pulses of finite duration and derive an ɛ -classical model for the dynamics of the gas atoms which is capable of reproducing quantum resonant behavior for both zero-temperature and finite-temperature noninteracting gases. We show that this model agrees well with the fully quantum treatment of the system over a time scale set by the choice of experimental parameters. We also show that this model is capable of correctly treating the time-reversal mechanism necessary for implementing an interferometer with this physical configuration and that it explains an unexpected universality in the dynamics.
Rathore, Bhavna
2015-01-01
The 133.5 nm lines are important observables for the NASA/SMEX mission Interface Region Imaging Spectrograph (IRIS). To make 3D non-LTE radiative transfer computationally feasible it is crucial to have a model atom with as few levels as possible while retaining the main physical processes. We here develop such a model atom and we study the general formation properties of the C II lines. We find that a nine-level model atom of C I-C III with the transitions treated assuming complete frequency redistribution (CRD) suffices to describe the 133.5 nm lines. 3D scattering effects are important for the intensity in the core of the line. The lines are formed in the optically thick regime. The core intensity is formed in layers where the temperature is about 10kK at the base of the transition region. The lines are 1.2-4 times wider than the atomic absorption profile due to the formation in the optically thick regime. The smaller opacity broadening happens for single peak intensity profiles where the chromospheric temp...
Nigam, Sandeep; Majumder, Chiranjib
2010-11-03
Using state-of-the-art first-principles calculations we report the interaction of M atoms (M = Cu, Ag and Au) with small Ag(n), Au(n) clusters (n = 3 and 6) and periodic Ag(111) and Au(111) surfaces. All calculations were performed using the plane wave pseudo-potential approach under the spin polarized version of the generalized gradient approximation scheme. The result shows that the equilibrium geometry of all MAg(3) and MAu(3) clusters favor a planar rhombus structure. From the charge distribution analysis of MAg(n)/MAu(n) clusters it is found that, while Cu and Ag donates electronic charge towards the host clusters, the Au atom acts as an acceptor, thus creating charge polarization in the system. The difference in orbital decomposed charges before and after the M interaction reveals that enhanced s-d hybridization is responsible for keeping the MAu(6) cluster planar, and increased p-orbital participation induces three-dimensional configurations in MAg(6) clusters. The optimization of M atom deposition on the Ag(111) and Au(111) surfaces shows that M atoms prefer to adsorb on the threefold fcc site over other well-defined sites. From the orbital decomposed charge analysis it is inferred that, although there is significant difference in the absolute magnitude of the interaction energy between M atoms and the Ag or Au substrates, the nature of chemical bonding is similar for the finite size clusters as well as in slab models.