WorldWideScience

Sample records for atom molecular dynamics

  1. Dynamical processes in atomic and molecular physics

    CERN Document Server

    Ogurtsov, Gennadi

    2012-01-01

    Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

  2. Molecular dynamics study of atomic displacements in disordered solid alloys

    Science.gov (United States)

    Puzyrev, Yevgeniy S.

    The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

  3. Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

    Directory of Open Access Journals (Sweden)

    Dirk-Sören Lühmann

    2015-08-01

    Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

  4. Microsecond atomic-scale molecular dynamics simulations of polyimides

    NARCIS (Netherlands)

    Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

    2013-01-01

    We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

  5. Thermodynamics of small clusters of atoms: A molecular dynamics simulation

    DEFF Research Database (Denmark)

    Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J

    1974-01-01

    The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...... transition was investigated, and a number of properties, such as melting temperature, latent heat of melting, and premelting phenomena, were found to vary with cluster size. These properties were also found to depend on the structure of the solid phase. In this phase the configuration of lowest free energy...

  6. Molecular dynamics simulation of amplitude modulation atomic force microscopy

    International Nuclear Information System (INIS)

    Hu, Xiaoli; Martini, Ashlie; Egberts, Philip; Dong, Yalin

    2015-01-01

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip–substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip–sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement. (paper)

  7. Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets

    Science.gov (United States)

    Lehmann, Kevin K.

    2003-03-01

    Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.

  8. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  9. Imaging Multi-Particle Atomic and Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Landers, Allen [Auburn Univ., AL (United States)

    2016-02-12

    Final Report for Grant Number: DE- FG02-10ER16146 This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms and molecules with photons and electrons. The duration of the grant was the 5 year period from 4/1/2010 – 10/31/2015. All of the support from the grant was used to pay salaries of the PI, graduate students, and undergraduates and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals. There were 20 peer reviewed publications over these 5 years with 2 of the publications in Physical Review Letters and 1 in Nature; all of the other articles were in respected peer reviewed journals (Physical Review A, New Journal of Physics, Journal of Physics B ...).

  10. Applications of the semiclassical spectral method to nuclear, atomic, molecular, and polymeric dynamics

    International Nuclear Information System (INIS)

    Koszykowski, M.L.; Pfeffer, G.A.; Noid, D.W.

    1987-01-01

    Nonlinear dynamics plays a dominant role in a variety of important problems in chemical physics. Examples are unimolecular reactions, infrared multiphoton decomposition of molecules, the pumping process of the gamma ray laser, dissociation of vibrationally excited state-selected van der Waals's complexes, and many other chemical and atomic processes. The present article discusses recent theoretical studies on the quasi-periodic and chaotic dynamic aspects of vibrational-rotational states of atomic, nuclear, and molecular systems using the semiclassical spectral method (SSM). The authors note that the coordinates, momenta, and so on, are found using classical mechanics in the studies included in this review. They outline the semiclassical spectral method and a wide variety of applications. Although this technique was first developed ten years ago, it has proved to be tremendously successful as a tool used in dynamics problems. Applications include problems in nonlinear dynamics, molecular and atomic spectra, surface science, astronomy and stellar dynamics, nuclear physics, and polymer physics

  11. Molecular dynamics simulation study of the influence of the lattice atom potential function upon atom ejection processes

    International Nuclear Information System (INIS)

    Harrison, D.E. Jr.; Webb, R.P.

    1982-01-01

    A molecular dynamics simulation has been used to investigate the sensitivity of atom ejection processes from a single-crystal target to changes in the atom-atom potential function. Four functions, three constructed from the Gibson potentials with Anderman's attractive well, and a fouth specifically developed for this investigation, were investigated in the Cu/Ar/sup +/ system over a range of ion energies from 1.0 to 10.0 kev with the KSE-B ion-atom potential. Well depths and widths also were varied. The calculations were done at normal incidence on the fcc (111) crystal orientation. Computed values were compared with experimental data where they exist. Sputtering yields, multimer yield ratios, layer yield ratios, and the ejected atom energy distribution vary systematically with the parameters of the atom-atom potential function. Calculations also were done with the modified Moliere function. Yields and other properties fall exactly into the positions predicted from the Born-Mayer function analysis. Simultaneous analysis of the ejected atom energy distribution and the ion energy dependence of the sputtering yield curve provides information about the parameters of both the wall and well portions of the atom-atom potential function

  12. Molecular dynamic simulation of the atomic structure of aluminum solid–liquid interfaces

    International Nuclear Information System (INIS)

    Men, H; Fan, Z

    2014-01-01

    In this paper, molecular dynamic (MD) simulation was used to investigate the equilibrium atomic arrangement at aluminum solid–liquid (S/L) interfaces with {111}, {110} and {100} orientations. The simulation results reveal that the aluminum S/L interfaces are diffuse for all the orientations, and extend up to 7 atomic layers. Within the diffuse interfaces there exists substantial atomic ordering, which is manifested by atomic layering perpendicular to the interface and in-plane atomic ordering parallel to the interface. Atomic layering can be quantified by the atomic density profile (ρ(z)) while the in-plane atomic ordering can be described by the in-plane ordering parameter (S(z)). The detailed MD simulation suggests that atomic layering at the interface always occurs within 7 atomic layers independent of the interface orientation while the in-plane ordering is highly dependent on the interface orientations, with the {111} interface being less diffuse than the {100} and {110} interfaces. This study demonstrates clearly that the physical origin of the diffuse interface is atomic layering and in-plane atomic ordering at the S/L interfaces. It is suggested that the difference in atomic layering and in-plane ordering at the S/L interface with different orientations is responsible for the observed growth anisotropy. (papers)

  13. Atomic and molecular sciences

    International Nuclear Information System (INIS)

    Lane, N.F.

    1989-01-01

    The theoretical atomic and molecular physics program at Rice University addresses basic questions about the collision dynamics of electrons, atoms, ions and molecules, emphasizing processes related to possible new energy technologies and other applications. The program focuses on inelastic collision processes that are important in understanding energy and ionization balance in disturbed gases and plasmas. Emphasis is placed on systems and processes where some experimental information is available or where theoretical results may be expected to stimulate new measurements. Examples of current projects include: excitation and charge-transfer processes; orientation and alignment of excited states following collisions; Rydberg atom collisions with atoms and molecules; Penning ionization and ion-pair formation in atom-atom collisions; electron-impact ionization in dense, high-temperature plasmas; electron-molecule collisions; and related topics

  14. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob

    2002-01-01

    The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the simulati......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

  15. Molecular dynamics modeling of bonding two materials by atomic scale friction stir welding

    Science.gov (United States)

    Konovalenko S., Iv.; Konovalenko, Ig. S.; Psakhie, S. G.

    2017-12-01

    Molecular dynamics model of atomic scale friction stir welding has been developed. Formation of a butt joint between two crystallites was modeled by means of rotating rigid conical tool traveling along the butt joint line. The formed joint had an intermixed atomic structure composed of atoms initially belonged to the opposite mated piece of metal. Heat removal was modeled by adding the extra viscous force to peripheral atomic layers. This technique provides the temperature control in the tool-affected zone during welding. Auxiliary vibration action was added to the rotating tool. The model provides the variation of the tool's angular velocity, amplitude, frequency and direction of the auxiliary vibration action to provide modeling different welding modes.

  16. Rabi dynamics of coupled atomic and molecular Bose-Einstein condensates

    International Nuclear Information System (INIS)

    Ishkhanyan, Artur; Chernikov, G.P.; Nakamura, Hiroki

    2004-01-01

    The dynamics of coherent Rabi oscillations in coupled atomic and molecular Bose-Einstein condensates is considered taking into account the atom-atom, atom-molecule, and molecule-molecule elastic interactions. The exact solution for the molecule formation probability is derived in terms of the elliptic functions. The two-dimensional space of the involved parameters intensity and detuning is analyzed and divided into two regions where the Rabi oscillations show different characteristics. A resonance curve is found, on which the molecular formation probability monotonically increases as a function of time. The maximum value of the final transition probability on this curve is 1/2 (i.e., total transition to the molecular state) and it is achieved at high field intensities starting from a minimal threshold defined by the interspecies interaction scattering lights. The explicit form of the resonance curve is determined, and it is shown that the resonance frequency position reveals a nonlinear dependence on the Rabi frequency of the applied field. A singular point is found on the resonance curve, where a power-law time evolution of the system is observed

  17. Atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    Science.gov (United States)

    Pabst, Stefan

    2013-04-01

    Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in recent years made it possible to generate ultrashort pulses, which can be used to trigger, to watch, and to control atomic and molecular motion. This tutorial focuses on experimental and theoretical advances which are used to study the dynamics of electrons and molecules in the presence of ultrashort pulses. In the first part, the rotational dynamics of molecules, which happens on picosecond and femtosecond time scales, is reviewed. Well-aligned molecules are particularly suitable for angle-dependent investigations like x-ray diffraction or strong-field ionization experiments. In the second part, the ionization dynamics of atoms is studied. The characteristic time scale lies, here, in the attosecond to few-femtosecond regime. Although a one-particle picture has been successfully applied to many processes, many-body effects do constantly occur. After a broad overview of the main mechanisms and the most common tools in attosecond physics, examples of many-body dynamics in the attosecond world (e.g., in high-harmonic generation and attosecond transient absorption spectroscopy) are discussed.

  18. Control of the dynamics of coupled atomic-molecular Bose-Einstein condensates: Modified Gross-Pitaevskii approach

    International Nuclear Information System (INIS)

    Gupta, Moumita; Dastidar, Krishna Rai

    2009-01-01

    We study the dynamics of the atomic and molecular Bose-Einstein condensates (BECs) of 87 Rb in a spherically symmetric trap coupled by stimulated Raman photoassociation process. Considering the higher order nonlinearity in the atom-atom interaction we analyze the dynamics of the system using coupled modified Gross-Pitaevskii (MGP) equations and compare it with mean-field coupled Gross-Pitaevskii (GP) dynamics. Considerable differences in the dynamics are obtained in these two approaches at large scattering length, i.e., for large values of peak-gas parameter x pk ≥10 -3 . We show how the dynamics of the coupled system is affected when the atom-molecule and molecule-molecule interactions are considered together with the atom-atom interaction and also when the strengths of these three interactions are increased. The effect of detuning on the efficiency of conversion of atomic fractions into molecules is demonstrated and the feasibility of maximum molecular BEC formation by varying the Raman detuning parameter at different values of time is explored. Thus by varying the Raman detuning and the scattering length for atom-atom interaction one can control the dynamics of the coupled atomic-molecular BEC system. We have also solved coupled Gross-Pitaevskii equations for atomic to molecular condensate formation through magnetic Feshbach resonance in a BEC of 85 Rb. We found similar features for oscillations between atomic and molecular condensates noted in previous theoretical study and obtained fairly good agreement with the evolution of total atomic condensate observed experimentally.

  19. Mechanisms of defect production and atomic mixing in high energy displacement cascades: A molecular dynamics study

    International Nuclear Information System (INIS)

    Diaz de la Rubia, T.; Guinan, M.W.

    1991-01-01

    We have performed molecular dynamics computer simulation studies of displacement cascades in Cu at low temperature. For 25 keV recoils we observe the splitting of a cascade into subcascades and show that cascades in Cu may lead to the formation of vacancy and interstitial dislocation loops. We discuss a new mechanism of defect production based on the observation of interstitial prismatic dislocation loop punching from cascades at 10 K. We also show that below the subcascade threshold, atomic mixing in the cascade is recoil-energy dependent and obtain a mixing efficiency that scales as the square root of the primary recoil energy. 44 refs., 12 figs

  20. Molecular dynamics simulation of chemical sputtering of hydrogen atom on layer structured graphite

    International Nuclear Information System (INIS)

    Ito, A.; Wang, Y.; Irle, S.; Morokuma, K.; Nakamura, H.

    2008-10-01

    Chemical sputtering of hydrogen atom on graphite was simulated using molecular dynamics. Especially, the layer structure of the graphite was maintained by interlayer intermolecular interaction. Three kinds of graphite surfaces, flat (0 0 0 1) surface, armchair (1 1 2-bar 0) surface and zigzag (1 0 1-bar 0) surface, are dealt with as targets of hydrogen atom bombardment. In the case of the flat surface, graphene layers were peeled off one by one and yielded molecules had chain structures. On the other hand, C 2 H 2 and H 2 are dominant yielded molecules on the armchair and zigzag surfaces, respectively. In addition, the interaction of a single hydrogen isotope on a single graphene is investigated. Adsorption, reflection and penetration rates are obtained as functions of incident energy and explain hydrogen retention on layered graphite. (author)

  1. Molecular dynamics simulation of effect of hydrogen atoms on crack propagation behavior of α-Fe

    Energy Technology Data Exchange (ETDEWEB)

    Song, H.Y., E-mail: gsfshy@sohu.com; Zhang, L.; Xiao, M.X.

    2016-12-16

    The effect of the hydrogen concentration and hydrogen distribution on the mechanical properties of α-Fe with a pre-existing unilateral crack under tensile loading is investigated by molecular dynamics simulation. The results reveal that the models present good ductility when the front region of crack tip has high local hydrogen concentration. The peak stress of α-Fe decreases with increasing hydrogen concentration. The studies also indicate that for the samples with hydrogen atoms, the crack propagation behavior is independent of the model size and boundaries. In addition, the crack propagation behavior is significantly influenced by the distribution of hydrogen atoms. - Highlights: • The distribution of hydrogen plays a critical role in the crack propagation. • The peak stress decrease with the hydrogen concentration increasing. • The crack deformation behavior is disclosed and analyzed.

  2. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Samuel Hertig

    2016-06-01

    Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

  3. Atomic and electronic structures of a-SiC:H from tight-binding molecular dynamics

    CERN Document Server

    Ivashchenko, V I; Shevchenko, V I; Ivashchenko, L A; Rusakov, G V

    2003-01-01

    The atomic and electronic properties of amorphous unhydrogenated (a-SiC) and hydrogenated (a-SiC:H) silicon carbides are studied using an sp sup 3 s sup * tight-binding force model with molecular dynamics simulations. The parameters of a repulsive pairwise potential are determined from ab initio pseudopotential calculations. Both carbides are generated from dilute vapours condensed from high temperature, with post-annealing at low temperature for a-SiC:H. A plausible model for the inter-atomic correlations and electronic states in a-SiC:H is suggested. According to this model, the formation of the amorphous network is weakly sensitive to the presence of hydrogen. Hydrogen passivates effectively only the weak bonds of threefold-coordinated atoms. Chemical ordering is very much affected by the cooling rate and the structure of the high-temperature vapour. The as-computed characteristics are in rather good agreement with the results for a-SiC and a-Si:H from ab initio calculations.

  4. Mechanical Properties of Boehmite Evaluated by Atomic Force Microscopy Experiments and Molecular Dynamic Finite Element Simulations

    International Nuclear Information System (INIS)

    Fankhanel, J.; Daum, B.; Kempe, A.; Rolfes, R.; Silbernagl, D.; Khorasani, M.Gh.Z.; Sturm, H.; Sturm, H.

    2016-01-01

    Boehmite nanoparticles show great potential in improving mechanical properties of fiber reinforced polymers. In order to predict the properties of nanocomposites, knowledge about the material parameters of the constituent phases, including the boehmite particles, is crucial. In this study, the mechanical behavior of boehmite is investigated using Atomic Force Microscopy (AFM) experiments and Molecular Dynamic Finite Element Method (MDFEM) simulations. Young’s modulus of the perfect crystalline boehmite nanoparticles is derived from numerical AFM simulations. Results of AFM experiments on boehmite nanoparticles deviate significantly. Possible causes are identified by experiments on complementary types of boehmite, that is, geological and hydrothermally synthesized samples, and further simulations of imperfect crystals and combined boehmite/epoxy models. Under certain circumstances, the mechanical behavior of boehmite was found to be dominated by inelastic effects that are discussed in detail in the present work. The studies are substantiated with accompanying X-ray diffraction and Raman experiments.

  5. Incident angle dependence of reactions between graphene and hydrogen atom by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Saito, Seiki; Nakamura, Hiroaki; Ito, Atsushi

    2010-01-01

    Incident angle dependence of reactions between graphene and hydrogen atoms are obtained qualitatively by classical molecular dynamics simulation under the NVE condition with modified Brenner reactive empirical bond order (REBO) potential. Chemical reaction depends on two parameters, i.e., polar angle θ and azimuthal angle φ of the incident hydrogen. From the simulation results, it is found that the reaction rates strongly depend on polar angle θ. Reflection rate becomes larger with increasing θ, and the θ dependence of adsorption rate is also found. The θ dependence is caused by three dimensional structure of the small potential barrier which covers adsorption sites. φ dependence of penetration rate is also found for large θ. (author)

  6. Multibillion-atom Molecular Dynamics Simulations of Plasticity, Spall, and Ejecta

    Science.gov (United States)

    Germann, Timothy C.

    2007-06-01

    Modern supercomputing platforms, such as the IBM BlueGene/L at Lawrence Livermore National Laboratory and the Roadrunner hybrid supercomputer being built at Los Alamos National Laboratory, are enabling large-scale classical molecular dynamics simulations of phenomena that were unthinkable just a few years ago. Using either the embedded atom method (EAM) description of simple (close-packed) metals, or modified EAM (MEAM) models of more complex solids and alloys with mixed covalent and metallic character, simulations containing billions to trillions of atoms are now practical, reaching volumes in excess of a cubic micron. In order to obtain any new physical insights, however, it is equally important that the analysis of such systems be tractable. This is in fact possible, in large part due to our highly efficient parallel visualization code, which enables the rendering of atomic spheres, Eulerian cells, and other geometric objects in a matter of minutes, even for tens of thousands of processors and billions of atoms. After briefly describing the BlueGene/L and Roadrunner architectures, and the code optimization strategies that were employed, results obtained thus far on BlueGene/L will be reviewed, including: (1) shock compression and release of a defective EAM Cu sample, illustrating the plastic deformation accompanying void collapse as well as the subsequent void growth and linkup upon release; (2) solid-solid martensitic phase transition in shock-compressed MEAM Ga; and (3) Rayleigh-Taylor fluid instability modeled using large-scale direct simulation Monte Carlo (DSMC) simulations. I will also describe our initial experiences utilizing Cell Broadband Engine processors (developed for the Sony PlayStation 3), and planned simulation studies of ejecta and spall failure in polycrystalline metals that will be carried out when the full Petaflop Opteron/Cell Roadrunner supercomputer is assembled in mid-2008.

  7. Molecular Dynamics Analyses on Microscopic Contact Angle - Effect of Wall Atom Configuration

    International Nuclear Information System (INIS)

    Takahiro Ito; Yosuke Hirata; Yutaka Kukita

    2006-01-01

    Boiling or condensing phenomena of liquid on the solid surface is greatly affected by the wetting condition of the liquid to the solid. Although the contact angle is one of the most important parameter to represent the wetting condition, the behavior of the contact angle is not understood well, especially in the dynamic condition. In this study we made molecular dynamics simulations to investigate the microscopic contact angle behavior under several conditions on the numerical density of the wall atoms. In the analyses, when the number density of the wall is lower, the changing rate of the dynamics contact angles for the variation of ΔV was higher than those for the case where the wall density is higher. This is mainly due to the crystallization of the fluid near the wall and subsequent decrease in the slip between the fluid and the wall. The analyses also show that the static contact angle decreases with increase in the number density of the wall. This was mainly induced by the increase in the number density of the wall itself. (authors)

  8. Basic mechanisms of atomic displacement production in cubic silicon carbide: A molecular dynamics study

    International Nuclear Information System (INIS)

    Malerba, L.; Perlado, J.M.

    2002-01-01

    Studying the effects of radiation in silicon carbide (SiC) is important for its possible use in both nuclear and electronic technology. One of the most important parameters to describe radiation damage in a material is the threshold displacement energy (TDE). In this paper, the computational technique known as molecular dynamics (MD) is used to determine the TDE's along different crystallographic directions for Si and C atoms in SiC, also allowing for irradiation temperature effects, and to study in detail the mechanisms of atomic displacement production in this material. For this purpose, the widely tested Tersoff potential, implemented in a MD code optimized to study the interaction of high-energy ions with crystals, is used to describe the interatomic forces in SiC. It is found that it is difficult to define a single threshold for this material. Instead, the introduction of two thresholds, upper and lower, becomes necessary. These two thresholds delimit an uncertainty band, within which the displacement may or may not be produced, because the Frenkel pairs generated in such a transferred-kinetic-energy range are metastable. The Arrhenius law expressing the lifetime of one of these metastable defects has also been deduced from the simulation. Finally, on the basis of the results of the simulation, possible values for the recombination distance and the average threshold energy (E d,Si and E d,C ) in SiC are proposed and discussed

  9. Reinforced dynamics for enhanced sampling in large atomic and molecular systems

    Science.gov (United States)

    Zhang, Linfeng; Wang, Han; E, Weinan

    2018-03-01

    A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. The method is illustrated by studying the full-atom explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables.

  10. Atomic and molecular manipulation

    CERN Document Server

    Mayne, Andrew J

    2011-01-01

    Work with individual atoms and molecules aims to demonstrate that miniaturized electronic, optical, magnetic, and mechanical devices can operate ultimately even at the level of a single atom or molecule. As such, atomic and molecular manipulation has played an emblematic role in the development of the field of nanoscience. New methods based on the use of the scanning tunnelling microscope (STM) have been developed to characterize and manipulate all the degrees of freedom of individual atoms and molecules with an unprecedented precision. In the meantime, new concepts have emerged to design molecules and substrates having specific optical, mechanical and electronic functions, thus opening the way to the fabrication of real nano-machines. Manipulation of individual atoms and molecules has also opened up completely new areas of research and knowledge, raising fundamental questions of "Optics at the atomic scale", "Mechanics at the atomic scale", Electronics at the atomic scale", "Quantum physics at the atomic sca...

  11. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    Energy Technology Data Exchange (ETDEWEB)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  12. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    Science.gov (United States)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  13. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    International Nuclear Information System (INIS)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

    2014-01-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10 6 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it

  14. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

    2002-01-01

    The Gordon Research Conference (GRC) on Atomic and Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field

  15. Molecular dynamics for near melting temperatures simulations of metals using modified embedded-atom method

    Science.gov (United States)

    Etesami, S. Alireza; Asadi, Ebrahim

    2018-01-01

    Availability of a reliable interatomic potential is one of the major challenges in utilizing molecular dynamics (MD) for simulations of metals at near the melting temperatures and melting point (MP). Here, we propose a novel approach to address this challenge in the concept of modified-embedded-atom (MEAM) interatomic potential; also, we apply the approach on iron, nickel, copper, and aluminum as case studies. We propose adding experimentally available high temperature elastic constants and MP of the element to the list of typical low temperature properties used for the development of MD interatomic potential parameters. We show that the proposed approach results in a reasonable agreement between the MD calculations of melting properties such as latent heat, expansion in melting, liquid structure factor, and solid-liquid interface stiffness and their experimental/computational counterparts. Then, we present the physical properties of mentioned elements near melting temperatures using the new MEAM parameters. We observe that the behavior of elastic constants, heat capacity and thermal linear expansion coefficient at room temperature compared to MP follows an empirical linear relation (α±β × MP) for transition metals. Furthermore, a linear relation between the tetragonal shear modulus and the enthalpy change from room temperature to MP is observed for face-centered cubic materials.

  16. All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

    KAUST Repository

    Di Marino, Daniele

    2015-08-06

    © 2015 American Chemical Society. Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

  17. All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

    KAUST Repository

    Di Marino, Daniele; Bonome, Emma Letizia; Tramontano, Anna; Chinappi, Mauro

    2015-01-01

    © 2015 American Chemical Society. Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

  18. New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    International Nuclear Information System (INIS)

    Pabst, Stefan Ulf

    2013-04-01

    The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO 2 is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

  19. New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    Energy Technology Data Exchange (ETDEWEB)

    Pabst, Stefan Ulf

    2013-04-15

    The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO{sub 2} is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

  20. Molecular dynamics study of the interactions of incident N or Ti atoms with the TiN(001) surface

    International Nuclear Information System (INIS)

    Xu, Zhenhai; Zeng, Quanren; Yuan, Lin; Qin, Yi; Chen, Mingjun; Shan, Debin

    2016-01-01

    Graphical abstract: - Highlights: • Interactions of incident N or Ti atoms with TiN(001) surface are studied by CMD. • The impact position of incident N on the surface determines the interaction modes. • Adsorption could occur due to the atomic exchange process. • Resputtering and reflection may simultaneously occur. • The initial sticking coefficient of N on TiN(001) is much smaller than that of Ti. - Abstract: The interaction processes between incident N or Ti atoms and the TiN(001) surface are simulated by classical molecular dynamics based on the second nearest-neighbor modified embedded-atom method potentials. The simulations are carried out for substrate temperatures between 300 and 700 K and kinetic energies of the incident atoms within the range of 0.5–10 eV. When N atoms impact against the surface, adsorption, resputtering and reflection of particles are observed; several unique atomic mechanisms are identified to account for these interactions, in which the adsorption could occur due to the atomic exchange process while the resputtering and reflection may simultaneously occur. The impact position of incident N atoms on the surface plays an important role in determining the interaction modes. Their occurrence probabilities are dependent on the kinetic energy of incident N atoms but independent on the substrate temperature. When Ti atoms are the incident particles, adsorption is the predominant interaction mode between particles and the surface. This results in the much smaller initial sticking coefficient of N atoms on the TiN(001) surface compared with that of Ti atoms. Stoichiometric TiN is promoted by N/Ti flux ratios larger than one.

  1. Atomic force microscope adhesion measurements and atomistic molecular dynamics simulations at different humidities

    International Nuclear Information System (INIS)

    Seppä, Jeremias; Sairanen, Hannu; Korpelainen, Virpi; Husu, Hannu; Heinonen, Martti; Lassila, Antti; Reischl, Bernhard; Raiteri, Paolo; Rohl, Andrew L; Nordlund, Kai

    2017-01-01

    Due to their operation principle atomic force microscopes (AFMs) are sensitive to all factors affecting the detected force between the probe and the sample. Relative humidity is an important and often neglected—both in experiments and simulations—factor in the interaction force between AFM probe and sample in air. This paper describes the humidity control system designed and built for the interferometrically traceable metrology AFM (IT-MAFM) at VTT MIKES. The humidity control is based on circulating the air of the AFM enclosure via dryer and humidifier paths with adjustable flow and mixing ratio of dry and humid air. The design humidity range of the system is 20–60 %rh. Force–distance adhesion studies at humidity levels between 25 %rh and 53 %rh are presented and compared to an atomistic molecular dynamics (MD) simulation. The uncertainty level of the thermal noise method implementation used for force constant calibration of the AFM cantilevers is 10 %, being the dominant component of the interaction force measurement uncertainty. Comparing the simulation and the experiment, the primary uncertainties are related to the nominally 7 nm radius and shape of measurement probe apex, possible wear and contamination, and the atomistic simulation technique details. The interaction forces are of the same order of magnitude in simulation and measurement (5 nN). An elongation of a few nanometres of the water meniscus between probe tip and sample, before its rupture, is seen in simulation upon retraction of the tip in higher humidity. This behaviour is also supported by the presented experimental measurement data but the data is insufficient to conclusively verify the quantitative meniscus elongation. (paper)

  2. Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

    Science.gov (United States)

    Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

    2014-09-01

    Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.

  3. Mixed DPPC/POPC Monolayers: All-atom Molecular Dynamics Simulations and Langmuir Monolayer Experiments

    Czech Academy of Sciences Publication Activity Database

    Olžyńska, Agnieszka; Zubek, M.; Roeselová, Martina; Korchowiec, J.; Cwiklik, Lukasz

    2016-01-01

    Roč. 1858, č. 12 (2016), s. 3120-3130 ISSN 0005-2736 R&D Projects: GA ČR GA15-14292S Institutional support: RVO:61388955 ; RVO:61388963 Keywords : phospholipid monolayers * Lung surfactant * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.498, year: 2016

  4. Translational-rotational interaction in dynamics and thermodynamics of 2D atomic crystal with molecular impurity

    International Nuclear Information System (INIS)

    Antsygina, T.N.; Poltavskaya, M.I.; Chishko, K.A.

    2003-01-01

    The interaction between the rotational degrees of freedom of a diatomic molecular impurity and the phonon excitations of a two-dimensional atomic matrix commensurate with a substrate is investigated theoretically. It is shown, that the translational-rotational interaction changes the form of the rotational kinetic energy operator as compared to the corresponding expression for a free rotator, and also renormalized the parameters of the crystal field without change in its initial form. The contribution of the impurity rotational degrees of freedom to the low-temperature heat capacity for a dilute solution of diatomic molecules in an atomic two-dimensional matrix is calculated. The possibility of experimental observation of the effects obtained is discussed

  5. Dynamic and structural studies of molecular or atomic systems through the generation of high order harmonics

    International Nuclear Information System (INIS)

    Higuet, J.

    2010-10-01

    High harmonic generation is a well known phenomenon explained by a three step model: because of the high intensity field generated by an ultrashort laser pulse, an atom or a molecule can be tunnel ionized. The ejected electron is then accelerated by the intense electric field, and eventually can recombine on its parent ion, leading to the emission of a XUV photon. Because of the generating process in itself, this light source is a promising candidate to probe the electronic structure of atoms and molecules, with an atto-second/sub-nanometer potential resolution (1 as=10 -18 s). In this work, we have studied the sensitivity of the emitted light (in terms of amplitude, but also phase and polarization) towards the electronic structure of the generating medium. We have first worked on atomic medium, then on molecules (N 2 , CO 2 , O 2 ). Comparing the experimental results with numerical simulations shows the necessity to model finely the generation process and to go beyond commonly used approximations. We have also shown the possibility to perform high harmonic spectroscopy in order to measure dynamics of complex molecules, such as Nitrogen Dioxide (NO 2 ). This technic has obtained complementary results compared to classical spectroscopy and has revealed dynamics of the electronic wave packet along a conical intersection. In this experiment, we have adapted conventional optical spectroscopy technic to the XUV spectral area, which significantly improved the signal over noise ratio. (author)

  6. The effect of deposition energy of energetic atoms on the growth and structure of ultrathin amorphous carbon films studied by molecular dynamics simulations

    KAUST Repository

    Wang, N; Komvopoulos, K

    2014-01-01

    The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures

  7. Atomic and molecular theory

    International Nuclear Information System (INIS)

    Inokuti, Mitio.

    1990-01-01

    The multifaceted role of theoretical physics in understanding the earliest stages of radiation action is discussed. Scientific topics chosen for the present discourse include photoabsorption, electron collisions, and ionic collisions, and electron transport theory, Connections of atomic and molecular physics with condensed-matter physics are also discussed. The present article includes some historical perspective and an outlook for the future. 114 refs., 3 figs

  8. Atomic and molecular theory

    Energy Technology Data Exchange (ETDEWEB)

    Inokuti, Mitio.

    1990-01-01

    The multifaceted role of theoretical physics in understanding the earliest stages of radiation action is discussed. Scientific topics chosen for the present discourse include photoabsorption, electron collisions, and ionic collisions, and electron transport theory, Connections of atomic and molecular physics with condensed-matter physics are also discussed. The present article includes some historical perspective and an outlook for the future. 114 refs., 3 figs.

  9. Atomic structure of shear bands in Cu64Zr36 metallic glasses studied by molecular dynamics simulations

    International Nuclear Information System (INIS)

    Feng, Shidong; Qi, Li; Wang, Limin; Pan, Shaopeng; Ma, Mingzhen; Zhang, Xinyu; Li, Gong; Liu, Riping

    2015-01-01

    Graphical abstract: Figure shows that atoms in the shear band (SB) moved desultorily compared with those in the matrix. These atoms seriously interacted with each other similar to the grain boundary in crystalline materials. Figuratively, if these atoms wanted to “pass” the shear band, they should arrange their irritations. However, stress concentrations and high energy were observed in SB, which resulted in instability in the deformation process and finally led to a disastrously brittle fracture. - Abstract: Molecular dynamics simulations on the atomic structure of shear bands (SBs) in Cu 64 Zr 36 metallic glasses are presented. Results show that the atoms in the SB move desultorily, in contrast to those in the matrix. The saturated degree of bonded pairs considering the “liquid-like” character of SB quantitatively provides important details in extending earlier studies on SBs. Zr-centered 〈0, 2, 8, 5〉 clusters exhibit strong spatial correlations and tendency to connect with each other in short-range order. The 〈0, 2, 8, 5〉 cluster-type medium-range order is the main feature inside the SB relative to the matrix. The fractal results demonstrate the planar-like fashion of the 〈0, 2, 8, 5〉 network in SB, forming an interpenetrating solid-like backbone. Such heterogeneous structure provides a fundamental structural perspective of mechanical instability in SB

  10. Molecular dynamics modeling of bonding two materials by atomic scale friction stir welding at different process parameters

    Science.gov (United States)

    Konovalenko S., Iv.; Psakhie, S. G.

    2017-12-01

    Using the molecular dynamics method, we simulated the atomic scale butt friction stir welding on two crystallites and varied the onset FSW tool plunge depth. The effects of the plunge depth value on the thermomechanical evolution of nanosized crystallites and mass transfer in the course of FSW have been studied. The increase of plunge depth values resulted in more intense heating and reducing the plasticized metal resistance to the tool movement. The mass transfer intensity was hardly dependent on the plunge depth value. The plunge depth was recommended to be used as a FSW process control parameter in addition to the commonly used ones.

  11. Experimental atomic and molecular physics research

    International Nuclear Information System (INIS)

    Anon.

    1980-01-01

    The Atomic Physics research in the Physics Division consists of five ongoing experimental programs: dissociation and other interactions of energetic molecular ions in solid and gaseous targets; beam-foil research and collision dynamics of heavy ions; photoionization-photoelectron research; spectroscopy of free atoms and molecules, high precision laser-rf double-resonance spectroscopy with atomic and molecular beams; and Moessbauer effect research

  12. Heavy atoms as molecular probes in studying the solvent dependence of the dynamics of triplet exciplexes

    International Nuclear Information System (INIS)

    Steiner, U.; Winter, G.

    1981-01-01

    Electron transfer reactions between thiopyronine triplet (acceptor 3 A + ) and the electron donors (D), aniline, p-Br-aniline and p-I-aniline, are investigated by flash spectroscopy in solvents of different viscosity and polarity. Due to the heavy-atom effect the radical yield becomes very sensitive to the solvent influence, which can be explained by the dynamic properties of a triplet exciplex ( 3 (AD + )) formed as a primary product in the reaction between acceptor triplet and donor. Whereas on variation of solvent viscosity the solvent cage effect on the dissociation of 3 (AD + ) is observed, a change in solvent polarity is suggested to affect the radiationless deactivation of 3 (AD + ) to the ground state of the components. (author)

  13. Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111)

    Energy Technology Data Exchange (ETDEWEB)

    Kroes, Geert-Jan, E-mail: g.j.kroes@chem.leidenuniv.nl; Pavanello, Michele [Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden (Netherlands); Blanco-Rey, María [Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20080 Donostia-San Sebastián (Spain); Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Alducin, Maite [Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastián (Spain); Auerbach, Daniel J. [Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden (Netherlands); Max Planck Institute for Biophysical Chemistry, Göttingen (Germany); Institute for Physical Chemistry, Georg-August University of Göttingen, Göttingen (Germany)

    2014-08-07

    Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction (“EF”) model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated “post” (“p”) the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy

  14. Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111).

    Science.gov (United States)

    Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J

    2014-08-07

    Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the

  15. Effects of vacancies on atom displacement threshold energy calculations through Molecular Dynamics Methods in BaTiO3

    Science.gov (United States)

    Gonzalez Lazo, Eduardo; Cruz Inclán, Carlos M.; Rodríguez Rodríguez, Arturo; Guzmán Martínez, Fernando; Abreu Alfonso, Yamiel; Piñera Hernández, Ibrahin; Leyva Fabelo, Antonio

    2017-09-01

    A primary approach for evaluating the influence of point defects like vacancies on atom displacement threshold energies values Td in BaTiO3 is attempted. For this purpose Molecular Dynamics Methods, MD, were applied based on previous Td calculations on an ideal tetragonal crystalline structure. It is an important issue in achieving more realistic simulations of radiation damage effects in BaTiO3 ceramic materials. It also involves irradiated samples under severe radiation damage effects due to high fluency expositions. In addition to the above mentioned atom displacement events supported by a single primary knock-on atom, PKA, a new mechanism was introduced. It corresponds to the simultaneous excitation of two close primary knock-on atoms in BaTiO3, which might take place under a high flux irradiation. Therefore, two different BaTiO3 Td MD calculation trials were accomplished. Firstly, single PKA excitations in a defective BaTiO3 tetragonal crystalline structure, consisting in a 2×2×2 BaTiO3 perovskite like super cell, were considered. It contains vacancies on Ba and O atomic positions under the requirements of electrical charge balance. Alternatively, double PKA excitations in a perfect BaTiO3 tetragonal unit cell were also simulated. On this basis, the corresponding primary knock-on atom (PKA) defect formation probability functions were calculated at principal crystal directions, and compared with the previous one we calculated and reported at an ideal BaTiO3 tetrahedral crystal structure. As a general result, a diminution of Td values arises in present calculations in comparison with those calculated for single PKA excitation in an ideal BaTiO3 crystal structure.

  16. Dynamic grazing incidence fast atom diffraction during molecular beam epitaxial growth of GaAs

    Energy Technology Data Exchange (ETDEWEB)

    Atkinson, P., E-mail: atkinson@insp.jussieu.fr; Eddrief, M. [Sorbonne Universités, UPMC Univ. Paris 06, UMR 7588, INSP, F-75005 Paris (France); CNRS, UMR 7588, Institut des NanoSciences de Paris, 4 place Jussieu, F-75005 Paris (France); Etgens, V. H. [CNRS, UMR 7588, Institut des NanoSciences de Paris, 4 place Jussieu, F-75005 Paris (France); VeDeCom-Université Versailles Saint-Quentin en Yvelines, Versailles (France); Khemliche, H., E-mail: hocine.khemliche@u-psud.fr; Debiossac, M.; Mulier, M.; Lalmi, B.; Roncin, P. [ISMO UMR8214 CNRS-Université Paris-Sud, Orsay F-91400 (France); Momeni, A. [ISMO UMR8214 CNRS-Université Paris-Sud, Orsay F-91400 (France); Univ. Cergy Pontoise, F-95031 Cergy (France)

    2014-07-14

    A Grazing Incidence Fast Atom Diffraction (GIFAD) system has been mounted on a commercial molecular beam epitaxy chamber and used to monitor GaAs growth in real-time. In contrast to the conventionally used Reflection High Energy Electron Diffraction, all the GIFAD diffraction orders oscillate in phase, with the change in intensity related to diffuse scattering at step edges. We show that the scattered intensity integrated over the Laue circle is a robust method to monitor the periodic change in surface roughness during layer-by-layer growth, with oscillation phase and amplitude independent of incidence angle and crystal orientation. When there is a change in surface reconstruction at the start of growth, GIFAD intensity oscillations show that there is a corresponding delay in the onset of layer-by-layer growth. In addition, changes in the relative intensity of different diffraction orders have been observed during growth showing that GIFAD has the potential to provide insight into the preferential adatom attachment sites on the surface reconstruction during growth.

  17. Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates

    NARCIS (Netherlands)

    Baron, R; de Vries, AH; Hunenberger, PH; van Gunsteren, WF

    2006-01-01

    Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model

  18. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

    Science.gov (United States)

    Chen, Wei; Shen, Jana K.

    2014-01-01

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

  19. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

    Science.gov (United States)

    Chen, Wei; Shen, Jana K

    2014-10-15

    Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

  20. SELF-HEALING NANOMATERIALS: MULTIMILLION-ATOM REACTIVE MOLECULAR DYNAMICS SIMULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Hakamata, Tomoya [Kumamoto Univ., Kumamoto (Japan); Shimamura, Kohei [Kumamoto Univ., Kumamoto (Japan); Univ. of Southern California, Los Angeles, CA (United States); Kobe Univ., Kobe (Japan); Shimojo, Fuyuki [Kumamoto Univ., Kumamoto (Japan); Kalia, Rajiv K. [Univ. of Southern California, Los Angeles, CA (United States); Nakano, Aiichiro [Univ. of Southern California, Los Angeles, CA (United States); Vashishta, Priya [Univ. of Southern California, Los Angeles, CA (United States)

    2017-10-20

    Organometal halide perovskites are attracting great attention as promising material for solar cells because of their high power conversion efficiency. The high performance has been attributed to the existence of free charge carriers and their large diffusion lengths, but the nature of carrier transport at the atomistic level remains elusive. Here, nonadiabatic quantum molecular dynamics simulations elucidate the mechanisms underlying the excellent free-carrier transport in CH3NH3PbI3. Pb and I sublattices act as disjunct pathways for rapid and balanced transport of photoexcited electrons and holes, respectively, while minimizing efficiency-degrading charge recombination. On the other hand, CH3NH3 sublattice quickly screens out electrostatic electron-hole attraction to generate free carriers within 1 ps. Together this nano-architecture lets photoexcited electrons and holes dissociate instantaneously and travel far away to be harvested before dissipated as heat. As a result, this work provides much needed structure-property relationships and time-resolved information that potentially lead to rational design of efficient solar cells.

  1. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  2. Atomic structure of screw dislocations intersecting the Au(111) surface: A combined scanning tunneling microscopy and molecular dynamics study

    DEFF Research Database (Denmark)

    Engbæk, Jakob; Schiøtz, Jakob; Dahl-Madsen, Bjarke

    2006-01-01

    The atomic-scale structure of naturally occurring screw dislocations intersecting a Au(111) surface has been investigated both experimentally by scanning tunneling microscopy (STM) and theoretically using molecular dynamics (MD) simulations. The step profiles of 166 dislocations were measured using...... STM. Many of them exhibit noninteger step-height plateaus with different widths. Clear evidence was found for the existence of two different populations at the surface with distinct (narrowed or widened) partial-splitting widths. All findings are fully confirmed by the MD simulations. The MD...... simulations extend the STM-, i.e., surface-, investigation to the subsurface region. Due to this additional insight, we can explain the different partial-splitting widths as the result of the interaction between the partial dislocations and the surface....

  3. Hydrogen atom injection into carbon surfaces by comparison between Monte-Carlo, molecular dynamics and ab-initio calculations

    International Nuclear Information System (INIS)

    Ito, A.; Kenmotsu, T.; Kikuhara, Y.; Inai, K.; Ohya, K.; Wang, Y.; Irle, S.; Morokuma, K.; Nakamura, H.

    2009-01-01

    Full text: To understand the plasma-wall interaction on divertor plates, we investigate the interaction of hydrogen atoms and carbon materials used in the high heat flux components by the use of the following simulations. Monte-Carlo (MC) method based on binary collision approximation can calculate the sputtering process of hydrogen atoms on the carbon material quickly. Classical molecular dynamics (MD) method employs multi-body potential models and can treat realistic structures of crystal and molecule. The ab-initio method can calculate electron energy in quantum mechanics, which is regarded as realistic potential for atoms. In the present paper, the interaction of the hydrogen and the carbon material is investigated using the multi-scale (MC, MD and ab-initio) methods. The bombardment of hydrogen atoms onto the carbon material is simulated by the ACAT-code of the MC method, which cannot represent the structure of crystal, and the MD method using modified reactive empirical bond order (REBO) potential, which treats single crystal graphite and amorphous carbon. Consequently, we clarify that the sputtering yield and the reflection rate calculated by the ACAT-code agree with those on the amorphous carbon calculated by the MD. Moreover, there are many kinds of REBO potential for the MD. Adsorption, reflection and penetration rates between a hydrogen atom and a graphene surface are calculated by the MD simulations using the two kinds of potential model. For the incident energy of less than 1 eV, the MD simulation using the modified REBO potential, which is based on Brenner's REBO potential in 2002, shows that reflection is dominant, while the most popular Brenner's REBO potential in 1990 shows that adsorption is dominant. This reflection of the low energy injection is caused by a small potential barrier for the hydrogen atom in the modified REBO potential. The small potential barrier is confirmed by the ab-initio calculations, which are hybrid DFT (B3LYP/cc-pVDZ), ab

  4. Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

  5. Atomic structure and thermal stability of interfaces between metallic glass and embedding nano-crystallites revealed by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gao, X.Z.; Yang, G.Q.; Xu, B.; Qi, C.; Kong, L.T., E-mail: konglt@sjtu.edu.cn; Li, J.F.

    2015-10-25

    Molecular dynamics simulations were performed to investigate the atomic structure and thermal stability of interfaces formed between amorphous Cu{sub 50}Zr{sub 50} matrix and embedding B2 CuZr nano-crystallites. The interfaces are found to be rather abrupt, and their widths show negligible dependence on the nano-crystallite size. Local atomic configuration in the interfacial region is dominated by geometry characterized by Voronoi polyhedra <0,5,2,6> and <0,4,4,6>, and the contents of these polyhedra also exhibit apparent size dependence, which in turn results in an increasing trend in the interfacial energy against the nano-crystallite size. Annealing of the interface models at elevated temperatures will also enrich these characterizing polyhedra. While when the temperature is as high as the glass transition temperature of the matrix, growth of the nano-crystallites will be appreciable. The growth activation energy also shows size dependence, which is lower for larger nano-crystallites, suggesting that large nano-crystallites are prone to grow upon thermal disturbance. - Highlights: • Special clusters characterizing the local geometry are abundant in the interfaces. • Their content varies with the size of the embedding nano-crystallite. • In turn, size dependences in interfacial thermodynamics and kinetics are observed.

  6. A molecular dynamics study of the atomic structure of (CaO)x(SiO2)1-x glasses.

    Science.gov (United States)

    Mead, Robert N; Mountjoy, Gavin

    2006-07-27

    The local atomic environment of Ca in (CaO)x(SiO2)1-x glasses is of interest because of the role of Ca in soda-lime glass, the application of calcium silicate glasses as biomaterials, and the previous experimental measurement of the Ca-Ca correlation in CaSiO(3) glass. Molecular dynamics has been used to obtain models of (CaO)x(SiO2)1-x glasses with x = 0, 0.1, 0.2, 0.3, 0.4, and 0.5, and with approximately 1000 atoms and size approximately 25 A. As expected, the models contain a tetrahedral silica network, the connectivity of which decreases as x increases. In the glass-forming region, i.e., x = 0.4 and 0.5, Ca has a mixture of 6- and 7-fold coordination. Bridging oxygen makes an important contribution to the coordination of Ca, with most bridging oxygens coordinated to 2 Si plus 1 Ca. The x = 0.5 model is in reasonable agreement with previous experimental studies, and does not substantiate the previous theory of cation ordering, which predicted Ca arranged in sheets. In the phase-separated region, i.e., x = 0.1 and 0.2, there is marked clustering of Ca.

  7. Statistical study of defects caused by primary knock-on atoms in fcc Cu and bcc W using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Warrier, M., E-mail: Manoj.Warrier@gmail.com [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India); Bhardwaj, U.; Hemani, H. [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India); Schneider, R. [Computational Science, Ernst-Moritz-Arndt University, D-17489 Greifswald (Germany); Mutzke, A. [Max-Planck-Institut für Plasmaphysik, D-17491 Greifswald (Germany); Valsakumar, M.C. [School for Engineering Sciences and Technology, University of Hyderabad, Gachibowli, Hyderabad, Telangana State, 500046 (India)

    2015-12-15

    We report on molecular Dynamics (MD) simulations carried out in fcc Cu and bcc W using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code to study (i) the statistical variations in the number of interstitials and vacancies produced by energetic primary knock-on atoms (PKA) (0.1–5 keV) directed in random directions and (ii) the in-cascade cluster size distributions. It is seen that around 60–80 random directions have to be explored for the average number of displaced atoms to become steady in the case of fcc Cu, whereas for bcc W around 50–60 random directions need to be explored. The number of Frenkel pairs produced in the MD simulations are compared with that from the Binary Collision Approximation Monte Carlo (BCA-MC) code SDTRIM-SP and the results from the NRT model. It is seen that a proper choice of the damage energy, i.e. the energy required to create a stable interstitial, is essential for the BCA-MC results to match the MD results. On the computational front it is seen that in-situ processing saves the need to input/output (I/O) atomic position data of several tera-bytes when exploring a large number of random directions and there is no difference in run-time because the extra run-time in processing data is offset by the time saved in I/O. - Highlights: • MD simulations of collision cascades in 200 random directions explored in the energy range of 1–5 keV for fcc Cu and bcc W. • 60–80 random directions must be sampled for the number of displacements produced in a collision cascade to stabilize. • In-cascade clustering of interstitials and vacancies occur. • Direction averaged distribution of interstitials and vacancies around the origin of a PKA is presented. • Comparisons with MD indicate that the recoils produced in BCA-MC simulations be checked for recombination against all vacancies created.

  8. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  9. Atom dynamics in laser fields

    International Nuclear Information System (INIS)

    Jang, Su; Mi, No Gin

    2004-12-01

    This book introduces coherent dynamics of internal state, spread of atoms wave speed, semiclassical atoms density matrix such as dynamics equation in both still and moving atoms, excitation of atoms in movement by light, dipole radiating power, quantum statistical mechanics by atoms in movement, semiclassical atoms in movement, atoms in movement in the uniform magnetic field including effects of uniform magnetic field, atom cooling using laser such as Doppler cooling, atom traps using laser and mirrors, radiant heat which particles receive, and near field interactions among atoms in laser light.

  10. Dislocation glide in Ni-Al solid solutions from the atomic scale up: a molecular dynamics study

    International Nuclear Information System (INIS)

    Rodary, E.

    2003-01-01

    The glide of an edge dislocation in solid solutions is studied by molecular dynamics, at fixed temperature and imposed external stress. We have optimized an EAM potential for Ni(1 a 8% A1): it well reproduces the lattice expansion, local atomic order, stacking fault energy as a function of composition, as well as the elastic properties of the γ' phase with L1 2 structure. On increasing the stress, the dislocation is first immobile, then glides with a velocity proportional to the stress and the velocity saturates on reaching the transverse sound velocity. However, only beyond a static threshold stress, σ s , does the dislocation glide a distance large enough to allow macroscopic shear; the linear part of the velocity-stress curve extrapolates to zero at a dynamical threshold stress, σ d , The friction coefficient, and the threshold stresses (σ s and σ d ), increase with the A1 concentration and decrease with temperature (300 and 500 K). Close to the critical shear stress, σ s , the dislocation glide is analysed with a 'stop and go' model. The latter yields the flight velocity between obstacles, the mean obstacle density and the distribution of the waiting time on each obstacle as a function of stress, composition and temperature. The obstacle to the glide is proposed to be the strong repulsion between Al atoms brought into nearest neighbour position by the glide process, and not the dislocation-solute interaction. The microscopic parameters so defined are introduced into a micro-mechanical model, which well reproduces the known behaviour of nickel base solid solutions. (author)

  11. Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study

    Science.gov (United States)

    Man, Viet Hoang; Li, Mai Suan; Derreumaux, Philippe; Nguyen, Phuong H.

    2018-03-01

    The Rayleigh-Plesset (RP) equation was derived from the first principles to describe the bubble cavitation in liquids in terms of macroscopic hydrodynamics. A number of nonequilibrium molecular dynamics studies have been carried out to validate this equation in describing the bubble inertial cavitation, but their results are contradictory and the applicability of the RP equation still remains to be examined, especially for the stable cavitation. In this work, we carry out nonequilibrium all-atom simulation to validate the applicability of the RP equation in the description of the stable cavitation of nano-sized bubbles in water. We show that although microscopic effects are not explicitly included, this equation still describes the dynamics of subnano-bubbles quite well as long as the contributions of various terms including inertial, surface tension, and viscosity are correctly taken into account. These terms are directly and inversely proportional to the amplitude and period of the cavitation, respectively. Thus, their contributions to the RP equation depend on these two parameters. This may explain the discrepancy between the current results obtained using different parameters. Finally, the accuracy of the RP equation in the current mathematical modeling studies of the ultrasound-induced blood-brain-barrier experiments is discussed in some detail.

  12. Dynamical symmetries of molecular states in atomic, nuclear and hadron physics

    International Nuclear Information System (INIS)

    Iachello, F.; Cseh, J.; Levai, G.

    1995-01-01

    The algebraic description of dipole degrees of freedom is discussed. These degrees of freedom are relevant to two and few-body systems, as well as in the collective motion of many-body systems. Applications to molecular, nuclear and hadron spectroscopy are presented. Different internal degrees of freedom can also be coupled to the spatial ones, leading to realistic models of several complex systems. (author)

  13. Molecular invariants: atomic group valence

    International Nuclear Information System (INIS)

    Mundim, K.C.; Giambiagi, M.; Giambiagi, M.S. de.

    1988-01-01

    Molecular invariants may be deduced in a very compact way through Grassman algebra. In this work, a generalized valence is defined for an atomic group; it reduces to the Known expressions for the case of an atom in a molecule. It is the same of the correlations between the fluctions of the atomic charges qc and qd (C belongs to the group and D does not) around their average values. Numerical results agree with chemical expectation. (author) [pt

  14. Atomic molecular and optical physics

    International Nuclear Information System (INIS)

    Anon.

    1986-01-01

    Laser-assisted manufacturing and fiber-optics communications are but two of the products of atomic, molecular, and optical physics, (AMO) research. AMO physics provides theoretical and experimental methods and essential data to neighboring areas of science such as chemistry, astrophysics, condensed-matter physics, plasma physics, surface science, biology, and medicine. This book addresses advances in atomic, molecular, and optical fields and provides recommendations for further research. It also looks at scientific applications in national security, manufacturing, medicine, and other fields

  15. The atomic-scale nucleation mechanism of NiTi metallic glasses upon isothermal annealing studied via molecular dynamics simulations.

    Science.gov (United States)

    Li, Yang; Li, JiaHao; Liu, BaiXin

    2015-10-28

    Nucleation is one of the most essential transformation paths in phase transition and exerts a significant influence on the crystallization process. Molecular dynamics simulations were performed to investigate the atomic-scale nucleation mechanisms of NiTi metallic glasses upon devitrification at various temperatures (700 K, 750 K, 800 K, and 850 K). Our simulations reveal that at 700 K and 750 K, nucleation is polynuclear with high nucleation density, while at 800 K it is mononuclear. The underlying nucleation mechanisms have been clarified, manifesting that nucleation can be induced either by the initial ordered clusters (IOCs) or by the other precursors of nuclei evolved directly from the supercooled liquid. IOCs and other precursors stem from the thermal fluctuations of bond orientational order in supercooled liquids during the quenching process and during the annealing process, respectively. The simulation results not only elucidate the underlying nucleation mechanisms varied with temperature, but also unveil the origin of nucleation. These discoveries offer new insights into the devitrification mechanism of metallic glasses.

  16. Peptide insertion, positioning, and stabilization in a membrane: insight from an all-atom molecular dynamics simulation.

    Science.gov (United States)

    Babakhani, Arneh; Gorfe, Alemayehu A; Gullingsrud, Justin; Kim, Judy E; Andrew McCammon, J

    Peptide insertion, positioning, and stabilization in a model membrane are probed via an all-atom molecular dynamics (MD) simulation. One peptide (WL5) is simulated in each leaflet of a solvated dimyristoylglycero-3-phosphate (DMPC) membrane. Within the first 5 ns, the peptides spontaneously insert into the membrane and then stabilize during the remaining 70 ns of simulation time. In both leaflets, the peptides localize to the membrane interface, and this localization is attributed to the formation of peptide-lipid hydrogen bonds. We show that the single tryptophan residue in each peptide contributes significantly to these hydrogen bonds; specifically, the nitrogen heteroatom of the indole ring plays a critical role. The tilt angles of the indole rings relative to the membrane normal in the upper and lower leaflets are approximately 26 degrees and 54 degrees , respectively. The tilt angles of the entire peptide chain are 62 degrees and 74 degrees . The membrane induces conformations of the peptide that are characteristic of beta-sheets, and the peptide enhances the lipid ordering in the membrane. Finally, the diffusion rate of the peptides in the membrane plane is calculated (based on experimental peptide concentrations) to be approximately 6 A(2)/ns, thus suggesting a 500 ns time scale for intermolecular interactions.

  17. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Carles Calero

    2016-04-01

    Full Text Available Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs. We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.

  18. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  19. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    International Nuclear Information System (INIS)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-01-01

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems

  20. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

    Science.gov (United States)

    Wallace, Jason A; Shen, Jana K

    2012-11-14

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  1. Atomic, molecular and optical physics

    International Nuclear Information System (INIS)

    1990-01-01

    This is related to the actual situation and perspectives of atomic, molecular and optical physics in Brazil. It gives a general overview of the most important research groups in the above mentioned areas. It discusses as well, the future trends of Brazilian universities and the financing of these groups. (A.C.A.S.)

  2. Physics through the 1990s: Atomic, molecular, and optical physics

    International Nuclear Information System (INIS)

    1986-01-01

    This report was prepared by the Panel on Atomic, Molecular, and Optical Physics of the Physics Survey Committee in response to its charge to describe the field, to characterize the recent advances, and to identify the current frontiers of research. Some of the areas discussed are: atomic structure, atomic dynamics, accelerator-based atomic physics, molecular photoionization and electron-molecule scattering, astrophysics, laser spectroscopy, atmospheric physics, plasma physics, and applications

  3. Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

    Science.gov (United States)

    Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

    2017-10-01

    Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

  4. A statistical analysis of the lateral displacement of Si atoms in molecular dynamics simulations of successive bombardment with 20-keV C{sub 60} projectiles

    Energy Technology Data Exchange (ETDEWEB)

    Krantzman, K.D., E-mail: krantzmank@cofc.edu [Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424 (United States); Cook, E.L. [Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424 (United States); Wucher, A. [Faculty of Physics, University of Duisburg-Essen, 47048 Duisburg (Germany); Garrison, B.J. [Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 (United States)

    2011-07-15

    An important factor that determines the possible lateral resolution in sputter depth profiling experiments is ion induced lateral displacement of substrate atoms. Molecular dynamics (MD) simulations are performed to model the successive bombardment of Si with 20 keV C{sub 60} at normal incidence. A statistical analysis of the lateral displacement of atoms that originate from the topmost layer is presented and discussed. From these results, it is determined that the motion is isotropic and can be described mathematically by a simple diffusion equation. A 'diffusion coefficient' for lateral displacement is determined to be 3.5 A{sup 2}/impact. This value can be used to calculate the average lateral distance moved as a function of the number of impacts. The maximum distance an atom may move is limited by the time that it remains on the surface before it is sputtered. After 800 impacts, 99% of atoms from the topmost layer have been removed, and the average distance moved by these atoms is predicted to be 100 A. Although the behavior can be described mathematically by the diffusion equation, the behavior of the atoms is different than what is thought of as normal diffusion. Atoms are displaced a large distance due to infrequent large hops.

  5. Monolayer atomic crystal molecular superlattices

    Science.gov (United States)

    Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

    2018-03-01

    Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

  6. Atomic probes of surface structure and dynamics

    International Nuclear Information System (INIS)

    Heller, E.J.; Jonsson, H.

    1992-01-01

    Progress for the period Sept. 15, 1992 to Sept. 14, 1993 is discussed. Semiclassical methods that will allow much faster and more accurate three-dimensional atom--surface scattering calculations, both elastic and inelastic, are being developed. The scattering of He atoms from buckyballs is being investigated as a test problem. Somewhat more detail is given on studies of He atom scattering from defective Pt surfaces. Molecular dynamics simulations of He + and Ar + ion sputtering of Pt surfaces are also being done. He atom scattering from Xe overlayers on metal surfaces and the thermalized dissociation of H 2 on Cu(110) are being studied. (R.W.R.) 64 refs

  7. Molecular dynamics of bacteriorhodopsin.

    Science.gov (United States)

    Lupo, J A; Pachter, R

    1997-02-01

    A model of bacteriorhodopsin (bR), with a retinal chromophore attached, has been derived for a molecular dynamics simulation. A method for determining atomic coordinates of several ill-defined strands was developed using a structure prediction algorithm based on a sequential Kalman filter technique. The completed structure was minimized using the GROMOS force field. The structure was then heated to 293 K and run for 500 ps at constant temperature. A comparison with the energy-minimized structure showed a slow increase in the all-atom RMS deviation over the first 200 ps, leveling off to approximately 2.4 A relative to the starting structure. The final structure yielded a backbone-atom RMS deviation from the crystallographic structure of 2.8 A. The residue neighbors of the chromophore atoms were followed as a function of time. The set of persistent near-residue neighbors supports the theory that differences in pKa values control access to the Schiff base proton, rather than formation of a counterion complex.

  8. Molecular beam studies and hot atom chemistry

    International Nuclear Information System (INIS)

    Continetti, R.E.; Lee, Y.T.

    1993-01-01

    The application of the crossed molecular beam technique to the study of hot atom chemistry has provided significant insights into the dynamics of hot atom reaction. To illustrate this, two recent studies are discussed. Those are the study on the influence of translational energy in 0.6 to 1.5 eV range on endoergic reaction, and the experimental study on the detailed dynamics of elementary reaction at translational energy of 0.53 and 1.01 eV. The first example illustrates the contribution that molecular beam experiment can make in the understanding of the dynamics of endoergic substitution reaction. The second example illustrates the role that such studies can play in evaluating exact three-dimensional quantum scattering calculation and ab initio potential energy surfaces for chemical reaction. In the case of endoergic reaction of halogen substitution, it was observed that the reactive collision involved short lived collision complexes. It is suggested that energetic effect alone cannot account for the difference in cross sections, and dynamic effect most play a large role. In atom-diatom reaction, the differential cross section measurement of D+H 2 →DH+H reaction was carried out, and the results are discussed. (K.I.)

  9. Atomic and Molecular Data and their Applications★

    Science.gov (United States)

    Drake, Gordon W. F.; Yoon, Jung-Sik; Kato, Daiji; Karwasz, Grzegorz

    2018-03-01

    This topical issue on Atomic and molecular data and their applications was motivated by the 10th International Conference on Atomic and Molecular Data (ICAMDATA 2016), which was held from September 26 to 29, 2016 in Gunsan, Republic of Korea. The topics of this issue reflect those of the conference program. The scientific papers in the topical issue cover the fields of atomic and molecular structure, radiative transitions, scattering processes, data base development, and the applications of atomic and molecular data to plasma modeling. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, and Grzegorz Karwasz.

  10. The effect of deposition energy of energetic atoms on the growth and structure of ultrathin amorphous carbon films studied by molecular dynamics simulations

    KAUST Repository

    Wang, N

    2014-05-16

    The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures were simulated by varying the deposition energy of carbon atoms in the range of 1-120 eV. Intrinsic film characteristics (e.g. density and internal stress) were determined after the system reached equilibrium. Short- and intermediate-range carbon atom ordering is examined in the context of atomic hybridization and ring connectivity simulation results. It is shown that relatively high deposition energy (i.e., 80 eV) yields a multilayer film structure consisting of an intermixing layer, bulk film and surface layer, consistent with the classical subplantation model. The highest film density (3.3 g cm-3), sp3 fraction (∼43%), and intermediate-range carbon atom ordering correspond to a deposition energy of ∼80 eV, which is in good agreement with experimental findings. © 2014 IOP Publishing Ltd.

  11. Effect of solute atoms on glass-forming ability for Fe–Y–B alloy: An ab initio molecular dynamics study

    International Nuclear Information System (INIS)

    Han, J.J.; Wang, W.Y.; Liu, X.J.; Wang, C.P.; Hui, X.D.; Liu, Z.K.

    2014-01-01

    The glass-forming abilities of Fe 78 B 22 , Fe 70 Y 6 B 24 , Fe 72 Y 6 B 22 and Fe 72.5 Y 3.5 B 24 alloys were characterized comprehensively using ab initio molecular dynamics simulations. The calculated results were correlated with the properties and atomic structures. It was found that the Fe 72 Y 6 B 22 alloy consists of both the most stable and the least deformed body centered cubic atomic packing structures in the supercooled liquid and glassy states. It was observed that the local compositions in the Fe 72 Y 6 B 22 alloy significantly deviate from the compositions of stable crystalline phases, indicating that the Fe 72 Y 6 B 22 alloy has the best glass-forming ability among the alloys studied. However, Fe 72 Y 6 B 22 alloy has two flaws in terms of glass-forming ability, i.e. relatively large atomic diffusivity and insufficiently close atomic packing. The best performance in these two aspects is observed in the Fe 72.5 Y 3.5 B 24 alloy. Thus, the theoretical study predicts that the best glass former for the Fe–Y–B system is within the compositional range of 22–24 at.% B and 3.5–6 at.% Y

  12. Effects of guest atomic species on the lattice thermal conductivity of type-I silicon clathrate studied via classical molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Kumagai, Tomohisa, E-mail: kumagai@criepi.denken.or.jp; Nakamura, Kaoru; Yamada, Susumu; Ohnuma, Toshiharu [Materials Science Research Laboratory, Central Research Institute of Electric Power Industry, 2-6-1 Nagasaka, Yokosuka, Kanagawa 240-0196 (Japan)

    2016-08-14

    The effects of guest atomic species in Si clathrates on the lattice thermal conductivity were studied using classical molecular dynamics calculations. The interaction between a host atom and a guest atom was described by the Morse potential function while that between host atoms was described by the Tersoff potential. The parameters of the potentials were newly determined for this study such that the potential curves obtained from first-principles calculations for the insertion of a guest atom into a Si cage were successfully reproduced. The lattice thermal conductivities were calculated by using the Green-Kubo method. The experimental lattice thermal conductivity of Ba{sub 8}Ga{sub 16}Si{sub 30} can be successfully reproduced using the method. As a result, the lattice thermal conductivities of type-I Si clathrates, M{sub 8}Si{sub 46} (M = Na, Mg, K, Ca Rb, Sr, Cs, or Ba), were obtained. It is found that the lattice thermal conductivities of M{sub 8}Si{sub 46}, where M is IIA elements (i.e., M = Mg, Ca, Sr, or Ba) tend to be lower than those of M{sub 8}Si{sub 46}, where M is IA elements (i.e., M = Na, K, Rb, or Cs). Those of {sup m}M{sub 8}Si{sub 46}, where m was artificially modified atomic weight were also obtained. The obtained lattice thermal conductivity can be regarded as a function of a characteristic frequency, f{sub c}. That indicates minimum values around f{sub c}=2-4 THz, which corresponds to the center of the frequencies of the transverse acoustic phonon modes associated with Si cages.

  13. Dynamical polarizability of atoms

    International Nuclear Information System (INIS)

    Mukhopadhyay, G.; Lundqvist, S.

    1980-07-01

    The frequency-dependent polarizability of a closed-shell atom is considered in an RPA type approximation. This is usually done using many-body perturbation theory but can also be recast into the form of equations for the density oscillations as previously shown by the authors. The latter approach is known to lead to a non-hermitian problem because of the structure of the interaction kernel. This note shows that this is also true if using the reaction matrix method. The main result is to derive the expression for the polarizability function taking into account the non-hermitian nature of the problem. (author)

  14. Atomic and molecular collision processes

    International Nuclear Information System (INIS)

    Norcross, D.W.

    1991-01-01

    530Accomplishments during the course of a 44-month program of code development and high precision calculations for electron collisions with atoms, atomic ions, and molecules are summarized. In electron-atom and -ion collisions, we were primarily concerned with the fundamental physics of the process that controls excitation in high temperature plasmas. In the molecular work, we pursued the development of techniques for accurate calculations of ro-vibrational excitation of polyatomic molecules, to the modeling of gas-phase laser systems. Highlights from the seven technical paper published as a result of this contract include: The resolution of a long history of unexplained anomalies and experimental/theoretical discrepancies by a demonstration that the Coulomb phase must be included in scattering amplitudes for electron-ion collisions. Definitive close-coupling calculations of cross sections for electron impact excitation of Be + , using a very elaborate expansion for the collision system and inclusion of both one- and two-body terms for the effect of core polarization. Detailed state-of-the-art calculations for electron-impact excitation of the sodium-like ion A ell 2+ that included core-polarization interactions, and which also produced new data on bound-state energy levels for the magnesium-like ion A ell + and oscillator strengths for A ell 2+ . Partial cross sections for excitation of the 3p level of sodium at energies just above threshold calculated using a four-state close-coupling approach, including both total cross sections and those for excitation as a function of the change in the spin and orbital angular momentum projection quantum numbers of the target electron. Generalization of our electron-molecule scattering code to carry out full vibrational close-coupling calculations with an exact treatment of exchange and with a parameter-free representation of correlation and polarization interactions, and application to HF and H 2

  15. Analyses of Non-bonding Length, Partial Atomics Charge and Electrostatic Energy from Molecular Dynamics Simulation of Phospholipase A2 – Substrate

    Directory of Open Access Journals (Sweden)

    Nirwan Syarif

    2016-11-01

    Full Text Available This paper reports molecular dynamics simulation of phospholipase A2 (PLA2– substrate that has been done. Non-bonding length, partial atomic charge and electrostatic energy were used to evaluation the interaction between PLA2 and substrate. The research was subjected for three types of PLA2 of different sources, i.e, homo sapien, bovinus and porcinus, by using computer files of their molecular structures. The files with code 3elo, 1bp2, dan 1y6o were downloaded from protein data bank. Substrate structure can be found in 1y60 and was separated from its enzyme structure and docked into two other PLA2 structures for simulation purpose. Molecular dynamics simulations were done for 30000 steps with constant in number of molecules, volume and temperature (NVT. The results showed the existing of flip-flop mechanism as basic feature of PLA2 – substrate reactions. Interaction length analysis results indicated the presence of water molecules on the structures of 1bp2 and 3elo at the time of the simulation was completed. The existence of aspagine at the reaction site confirmed the theory that this amino acid is responsible for the survival of the reaction. the electrostatic energy increased substantially in the interaction after homo sapien PLA2 (3elo and Bovinus (1bp2 with the substrate. Inverse effect took place in the PLA porcinus (1y6o.

  16. Development of constraint algorithm for the number of electrons in molecular orbitals consisting mainly 4f atomic orbitals of rare-earth elements and its introduction to tight-binding quantum chemical molecular dynamics method

    International Nuclear Information System (INIS)

    Endou, Akira; Onuma, Hiroaki; Jung, Sun-ho

    2007-01-01

    Our original tight-binding quantum chemical molecular dynamics code, Colors', has been successfully applied to the theoretical investigation of complex materials including rare-earth elements, e.g., metal catalysts supported on a CeO 2 surface. To expand our code so as to obtain a good convergence for the electronic structure of a calculation system including a rare-earth element, we developed a novel algorithm to provide a constraint condition for the number of electrons occupying the selected molecular orbitals that mainly consist of 4f atomic orbitals of the rare-earth element. This novel algorithm was introduced in Colors. Using Colors, we succeeded in obtaining the classified electronic configurations of the 4f atomic orbitals of Ce 4+ and reduced Ce ions in a CeO 2 bulk model with one oxygen defect, which makes it difficult to obtain a good convergence using a conventional first-principles quantum chemical calculation code. (author)

  17. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

    Science.gov (United States)

    Prior, C; Danilāne, L; Oganesyan, V S

    2018-05-16

    We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

  18. A Molecular Dynamics of Cold Neutral Atoms Captured by Carbon Nanotube Under Electric Field and Thermal Effect as a Selective Atoms Sensor.

    Science.gov (United States)

    Santos, Elson C; Neto, Abel F G; Maneschy, Carlos E; Chen, James; Ramalho, Teodorico C; Neto, A M J C

    2015-05-01

    Here we analyzed several physical behaviors through computational simulation of systems consisting of a zig-zag type carbon nanotube and relaxed cold atoms (Rb, Au, Si and Ar). These atoms were chosen due to their different chemical properties. The atoms individually were relaxed on the outside of the nanotube during the simulations. Each system was found under the influence of a uniform electric field parallel to the carbon nanotube and under the thermal effect of the initial temperature at the simulations. Because of the electric field, the cold atoms orbited the carbon nanotube while increasing the initial temperature allowed the variation of the radius of the orbiting atoms. We calculated the following quantities: kinetic energy, potential energy and total energy and in situ temperature, molar entropy variation and average radius of the orbit of the atoms. Our data suggest that only the action of electric field is enough to generate the attractive potential and this system could be used as a selected atoms sensor.

  19. Modelling the local atomic structure of molybdenum in nuclear waste glasses with ab initio molecular dynamics simulations.

    Science.gov (United States)

    Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M

    2016-09-21

    The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO 2 ) 57.5 -(B 2 O 3 ) 10 -(Na 2 O) 15 -(CaO) 15 -(MoO 3 ) 2.5 and (SiO 2 ) 57.3 -(B 2 O 3 ) 20 -(Na 2 O) 6.8 -(Li 2 O) 13.4 -(MoO 3 ) 2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na 2 MoO 4 and CaMoO 4 ). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.

  20. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

    Science.gov (United States)

    Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie

    2011-08-10

    Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation

  1. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

    Directory of Open Access Journals (Sweden)

    Toofanny Rudesh D

    2011-08-01

    Full Text Available Abstract Background Molecular dynamics (MD simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster. For a 'full' simulation trajectory (51 ns spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster. Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36% was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery

  2. 2010 Atomic & Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Todd Martinez

    2010-07-23

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

  3. Atomic and molecular science with synchrotron radiation

    International Nuclear Information System (INIS)

    1989-01-01

    This paper discusses the following topics: electron correlation in atoms; atomic innershell excitation and decay mechanisms; timing experiments; x-ray scattering; properties of ionized species; electronic properties of actinide atoms; total photon-interaction cross sections; and molecular physics. 66 refs

  4. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Bederson, Benjamin

    1993-01-01

    Advances in Atomic, Molecular, and Optical Physics, established in 1965, continues its tradition of excellence with Volume 32, published in honor of Founding Editor Sir David Bates upon his retirement as editorof the series. This volume presents reviews of topics related to the applications of atomic and molecular physics to atmospheric physics and astrophysics.

  5. Molecular dynamics study of silver

    International Nuclear Information System (INIS)

    Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

    1995-03-01

    We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

  6. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

    Science.gov (United States)

    Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

    2016-06-16

    Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration

  7. Heavy Atom Substituents as Molecular Probes for Solvent Effects on the Dynamics of Short-lived Triplet Exciplexes

    OpenAIRE

    Winter, Gerhard; Steiner, Ulrich

    1980-01-01

    The influence of heavy atom substituents (Br, I) in the electron donor aniline on the electron transfer reaction with thiopyronine triplet is investigated by flash spectroscopy in solvents of different viscosity and polarity. Triplet quenching constants and radical yields are determined. The results are analysed in terms of decay constants of an intermediate triplet exciplex where the heavy atom substituents significantly enhance the intersystem crossing process leading to singlet ground stat...

  8. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

    Science.gov (United States)

    Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

  9. Pharmacophore generation, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on benzamide analogues as FtsZ inhibitors.

    Science.gov (United States)

    Tripathy, Swayansiddha; Azam, Mohammed Afzal; Jupudi, Srikanth; Sahu, Susanta Kumar

    2017-10-11

    FtsZ is an appealing target for the design of antimicrobial agent that can be used to defeat the multidrug-resistant bacterial pathogens. Pharmacophore modelling, molecular docking and molecular dynamics (MD) simulation studies were performed on a series of three-substituted benzamide derivatives. In the present study a five-featured pharmacophore model with one hydrogen bond acceptors, one hydrogen bond donors, one hydrophobic and two aromatic rings was developed using 97 molecules having MIC values ranging from .07 to 957 μM. A statistically significant 3D-QSAR model was obtained using this pharmacophore hypothesis with a good correlation coefficient (R 2  = .8319), cross validated coefficient (Q 2  = .6213) and a high Fisher ratio (F = 103.9) with three component PLS factor. A good correlation between experimental and predicted activity of the training (R 2  = .83) and test set (R 2  = .67) molecules were displayed by ADHRR.1682 model. The generated model was further validated by enrichment studies using the decoy test and MAE-based criteria to measure the efficiency of the model. The docking studies of all selected inhibitors in the active site of FtsZ protein showed crucial hydrogen bond interactions with Val 207, Asn 263, Leu 209, Gly 205 and Asn-299 residues. The binding free energies of these inhibitors were calculated by the molecular mechanics/generalized born surface area VSGB 2.0 method. Finally, a 15 ns MD simulation was done to confirm the stability of the 4DXD-ligand complex. On a wider scope, the prospect of present work provides insight in designing molecules with better selective FtsZ inhibitory potential.

  10. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    International Nuclear Information System (INIS)

    Cortini, Ruggero; Cheng, Xiaolin

    2017-01-01

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of 1k B T. Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

  11. Effects of spin orbital coupling on atomic and electronic structures in Al2Cu and Al2Au crystal and liquid phases via ab initio molecular dynamics simulations

    International Nuclear Information System (INIS)

    Wang, Y.; Lu, Y.H.; Wang, X.D.; Cao, Q.P.; Zhang, D.X.; Jiang, J.Z.

    2014-01-01

    Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al 2 Cu and Al 2 Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al 2 Cu and Al 2 Au

  12. Atomic and molecular beams production and collimation

    CERN Document Server

    Lucas, Cyril Bernard

    2013-01-01

    Atomic and molecular beams are employed in physics and chemistry experiments and, to a lesser extent, in the biological sciences. These beams enable atoms to be studied under collision-free conditions and allow the study of their interaction with other atoms, charged particles, radiation, and surfaces. Atomic and Molecular Beams: Production and Collimation explores the latest techniques for producing a beam from any substance as well as from the dissociation of hydrogen, oxygen, nitrogen, and the halogens.The book not only provides the basic expressions essential to beam design but also offers

  13. An investigation of the sites occupied by atomic barium in solid xenon—A 2D-EE luminescence spectroscopy and molecular dynamics study

    Science.gov (United States)

    Davis, Barry M.; Gervais, Benoit; McCaffrey, John G.

    2018-03-01

    A detailed characterisation of the luminescence recorded for the 6p 1P1-6s 1S0 transition of atomic barium isolated in annealed solid xenon has been undertaken using two-dimensional excitation-emission (2D-EE) spectroscopy. In the excitation spectra extracted from the 2D-EE scans, two dominant thermally stable sites were identified, consisting of a classic, three-fold split Jahn-Teller band, labeled the blue site, and an unusual asymmetric 2 + 1 split band, the violet site. A much weaker band has also been identified, whose emission is strongly overlapped by the violet site. The temperature dependence of the luminescence for these sites was monitored revealing that the blue site has a non-radiative channel competing effectively with the fluorescence even at 9.8 K. By contrast, the fluorescence decay time of the violet site was recorded to be 4.3 ns and independent of temperature up to 24 K. The nature of the dominant thermally stable trapping sites was investigated theoretically with Diatomics-in-Molecule (DIM) molecular dynamics simulations. The DIM model was parameterized with ab initio multi-reference configuration interaction calculations for the lowest energy excited states of the BaṡXe pair. The simulated absorption spectra are compared with the experimental results obtained from site-resolved excitation spectroscopy. The simulations allow us to assign the experimental blue feature spectrum to a tetra-vacancy trapping site in the bulk xenon fcc crystal—a site often observed when trapping other metal atoms in rare gas matrices. By contrast, the violet site is assigned to a specific 5-atom vacancy trapping site located at a grain boundary.

  14. Dynamics in atomic signaling games

    KAUST Repository

    Fox, Michael J.

    2015-04-08

    We study an atomic signaling game under stochastic evolutionary dynamics. There are a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with high probability or mutate with low probability. We analyze the long-run distribution of states and show that, for sufficiently small mutation probability, its support is limited to efficient communication systems. We find that this behavior is insensitive to the particular choice of evolutionary dynamic, a property that is due to the game having a potential structure with a potential function corresponding to average fitness. Consequently, the model supports conclusions similar to those found in the literature on language competition. That is, we show that efficient languages eventually predominate the society while reproducing the empirical phenomenon of linguistic drift. The emergence of efficiency in the atomic case can be contrasted with results for non-atomic signaling games that establish the non-negligible possibility of convergence, under replicator dynamics, to states of unbounded efficiency loss.

  15. Dynamics in atomic signaling games

    KAUST Repository

    Fox, Michael J.; Touri, Behrouz; Shamma, Jeff S.

    2015-01-01

    We study an atomic signaling game under stochastic evolutionary dynamics. There are a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with high probability or mutate with low probability. We analyze the long-run distribution of states and show that, for sufficiently small mutation probability, its support is limited to efficient communication systems. We find that this behavior is insensitive to the particular choice of evolutionary dynamic, a property that is due to the game having a potential structure with a potential function corresponding to average fitness. Consequently, the model supports conclusions similar to those found in the literature on language competition. That is, we show that efficient languages eventually predominate the society while reproducing the empirical phenomenon of linguistic drift. The emergence of efficiency in the atomic case can be contrasted with results for non-atomic signaling games that establish the non-negligible possibility of convergence, under replicator dynamics, to states of unbounded efficiency loss.

  16. Molecular dynamics study on atomic elastic stiffness in Si under tension: homogenization by external loading and its limit

    International Nuclear Information System (INIS)

    Yashiro, K; Fujihara, M

    2012-01-01

    As a series of studies that discuss the onset of inelastic deformation based on atomic elastic stiffness (AES), we investigated the AES in silicon by the Tersoff interatomic potential. For a comprehensive discussion including the effect of structural inhomogeneity by surface and grain boundaries, we performed tensile simulations on bulk/nanowire of Si single crystal, laminate bulk/bamboo nanowire with Σ5 twist grain boundary under a very low temperature (T = 1 K). Not only the stress–strain response, but also the AESs at each atom point, B ij α , were evaluated numerically by Δσ i α /Δε j (Voigt notation) against local strain perturbation. The deviation of detB ij α vanishes/diminishes by tension both in the homogeneous case of bulk perfect lattice and inhomogeneous ones with surface and grain boundaries; however, there is a certain limit for the homogenization. That is, the subtle deviation of AES in the perfect bulk vanishes by tension but it increases again like an onset of resonance, showing precursor stress decrease just before the unstable stress drop. In the inhomogeneous cases, we demonstrated that the near-zero AESs at the initial structural defects, e.g. surface or grain boundary, do not change but the positive AESs of other stable atoms approach zero by tension. When these distributions overlap each other, the standard deviation of AES increases again as if it were the first homogenization limit. However, the real homogenization starts at that point; that is, the AES distribution changes its shape to have a single peak at the detB ij α =0 border, suggesting that the difference of initial defects and other stable part vanishes before the system instability. (paper)

  17. Atomic and molecular data for radiotherapy

    International Nuclear Information System (INIS)

    Okamoto, K.

    1989-03-01

    This is the summary report of the First Research Co-ordination Meeting of the IAEA Co-ordinated Research Programme (CRP) on Atomic and Molecular Data for Radiotherapy, convened by the IAEA Nuclear Data Section in Vienna, from 30 January to 2 February 1989. The main objectives of the CRP are to generate, compile and evaluate the important atomic and molecular data relevant to radiotherapy. (author). 38 refs, 7 figs, 10 tabs

  18. Atomic and molecular processes in fusion plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Janev, R.K. [International Atomic Energy Agency, Vienna (Austria)

    1997-01-01

    The role of atomic and molecular processes in achieving and maintaining the conditions for thermonuclear burn in a magnetically confined fusion plasma is described. Emphasis is given to the energy balance and power and particle exhaust issues. The most important atomic and molecular processes which affect the radiation losses and impurity transport in the core plasma, the neutral particle transport in the plasma edge and the radiative cooling of divertor plasmas are discussed in greater detail. (author)

  19. Lasers in atomic, molecular and nuclear physics

    International Nuclear Information System (INIS)

    Letokhov, V.S.

    1986-01-01

    This book presents papers on laser applications in atomic, molecular and nuclear physics. Specifically discussed are: laser isotope separation; laser spectroscopy of chlorophyll; laser spectroscopy of molecules and cell membranes; laser detection of atom-molecule collisions and lasers in astrophysics

  20. 1985 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  1. 1984 Bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

    1985-04-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  2. Bibliography of atomic and molecular processes, 1983

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  3. Bibliography of atomic and molecular processes, 1983

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  4. 1982 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  5. 1985 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  6. 1978 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  7. 1982 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  8. 1979 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1980-08-01

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  9. 1980 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1982-02-01

    This annotated bibliography lists 2866 works on atomic and molecular processes reported in publications dated 1980. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  10. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Berman, Paul R; Arimondo, Ennio

    2006-01-01

    Volume 54 of the Advances Series contains ten contributions, covering a diversity of subject areas in atomic, molecular and optical physics. The article by Regal and Jin reviews the properties of a Fermi degenerate gas of cold potassium atoms in the crossover regime between the Bose-Einstein condensation of molecules and the condensation of fermionic atom pairs. The transition between the two regions can be probed by varying an external magnetic field. Sherson, Julsgaard and Polzik explore the manner in which light and atoms can be entangled, with applications to quantum information processing

  11. Molecular dynamics simulation for the influence of incident angles of energetic carbon atoms on the structure and properties of diamond-like carbon films

    International Nuclear Information System (INIS)

    Li, Xiaowei; Ke, Peiling; Lee, Kwang-Ryeol; Wang, Aiying

    2014-01-01

    The influence of incident angles of energetic carbon atoms (0–60°) on the structure and properties of diamond-like carbon (DLC) films was investigated by the molecular dynamics simulation using a Tersoff interatomic potential. The present simulation revealed that as the incident angles increased from 0 to 60°, the surface roughness of DLC films increased and the more porous structure was generated. Along the growth direction of DLC films, the whole system could be divided into four regions including substrate region, transition region, stable region and surface region except the case at the incident angle of 60°. When the incident angle was 45°, the residual stress was significantly reduced by 12% with little deterioration of mechanical behavior. The further structure analysis using both the bond angles and bond length distributions indicated that the compressive stress reduction mainly resulted from the relaxation of highly distorted C–C bond length. - Highlights: • The dependence of films properties on different incident angles was investigated. • The change of incident angles reduced the stress without obvious damage of density. • The stress reduction attributed to the relaxation of highly distorted bond length

  12. Line emission processes in atomic and molecular shocks

    International Nuclear Information System (INIS)

    Shull, J.M.

    1988-01-01

    The review discusses the observations and theoretical models of interstellar shock waves in diffuse and molecular clouds. After summarizing the relevant gas dynamics, atomic, molecular and grain processes, and physics of radiative and magnetic precursors, the author describes observational diagnostics of shocks. This paper concludes with a discussion of two topics: unstable or non-steady shocks and thermal conduction in metal-rich shocks

  13. Molecular dynamics for fermions

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    2000-02-01

    The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

  14. Atomic and molecular data for radiotherapy

    International Nuclear Information System (INIS)

    1989-05-01

    An Advisory Group Meeting devoted solely to review the atomic and molecular data needed for radiotherapy was held in Vienna from 13 to 16 June 1988. The following items as related to the atoms and molecules of human tissues were reviewed: Cross sections differential in energy loss for electrons and other charged particles. Secondary electron spectra, or differential ionization cross sections. Total cross sections for ionization and excitation. Subexcitation electrons. Cross sections for charged-particle collisions in condensed matter. Stopping power for low-energy electrons and ions. Initial yields of atomic and molecular ions and their excited states and electron degradation spectra. Rapid conversion of these initial ions and their excited states through thermal collisions with other atoms and molecules. Track-structure quantities. Other relevant data. Refs, figs and tabs

  15. The fundamentals of atomic and molecular physics

    CERN Document Server

    Brooks, Robert L

    2013-01-01

    The Fundamentals of Atomic and Molecular Physics is intended as an introduction to the field for advanced undergraduates who have taken quantum mechanics. Each chapter builds upon the previous, using the same tools and methods throughout. As the students progress through the book, their ability to use these tools will steadily increase, along with their confidence in their efficacy. The book treats the two-electron atom as the simplest example of the many-electron atom—as opposed to using techniques that are not applicable to many-electron atoms—so that it is unnecessary to develop additional equations when turning to multielectron atoms, such as carbon. External fields are treated using both perturbation theory and direct diagonalization and spontaneous emission is developed from first principles. Only diatomic molecules are considered with the hydrogen molecular ion and neutral molecule treated in some detail. This comprehensive coverage of the quantum mechanics of complex atoms and simple diatomic mole...

  16. Molecular-dynamics simulation of lateral friction in contact-mode atomic force microscopy of alkane films: The role of molecular flexibility

    DEFF Research Database (Denmark)

    Soza, P.; Hansen, Flemming Yssing; Taub, H.

    2011-01-01

    than on a surface of molecules with the long axis perpendicular to the surface, in agreement with experimental results. A major dissipation mechanism is the molecular flexibility as manifested in the torsional motion about the molecules' C-C bonds. The generation of gauche defects as a result...

  17. Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Haruki Nakamura

    2012-02-01

    Full Text Available The phosphorylated kinase-inducible activation domain (pKID adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity; the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.

  18. Atomic and Molecular Manipulation of Chemical Interactions

    National Research Council Canada - National Science Library

    Ho, Wilson

    2007-01-01

    .... In effect, the goal is to carry out chemical changes by manipulating individual atoms and molecules to induce different bonding geometry and to create new interactions with their environment. These studies provide the scientific basis for the advancement of technology in catalysis, molecular electronics, optics, chemical and biological sensing, and magnetic storage.

  19. Atomic and molecular adsorption on Rh(111)

    DEFF Research Database (Denmark)

    Mavrikakis, Manos; Rempel, J.; Greeley, Jeffrey Philip

    2002-01-01

    A systematic study of the chemisorption of both atomic (H, O, N, S, C), molecular (N-2, CO, NO), and radical (CH3, OH) species on Rh(111) has been performed. Self-consistent, periodic, density functional theory (DFT-GGA) calculations, using both PW91 and RPBE functionals, have been employed to de...

  20. Atomic and molecular phases through attosecond streaking

    DEFF Research Database (Denmark)

    Baggesen, Jan Conrad; Madsen, Lars Bojer

    2011-01-01

    phase of the atomic or molecular ionization matrix elements from the two states through the interference from the two channels. The interference may change the phase of the photoelectron streaking signal within the envelope of the infrared field, an effect to be accounted for when reconstructing short...... pulses from the photoelectron signal and in attosecond time-resolved measurements....

  1. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    1999-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics.

  2. On the dynamical supersymmetry of atomic hydrogen

    International Nuclear Information System (INIS)

    Slepchenko, L.A.

    1986-01-01

    In the framework of supersymmetric quantum mechanics a dynamical symmetry of the hydrogen atom is considered. New features of spectra for the dynamical supersymmetry of two-dimensional Kepler problem are found

  3. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

  4. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  5. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  6. The nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1992-03-01

    MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

  7. 2004 Atomic and Molecular Interactions Gordon Research Conference

    International Nuclear Information System (INIS)

    Dr. Paul J. Dagdigian

    2004-01-01

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference

  8. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  9. Orthonormal Wavelet Bases for Quantum Molecular Dynamics

    International Nuclear Information System (INIS)

    Tymczak, C.; Wang, X.

    1997-01-01

    We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

  10. Molecular dynamics simulations

    International Nuclear Information System (INIS)

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

  11. Atomic and molecular science: progress and opportunities

    International Nuclear Information System (INIS)

    Mathur, D.

    2000-01-01

    In the contemporary scenario, atomic, molecular and optical (AMO) science focuses on the physical and chemical properties of the common building blocks of matter - atoms, molecules and light. The main characteristic of AMO science is that it is both an intellectually stimulating fundamental science and a powerful enabling science that supports an increasing number of other important areas of science and technology. In brief, the fundamental interests in atoms, molecules and clusters (as well as their ions) include studies of their structure and properties, their optical interactions, collisional properties, including quantum state-resolved studies, and interactions with external fields, solids and surfaces. Fundamental aspects of present-day optical sciences include studies of laser spectroscopy, nonlinear optics, quantum optics, optical interactions with condensed matter, ultrafast optics and coherent light sources. The enabling aspect of AMO science derives from efforts to control atoms, molecules, clusters, charged particles and light more precisely, to accurately to determine, experimentally and theoretically, their properties, and to invent new, methods of generating light with tailor-made properties

  12. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    2005-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered include related applied areas, such as atmospheric science, astrophysics, surface physics and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments. · Reviews timely fields of atomic physics · Articles written by world leaders in those fields · In depth review of the subject with relevant literature · Suitable for researchers in other fields · Only book series of this kind.

  13. Atomic, molecular, and optical physics charged particles

    CERN Document Server

    Dunning, F B

    1995-01-01

    With this volume, Methods of Experimental Physics becomes Experimental Methods in the Physical Sciences, a name change which reflects the evolution of todays science. This volume is the first of three which will provide a comprehensive treatment of the key experimental methods of atomic, molecular, and optical physics; the three volumes as a set will form an excellent experimental handbook for the field. The wide availability of tunable lasers in the pastseveral years has revolutionized the field and lead to the introduction of many new experimental methods that are covered in these volumes. Traditional methods are also included to ensure that the volumes will be a complete reference source for the field.

  14. Atomic, molecular, and optical physics electromagnetic radiation

    CERN Document Server

    Dunning, F B; Lucatorto, Thomas

    1997-01-01

    Combined with Volumes 29A and 29B, this volume is a comprehensive treatment of the key experimental methods of atomic, molecular, and optical physics, as well as an excellent experimental handbook for the field. Thewide availability of tunable lasers in the past several years has revolutionized the field and lead to the introduction of many new experimental methods that are covered in these volumes. Traditional methods are also included to ensure that the volumes will be a complete reference source for the field.

  15. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    2001-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

  16. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    1998-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material as well as detailed descriptions of important recent developments.

  17. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    2000-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular, and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered also include related applied areas, such as atmospheric science, astrophysics, surface physics, and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

  18. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Walther, Herbert; Walther, Herbert

    2002-01-01

    This series, established in 1965, is concerned with recent developments in the general area of atomic, molecular and optical physics. The field is in a state of rapid growth, as new experimental and theoretical techniques are used on many old and new problems. Topics covered include related applied areas, such as atmospheric science, astrophysics, surface physics and laser physics. Articles are written by distinguished experts who are active in their research fields. The articles contain both relevant review material and detailed descriptions of important recent developments.

  19. Molecular Dynamics and Bioactivity of a Novel Mutated Human ...

    African Journals Online (AJOL)

    Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...

  20. Electron-nuclear dynamics of molecular systems

    International Nuclear Information System (INIS)

    Diz, A.; Oehrn, Y.

    1994-01-01

    The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

  1. International bulletin on atomic and molecular data for fusion

    International Nuclear Information System (INIS)

    Stephens, J.A.; Bannister, M.E.; Fuhr, J.

    1999-12-01

    The International Bulletin on Atomic and Molecular Data for Fusion is prepared by the Atomic and Molecular Data Unit of the International Atomic Energy Agency. It is distributed free of charge by the IAEA to assist in the development of fusion research and technology. In part 1, the Atomic and Molecular Data Information System (AMDIS) is presented. In Part 2, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Finally, the Author Index (part 4) refers to the bibliographic references contained in part 3

  2. Advances in molecular vibrations and collision dynamics molecular clusters

    CERN Document Server

    Bacic, Zatko

    1998-01-01

    This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

  3. Atomic and molecular adsorption on Fe(110)

    Science.gov (United States)

    Xu, Lang; Kirvassilis, Demetrios; Bai, Yunhai; Mavrikakis, Manos

    2018-01-01

    Iron is the principal catalyst for the ammonia synthesis process and the Fischer-Tropsch process, as well as many other heterogeneously catalyzed reactions. It is thus of fundamental importance to understand the interactions between the iron surface and various reaction intermediates. Here, we present a systematic study of atomic and molecular adsorption behavior over Fe(110) using periodic, self-consistent density functional theory (DFT-GGA) calculations. The preferred binding sites, binding energies, and the corresponding surface deformation energies of five atomic species (H, C, N, O, and S), six molecular species (NH3, CH4, N2, CO, HCN, and NO), and eleven molecular fragments (CH, CH2, CH3, NH, NH2, OH, CN, COH, HCO, NOH, and HNO) were determined on the Fe(110) surface at a coverage of 0.25 monolayer. The binding strengths calculated using the PW91 functional decreased in the following order: C > CH >N > O > S > NH > COH > CN > CH2 > NOH > OH > HNO > HCO > NH2 > H > NO > HCN > CH3 > CO > N2 > NH3. No stable binding structures were observed for CH4. The estimated diffusion barriers and pathways, as well as the adsorbate-surface and intramolecular vibrational modes of all the adsorbates at their preferred binding sites, were identified. Using the calculated adsorption energetics, we constructed the potential energy surfaces for a few surface reactions including the decomposition of methane, ammonia, dinitrogen, carbon monoxide, and nitric oxide. These potential energy surfaces provide valuable insight into the ability of Fe(110) to catalyze common elementary steps.

  4. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules.

    Science.gov (United States)

    Ren, Pengyu; Wu, Chuanjie; Ponder, Jay W

    2011-10-11

    An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.

  5. DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

    NARCIS (Netherlands)

    JUFFER, AH; BERENDSEN, HJC

    1993-01-01

    A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

  6. Chemical reaction dynamics of Rydberg atoms with neutral molecules: A comparison of molecular-beam and classical trajectory results for the H(n)+D2→HD+D(n') reaction

    International Nuclear Information System (INIS)

    Song Hui; Dai Dongxu; Wu Guorong; Wang, C.-C.; Harich, Steven A.; Hayes, Michael Y.; Wang Xiuyan; Gerlich, Dieter; Yang Xueming; Skodje, Rex T.

    2005-01-01

    Recent molecular-beam experiments have probed the dynamics of the Rydberg-atom reaction, H(n)+D 2 →HD+D(n) at low collision energies. It was discovered that the rotationally resolved product distribution was remarkably similar to a much more limited data set obtained at a single scattering angle for the ion-molecule reaction H + +D 2 →D + +HD. The equivalence of these two problems would be consistent with the Fermi-independent-collider model (electron acting as a spectator) and would provide an important new avenue for the study of ion-molecule reactions. In this work, we employ a classical trajectory calculation on the ion-molecule reaction to facilitate a more extensive comparison between the two systems. The trajectory simulations tend to confirm the equivalence of the ion+molecule dynamics to that for the Rydberg-atom+molecule system. The theory reproduces the close relationship of the two experimental observations made previously. However, some differences between the Rydberg-atom experiments and the trajectory simulations are seen when comparisons are made to a broader data set. In particular, the angular distribution of the differential cross section exhibits more asymmetry in the experiment than in the theory. The potential breakdown of the classical model is discussed. The role of the 'spectator' Rydberg electron is addressed and several crucial issues for future theoretical work are brought out

  7. Molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Dehmer, J.L.

    1982-01-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed

  8. Applications in atomic and molecular physics

    International Nuclear Information System (INIS)

    Todd, J.F.J.

    1976-01-01

    Probably the most extensive area of application of quadrupole mass spectrometry has been that of atomic and molecular physics: it was for this market that the commercial instruments were first introduced and the variety of investigations which have consequently been made possible provides an obvious basis for illustrating the unique features possessed by the mass filter. The account which follows is divided into two main sections. The first deals with general applications of the quadrupole, in which the instrument is used essentially as an analyser for neutral or ionic species, e.g. the monitoring of residual gases and reaction products. The fields of vacuum technology, surface studies and gas phase studies are considered in turn. The second section is devoted to an account of the special applications of quadrupole fields in which use is made of properties such as ion containment. (Auth.)

  9. Delocalized electrons in atomic and molecular nanoclusters

    Energy Technology Data Exchange (ETDEWEB)

    Kresin, Vitaly [Univ. of Southern California, Los Angeles, CA (United States)

    2018-01-17

    The aim of the award (Program director: Dr. Mark Pederson) was to facilitate the attendance of researchers, students, and postdocs from the U.S. at the international workshop co-organized by the applicant. The award succeeded in making it possible for a number of US attendees to present their work and participate in the meeting, which was a significant event in the research community at the interdisciplinary interface of physical chemistry, nanoscience, atomic and molecular physics, condensed matter physics, and spectroscopy. The workshop did not issue proceedings, but the present report includes present the schedule, the abstracts, and the attendance list of the July 2016 Workshop. DOE sponsorship is gratefully acknowledged in the program.

  10. Molecular dynamics simulation of defect formation during energetic Cu deposition

    International Nuclear Information System (INIS)

    Gilmore, Charles M.; Sprague, James A.

    2002-01-01

    The deposition of energetic Cu atoms from 5 to 80 eV onto (0 0 1) Cu was simulated with molecular dynamics. The Cu-Cu interaction potential was a spline of the embedded atom potential developed from equilibrium data, and the universal scattering potential. Incident Cu atoms substituted for first layer substrate atoms by an exchange process at energies as low as 5 eV. Incident Cu atoms of 20 eV penetrated to the second substrate layer, and 20 eV was sufficient energy to produce interstitial defects. Incident atoms of 80 eV penetrated to the third atomic layer, produced interstitials 12 atomic layers into the substrate by focused replacement collision sequences, and produced sputtered atoms with a 16% yield. Interstitial clusters of up to 7 atoms were observed. The observed mechanisms of film growth included: the direct deposition of atoms into film equilibrium atom positions, the exchange of substrate atoms to equilibrium film atoms positions, and the migration of interstitials to equilibrium film atom positions. The relative frequency of each process was a function of incident energy. Since all observed growth mechanisms resulted in film atoms in equilibrium atomic positions, these simulations suggest that stresses in homoepitaxial Cu thin films are due to point defects. Vacancies would produce tensile strain and interstitial atoms would produce compressive strain in the films. It is proposed that immobile interstitial clusters could be responsible for retaining interstitial atoms and clusters in growing metal thin films

  11. Atomic insight into tribochemical wear mechanism of silicon at the Si/SiO{sub 2} interface in aqueous environment: Molecular dynamics simulations using ReaxFF reactive force field

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Jialin; Ma, Tianbao [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Zhang, Weiwei; Psofogiannakis, George; Duin, Adri C.T. van [Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, PA 16802 (United States); Chen, Lei; Qian, Linmao [Tribology Research Institute, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031 (China); Hu, Yuanzhong [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Lu, Xinchun, E-mail: xclu@tsinghua.edu.cn [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China)

    2016-12-30

    Highlights: • New ReaxFF reactive force field was applied to simulate the tribochemical wear process at Si/SiO{sub 2} interface. • Wear of silicon atoms is due to the breaking of Si–O–Si bonds and Si–Si–O–Si bond chains on the Si substrate. • Interfacial bridge bonds play an important role during the tribochemical wear process. • Higher pressures applied to the silica phase can cause more Si atoms to be removed by forming more interfacial bridge bonds. • Water plays an opposing role in the wear process because of its both chemical and mechanical effects. - Abstract: In this work, the atomic mechanism of tribochemical wear of silicon at the Si/SiO{sub 2} interface in aqueous environment was investigated using ReaxFF molecular dynamics (MD) simulations. Two types of Si atom removal pathways were detected in the wear process. The first is caused by the destruction of stretched Si–O–Si bonds on the Si substrate surface and is assisted by the attachment of H atoms on the bridging oxygen atoms of the bonds. The other is caused by the rupture of Si–Si bonds in the stretched Si–Si–O–Si bond chains at the interface. Both pathways effectively remove Si atoms from the silicon surface via interfacial Si–O–Si bridge bonds. Our simulations also demonstrate that higher pressures applied to the silica phase can cause more Si atoms to be removed due to the formation of increased numbers of interfacial Si–O–Si bridge bonds. Besides, water plays a dual role in the wear mechanism, by oxidizing the Si substrate surface as well as by preventing the close contact of the surfaces. This work shows that the removal of Si atoms from the substrate is a result of both chemical reaction and mechanical effects and contributes to the understanding of tribochemical wear behavior in the microelectromechanical systems (MEMS) and Si chemical mechanical polishing (CMP) process.

  12. Computational challenges in atomic, molecular and optical physics.

    Science.gov (United States)

    Taylor, Kenneth T

    2002-06-15

    Six challenges are discussed. These are the laser-driven helium atom; the laser-driven hydrogen molecule and hydrogen molecular ion; electron scattering (with ionization) from one-electron atoms; the vibrational and rotational structure of molecules such as H(3)(+) and water at their dissociation limits; laser-heated clusters; and quantum degeneracy and Bose-Einstein condensation. The first four concern fundamental few-body systems where use of high-performance computing (HPC) is currently making possible accurate modelling from first principles. This leads to reliable predictions and support for laboratory experiment as well as true understanding of the dynamics. Important aspects of these challenges addressable only via a terascale facility are set out. Such a facility makes the last two challenges in the above list meaningfully accessible for the first time, and the scientific interest together with the prospective role for HPC in these is emphasized.

  13. Physical adsorption and molecular dynamics

    International Nuclear Information System (INIS)

    Cohan, N.V.

    1981-01-01

    Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

  14. Toluene model for molecular dynamics simulations in the ranges 298

    NARCIS (Netherlands)

    Fioroni, M.; Vogt, D.

    2004-01-01

    An all-atom model for toluene is presented in the framework of classical molecular dynamics (MD). The model has been parametrized under the GROMOS96 force field to reproduce the physicochemical properties of the neat liquid. Four new atom types have been introduced, distinguishing between carbons

  15. Chirality in molecular collision dynamics

    Science.gov (United States)

    Lombardi, Andrea; Palazzetti, Federico

    2018-02-01

    Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

  16. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

    Niemelä, Perttu S; Hyvönen, Marja T; Vattulainen, Ilpo

    2009-01-01

    We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular...... dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis...... examples of this issue. The third part concentrates on the specificity of intermolecular interactions in three-component mixtures of SM, PC and cholesterol (CHOL) under conditions where the concentrations of SM and CHOL are dilute with respect to that of PC. The results show how SM and CHOL favor one...

  17. Theoretical atomic and molecular physics: Progress report, July 1, 1988 through June 30, 1989

    International Nuclear Information System (INIS)

    Lane, N.F.

    1989-01-01

    The theoretical atomic and molecular physics program at Rice University emphasizes fundamental questions regarding the structure and collision dynamics of various atomic and molecular systems with some attention given to atomic processes at surfaces. Our activities have been centered on continuing the projects initiated last year as well as beginning some new studies. These include: differential elastic and charge-transfer scattering and alignment and orientation of the excited electron cloud in ion-atom, atom-atom and ion-molecule collisions, using a molecular-orbital representation and both semiclassical and quantal methods; quenching of low-lying Rydberg states of a sodium atom in a collision with a rare-gas atom, using a semiclassical representation; so far, target atoms He, Ne and Ar have been studied; chemiionization and ion-pair formation in a collision of a Li atom with a metastable He atom at intermediate collision energies, using a combination of quantal and semi-classical methods; Penning ionization of alkali atoms Na and K, using advanced Cl and Stieltjes imaging methods; radiative and nonradiative charge-transfer in He + + H collisions at ultra-low collision energies, using quantal methods; elastic and inelastic processes in electron-molecule collisions, using the continuum-multiple-scattering method; and inelastic collision processes in dense, high-temperature plasmas. Selected highlights of our research progress are briefly summarized in this paper

  18. Thermal transpiration: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  19. Examples how to use atomic and molecular databases

    International Nuclear Information System (INIS)

    Murakami, Izumi

    2012-01-01

    As examples how to use atomic and molecular databases, atomic spectra database (ASD) and molecular chemical kinetics database of National Institute of Standards and Technology (NIST), collision cross sections of National Institute of Fusion Science (NIFS), Open-Atomic Data and Analysis Structure (ADAS) and chemical reaction rate coefficients of GRI-Mech were presented. Sorting method differed in each database and several options were prepared. Atomic wavelengths/transition probabilities and electron collision ionization, excitation and recombination cross sections/rate coefficients were simply searched with just specifying atom or ion using a general internet search engine (GENIE) of IAEA. (T. Tanaka)

  20. Laser manipulation of atomic and molecular flows

    Science.gov (United States)

    Lilly, Taylor C.

    The continuing advance of laser technology enables a range of broadly applicable, laser-based flow manipulation techniques. The characteristics of these laser-based flow manipulations suggest that they may augment, or be superior to, such traditional electro-mechanical methods as ionic flow control, shock tubes, and small scale wind tunnels. In this study, methodology was developed for investigating laser flow manipulation techniques, and testing their feasibility for a number of aerospace, basic physics, and micro technology applications. Theories for laser-atom and laser-molecule interactions have been under development since the advent of laser technology. The theories have yet to be adequately integrated into kinetic flow solvers. Realizing this integration would greatly enhance the scaling of laser-species interactions beyond the realm of ultra-cold atomic physics. This goal was realized in the present study. A representative numerical investigation, of laser-based neutral atomic and molecular flow manipulations, was conducted using near-resonant and non-resonant laser fields. To simulate the laser interactions over a range of laser and flow conditions, the following tools were employed: a custom collisionless gas particle trajectory code and a specifically modified version of the Direct Simulation Monte Carlo statistical kinetic solver known as SMILE. In addition to the numerical investigations, a validating experiment was conducted. The experimental results showed good agreement with the numerical simulations when experimental parameters, such as finite laser line width, were taken into account. Several areas of interest were addressed: laser induced neutral flow steering, collimation, direct flow acceleration, and neutral gas heating. Near-resonant continuous wave laser, and non-resonant pulsed laser, interactions with cesium and nitrogen were simulated. These simulations showed trends and some limitations associated with these interactions, used for flow

  1. Molecular dynamics computer simulations based on NMR data

    International Nuclear Information System (INIS)

    Vlieg, J. de.

    1989-01-01

    In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs

  2. Atomic and molecular effects in the VUV spectra of solids

    International Nuclear Information System (INIS)

    Sonntag, B.

    1977-10-01

    The VUV spectra of solids are often dominated by atomic or molecular effects, which clearly manifest themselves in the gross features of the spectra and the fine structure at inner shell excitation thresholds. Evidence for the influence of atomic and molecular matrix elements, multiplet-splitting and correlation is presented. Special emphasis is given to the direct experimental verification based on the comparison of atomic and solid state spectra. (orig.) [de

  3. Uncertainty estimates for theoretical atomic and molecular data

    International Nuclear Information System (INIS)

    Chung, H-K; Braams, B J; Bartschat, K; Császár, A G; Drake, G W F; Kirchner, T; Kokoouline, V; Tennyson, J

    2016-01-01

    Sources of uncertainty are reviewed for calculated atomic and molecular data that are important for plasma modeling: atomic and molecular structures and cross sections for electron-atom, electron-molecule, and heavy particle collisions. We concentrate on model uncertainties due to approximations to the fundamental many-body quantum mechanical equations and we aim to provide guidelines to estimate uncertainties as a routine part of computations of data for structure and scattering. (topical review)

  4. Vibration dynamics of single atomic nanocontacts

    International Nuclear Information System (INIS)

    Khater, A; Bourahla, B; Tigrine, R

    2007-01-01

    The motivation for this work is to introduce a model for an atomic nanocontact, whereby its mechanical properties can be analysed via the local spectra. The model system consists of two sets of triple parallel semi-infinite atomic chains joined by a single atom in between. We calculate the vibration spectra and the local densities of vibration states, in the harmonic approximation, for the irreducible set of sites that constitute the nanocontact domain. The nanocontact observables are numerically calculated for different cases of elastic hardening and softening, to investigate how the local dynamics can respond to changes in the microscopic environment on the domain. We have also calculated the phonon scattering and coherent conductance at the nanocontact, derived in a Landauer-Buettiker matrix approach. The analysis of the spectra, of the densities of vibration states, and of the phonon conductance, identifies characteristic features and demonstrates the central role of a core subset of sites in the nanocontact domain

  5. Atomic-scale investigation of the interactions between tetrabromobisphenol A, tetrabromobisphenol S and bovine trypsin by spectroscopies and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Ding, Keke; Zhang, Huanxin; Wang, Haifei; Lv, Xuan; Pan, Liumeng; Zhang, Wenjing; Zhuang, Shulin

    2015-01-01

    Highlights: • The interaction of TBBPA/TBBPS with bovine trypsin was deciphered for the first time. • The fluorescence of bovine trypsin was quenched in a concentration-dependent mode. • TBBPA and TBBPS bind at the ANS binding site with distinct binding modes. • TBBPS has a higher binding affinity toward bovine trypsin than TBBPA. • Our in vitro and in silico approach is helpful to assess risk of TBBPA-related BFRs. - Abstract: Tetrabromobisphenol A (TBBPA) and its replacement alternative tetrabromobisphenol S (TBBPS) are used widely as brominated flame retardants (BFRs). However, the potential risk of their effects on bovine trypsin remains largely unknown. We investigated the effects of TBBPA and TBBPS to bovine trypsin by the fluorescence spectroscopy, circular dichroism and molecular dynamics (MD) simulations. They statically quenched the intrinsic fluorescence of bovine trypsin in a concentration-dependent mode and caused slight red-shifted fluorescence. The short and long fluorescence lifetime decay components of bovine trypsin were both affected, partly due to the disturbed microenvironmental changes of Trp215. The β-sheet content of bovine trypsin was significantly reduced from 82.4% to 75.7% and 76.6% by TBBPA and TBBPS, respectively, possibly impairing the physiological function of bovine trypsin. TBBPA and TBBPS bind at the 8-anilinonaphthalene-1-sulfonate (ANS) binding site with an association constant of 1.09 × 10 4 M −1 and 2.41 × 10 4 M −1 at 298 K, respectively. MD simulations revealed that van der Waals interactions and hydrogen bond interactions are dominant for TBBPA, whereas electrostatic interactions are critical for TBBPS. Our in vitro and in silico studies are beneficial to the understanding of risk assessment and future design of environmental benign BFRs.

  6. Binding modes and pathway of RHPS4 to human telomeric G-quadruplex and duplex DNA probed by all-atom molecular dynamics simulations with explicit solvent.

    Science.gov (United States)

    Mulholland, Kelly; Siddiquei, Farzana; Wu, Chun

    2017-07-19

    RHPS4, a potent binder to human telomeric DNA G-quadruplex, shows high efficacy in tumor cell growth inhibition. However, it's preferential binding to DNA G-quadruplex over DNA duplex (about 10 fold) remains to be improved toward its clinical application. A high resolution structure of the single-stranded telomeric DNA G-quadruplexes, or B-DNA duplex, in complex with RHPS4 is not available yet, and the binding nature of this ligand to these DNA forms remains to be elusive. In this study, we carried out 40 μs molecular dynamics binding simulations with a free ligand to decipher the binding pathway of RHPS4 to a DNA duplex and three G-quadruplex folders (parallel, antiparallel and hybrid) of the human telomeric DNA sequence. The most stable binding mode identified for the duplex, parallel, antiparallel and hybrid G-quadruplexes is an intercalation, bottom stacking, top intercalation and bottom intercalation mode, respectively. The intercalation mode with similar binding strength to both the duplex and the G-quadruplexes, explains the lack of binding selectivity of RHPS4 to the G-quadruplex form. Therefore, a ligand modification that destabilizes the duplex intercalation mode but stabilizes the G-quadruplex intercalation mode will improve the binding selectivity toward G-quadruplex. The intercalation mode of RHPS4 to both the duplex and the antiparallel and the hybrid G-quadruplex follows a base flipping-insertion mechanism rather than an open-insertion mechanism. The groove binding, the side binding and the intercalation with flipping out of base were observed to be intermediate states before the full intercalation state with paired bases.

  7. Nonequilibrium molecular dynamics theory, algorithms and applications

    CERN Document Server

    Todd, Billy D

    2017-01-01

    Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

  8. Gas Phase Molecular Dynamics

    International Nuclear Information System (INIS)

    Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.

    1999-01-01

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wave packet calculations that provide insights into energy flow between the vibrational modes of the molecule

  9. Viscosity calculations at molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kirova, E M; Norman, G E

    2015-01-01

    Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)

  10. A molecular dynamics study of the atomic structure of (CaO)x(Al2O3)1-x glass with x = 0.625 close to the eutectic

    Science.gov (United States)

    Thomas, B. W. M.; Mead, R. N.; Mountjoy, G.

    2006-05-01

    Aluminate glasses are difficult to prepare as they do not contain traditional network formers, but they are promising materials for optical applications. The atomic structure of calcium aluminate glasses has been studied using several experimental techniques. The current study uses molecular dynamics to obtain a model of a (CaO)0.625(Al2O3)0.375 glass close to the eutectic. The glass consists of a tetrahedral alumina network with average network polymerization \\langle Q^{n}\\rangle of n = 3.3. Ca acts as a network modifier with average coordination of 6.2. Ca is typically coordinated to three bridging oxygens (Ob) and three non-bridging oxygens (Onb), with Ca-Onb bonds noticeably shorter than the Ca-Ob bonds. A new method of analysing modifier cation coordination is presented, which specifically shows the distribution of Ca coordination NCaO in terms of combinations of NCaOb and NCaOnb. Ob is most often coordinated to two Al plus two Ca, and Onb is most often coordinated to one Al plus three Ca. The typical coordinations of Ca, Ob, and Onb all have a noticeable similarity to those for the 5CaO·3Al2O3 crystal. The Ca-Ca distribution shows a clear similarity to that for (CaO)0.5(SiO2)0.5 glass, and this is attributed to the equal atomic number densities of Ca in these glasses.

  11. Effects of spin orbital coupling on atomic and electronic structures in Al{sub 2}Cu and Al{sub 2}Au crystal and liquid phases via ab initio molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y. [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Lu, Y.H., E-mail: luyh@zju.edu.cn [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Wang, X.D.; Cao, Q.P. [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Zhang, D.X. [State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310027 (China); Jiang, J.Z., E-mail: jiangjz@zju.edu.cn [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China)

    2014-11-15

    Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al{sub 2}Cu and Al{sub 2}Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al{sub 2}Cu and Al{sub 2}Au.

  12. Atomic and molecular databases in the context of virtual observatories

    International Nuclear Information System (INIS)

    Dubernet, Marie-Lise; Roueff, Evelyne

    2006-01-01

    Numerical and bibliographic Databases in Atomic and Molecular Physics are essential for both the modelling of various astrophysical media and the interpretation of astrophysical spectra provided by ground or space-based telescopes. We report here on our current project concerning the access to Atomic and Molecular Databases within the Virtual Observatories. This presentation aims at informing people about interoperability matters, in order to put together the efforts which have already started in this domain, to evaluate the needs and requirements of the targeted interrelation between atomic and molecular data bases and VO projects. Collaborations in this domain are welcome. (author)

  13. Atomic and molecular physics of controlled thermonuclear fusion

    International Nuclear Information System (INIS)

    Joachain, C.J.; Post, D.E.

    1983-01-01

    This book attempts to provide a comprehensive introduction to the atomic and molecular physics of controlled thermonuclear fusion, and also a self-contained source from which to start a systematic study of the field. Presents an overview of fusion energy research, general principles of magnetic confinement, and general principles of inertial confinement. Discusses the calculation and measurement of atomic and molecular processes relevant to fusion, and the atomic and molecular physics of controlled thermonuclear research devices. Topics include recent progress in theoretical methods for atomic collisions; current theoretical techniques for electron-atom and electronion scattering; experimental aspects of electron impact ionization and excitation of positive ions; the theory of charge exchange and ionization by heavy particles; experiments on electron capture and ionization by multiply charged ions; Rydberg states; atomic and molecular processes in high temperature, low-density magnetically confined plasmas; atomic processes in high-density plasmas; the plasma boundary region and the role of atomic and molecular processes; neutral particle beam production and injection; spectroscopic plasma diagnostics; and particle diagnostics for magnetic fusion experiments

  14. Roadmap of ultrafast x-ray atomic and molecular physics

    Science.gov (United States)

    Young, Linda; Ueda, Kiyoshi; Gühr, Markus; Bucksbaum, Philip H.; Simon, Marc; Mukamel, Shaul; Rohringer, Nina; Prince, Kevin C.; Masciovecchio, Claudio; Meyer, Michael; Rudenko, Artem; Rolles, Daniel; Bostedt, Christoph; Fuchs, Matthias; Reis, David A.; Santra, Robin; Kapteyn, Henry; Murnane, Margaret; Ibrahim, Heide; Légaré, François; Vrakking, Marc; Isinger, Marcus; Kroon, David; Gisselbrecht, Mathieu; L'Huillier, Anne; Wörner, Hans Jakob; Leone, Stephen R.

    2018-02-01

    X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (1020 W cm-2) of x-rays at wavelengths down to ˜1 Ångstrom, and HHG provides unprecedented time resolution (˜50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scales can be referenced to the chemically significant carbon K-edge at a photon energy of ˜280 eV (44 Ångstroms) and the bond length in methane of ˜1 Ångstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and Ångstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at Ångstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities since

  15. Laser-cooled atomic ions as probes of molecular ions

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kenneth R.; Viteri, C. Ricardo; Clark, Craig R.; Goeders, James E.; Khanyile, Ncamiso B.; Vittorini, Grahame D. [Schools of Chemistry and Biochemistry, Computational Science and Engineering and Physics, Georgia Institute of Technology, Atlanta, GA 30332 (United States)

    2015-01-22

    Trapped laser-cooled atomic ions are a new tool for understanding cold molecular ions. The atomic ions not only sympathetically cool the molecular ions to millikelvin temperatures, but the bright atomic ion fluorescence can also serve as a detector of both molecular reactions and molecular spectra. We are working towards the detection of single molecular ion spectra by sympathetic heating spectroscopy. Sympathetic heating spectroscopy uses the coupled motion of two trapped ions to measure the spectra of one ion by observing changes in the fluorescence of the other ion. Sympathetic heating spectroscopy is a generalization of quantum logic spectroscopy, but does not require ions in the motional ground state or coherent control of the ion internal states. We have recently demonstrated this technique using two isotopes of Ca{sup +} [Phys. Rev. A, 81, 043428 (2010)]. Limits of the method and potential applications for molecular spectroscopy are discussed.

  16. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

    Science.gov (United States)

    Armen, Roger S; Chen, Jianhan; Brooks, Charles L

    2009-10-13

    Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

  17. Dislocation glide in Ni-Al solid solutions from the atomic scale up: a molecular dynamics study; Etude du glissement des dislocations dans la solution solide Ni-Al par simulation a l'echelle atomique

    Energy Technology Data Exchange (ETDEWEB)

    Rodary, E

    2003-01-01

    The glide of an edge dislocation in solid solutions is studied by molecular dynamics, at fixed temperature and imposed external stress. We have optimized an EAM potential for Ni(1 a 8% A1): it well reproduces the lattice expansion, local atomic order, stacking fault energy as a function of composition, as well as the elastic properties of the {gamma}' phase with L1{sub 2} structure. On increasing the stress, the dislocation is first immobile, then glides with a velocity proportional to the stress and the velocity saturates on reaching the transverse sound velocity. However, only beyond a static threshold stress, {sigma}{sub s}, does the dislocation glide a distance large enough to allow macroscopic shear; the linear part of the velocity-stress curve extrapolates to zero at a dynamical threshold stress, {sigma}{sub d}, The friction coefficient, and the threshold stresses ({sigma}{sub s} and {sigma}{sub d}), increase with the A1 concentration and decrease with temperature (300 and 500 K). Close to the critical shear stress, {sigma}{sub s}, the dislocation glide is analysed with a 'stop and go' model. The latter yields the flight velocity between obstacles, the mean obstacle density and the distribution of the waiting time on each obstacle as a function of stress, composition and temperature. The obstacle to the glide is proposed to be the strong repulsion between Al atoms brought into nearest neighbour position by the glide process, and not the dislocation-solute interaction. The microscopic parameters so defined are introduced into a micro-mechanical model, which well reproduces the known behaviour of nickel base solid solutions. (author)

  18. Atomic-scale dislocation dynamics in radiation damage environment

    International Nuclear Information System (INIS)

    Osetsky, Y.; Stoller, R.; Bacon, D.J.

    2007-01-01

    Full text of publication follows: The dynamics behavior of dislocations determines mechanical properties of crystalline materials. Long-range interactions between a moving dislocation and other defects can be treated within a continuum approach via interaction of their stress and strain fields. However, a vast contribution to mechanical properties depends on the direct interaction between dislocations and other defects and depends very much on the particular atomic scale structure of the both moving dislocation core and the obstacle. In this work we review recent progress in large-scale modeling of dislocation dynamics in metals at the atomic level by molecular dynamics and statics. We review the modem techniques used to simulate dynamics of dislocations in different lattice structures, the dependence on temperature, strain rate and obstacle size. Examples are given for bcc, fcc and hcp metals where edge and screw dislocations interact with vacancy (loops, voids, stacking fault tetrahedra, etc), self-interstitial clusters and secondary phase precipitates. Attention is paid to interpretation of atomistic results from the point of view of parameterization of continuum models. The latter is vitally necessary for further application in 3-dimensional dislocation dynamics within the multi-scale materials modeling approach. Research sponsored by the Division of Materials Sciences and Engineering and the Office of Fusion Energy Sciences, U.S. Department of Energy, under contract DE-AC0S-00OR22725 with UT-Battelle, LLC. (authors)

  19. Reaction dynamics of electronically excited alkali atoms with simpler molecules

    International Nuclear Information System (INIS)

    Weiss, P.S.; Mestdagh, J.M.; Schmidt, H.; Vernon, M.F.; Covinsky, M.H.; Balko, B.A.; Lee, Y.T.

    1985-05-01

    The reactions of electronically excited sodium atoms with simple molecules have been studied in crossed molecular beams experiments. Electronically excited Na(3 2 P/sub 3/2/, 4 2 D/sub 5/2/, and 5 2 S/sub 1/2/) were produced by optical pumping using single frequency dye lasers. The effects of the symmetry, and the orientation and alignment of the excited orbital on the chemical reactivity, and detailed information on the reaction dynamics were derived from measurements of the product angular and velocity distributions. 12 refs., 9 figs

  20. R-Matrix Theory of Atomic Collisions Application to Atomic, Molecular and Optical Processes

    CERN Document Server

    Burke, Philip George

    2011-01-01

    Commencing with a self-contained overview of atomic collision theory, this monograph presents recent developments of R-matrix theory and its applications to a wide-range of atomic molecular and optical processes. These developments include electron and photon collisions with atoms, ions and molecules required in the analysis of laboratory and astrophysical plasmas, multiphoton processes required in the analysis of superintense laser interactions with atoms and molecules and positron collisions with atoms and molecules required in antimatter studies of scientific and technologial importance. Basic mathematical results and general and widely used R-matrix computer programs are summarized in the appendices.

  1. Thomas-Fermi molecular dynamics

    International Nuclear Information System (INIS)

    Clerouin, J.; Pollock, E.L.; Zerah, G.

    1992-01-01

    A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

  2. Symmetry of quantum molecular dynamics

    International Nuclear Information System (INIS)

    Burenin, A.V.

    2002-01-01

    The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

  3. 1979 bibliography of atomic and molecular processes. [Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-08-01

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  4. 1978 bibliography of atomic and molecular processes. [Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  5. Atomic and Molecular Data activities at NDC/JAERI

    International Nuclear Information System (INIS)

    Shirai, Toshizo

    2000-01-01

    The NDC/JAERI is a member of the international atomic and molecular (A+M) data center network for fusion, coordinated by the International Atomic Energy Agency. In this poster we introduce our Evaluated Atomic and Molecular Data Library (JEAMDL) developed in collaboration with the JAERI Research Committee on A+M Data and with researchers of ORNL and NIST under the US-Japan fusion cooperation program. JEAMDL comprises databases of collision cross section data and of spectroscopic data. We briefly summarize these two databases below. (author)

  6. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  7. Entanglement dynamics between an isolated atom and a moving atom in the cavity

    International Nuclear Information System (INIS)

    Xiao-Juan, Deng; Mao-Fa, Fang; Guo-Dong, Kang

    2009-01-01

    The entanglement dynamics between an isolated atom and a moving atom interacting with a cavity field is investigated. The results show that there appears sudden death of entanglement between the isolated atom and the moving atom and that the time of entanglement sudden death (ESD) is independent of the initial state of the system. It is interesting that the isolated atom can also entangle with a cavity field, though they do not interact with each other originally, which stems from the fact that the entanglement between the isolated atom and the moving atom may turn into the entanglement between the isolated atom and the cavity. (general)

  8. New trends in atomic and molecular physics advanced technological applications

    CERN Document Server

    2013-01-01

    The field of Atomic and Molecular Physics (AMP) has reached significant advances in high–precision experimental measurement techniques. The area covers a wide spectrum ranging from conventional to new emerging multi-disciplinary areas like physics of highly charged ions (HCI), molecular physics, optical science, ultrafast laser technology etc. This book includes the important topics of atomic structure, physics of atomic collision, photoexcitation, photoionization processes, Laser cooling and trapping, Bose Einstein condensation and advanced technology applications of AMP in the fields of astronomy , astrophysics , fusion, biology and nanotechnology. This book is useful for researchers, professors, graduate, post graduate and PhD students dealing with atomic and molecular physics. The book has a wide scope with applications in neighbouring fields like plasma physics, astrophysics, cold collisions, nanotechnology and future fusion energy sources like ITER (international Thermonuclear Experimental Reactor) To...

  9. Molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

    2012-01-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

  10. Molecular dynamics for dense matter

    Science.gov (United States)

    Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

    2012-08-01

    We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

  11. Manipulating localized molecular orbitals by single-atom contacts.

    Science.gov (United States)

    Wang, Weihua; Shi, Xingqiang; Lin, Chensheng; Zhang, Rui Qin; Minot, Christian; Van Hove, Michel A; Hong, Yuning; Tang, Ben Zhong; Lin, Nian

    2010-09-17

    We have fabricated atom-molecule contacts by attachment of single Cu atoms to terpyridine side groups of bis-terpyridine tetra-phenyl ethylene molecules on a Cu(111) surface. By means of scanning tunneling microscopy, spectroscopy, and density functional calculations, we have found that, due to the localization characteristics of molecular orbitals, the Cu-atom contact modifies the state localized at the terpyridine side group which is in contact with the Cu atom but does not affect the states localized at other parts of the molecule. These results illustrate the contact effects at individual orbitals and offer possibilities to manipulate orbital alignments within molecules.

  12. Atomic and Molecular Data Activities at NIFS in 2009 - 2011

    International Nuclear Information System (INIS)

    Murakami, I.

    2011-01-01

    We open and maintain the NIFS atomic and molecular numerical databases. Numbers of data records increase to 476,048 in total (as of Aug. 23, 2011) and mainly new data are added for AMDIS (electron impact ionization, excitation, and recombination cross sections and rate coefficients) and CHART (charge transfer of atom - ion collisions cross sections) during last two years. A collaboration group has started for research on atomic and molecular processes in plasma using the Large Helical Device and we measure visible and extreme ultraviolet spectra of W and rare earth elements. We also organize a collaboration group with atomic physicists from Japanese universities for research on W to study atomic data, spectra and collisional-radiative models for W ions. (author)

  13. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  14. Simulation and understanding of atomic and molecular quantum crystals

    Science.gov (United States)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

    Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

  15. Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

    International Nuclear Information System (INIS)

    Jee, Jun Goo

    2010-01-01

    It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

  16. Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

    International Nuclear Information System (INIS)

    Perez, Danny

    2012-01-01

    We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

  17. Molecular beam studies of hot atom chemical reactions: Reactive scattering of energetic deuterium atoms

    International Nuclear Information System (INIS)

    Continetti, R.E.; Balko, B.A.; Lee, Y.T.

    1989-02-01

    A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H 2 /minus/> DH + H and the substitution reaction D + C 2 H 2 /minus/> C 2 HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible. 18 refs., 9 figs

  18. Molecular Beam Studies of Hot Atom Chemical Reactions: Reactive Scattering of Energetic Deuterium Atoms

    Science.gov (United States)

    Continetti, R. E.; Balko, B. A.; Lee, Y. T.

    1989-02-01

    A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H{sub 2} -> DH + H and the substitution reaction D + C{sub 2}H{sub 2} -> C{sub 2}HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible.

  19. Rheology via nonequilibrium molecular dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.

    1982-10-01

    The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

  20. Atoms

    International Nuclear Information System (INIS)

    Fuchs, Alain; Villani, Cedric; Guthleben, Denis; Leduc, Michele; Brenner, Anastasios; Pouthas, Joel; Perrin, Jean

    2014-01-01

    Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)

  1. Molecular dynamics studies of displacement cascades

    International Nuclear Information System (INIS)

    Averback, R.S.; Hsieh, Horngming; Diaz de la Rubia, T.

    1990-02-01

    Molecular-dynamics simulations of cascades in Cu and Ni with primary-knock-on energies up to 5 keV and lattice temperatures in the range 0 K--700 K are described. Interatomic forces were represented by either the Gibson II (Cu) or Johnson-Erginsoy (Ni) potentials in most of this work, although some simulations using ''Embedded Atom Method'' potentials, e.g., for threshold events in Ni 3 Al, are also presented. The results indicate that the primary state of damage produced by displacement cascades is controlled by two phenomena, replacement collision sequences during the collisional phase of the cascade and local melting during the thermal spike. As expected, the collisional phase is rather similar in Cu and Ni, however, the thermal spike is of longer duration and has a more pronounced influence in Cu than Ni. When the ambient temperature of the lattice is increased, the melt zones are observed to both increase in size and cool more slowly. This has the effect of reducing defect production and enhancing atomic mixing and disordering. The implications of these results for defect production, cascade collapse, atomic disordering will be discussed. 34 refs., 7 figs., 2 tabs

  2. Light absorption during alkali atom-noble gas atom interactions at thermal energies: a quantum dynamics treatment.

    Science.gov (United States)

    Pacheco, Alexander B; Reyes, Andrés; Micha, David A

    2006-10-21

    The absorption of light during atomic collisions is treated by coupling electronic excitations, treated quantum mechanically, to the motion of the nuclei described within a short de Broglie wavelength approximation, using a density matrix approach. The time-dependent electric dipole of the system provides the intensity of light absorption in a treatment valid for transient phenomena, and the Fourier transform of time-dependent intensities gives absorption spectra that are very sensitive to details of the interaction potentials of excited diatomic states. We consider several sets of atomic expansion functions and atomic pseudopotentials, and introduce new parametrizations to provide light absorption spectra in good agreement with experimentally measured and ab initio calculated spectra. To this end, we describe the electronic excitation of the valence electron of excited alkali atoms in collisions with noble gas atoms with a procedure that combines l-dependent atomic pseudopotentials, including two- and three-body polarization terms, and a treatment of the dynamics based on the eikonal approximation of atomic motions and time-dependent molecular orbitals. We present results for the collision induced absorption spectra in the Li-He system at 720 K, which display both atomic and molecular transition intensities.

  3. Laser Controlled Molecular Orientation Dynamics

    International Nuclear Information System (INIS)

    Atabek, O.

    2004-01-01

    Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

  4. Molecular beam studies of reaction dynamics

    International Nuclear Information System (INIS)

    Lee, Yuan T.

    1991-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation

  5. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  6. Atomic and molecular gas phase spectrometry

    Science.gov (United States)

    Winefordner, J. D.

    1985-10-01

    The major goals of this research have been to develop diagnostical spectroscopic methods for measuring spatial/temporal temperatures and species of combustion flames and plasmas and to develop sensitive, selective, precise, reliable, rapid spectrometric methods of trace analysis of elements present in jet engine lubricating oils, metallurgical samples, and engine exhausts. The diagnostical approaches have been based upon the measurement of metal probes introduced into the flame or plasmas and the measurement of OH in flames. The measurement approaches have involved the use of laser-excited fluorescence, saturated absorption, polarization, and linear absorption. The spatial resolution in most studies is less than 1 cu mm and the temporal resolution is less than 10 ns with the use of pulsed lasers. Single pulse temperature and species measurements have also been carried out. Other diagnostical studies have involved the measurement of collisional redistribution of radiatively excited levels of Na and Tl in acetylene/02/Ar flames and the measurement of lifetimes and quantum efficiencies of atoms and ions in the inductively coupled plasmas, ICP. The latter studies indicate that the high electron number densities in ICPs are not efficient quenchers of excited atoms/ions. Temperatures of microwave atmospheric plasmas produced capacitatively and cool metastable N2 discharge produced by a dielectric discharge have also been measured.

  7. Committee on Atomic, Molecular, and Optical Sciences (CAMOS)

    International Nuclear Information System (INIS)

    1992-01-01

    The Committee on Atomic, Molecular and Optical Sciences (CAMOS) of the National Research Council (NRC) is charged with monitoring the health of the field of atomic, molecular, and optical (AMO) science in the United States. Accordingly, the Committee identifies and examines both broad and specific issues affecting the field. Regular meetings, teleconferences, briefings from agencies and the scientific community, the formation of study panels to prepare reports, and special symposia are among the mechanisms used by the CAMOS to meet its charge. This progress report presents a review of CAMOS activities from February 1, 1992 to January 31, 1993. This report also includes the status of activities associated with the CAMOS study on the field that is being conducted by the Panel on the Future of Atomic, Molecular, and Optical Sciences (FAMOS)

  8. The role of atomic and molecular processes in fusion research

    International Nuclear Information System (INIS)

    Harrison, M.F.A.

    1977-01-01

    This paper considers the relevance of atomic and molecular processes to research into controlled nuclear fusion and in particular their effects upon the magnetically confined plasma in Tokamak experiments and conceptual Tokamak reactors. The relative significance of collective phenomena and of single particle collisions to both plasma heating and loss processes are discussed and the pertinent principles of plasma refuelling and plasma diagnostics are outlined. The methods by which atomic and molecular data are applied to these problems, the contributing effects of surface interactions and the consequent implications upon the accuracy and the type of data needed are described in a qualitative manner. Whilst particular atomic and molecular processes are not discussed in detail, sufficient information is given of the physical environments of Tokamak devices for significant processes to be self evident. (author)

  9. The calculation of the viscosity from the autocorrelation function using molecular and atomic stress tensors

    Science.gov (United States)

    Cui, S. T.

    The stress-stress correlation function and the viscosity of a united-atom model of liquid decane are studied by equilibrium molecular dynamics simulation using two different formalisms for the stress tensor: the atomic and the molecular formalisms. The atomic and molecular correlation functions show dramatic difference in short-time behaviour. The integrals of the two correlation functions, however, become identical after a short transient period whichis significantly shorter than the rotational relaxation time of the molecule. Both reach the same plateau value in a time period corresponding to this relaxation time. These results provide a convenient guide for the choice of the upper integral time limit in calculating the viscosity by the Green-Kubo formula.

  10. New trends in atomic and molecular physics. Advanced technological applications

    International Nuclear Information System (INIS)

    Mohan, Man

    2013-01-01

    Represents an up-to-date scientific status report on new trends in atomic and molecular physics. Multi-disciplinary approach. Also of interest to researchers in astrophysics and fusion plasma physics. Contains material important for nano- and laser technology. The field of Atomic and Molecular Physics (AMP) has reached significant advances in high-precision experimental measurement techniques. The area covers a wide spectrum ranging from conventional to new emerging multi-disciplinary areas like physics of highly charged ions (HCI), molecular physics, optical science, ultrafast laser technology etc. This book includes the important topics of atomic structure, physics of atomic collision, photoexcitation, photoionization processes, Laser cooling and trapping, Bose Einstein condensation and advanced technology applications of AMP in the fields of astronomy, astrophysics, fusion, biology and nanotechnology. This book is useful for researchers, professors, graduate, post graduate and PhD students dealing with atomic and molecular physics. The book has a wide scope with applications in neighbouring fields like plasma physics, astrophysics, cold collisions, nanotechnology and future fusion energy sources like ITER (international Thermonuclear Experimental Reactor) Tokomak plasma machine which need accurate AMP data.

  11. Classical molecular dynamics simulation of nuclear fuels

    International Nuclear Information System (INIS)

    Devanathan, R.; Krack, M.; Bertolus, M.

    2015-01-01

    Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

  12. Optically pumped semiconductor lasers for atomic and molecular physics

    Science.gov (United States)

    Burd, S.; Leibfried, D.; Wilson, A. C.; Wineland, D. J.

    2015-03-01

    Experiments in atomic, molecular and optical (AMO) physics rely on lasers at many different wavelengths and with varying requirements on spectral linewidth, power and intensity stability. Optically pumped semiconductor lasers (OPSLs), when combined with nonlinear frequency conversion, can potentially replace many of the laser systems currently in use. We are developing a source for laser cooling and spectroscopy of Mg+ ions at 280 nm, based on a frequency quadrupled OPSL with the gain chip fabricated at the ORC at Tampere Univ. of Technology, Finland. This OPSL system could serve as a prototype for many other sources used in atomic and molecular physics.

  13. International bulletin on atomic and molecular data for fusion. No. 60

    International Nuclear Information System (INIS)

    Stephens, J.A.; Bannister, M.E.; Delcroix, J.L.; Fuhr, J.

    2001-06-01

    This bulletin comprises updated atomic and molecular data for fusion. It includes the Atomic and Molecular Data Information System (AMDIS) of the IAEA. It contains two parts: a bibliographic database for atomic and molecular data for fusion research, and numerical databases of recommended and evaluated atomic, molecular and plasma-surface interaction data. The indexed papers are also listed separately for structure and spectra, atomic and molecular collisions, and surface interactions

  14. A concurrent multiscale micromorphic molecular dynamics

    International Nuclear Information System (INIS)

    Li, Shaofan; Tong, Qi

    2015-01-01

    In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

  15. Color molecular dynamics for dense matter

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Hatsuda, Tetsuo

    2000-01-01

    We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

  16. Atomic probes of surface structure and dynamics

    International Nuclear Information System (INIS)

    Heller, E.J.; Jonsson, H.

    1992-01-01

    The following were studied: New semiclassical method for scattering calculations, He atom scattering from defective Pt surfaces, He atom scattering from Xe overlayers, thermal dissociation of H 2 on Cu(110), spin flip scattering of atoms from surfaces, and Car-Parrinello simulations of surface processes

  17. Atomic and Molecular Data and Their Applications. Proceedings

    International Nuclear Information System (INIS)

    Mohr, P.J.; Wiese, W.L.

    1998-01-01

    These proceedings contain papers based on invited talks at the First International Conference on Atomic and Molecular Data and Their Applications held at the National Institute of Standards and Technology (INIST) in Gaithersburg, Maryland in October, 1997. The invited presentations addressed four major areas of importance to atomic and molecular data activities: Global trends affecting scientific data, collisions and spectral radiation data, date assessment and database and data management activities and lastly, data needs of the main user communities such as the magnetic and inertial fusion research communities, semiconductor-related plasma processing, the atmospheric research community and the space astronomy community, etc. These proceedings are expected to be of interest to both producers and users of data and provide up-to-date surveys on atomic and molecular data. A wide range of data has been presented including X-ray transition energies, atomic transition probabilities, atomic collisions data, data for cosmology and X-ray astronomy, data for fusion plasma diagnostics, etc. There were 27 invited talks and consequently 27 articles in these Proceedings. Out of these, 9 have been abstracted for the Energy Science and Technology database

  18. Atomic and molecular physics with ion storage rings

    International Nuclear Information System (INIS)

    Larsson, M.

    1995-01-01

    Advances in ion-source, accelerator and beam-cooling technology have made it possible to produce high-quality beams of atomic ions in arbitrary charged states as well as molecular and cluster ions are internally cold. Ion beams of low emittance and narrow momentum spread are obtained in a new generation of ion storage-cooler rings dedicated to atomic and molecular physics. The long storage times (∼ 5 s ≤ τ ≤ days) allow the study of very slow processes occurring in charged (positive and negative) atoms, molecules and clusters. Interactions of ions with electrons and/or photons can be studied by merging the stored ion beam with electron and laser beams. The physics of storage rings spans particles having a charge-to-mass ratio ranging from 60 + and C 70 + ) to 0.4 - 1.0 (H + , D + , He 2+ , ..., U 92+ ) and collision processes ranging from <1 meV to ∼ 70 GeV. It incorporates, in addition to atomic and molecular physics, tests of fundamental physics theories and atomic physics bordering on nuclear and chemical physics. This exciting development concerning ion storage rings has taken place within the last five to six years. (author)

  19. Molecular dynamics of liquid crystals

    Science.gov (United States)

    Sarman, Sten

    1997-02-01

    We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.

  20. Harwell's atomic, molecular and solid state computer programs

    International Nuclear Information System (INIS)

    Harker, A.H.

    1976-02-01

    This document is intended to introduce the computational facilities available in the fields of atomic, molecular the solid state theory on the IBM370/165 at Harwell. The programs have all been implemented and thoroughly tested by the Theory of Solid State Materials Group. (author)

  1. Committee on Atomic, Molecular, and Optical Sciences (CAMOS)

    International Nuclear Information System (INIS)

    1992-01-01

    The Committee on Atomic, Molecular, and Optical Sciences is a standing committee under the auspices of the Board on Physics and Astronomy, Commission on Physical Sciences, Mathematics, and Applications of the National Academy of Sciences -- National Research Council. The atomic, molecular, and optical (AMO) sciences represent a broad and diverse field in which much of the research is carried out by small groups. These groups generally have not operated in concert with each other and, prior to the establishment of CAMOS, there was no single committee or organization that accepted the responsibility of monitoring the continuing development and assessing the general public health of the field as a whole. CAMOS has accepted this responsibility and currently provides a focus for the AMO community that is unique and essential. The membership of CAMOS is drawn from research laboratories in universities, industry, and government. Areas of expertise on the committee include atomic physics, molecular science, and optics. A special effort has been made to include a balanced representation from the three subfields. (A roster is attached.) CAMOS has conducted a number of studies related to the health of atomic and molecular science and is well prepared to response to requests for studies on specific issues. This report brief reviews the committee work of progress

  2. Bibliographic data base on atomic and molecular data

    International Nuclear Information System (INIS)

    Itikawa, Yukikazu.

    1983-03-01

    A comparative study is made on three bibliographic data bases: INSPEC, ORNL - AMPIC, GAPHYOR. An on - line retrieval is carried out for searching a number of specific atomic and molecular data. Characteristics of each data base are clarified and suggestions are given for use of those data bases. (author)

  3. Atomic and molecular processes with lithium in peripheral plasmas

    International Nuclear Information System (INIS)

    Murakami, I.; Kato, D.; Hirooka, Y.; Sawada, K.

    2010-01-01

    Atomic and molecular processes for Li chemistry are examined for low temperature plasma such as peripheral plasmas in fusion research laboratory devices. Particle abundances of Li, Li ions, LiH and LiH ion are calculated by solving rate equations in which all reactions of the Li chemistry are considered for low temperature plasma.

  4. Springer handbook of atomic, molecular, and optical physics

    CERN Document Server

    Cassar, Mark M

    2006-01-01

    This Springer Handbook of Atomic, Molecular, and Optical Physics comprises a comprehensive reference source that unifies the entire fields of atomic, molecular, and optical (AMO) physics, assembling the principal ideas, techniques and results of the field from atomic spectroscopy to applications in comets. Its 92 chapters are written by over 100 authors, all leaders in their respective disciplines. Carefully edited to ensure uniform coverage and style, with extensive cross references, and acting as a guide to the primary research literature, it is both a source of information and an inspiration for graduate students and other researchers new to the field. Relevant diagrams, graphs, and tables of data are provided throughout the text. Substantially updated and expanded since the 1996 edition and published in conjunction with the 2005 World Year of Physics (commemorating Einstein’s 1905 "miracle year"), it contains several entirely new chapters covering current areas of great research interest, such as Bose �...

  5. Multiscale equation-free algorithms for molecular dynamics

    Science.gov (United States)

    Abi Mansour, Andrew

    Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

  6. Theoretical Concepts in Molecular Photodissociation Dynamics

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm

    1995-01-01

    This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

  7. Modeling shockwave deformation via molecular dynamics

    International Nuclear Information System (INIS)

    Holian, B.L.

    1987-01-01

    Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too

  8. Atomic and molecular data for optical stellar spectroscopy

    International Nuclear Information System (INIS)

    Heiter, U; Lind, K; Barklem, P S; Asplund, M; Bergemann, M; Magrini, L; Masseron, T; Mikolaitis, Š; Pickering, J C; Ruffoni, M P

    2015-01-01

    High-precision spectroscopy of large stellar samples plays a crucial role for several topical issues in astrophysics. Examples include studying the chemical structure and evolution of the Milky Way Galaxy, tracing the origin of chemical elements, and characterizing planetary host stars. Data are accumulating from instruments that obtain high-quality spectra of stars in the ultraviolet, optical and infrared wavelength regions on a routine basis. These instruments are located at ground-based 2–10 m class telescopes around the world, in addition to the spectrographs with unique capabilities available at the Hubble Space Telescope. The interpretation of these spectra requires high-quality transition data for numerous species, in particular neutral and singly ionized atoms, and di- or triatomic molecules. We rely heavily on the continuous efforts of laboratory astrophysics groups that produce and improve the relevant experimental and theoretical atomic and molecular data. The compilation of the best available data is facilitated by databases and electronic infrastructures such as the NIST Atomic Spectra Database, the VALD database, or the Virtual Atomic and Molecular Data Centre. We illustrate the current status of atomic data for optical stellar spectra with the example of the Gaia-ESO Public Spectroscopic Survey. Data sources for 35 chemical elements were reviewed in an effort to construct a line list for a homogeneous abundance analysis of up to 10 5 stars. (paper)

  9. Atomic and molecular data for optical stellar spectroscopy

    Science.gov (United States)

    Heiter, U.; Lind, K.; Asplund, M.; Barklem, P. S.; Bergemann, M.; Magrini, L.; Masseron, T.; Mikolaitis, Š.; Pickering, J. C.; Ruffoni, M. P.

    2015-05-01

    High-precision spectroscopy of large stellar samples plays a crucial role for several topical issues in astrophysics. Examples include studying the chemical structure and evolution of the Milky Way Galaxy, tracing the origin of chemical elements, and characterizing planetary host stars. Data are accumulating from instruments that obtain high-quality spectra of stars in the ultraviolet, optical and infrared wavelength regions on a routine basis. These instruments are located at ground-based 2-10 m class telescopes around the world, in addition to the spectrographs with unique capabilities available at the Hubble Space Telescope. The interpretation of these spectra requires high-quality transition data for numerous species, in particular neutral and singly ionized atoms, and di- or triatomic molecules. We rely heavily on the continuous efforts of laboratory astrophysics groups that produce and improve the relevant experimental and theoretical atomic and molecular data. The compilation of the best available data is facilitated by databases and electronic infrastructures such as the NIST Atomic Spectra Database, the VALD database, or the Virtual Atomic and Molecular Data Centre. We illustrate the current status of atomic data for optical stellar spectra with the example of the Gaia-ESO Public Spectroscopic Survey. Data sources for 35 chemical elements were reviewed in an effort to construct a line list for a homogeneous abundance analysis of up to 105 stars.

  10. Dynamics and applications of excited cold atoms

    NARCIS (Netherlands)

    Claessens, B.J.

    2006-01-01

    In a Magneto-Optical Trap (MOT), realized for the first time in 1987, one can trap and cool neutral atoms to temperatures below a mK. The invention of this device caused a revolution in atomic physics. With an MOT collision and spectroscopy experiments could be performed with unprecedented accuracy.

  11. Atomic and molecular excitation mechanisms in the interstellar medium

    International Nuclear Information System (INIS)

    Sternberg, A.

    1986-01-01

    The detailed infrared response of dense molecular hydrogen gas to intense ultraviolet radiation fields in photodissociation regions is presented. The thermal and chemical structures of photodissociation regions are analyzed, and the relationship between the emission by molecular hydrogen and trace atomic and molecular species is explored. The ultraviolet spectrum of radiation generated by cosmic rays inside dense molecular clouds is presented, and the resulting rates of photodissociation for a variety of interstellar molecules are calculated. Effects of this radiation on the chemistry of dense molecular clouds are discussed, and it is argued that the cosmic ray induced photons will significantly inhibit the production of complex molecular species. It is argued that the annihilation of electrons and positrons at the galactic center may result in observable infrared line emission by atomic hydrogen. A correlation between the intensity variations of the 511 keV line and the hydrogen infrared lines emitted by the annihilation region is predicted. The observed infrared fluxes from compact infrared sources at the galactic center may be used to constrain theories of pair production there

  12. Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril

    Energy Technology Data Exchange (ETDEWEB)

    Okumura, Hisashi [Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585 (Japan); Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585 (Japan)

    2015-12-31

    Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. We perform all-atom molecular dynamics simulations of amyloid fibril assembly and disassembly.

  13. Single asperity nanocontacts: Comparison between molecular dynamics simulations and continuum mechanics models

    NARCIS (Netherlands)

    Solhjoo, Soheil; Vakis, Antonis I.

    Abstract Using classical molecular dynamics, atomic scale simulations of normal contact between a nominally flat substrate and different atomistic and non-atomistic spherical particles were performed to investigate the applicability of classical contact theories at the nanoscale, and further

  14. Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations

    KAUST Repository

    Sun, Sheng; Yin, Guangyao; Lee, Yi-Kuen; Wong, Joseph T.Y.; Zhang, Tong-Yi

    2011-01-01

    Effects of mechanical properties and thermal motion of POPE lipid membrane on electroporation were studied by molecular dynamics simulations. Among simulations in which specific atoms of lipids were artificially constrained at their equilibrium

  15. Atomic and molecular physics in the gas phase

    International Nuclear Information System (INIS)

    Toburen, L.H.

    1990-09-01

    The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets

  16. Molecular dynamics for irradiation driven chemistry

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

    2016-01-01

    A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

  17. Atomic and molecular processes in JT-60U divertor plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Takenaga, H.; Shimizu, K.; Itami, K. [Japan Atomic Energy Research Inst., Naka, Ibaraki (Japan). Naka Fusion Research Establishment] [and others

    1997-01-01

    Atomic and molecular data are indispensable for the understanding of the divertor characteristics, because behavior of particles in the divertor plasma is closely related to the atomic and molecular processes. In the divertor configuration, heat and particles escaping from the main plasma flow onto the divertor plate along the magnetic field lines. In the divertor region, helium ash must be effectively exhausted, and radiation must be enhanced for the reduction of the heat load onto the divertor plate. In order to exhaust helium ash effectively, the difference between behavior of neutral hydrogen (including deuterium and tritium) and helium in the divertor plasma should be understood. Radiation from the divertor plasma generally caused by the impurities which produced by the erosion of the divertor plate and/or injected by gas-puffing. Therefore, it is important to understand impurity behavior in the divertor plasma. The ions hitting the divertor plate recycle through the processes of neutralization, reflection, absorption and desorption at the divertor plates and molecular dissociation, charge-exchange reaction and ionization in the divertor plasma. Behavior of hydrogen, helium and impurities in the divertor plasmas can not be understood without the atomic and molecular data. In this report, recent results of the divertor study related to the atomic and molecular processes in JT-60U were summarized. Behavior of neural deuterium and helium was discussed in section 2. In section 3, the comparisons between the modelling of the carbon impurity transport and the measurements of C II and C IV were discussed. In section 4, characteristics of the radiative divertor using Ne puffing were reported. The new diagnostic method for the electron density and temperature in the divertor plasmas using the intensity ratios of He I lines was described in section 5. (author)

  18. Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

    Science.gov (United States)

    Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

    2009-07-02

    Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or

  19. Atomic and molecular sciences. Progress report No. 8, April 1, 1981-March 31, 1982

    International Nuclear Information System (INIS)

    Walters, G.K.; Lane, N.F.

    1981-01-01

    The atomic and molecular physics program at Rice University addresses fundamental problems in structure, radiation-induced gas- and condensed-phase reaction kinetics and dynamics, and the mutual interactions of radiation, atoms, molecules, electrons and ions, particularly in highly unusual or exotic environments. The program emphasizes fundamental studies relating to new sources of energy, with close interaction between experimental and theoretical aspects of the research. Progress in the experimental program is reported in two principal areas, A) time resolved spectroscopy, and B) reactions in a flowing helium afterglow

  20. Molecular dynamics beyonds the limits: Massive scaling on 72 racks of a BlueGene/P and supercooled glass dynamics of a 1 billion particles system

    KAUST Repository

    Allsopp, Nicholas; Ruocco, Giancarlo; Fratalocchi, Andrea

    2012-01-01

    We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the short-range atomic dynamics

  1. Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

    Science.gov (United States)

    Saenz, A.

    2008-07-01

    The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some

  2. Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

    Directory of Open Access Journals (Sweden)

    Jenny Farmer

    2017-11-01

    Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

  3. Non-destructive Faraday imaging of dynamically controlled ultracold atoms

    Science.gov (United States)

    Gajdacz, Miroslav; Pedersen, Poul; Mørch, Troels; Hilliard, Andrew; Arlt, Jan; Sherson, Jacob

    2013-05-01

    We investigate non-destructive measurements of ultra-cold atomic clouds based on dark field imaging of spatially resolved Faraday rotation. In particular, we pursue applications to dynamically controlled ultracold atoms. The dependence of the Faraday signal on laser detuning, atomic density and temperature is characterized in a detailed comparison with theory. In particular the destructivity per measurement is extremely low and we illustrate this by imaging the same cloud up to 2000 times. The technique is applied to avoid the effect of shot-to-shot fluctuations in atom number calibration. Adding dynamic changes to system parameters, we demonstrate single-run vector magnetic field imaging and single-run spatial imaging of the system's dynamic behavior. The method can be implemented particularly easily in standard imaging systems by the insertion of an extra polarizing beam splitter. These results are steps towards quantum state engineering using feedback control of ultracold atoms.

  4. Ultrafast dissociation: An unexpected tool for probing molecular dynamics

    International Nuclear Information System (INIS)

    Morin, Paul; Miron, Catalin

    2012-01-01

    Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.

  5. Energetics and dynamics of atomic uranium levels

    International Nuclear Information System (INIS)

    Miron, E.

    1978-01-01

    New methods for discovering and identifying new electronic levels of atomic uranium and measuring parameters, such as radiative lifetimes and absorption cross-sections, are described. The uranium atoms are produced within an especially designed induction-heated oven. The uranium vapor is irradiated by nitrogen laser pumped, pulsed dye lasers. The various measurements are accomplished by detection of laser induced fluorescence from selectively excited levels. 138 atomic-uranium odd levels in the region 32260-34900 cm -1 and 16 even levels in the region 49500-49900 cm -1 are reported. Unique J values are presented for 64 levels and partial assignment (two possibilities) for 42 levels. Radiative lifetimes are presented for 134 levels. Absorption cross sections were measured for 12 transitions. Isotope shifts of 17 levels are given. Cross-sections for internal excitation transfer in uranium which are induced by collisions with argon atoms, are presented for 11 levels. (author)

  6. A molecular dynamics study of helium bombardments on tungsten nanoparticles

    Science.gov (United States)

    Li, Min; Hou, Qing; Cui, Jiechao; Wang, Jun

    2018-06-01

    Molecular dynamics simulations were conducted to study the bombardment process of a single helium atom on a tungsten nanoparticle. Helium atoms ranging from 50 eV to 50 keV were injected into tungsten nanoparticles with a diameter in the range of 2-12 nm. The retention and reflection of projectiles and sputtering of nanoparticles were calculated at various times. The results were found to be relative to the nanoparticle size and projectile energy. The projectile energy of 100 eV contributes to the largest retention of helium atoms in tungsten nanoparticles. The most obvious difference in reflection exists in the range of 3-10 keV. Around 66% of sputtering atoms is in forward direction for projectiles with incident energy higher than 10 keV. Moreover, the axial direction of the nanoparticles was demonstrated to influence the bombardment to some degree.

  7. Barium atoms and N20 molecular agregates reaction

    International Nuclear Information System (INIS)

    Visticot, J.P.; Mestdagh, J.M.; Alcaraz, C.; Cuvellier, J.; Berlande, J.

    1988-06-01

    The collisions between a barium atom and N20 molecular agregates are studied, for a better understanding of the solvation part in a chemical reaction. The experiments are carried out in a crossed molecular beam device. The light coming from the collision zone is scattered, and analysed by means of a photon detector. A time-of-flight technique is applied in the investigation of the beam's polymer concentration. The results show a nearly negligible chemiluminescent effect in the reaction between barium and N20 polymer. A solvated BaO formation mechanism is proposed to justify the experimental results [fr

  8. Survey of atomic and molecular data needs for fusion

    International Nuclear Information System (INIS)

    Lorenz, A.; Phillips, J.; Schmidt, J.J.; Lemley, J.R.

    1976-01-01

    Atomic and molecular data needs in five areas of plasma research and fusion technology are considered: Injection Systems (plasma heating by neutral particle beam injection and particle cluster beam injection); Plasma-Surface Interaction (sputtering, absorption, adsorption, reflection, evaporation, surface electron emission, interactions of atomic hydrogen isotopes, synchrotron radiation); Plasma Impurities and Cooling (electron impact ionization and excitation, recombination processes, charge exchange, reflection of H from wall surfaces); Plasma Diagnostics (atomic structure and transition probabilities, X-ray wave-length shift for highly ionized metals, electron capture collisions with H + and D + , heavy-ion collision ionization probe, photon scattering, emission spectroscopy); Laser-fusion Compression (microexplosion physics, diagnostics, microtarget design, laser systems requirements, laser development, reactor design needs)

  9. Assembly, destruction and manipulation of atomic, molecular and complex systems

    International Nuclear Information System (INIS)

    Le Padellec, Arnaud Pierre Frederic

    2003-04-01

    In this report for Accreditation to Supervise Researches (HDR), the author first indicates his professional curriculum (diplomas, teaching activities, responsibilities in the field of education and research, publications), and then proposes a presentation of his scientific works and researches. He notably proposes an overview of the different experimental techniques he implemented: CRYRING storage ring, confluent beams, flow post-discharge with mass spectrometry and Langmuir probe, crossed beams, and so on. He reports works dealing with the manipulation and destruction of atomic, molecular and complex systems: detachment of atomic anions by electronic impact, detachment and dissociation of small carbon aggregates by electronic impact, dissociative recombination, dissociative ionisation and excitation, creation of pairs of ions, manipulation of sodium fluoride aggregates. He finally presents research projects regarding the assembly of molecular and complex systems

  10. MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

    Science.gov (United States)

    Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

    2011-01-01

    We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

  11. On the dynamic polarizability of atoms

    International Nuclear Information System (INIS)

    Nuroh, K.; Zaremba, E.

    1989-04-01

    The positive frequency dependent polarizability of atoms is discussed in terms of the particle-hole polarization propagator. It is considered in the simplest approximation defined by the Bethe-Salpeter equation which includes a subset of particle-hole interactions to all orders in the Coulomb potential. Its solution is used to show the relationship between different formulations of atomic photoabsorption via the effective dipole matrix element (Fermi's 'golden rule'), the TDLDA and the reaction matrix. (author). 21 refs, 7 figs

  12. Observation of dynamic atom-atom correlation in liquid helium in real space.

    Science.gov (United States)

    Dmowski, W; Diallo, S O; Lokshin, K; Ehlers, G; Ferré, G; Boronat, J; Egami, T

    2017-05-04

    Liquid 4 He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4 He atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.

  13. Accelerating Molecular Dynamic Simulation on Graphics Processing Units

    Science.gov (United States)

    Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.

    2009-01-01

    We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337

  14. Molecular dynamics simulation of cascade damage in gold

    International Nuclear Information System (INIS)

    Alonso, E.; Caturla, M.J.; Tang, M.; Huang, H.; Diaz de la Rubia, T.

    1997-01-01

    High-energy cascades have been simulated in gold using molecular dynamics with a modified embedded atom method potential. The results show that both vacancy and interstitial clusters form with high probability as a result of intracascade processes. The formation of clusters has been interpreted in terms of the high pressures generated in the core of the cascade during the early stages. The authors provide evidence that correlation between interstitial and vacancy clustering exists

  15. Thermal conductivity of ZnTe investigated by molecular dynamics

    International Nuclear Information System (INIS)

    Wang Hanfu; Chu Weiguo

    2009-01-01

    The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.

  16. International Bulletin on Atomic and Molecular Data for Fusion. No. 28

    International Nuclear Information System (INIS)

    Hughes, J.G.

    1985-03-01

    The bulletin presents a selected bibliography (462 literature pieces) on atomic and molecular data relevant to fusion research and technology. It also gives a list of indexed papers, separately on structure and spectra, atomic and molecular collisions, and surface effects

  17. International Bulletin on Atomic and Molecular Data for Fusion. No. 31

    International Nuclear Information System (INIS)

    Hughes, J.G.

    1985-12-01

    This bulletin presents a selected bibliography (363 literature pieces) on atomic and molecular data for fusion. It also gives a list of indexed papers on structure and spectra, atomic and molecular collisions, and surface interactions

  18. Molecular dynamics using quasielastic neutron scattering

    CERN Document Server

    Mitra, S

    2003-01-01

    Quasielastic neutron scattering (QENS) technique is well suited to study the molecular motions (rotations and translations) in solids or liquids. It offers a unique possibility of analysing spatial dimensions of atomic or molecular processes in their development over time. We describe here some of the systems studied using the QENS spectrometer, designed, developed and commissioned at Dhruva reactor in Trombay. We have studied a variety of systems to investigate the molecular motion, for example, simple molecular solids, molecules adsorbed in confined medium like porous systems or zeolites, monolayer-protected nano-sized metal clusters, water in Portland cement as it cures with time, etc. (author)

  19. Thermally driven molecular linear motors - A molecular dynamics study

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

    2009-01-01

    We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

  20. Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Saiz, Fernan [Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, London, SW7 2A7 (United Kingdom); Gamero-Castaño, Manuel, E-mail: mgameroc@uci.edu [Department of Mechanical and Aerospace Engineering, University of California, Irvine, California, 92697 (United States)

    2016-06-15

    The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.

  1. Molecular dynamics of nanodroplet impact: The effect of the projectile’s molecular mass on sputtering

    International Nuclear Information System (INIS)

    Saiz, Fernan; Gamero-Castaño, Manuel

    2016-01-01

    The impact of electrosprayed nanodroplets on ceramics at several km/s alters the atomic order of the target, causing sputtering, surface amorphization and cratering. The molecular mass of the projectile is known to have a strong effect on the impact phenomenology, and this article aims to rationalize this dependency using molecular dynamics. To achieve this goal, the article models the impact of four projectiles with molecular masses between 45 and 391 amu, and identical diameters and kinetic energies, 10 nm and 63 keV, striking a silicon target. In agreement with experiments, the simulations show that the number of sputtered atoms strongly increases with molecular mass. This is due to the increasing intensity of collision cascades with molecular mass: when the fixed kinetic energy of the projectile is distributed among fewer, more massive molecules, their collisions with the target produce knock-on atoms with higher energies, which in turn generate more energetic and larger numbers of secondary and tertiary knock-on atoms. The more energetic collision cascades intensify both knock-on sputtering and, upon thermalization, thermal sputtering. Besides enhancing sputtering, heavier molecules also increase the fraction of the projectile’s energy that is transferred to the target, as well as the fraction of this energy that is dissipated.

  2. Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

    Science.gov (United States)

    Negre, Christian

    2017-06-01

    A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

  3. Atomic and molecular layer deposition for surface modification

    Energy Technology Data Exchange (ETDEWEB)

    Vähä-Nissi, Mika, E-mail: mika.vaha-nissi@vtt.fi [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland); Sievänen, Jenni; Salo, Erkki; Heikkilä, Pirjo; Kenttä, Eija [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland); Johansson, Leena-Sisko, E-mail: leena-sisko.johansson@aalto.fi [Aalto University, School of Chemical Technology, Department of Forest Products Technology, PO Box 16100, FI‐00076 AALTO (Finland); Koskinen, Jorma T.; Harlin, Ali [VTT Technical Research Centre of Finland, PO Box 1000, FI‐02044 VTT (Finland)

    2014-06-01

    Atomic and molecular layer deposition (ALD and MLD, respectively) techniques are based on repeated cycles of gas–solid surface reactions. A partial monolayer of atoms or molecules is deposited to the surface during a single deposition cycle, enabling tailored film composition in principle down to molecular resolution on ideal surfaces. Typically ALD/MLD has been used for applications where uniform and pinhole free thin film is a necessity even on 3D surfaces. However, thin – even non-uniform – atomic and molecular deposited layers can also be used to tailor the surface characteristics of different non-ideal substrates. For example, print quality of inkjet printing on polymer films and penetration of water into porous nonwovens can be adjusted with low-temperature deposited metal oxide. In addition, adhesion of extrusion coated biopolymer to inorganic oxides can be improved with a hybrid layer based on lactic acid. - Graphical abstract: Print quality of a polylactide film surface modified with atomic layer deposition prior to inkjet printing (360 dpi) with an aqueous ink. Number of printed dots illustrated as a function of 0, 5, 15 and 25 deposition cycles of trimethylaluminum and water. - Highlights: • ALD/MLD can be used to adjust surface characteristics of films and fiber materials. • Hydrophobicity after few deposition cycles of Al{sub 2}O{sub 3} due to e.g. complex formation. • Same effect on cellulosic fabrics observed with low temperature deposited TiO{sub 2}. • Different film growth and oxidation potential with different precursors. • Hybrid layer on inorganic layer can be used to improve adhesion of polymer melt.

  4. The 2011 Dynamics of Molecular Collisions Conference

    Energy Technology Data Exchange (ETDEWEB)

    Nesbitt, David J. [JILA, NIST

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

  5. Reactions of carbon atoms in pulsed molecular beams

    Energy Technology Data Exchange (ETDEWEB)

    Reisler, H. [Univ. of Southern California, Los Angeles (United States)

    1993-12-01

    This research program consists of a broad scope of experiments designed to unravel the chemistry of atomic carbon in its two spin states, P and D, by using well-controlled initial conditions and state-resolved detection of products. Prerequisite to the proposed studies (and the reason why so little is known about carbon atom reactions), is the development of clean sources of carbon atoms. Therefore, in parallel with the studies of its chemistry and reaction dynamics, the authors continuously explore new, state-specific and efficient ways of producing atomic carbon. In the current program, C({sup 3}P) is produced via laser ablation of graphite, and three areas of study are being pursued: (i) exothermic reactions with small inorganic molecules (e.g., O{sub 2}, N{sub 2}O, NO{sub 2}) that can proceed via multiple pathways; (ii) the influence of vibrational and translational energy on endothermic reactions involving H-containing reactants that yield CH products (e.g., H{sub 2}O H{sub 2}CO); (iii) reactions of C({sup 3}P) with free radicals (e.g., HCO, CH{sub 3}O). In addition, the authors plan to develop a source of C({sup 1}D) atoms by exploiting the pyrolysis of diazotetrazole and its salts in the ablation source. Another important goal involves collaboration with theoreticians in order to obtain relevant potential energy surfaces, rationalize the experimental results and predict the roles of translational and vibrational energies.

  6. Dynamic polarizability of a complex atom in strong laser fields

    International Nuclear Information System (INIS)

    Rapoport, L.P.; Klinskikh, A.F.; Mordvinov, V.V.

    1997-01-01

    An asymptotic expansion of the dynamic polarizability of a complex atom in a strong circularly polarized light field is found for the case of high frequencies. The self-consistent approximation of the Hartree-Fock type for the ''atom+field'' system is developed, within the framework of which a numerical calculation of the dynamic polarizability of Ne, Kr, and Ar atoms in a strong radiation field is performed. The strong field effect is shown to manifest itself not only in a change of the energy spectrum and the character of behavior of the wave functions of atomic electrons, but also in a modification of the one-electron self-consistent potential for the atom in the field

  7. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    African Journals Online (AJOL)

    A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

  8. Spin-diffusions and diffusive molecular dynamics

    Science.gov (United States)

    Farmer, Brittan; Luskin, Mitchell; Plecháč, Petr; Simpson, Gideon

    2017-12-01

    Metastable configurations in condensed matter typically fluctuate about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of classical molecular dynamics (MD) methods and has spurned the development of a host of approximate algorithms. One recently proposed method is diffusive MD which aims at integrating a system of ordinary differential equations describing the likelihood of occupancy by one of two species, in the case of a binary alloy, while quasistatically evolving the locations of the atoms. While diffusive MD has shown itself to be efficient and provide agreement with observations, it is fundamentally a model, with unclear connections to classical MD. In this work, we formulate a spin-diffusion stochastic process and show how it can be connected to diffusive MD. The spin-diffusion model couples a classical overdamped Langevin equation to a kinetic Monte Carlo model for exchange amongst the species of a binary alloy. Under suitable assumptions and approximations, spin-diffusion can be shown to lead to diffusive MD type models. The key assumptions and approximations include a well-defined time scale separation, a choice of spin-exchange rates, a low temperature approximation, and a mean field type approximation. We derive several models from different assumptions and show their relationship to diffusive MD. Differences and similarities amongst the models are explored in a simple test problem.

  9. Dynamic of cold-atom tips in anharmonic potentials

    Science.gov (United States)

    Menold, Tobias; Federsel, Peter; Rogulj, Carola; Hölscher, Hendrik; Fortágh, József

    2016-01-01

    Background: Understanding the dynamics of ultracold quantum gases in an anharmonic potential is essential for applications in the new field of cold-atom scanning probe microscopy. Therein, cold atomic ensembles are used as sensitive probe tips to investigate nanostructured surfaces and surface-near potentials, which typically cause anharmonic tip motion. Results: Besides a theoretical description of this anharmonic tip motion, we introduce a novel method for detecting the cold-atom tip dynamics in situ and real time. In agreement with theory, the first measurements show that particle interactions and anharmonic motion have a significant impact on the tip dynamics. Conclusion: Our findings will be crucial for the realization of high-sensitivity force spectroscopy with cold-atom tips and could possibly allow for the development of advanced spectroscopic techniques such as Q-control. PMID:28144505

  10. Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups

    Science.gov (United States)

    Kurbatov, A. O.; Balabaev, N. K.; Mazo, M. A.; Kramarenko, E. Yu.

    2018-01-01

    Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.

  11. Metal-halide lamp design: atomic and molecular data needed

    International Nuclear Information System (INIS)

    Lapatovich, Walter P

    2009-01-01

    Metal-halide lamps are a subset of high intensity discharge (HID) lamps so named because of their high radiance. These lamps are low temperature (∼0.5 eV), weakly ionized plasmas sustained in refractory but light transmissive envelopes by the passage of electric current through atomic and molecular vapors. For commercial applications, the conversion of electric power to light must occur with good efficiency and with sufficient spectral content throughout the visible (380-780 nm) to permit the light so generated to render colors comparable to natural sunlight. This is achieved by adding multiple metals to a basic mercury discharge. Because the vapor pressure of most metals is very much lower than mercury itself, metal-halide salts of the desired metals, having higher vapor pressures, are used to introduce the material into the basic discharge. The metal compounds are usually polyatomic iodides, which vaporize and subsequently dissociate as they diffuse into the bulk plasma. Metals with multiple visible transitions are necessary to achieve high photometric efficiency (efficacy) and good color. Compounds of Sc, Dy, Ho, Tm, Ce, Pr, Yb and Nd are commonly used. The electrons, atoms and radicals are in local thermodynamic equilibrium (LTE), but not with the radiation field. Strong thermal (10 6 K m -1 ) and density gradients are sustained in the discharge. Atomic radiation produced in the high-temperature core transits through colder gas regions where it interacts with cold atoms and un-dissociated molecules before exiting the lamp. Power balance and spectral output of the lamp are directly affected by the strength of atomic transitions. Attempts to simulate the radiative output of functional metal-halide lamps have been successful only in very simple cases. More data (e.g. the atomic transition probabilities of Ce i) are necessary to improve lamp performance, to select appropriate radiators and in scaling the lamp geometry to various wattages for specific applications.

  12. Molecular dynamics for reactions of heterogeneous catalysis

    NARCIS (Netherlands)

    Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

    1991-01-01

    An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

  13. molecular dynamics simulations and quantum chemical calculations

    African Journals Online (AJOL)

    ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

  14. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2011-01-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

  15. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

  16. Atomistic simulation of damage production by atomic and molecular ion irradiation in GaN

    International Nuclear Information System (INIS)

    Ullah, M. W.; Kuronen, A.; Nordlund, K.; Djurabekova, F.; Karaseov, P. A.; Titov, A. I.

    2012-01-01

    We have studied defect production during single atomic and molecular ion irradiation having an energy of 50 eV/amu in GaN by molecular dynamics simulations. Enhanced defect recombination is found in GaN, in accordance with experimental data. Instantaneous damage shows non-linearity with different molecular projectile and increasing molecular mass. Number of instantaneous defects produced by the PF 4 molecule close to target surface is four times higher than that for PF 2 molecule and three times higher than that calculated as a sum of the damage produced by one P and four F ion irradiation (P+4×F). We explain this non-linearity by energy spike due to molecular effects. On the contrary, final damage created by PF 4 and PF 2 shows a linear pattern when the sample cools down. Total numbers of defects produced by Ag and PF 4 having similar atomic masses are comparable. However, defect-depth distributions produced by these species are quite different, also indicating molecular effect.

  17. Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

    International Nuclear Information System (INIS)

    Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.

    2011-01-01

    This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.

  18. Molecular ions, Rydberg spectroscopy and dynamics

    International Nuclear Information System (INIS)

    Jungen, Ch.

    2015-01-01

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

  19. Pattern recognition in molecular dynamics. [FORTRAN

    Energy Technology Data Exchange (ETDEWEB)

    Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

    1977-07-01

    An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

  20. Molecular ions, Rydberg spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

    2015-01-22

    Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

  1. Tuning the Electronic and Dynamical Properties of a Molecule by Atom Trapping Chemistry.

    Science.gov (United States)

    Pham, Van Dong; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie; Abad, Enrique; Dappe, Yannick J; Smogunov, Alexander; Lagoute, Jérôme

    2017-11-28

    The ability to trap adatoms with an organic molecule on a surface has been used to obtain a range of molecular functionalities controlled by the choice of the molecular trapping site and local deprotonation. The tetraphenylporphyrin molecule used in this study contains three types of trapping sites: two carbon rings (phenyl and pyrrole) and the center of a macrocycle. Catching a gold adatom on the carbon rings leads to an electronic doping of the molecule, whereas trapping the adatom at the macrocycle center with single deprotonation leads to a molecular rotor and a second deprotonation leads to a molecular jumper. We call "atom trapping chemistry" the control of the structure, electronic, and dynamical properties of a molecule achieved by trapping metallic atoms with a molecule on a surface. In addition to the examples previously described, we show that more complex structures can be envisaged.

  2. Lattice dynamics and molecular dynamics simulation of complex materials

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1997-01-01

    In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

  3. European Virtual Atomic And Molecular Data Center - VAMDC

    Science.gov (United States)

    Dimitrijevic, M. S.; Sahal-Brechot, S.; Kovacevic, A.; Jevremovic, D.; Popovic, L. C.

    2010-07-01

    Reliable atomic and molecular data are of great importance for different applications in astrophysics, atmospheric physics, fusion, environmental sciences, combustion chemistry, and in industrial applications from plasmas and lasers to lighting. Currently, very important resources of such data are highly fragmented, presented in different, nonstandardized ways, available through a variety of highly specialized and often poorly documented interfaces, so that the full exploitation of all their scientific worth is limited, hindering research in many topics like e.g. the characterization of extrasolar planets, understanding the chemistry of our local solar system and of the wider universe, the study of the terrestrial atmosphere and quantification of climate change; the development of the fusion rersearch, etc. The Virtual Atomic and Molecular Data Centre (http://www.vamdc.eu, VAMDC) is an European Union funded FP7 project aiming to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data. It will also provide a forum for training potential users and dissemination of expertise worldwide. Partners in the Consortium of the Project are: 1) Centre National de Recherche Scientifique - CNRS (Paris, Reims, Grenoble, Bordeaux, Dijon, Toulouse); 2) The Chancellor, Masters and Scholars of the University of Cambridge - CMSUC; 3) University College London - UCL; 4) Open University - OU; (Milton Keynes, England); 5) Universitaet Wien - UNIVIE; 6) Uppsala Universitet - UU; 7) Universitaet zu Koeln - KOLN; 8) Istituto Nazionale di Astrofisica - INAF (Catania, Cagliari); 9) Queen's University Belfast - QUB; 10) Astronomska Opservatorija - AOB (Belgrade, Serbia); 11) Institute of Spectroscopy RAS - ISRAN (Troitsk, Russia); 12) Russian Federal Nuclear Center - All-Russian Institute of Technical Physics - RFNC-VNIITF (Snezhinsk, Chelyabinsk Region, Russia; 13) Institute of Atmospheric Optics - IAO (Tomsk, Russia

  4. Percolation approach for atomic and molecular cluster formation

    International Nuclear Information System (INIS)

    Knospe, O.; Seifert, G.

    1987-12-01

    We apply a percolation approach for the theoretical analysis of mass spectra of molecular microclusters obtained by adiabatic expansion technique. The evolution of the shape of the experimental size distributions as function of stagnation pressure and stagnation temperature are theoretically reproduced by varying the percolation parameter. Remaining discrepancies between theory and experiment are discussed. In addition, the even-odd alternation as well as the 'magic' shell structure within metallic, secondary ion mass spectra are investigated by introducing statistical weights for the cluster formation probabilities. Shell correction energies of atomic clusters as function of cluster-size are deduced from the experimental data. (orig.)

  5. Application of atomic absorption in molecular analysis (spectrophotometry)

    International Nuclear Information System (INIS)

    Baliza, S.V.; Soledade, L.E.B.

    1981-01-01

    The apparatus of atomic absorption has been considered by all the experts in chemical analysis as one of the most important equipments in actual utilization in such field. Among its several applications one should emphasize direct and indirect metals analyses using flame, graphite furnace, cold vapor generator,... Besides such known applications, the authors have developed at the R and D Center of CSN a patent pendent method for the utilization of such equipment for molecular analysis, in substitution of a sophisticated and specific apparatus. (Author) [pt

  6. Dynamics of Oxidation of Aluminum Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers

    Science.gov (United States)

    Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen

    1999-06-01

    Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.

  7. Melting of Cu nanoclusters by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Li; Zhang, Yanning; Bian, Xiufang; Chen, Ying

    2003-04-14

    We present a detailed molecular dynamics study of the melting of copper nanoclusters with up to 8628 atoms within the framework of the embedded-atom method. The finding indicates that there exists an intermediate nanocrystal regime above 456 atoms. The linear relation between the cluster size and its thermodynamics properties is obeyed in this regime. Melting first occurs at the surface of the clusters, leading to T{sub m,N}=T{sub m,Bulk}-{alpha}N{sup -1/3}, dropping from T{sub m,Bulk}=1360 K to T{sub m,456}=990 K. In addition, the size, surface energy as well as the root mean square displacement (RMSD) of the clusters in the intermediate regime have been investigated.

  8. Crossed molecular beam studies of unimolecular reaction dynamics

    International Nuclear Information System (INIS)

    Buss, R.J.

    1979-04-01

    The study of seven radical-molecule reactions using the crossed molecular beam technique with supersonic nozzle beams is reported. Product angular and velocity distributions were obtained and compared with statistical calculations in order to identify dynamical features of the reactions. In the reaction of chlorine and fluorine atoms with vinyl bromide, the product energy distributions are found to deviate from predictions of the statistical model. A similar effect is observed in the reaction of chlorine atoms with 1, 2 and 3-bromopropene. The reaction of oxygen atoms with ICl and CF 3 I has been used to obtain an improved value of the IO bond energy, 55.0 +- 2.0 kcal mol -1 . In all reactions studied, the product energy and angular distributions are found to be coupled, and this is attributed to a kinematic effect of the conservation of angular momentum

  9. Understanding Molecular-Ion Neutral Atom Collisions for the Production of Ultracold Molecular Ions

    Science.gov (United States)

    2014-02-03

    SECURITY CLASSIFICATION OF: This project was superseded and replaced by another ARO-funded project of the same name, which is still continuing. The goal...cooled atoms," IOTA -COST Workshop on molecular ions, Arosa, Switzerland. 5. E.R. Hudson, "Sympathetic cooling of molecules with laser cooled

  10. A dynamical atomic simulation for the Ni-Al Wulff nanoparticle

    International Nuclear Information System (INIS)

    Tang, Jianfeng; Yang, Jianyu

    2013-01-01

    Ni-Al bimetallic nanoparticle structures are studied from a kinetic point of view. The diffusion and growth of Ni (or Al) atoms on Al (or Ni) cores with the Wulff structure are simulated by molecular dynamics and nudged elastic band methods. An analytic embedded atom model is applied to the two metals. The energy barriers of several typical diffusion processes of the adatoms on the nanoparticle surface are calculated. Results show that the incorporation of the Ni atoms into the Al core easily occurs, and the reverse process does not readily proceed. The growth simulations reveal that a better core-shell nanoparticle is obtained when the Al atoms are deposited on the Ni core at lower temperatures, and the deposition of the Ni atoms on the Al core leads to an amorphous surface. - Highlights: • The diffusion barrier of Ni (or Al) on Al (or Ni) Wulff nanoparticle is studied. • Ni atom can diffuse easily into Al core, and Al atom generally segregate on surface. • A core-shell nanoparticle is obtained for the deposition of Al atoms on Ni core. • Amorphous nanoparticle surface is obtained by depositing Ni atoms on Al core

  11. Molecular dynamics simulation of radiation damage cascades in diamond

    Energy Technology Data Exchange (ETDEWEB)

    Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  12. Pressure shifts and electron scattering in atomic and molecular gases

    International Nuclear Information System (INIS)

    Rupnik, K.; McGlynn, S.P.; Asaf, U.

    1994-01-01

    In this work, the authors focus on one aspect of Rydberg electron scattering, namely number density effects in molecular gases. The recent study of Rydberg states of CH 3 I and C 6 H 6 perturbed by H 2 is the first attempt to investigate number density effects of a molecular perturber on Rydberg electrons. Highly excited Rydberg states, because of their ''large orbital'' nature, are very sensitive to the surrounding medium. Photoabsorption or photoionization spectra of CH 3 I have also been measured as a function of perturber pressure in 11 different binary gas mixtures consisting of CH 3 I and each one of eleven different gaseous perturbers. Five of the perturbers were rare gases (He, Ne, Ar, Kr, Xe) and six were non-dipolar molecules (H 2 , CH 4 , N 2 , C 2 H 6 , C 3 H 8 ). The goal of this work is to underline similarities and differences between atomic and molecular perturbers. The authors first list some results of the molecular study

  13. Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kim, Woongkee; Kaviany, Massoud; Shim, J. H.

    2014-01-01

    It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments

  14. Photoionization cross section of atomic and molecular oxygen

    International Nuclear Information System (INIS)

    Pareek, P.N.

    1983-01-01

    Photoionization cross sections of atomic oxygen and dissociative photoionization cross sections of molecular oxygen were measured from their respective thresholds to 120 angstrom by use of a photoionization mass spectrometer in conjunction with a spark light source. The photoionization cross sections O 2 + parent ion and O + fragment ion from neutral O 2 were obtained by a technique that eliminated the serious problem of identifying the true abundances of O + ions. These ions are generally formed with considerable kinetic energy and, because most mass spectrometers discriminate against energetic ions, true O + abundances are difficult to obtain. In the present work the relative cross sections for producing O + ions are obtained and normalized against the total cross sections in a spectral region where dissociative ionization is not possible. The fragmentation cross sections for O + were then obtained by subtraction of O 2 + cross sections from the known total photoionization cross sections. The results are compared with the previously published measurements. The absolute photoionization cross section of atomic oxygen sigma 8 /sub +/ was measured at 304 A. The actual number density of oxygen atoms within the ionization region was obtained by measuring the fraction of 0 2 molecules dissociated. This sigma/sub +/ at 304 angstrom was used to convert the relative photoinization cross sections, measured as a function of wavelength using a calibrated photodiode, to absolute cross sections. The results are compared with previous measurements and calculated cross sections. angstrom Rydberg series converging to the OII 4 P state was observed

  15. Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals.

    Science.gov (United States)

    Sayfutyarova, Elvira R; Sun, Qiming; Chan, Garnet Kin-Lic; Knizia, Gerald

    2017-09-12

    We introduce the atomic valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multiconfiguration and multireference (MR) electronic structure calculations. Concretely, the technique constructs active molecular orbitals capable of describing all relevant electronic configurations emerging from a targeted set of atomic valence orbitals (e.g., the metal d orbitals in a coordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-reference wave function (such as from a Hartree-Fock or Kohn-Sham calculations) based on projectors to targeted atomic valence orbitals. We discuss the premises, theory, and implementation of the idea, and several of its variations are tested. To investigate the performance and accuracy, we calculate the excitation energies for various transition-metal complexes in typical application scenarios. Additionally, we follow the homolytic bond breaking process of a Fenton reaction along its reaction coordinate. While the described AVAS technique is not a universal solution to the active space problem, its premises are fulfilled in many application scenarios of transition-metal chemistry and bond dissociation processes. In these cases the technique makes MR calculations easier to execute, easier to reproduce by any user, and simplifies the determination of the appropriate size of the active space required for accurate results.

  16. Atomically precise graphene nanoribbon heterojunctions from a single molecular precursor

    Science.gov (United States)

    Nguyen, Giang D.; Tsai, Hsin-Zon; Omrani, Arash A.; Marangoni, Tomas; Wu, Meng; Rizzo, Daniel J.; Rodgers, Griffin F.; Cloke, Ryan R.; Durr, Rebecca A.; Sakai, Yuki; Liou, Franklin; Aikawa, Andrew S.; Chelikowsky, James R.; Louie, Steven G.; Fischer, Felix R.; Crommie, Michael F.

    2017-11-01

    The rational bottom-up synthesis of atomically defined graphene nanoribbon (GNR) heterojunctions represents an enabling technology for the design of nanoscale electronic devices. Synthetic strategies used thus far have relied on the random copolymerization of two electronically distinct molecular precursors to yield GNR heterojunctions. Here we report the fabrication and electronic characterization of atomically precise GNR heterojunctions prepared through late-stage functionalization of chevron GNRs obtained from a single precursor. Post-growth excitation of fully cyclized GNRs induces cleavage of sacrificial carbonyl groups, resulting in atomically well-defined heterojunctions within a single GNR. The GNR heterojunction structure was characterized using bond-resolved scanning tunnelling microscopy, which enables chemical bond imaging at T = 4.5 K. Scanning tunnelling spectroscopy reveals that band alignment across the heterojunction interface yields a type II heterojunction, in agreement with first-principles calculations. GNR heterojunction band realignment proceeds over a distance less than 1 nm, leading to extremely large effective fields.

  17. Phase-sensitive atomic dynamics in quantum light

    Science.gov (United States)

    Balybin, S. N.; Zakharov, R. V.; Tikhonova, O. V.

    2018-05-01

    Interaction between a quantum electromagnetic field and a model Ry atom with possible transitions to the continuum and to the low-lying resonant state is investigated. Strong sensitivity of atomic dynamics to the phase of applied coherent and squeezed vacuum light is found. Methods to extract the quantum field phase performing the measurements on the atomic system are proposed. In the case of the few-photon coherent state high accuracy of the phase determination is demonstrated, which appears to be much higher in comparison to the usually used quantum-optical methods such as homodyne detection.

  18. Atomic and Molecular Data Activities for Fusion Research in JAEA

    International Nuclear Information System (INIS)

    Nakano, T.

    2011-01-01

    The Japan Atomic Energy Agency (JAEA) has been producing, collecting and compiling cross-section data for atomic and molecular collisions and spectral data relevant to fusion research. In this talk, an overview of our activities since the last meeting in September 2009 will be presented. The state selective charge transfer cross-section data of Be 4+ , C 4+ and C 6+ by collision with H(n=2) in the collision energy range between 62 eV/amu and 6.2 keV/amu have been calculated with a molecular-bases close-coupling method. The calculated charge transfer data of C 4+ was implemented in a collisional-radiative model code for C 3+ , and it is shown that in some cases the charge transfer from C 4+ to H(n=2) populates predominantly C 3+ (n = 6, 7). The cross-section data of dissociative recombination and excitation of HD + , D 2+ , DT + , T 2+ 3 HeH + and 4 HeH + were produced by theoretical calculation. The principal quantum number of dissociated H atom isotopes was also given. The analytical expressions for the cross-section data for 26 processes of He-collision systems were produced in order to facilitate practical use of the data. The compiled data are in preparation for the web site at the URL of http://www-jt60.naka.jaea.go.jp/engish/JEAMDL/. The chemical sputtering yield data of CFC materials with hydrogen isotope collisions have been compiled. The ionization rate of W 44+ and the radiative and the dielectronic recombination rates of W 45+ were calculated with FAC. The ratio of these rates was compared with experimentally measured ratio of W 45+ density to W 44+ density in JT-60U, showing that the calculated ratio of the recombination ratio of W 45+ to the ionization rate of W 44+ is accurate within the experimental uncertainty (∼ 30%). The atomic and molecular data activities in JAEA are pursued in collaboration with Japanese universities, and other department of JAEA. (author)

  19. Molecular dynamics of TBP and DBP studied by neutron transmission

    International Nuclear Information System (INIS)

    Salles Filho, J.B.V.; Refinetti, M.E.; Fulfaro, R.; Vinhas, L.A.

    1984-04-01

    Differences between the properties of TBP and DBP, concerning the uranium extraction processes, may be related to certain characteristics of the molecular dynamics of each compound. In order to investigate the dynamical behaviour of hydrogen in these molecules, neutron transmission of TBP and DBP has been measured as a function of neutron wavelenght in the range 4.0 - 6.0 A, at room temperature. Scattering cross sections per hydrogen atom have been obtained. From the comparison with results previously obtained for n-butanol, similar dynamical behaviour of butyl radicals in these compounds could be observed. This similarity indicates that the presence of two or three butyl radicals in butylphosphate molecules does not exert influence in the hydrogen motion of methyl and methylene groups. This suggests that the different chemical behaviour between TBP and DBP is related to the dynamics of the hydrogen directly bound to the DBP phosphate group.(Author) [pt

  20. Molecular dynamics simulations on PGLa using NMR orientational constraints

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

    2015-11-15

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  1. International bulletin on atomic and molecular data for fusion. No. 59

    International Nuclear Information System (INIS)

    Stephens, J.A.; Bannister, M.E.; Fuhr, J.; Gilbody, H.B.

    2001-03-01

    The International Bulletin on Atomic and Molecular Data for Fusion is prepared by the Atomic and Molecular Data Unit of the International Atomic Energy Agency. It is distributed free of charge by the IAEA to assist in the development of fusion research and technology. In part 1, the Atomic and Molecular Data Information System (AMDIS) is presented. In Part 2, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Finally, the Author Index (part 4) refers to the bibliographic references contained in part 3

  2. International bulletin on atomic and molecular data for fusion. No. 58

    International Nuclear Information System (INIS)

    Stephens, J.; Bannister, M.E.; Fuhr, J.; Gilbody, H.B.

    2000-06-01

    The International Bulletin on Atomic and Molecular Data for Fusion is prepared by the Atomic and Molecular Data Unit of the International Atomic Energy Agency. It is distributed free of charge by the IAEA to assist in the development of fusion research and technology. In part 1, the Atomic and Molecular Data Information System (AMDIS) is presented. In Part 2, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Finally, the Author Index (part 4) refers to the bibliographic references contained in part 3

  3. Colloquium on Atomic, Molecular and Optical Physics of the French Physics Society. Days of Molecular Spectroscopy, Lille, 7-10 July 2008

    International Nuclear Information System (INIS)

    Balcou, Philippe; Aspect, Alain; Merkt, Frederic; Haroche, Serge; Hendecourt, Louis d'; Dereux, Alain; Bloch, Daniel; Courty, Jean-Michel; Demaison, Jean; Hynes, James T.; Lievin, Jacky; Billy, J.; Josse, V.; Zuo, Z.; Bernard, A.; Hambrecht, B.; Lugan, P.; Clement, D.; Sanchez-Palencia, L.; Bouyer, P.; Aspect, A.; Garreau, Jean-Claude; Chabe, Julien; Szriftgiser, Pascal; Lemarie, Gabriel; Gremaud, Benoit; Delande, Dominique; Simoni, Andrea; Browaeys, Antoine; Kasparian, Jerome; Boutou, Veronique; Guyon, Laurent; Courvoisier, Francois; Roth, Matthias; Roslund, Jon; Rabitz, Herschel; Bonacina, Luigi; Rondi, Ariana; Extermann, Jerome; Wolf, Jean-Pierre; Maitre, Philippe; Zehnacker, Anne; Le Barbu-Debus, Katia; Sidis, Victor; Aguillon, Francois; Sizun, Muriel; Rougeau, Nathalie; Teillet-Billy, Dominique; Bachellerie, Damien; Jeloaica, Leonard; Morisset, Sabine; Picaud, Sylvain; Cacciani, Patrice; Grosliere, Marie-Christine; Joly, Gilles; Joly, Nicolas; Kudlinsky, Alexandre; Martinelli, Gilbert; Buchard, Virginie; Tudorie, Marcela; Khelkhal, Mohamed; Cosleou, Jean; Hennequin, Daniel; Beaugeois, Maxime; Lebrun, Nathalie; Droz, Daniel; El Aydam, Mohamed; Gama, Marie-Jose; Ferri, Sandrine; Schyns, Bernadette; Courty, Jean Michel

    2008-07-01

    This colloquium of the French Physics Society on atomic, molecular and optical physics (and more particularly on molecular spectroscopy) comprised several mini-colloquia: methane and its applications in planetology, moving mirrors and Casimir, atoms and molecules in interaction with surfaces, electronic properties of small molecules, molecular spectroscopy for atmospheric applications, quantum memories in atomic sets, methods and applications of reaction dynamics, dynamics of super-excited molecular statuses, mass spectrometry, quantum spectroscopy and chemistry, spectroscopy and reactivity of of confined molecules, electronic and molecular dynamics, dipolar quantum gases. It also comprised plenary sessions: atto-second optics, the atomic Hanbury-Brown-Twiss effect with fermions and bosons, atom and molecule slowing down by Zeeman effect and by Stark effect on Rydberg levels, non destructive counting of photons trapped in a cavity, interstellar chemistry, atom-surface van der Waals interaction noticed in the exotic regime of short distances, communication, vulgarisation and education (the multiple lives of a scientific result), the actual precision of molecular parameters, towards the formation of an amine acid precursor in the interstellar medium via proton transfer, prediction of the ionized and excited molecular electronic structure by Quantum Chemistry (from bi-atomic to bio-molecules), direct observation of Anderson location of matter waves in a controlled disordered potential, experimental observation of the Anderson transition of cold atoms, ultra-cold collisions as a key towards the quantum world, Quantum physics with a single atom, Teramobile or plasma filaments to study the atmosphere, optimal control or how to discriminate two almost identical bio-molecules, infrared spectroscopy as a new dimension for mass spectrometry, chiral recognition in gaseous phase, interactions and reactions between H atoms and graphite surfaces, modelling of gas

  4. Element selective detection of molecular species applying chromatographic techniques and diode laser atomic absorption spectrometry.

    Science.gov (United States)

    Kunze, K; Zybin, A; Koch, J; Franzke, J; Miclea, M; Niemax, K

    2004-12-01

    Tunable diode laser atomic absorption spectroscopy (DLAAS) combined with separation techniques and atomization in plasmas and flames is presented as a powerful method for analysis of molecular species. The analytical figures of merit of the technique are demonstrated by the measurement of Cr(VI) and Mn compounds, as well as molecular species including halogen atoms, hydrogen, carbon and sulfur.

  5. Photo induced multiple fragmentation of atoms and molecules: Dynamics of Coulombic many-particle systems studied with the COLTRIMS reaction microscope

    International Nuclear Information System (INIS)

    Czasch, A.; Schmidt, L.Ph.H.; Jahnke, T.; Weber, Th.; Jagutzki, O.; Schoessler, S.; Schoeffler, M.S.; Doerner, R.; Schmidt-Boecking, H.

    2005-01-01

    Many-particle dynamics in atomic and molecular physics has been investigated by using the COLTRIMS reaction microscope. The COLTRIMS technique visualizes photon and ion induced many-particle fragmentation processes in the eV and milli-eV regime. It reveals the complete momentum pattern in atomic and molecular many-particle reactions comparable to the bubble chamber in nuclear physics

  6. Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

    2007-01-01

    The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

  7. Indistinguishability and interference in the coherent control of atomic and molecular processes

    International Nuclear Information System (INIS)

    Gong Jiangbin; Brumer, Paul

    2010-01-01

    The subtle and fundamental issue of indistinguishability and interference between independent pathways to the same target state is examined in the context of coherent control of atomic and molecular processes, with emphasis placed on possible 'which-way' information due to quantum entanglement established in the quantum dynamics. Because quantum interference between independent pathways to the same target state occurs only when the independent pathways are indistinguishable, it is first shown that creating useful coherence between nondegenerate states of a molecule for subsequent quantum interference manipulation cannot be achieved by collisions between atoms or molecules that are prepared in momentum and energy eigenstates. Coherence can, however, be transferred from light fields to atoms or molecules. Using a particular coherent control scenario, it is shown that this coherence transfer and the subsequent coherent phase control can be readily realized by the most classical states of light, i.e., coherent states of light. It is further demonstrated that quantum states of light may suppress the extent of phase-sensitive coherent control by leaking out some which-way information while 'incoherent interference control' scenarios proposed in the literature have automatically ensured the indistinguishability of multiple excitation pathways. The possibility of quantum coherence in photodissociation product states is also understood in terms of the disentanglement between photodissociation fragments. Results offer deeper insights into quantum coherence generation in atomic and molecular processes.

  8. Wavelet Analysis for Molecular Dynamics

    Science.gov (United States)

    2015-06-01

    Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific...problems, such as modeling crack initiation and propagation, or interfacial phenomena. In the present work, we introduce a wavelet-based approach to extend...Several functional forms are common for angle poten- tials complicating not only implementation but also choice of approximation. In all cases, the

  9. Proposal of flexible atomic and molecular process management for Monte Carlo impurity transport code based on object oriented method

    International Nuclear Information System (INIS)

    Asano, K.; Ohno, N.; Takamura, S.

    2001-01-01

    Monte Carlo simulation code on impurity transport has been developed by several groups to be utilized mainly for fusion related edge plasmas. State of impurity particle is determined by atomic and molecular processes such as ionization, charge exchange in plasma. A lot of atomic and molecular processes have been considered because the edge plasma has not only impurity atoms, but also impurity molecules mainly related to chemical erosion of carbon materials, and their cross sections have been given experimentally and theoretically. We need to reveal which process is essential in a given edge plasma condition. Monte Carlo simulation code, which takes such various atomic and molecular processes into account, is necessary to investigate the behavior of impurity particle in plasmas. Usually, the impurity transport simulation code has been intended for some specific atomic and molecular processes so that the introduction of a new process forces complicated programming work. In order to evaluate various proposed atomic and molecular processes, a flexible management of atomic and molecular reaction should be established. We have developed the impurity transport simulation code based on object-oriented method. By employing object-oriented programming, we can handle each particle as 'object', which enfolds data and procedure function itself. A user (notice, not programmer) can define property of each particle species and the related atomic and molecular processes and then each 'object' is defined by analyzing this information. According to the relation among plasma particle species, objects are connected with each other and change their state by themselves. Dynamic allocation of these objects to program memory is employed to adapt for arbitrary number of species and atomic/molecular reactions. Thus we can treat arbitrary species and process starting from, for instance, methane and acetylene. Such a software procedure would be useful also for industrial application plasmas

  10. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

    Science.gov (United States)

    Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C

    2013-11-07

    Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

  11. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

  12. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. As an example, recent calculations of the chi 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the chi 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, highly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate

  13. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  14. Molecular dynamics on diffusive time scales from the phase-field-crystal equation.

    Science.gov (United States)

    Chan, Pak Yuen; Goldenfeld, Nigel; Dantzig, Jon

    2009-03-01

    We extend the phase-field-crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of them. By solving the dynamical equation of the model, which is a partial differential equation, we are essentially performing molecular dynamics simulations on diffusive time scales. To illustrate this approach, we calculate the two-point correlation function of a fluid.

  15. Molecular dynamics and diffusion a compilation

    CERN Document Server

    Fisher, David

    2013-01-01

    The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

  16. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

  17. Recent developments at the atomic and molecular data unit of the International Atomic Energy Agency

    International Nuclear Information System (INIS)

    Clark, R.E.H.; )

    2002-01-01

    The Atomic and Molecular (A+M) Data Unit of the IAEA main purpose is to establish and maintain databases in support of nuclear fusion energy research. This encompasses a very large number of processes in atomic, molecular, and plasma - material interaction physics. Recent improvements and additions to these databases are presented. A prototype search engine, which searches five different sites for radiative data and two sites for electron impact excitation and ionization data is introduced. It is available at the IAEA, Weizmann Institute and GAPHYOR web sites. Data on erosion materials produced by the Co-ordinated research project (CRP) 'Plasma-interaction induced erosion of fusion reactor materials' was evaluated, fitted to physically realistic forms for angle and energy dependence and the resulting fits were added to the online electronic database. In a CRP on radiative power losses in plasmas, many lenghtly modelling calculations were carried out. In addition to providing the calculated radiated power, effective ionisation and recombination rate coefficients were derived. These data were stored along with the populations of the ion stages as well as the total radiation from each ion stage. Thus, it is possible to use these data to interpolate in temperature and electron density to obtain the radiated power at an arbitrary temperature and density. A preliminary version of a new interface to the bibliographic database at the A+M Data unit was developed, it allows the user to search by author and/or keyword. The resulting references are displayed along with a link to the home page of the journal where possible. A code for calculation electron impact excitation cross sections using the so-called 'average approximation' and a version of the Hartree-Fock atomic structure code were installed in the unit and can be run through an interface at the web page. (nevyjel)

  18. Vision-Augmented Molecular Dynamics Simulation of Nanoindentation

    Directory of Open Access Journals (Sweden)

    Rajab Al-Sayegh

    2015-01-01

    Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.

  19. Molecular dynamics modeling of polymer flammability

    International Nuclear Information System (INIS)

    Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

    1992-01-01

    Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

  20. Proceedings of the first European conference on atomic and molecular physics

    International Nuclear Information System (INIS)

    Delgado-Barrio, G.; Nebot, I.

    1994-01-01

    This monograph contains the proceedings of the ''First European Conference on Atomic and Molecular Physics'', held in Gandia (Spain) 1992. Among the several possibilities for the organization of the contributions to this monographic issue, we have chosen the following one. At the beginning of the book, we have placed the Experimental Papers, which we hope will be larger in future issues. This section is followed by the Quantum Chemical Contributions. Finally to close the monograph, we have presented the Dynamical Studies. The general idea behind this organization has been that the basic studies precede the applications and that the small systems come before the analysis of larger ones

  1. A MOLECULAR DYNAMICS STUDY ON SLOW ION INTERACTIONS WITH THE POLYCYCLIC AROMATIC HYDROCARBON MOLECULE ANTHRACENE

    NARCIS (Netherlands)

    Postma, J.; Hoekstra, Ronnie; Tielens, A. G. G. M.; Schlathölter, Thomas

    2014-01-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on

  2. First-principles molecular dynamics for metals

    International Nuclear Information System (INIS)

    Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

    1989-01-01

    A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

  3. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  4. Theory and application of quantum molecular dynamics

    CERN Document Server

    Zeng Hui Zhang, John

    1999-01-01

    This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

  5. Dynamic bremsstrahlung from relativistic particles scattered by atom

    International Nuclear Information System (INIS)

    Astapenko, V.A.; Bujmistrov, V.M.; Krotov, Yu.A.; Mikhajlov, L.K.; Trakhtenberg, L.I.

    1985-01-01

    The bremsstrahlung cross section for a relativistic particle scattered by an atom is calculated. In contrast to the screening approximation usually employed, the influence of the atomic electron on the bremsstrahlung is taken into account exactly, viz., the atomic electron is considered as a moving particle interacting with the electromagnetic field and not only as the source of a static external field. Consequently, along with the static term which leads to the Bethe-Heitw,ler formula, a ne dynamic, term appears in the transition amplitude. The corresponding cross section, the dynamic bremsstrahlung cross section, in certain frequensy ranges and certain ranges of the directions of photon emission exceeds considerably the static bremsstrahlung cross section

  6. Nonadiabatic electron wavepacket dynamics behind molecular autoionization

    Science.gov (United States)

    Matsuoka, Takahide; Takatsuka, Kazuo

    2018-01-01

    A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

  7. Ultrafast molecular dynamics illuminated with synchrotron radiation

    International Nuclear Information System (INIS)

    Bozek, John D.; Miron, Catalin

    2015-01-01

    Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

  8. Dynamic signature of molecular association in methanol

    International Nuclear Information System (INIS)

    Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.

    2016-01-01

    Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

  9. First-principles molecular dynamics study of Al/Alq3 interfaces

    Directory of Open Access Journals (Sweden)

    Kousuke Takeuchi et al

    2007-01-01

    Full Text Available We have carried out first-principles molecular dynamics simulations of Al deposition on tris (8-hydroxyquinoline aluminum (Alq3 layers to investigate atomic geometries and electronic properties of Al/Alq3 interfaces. Al atoms were ejected to Alq3 one by one with the kinetic energy of 37.4 kJ/mol, which approximately corresponds to the average kinetic energy of Al at the boiling temperature of metal Al. The first Al atom interacts with two of the three O atoms of meridional Alq3. Following Al atoms interact with Alq3 rather weakly and they tend to aggregate each other to form Al clusters. During the deposition process, Alq3 was not broken and its molecular structure remained essentially intact. At the interface, weak bonds between deposited Al atoms and N and C atoms were formed. The projected density of states (PDOS onto the Alq3 molecular orbitals shows gap states in between the highest occupied molecular orbitals (HOMOs and the lowest unoccupied molecular orbitals (LUMOs, which were experimentally observed by ultraviolet photoelectron spectroscopy (UPS and metastable atom electron spectroscopy (MAES. Our results show that even though the Alq3 molecular structure is retained, weak N–Al and C–Al bonds induce gap states.

  10. Quantum and semiclassical spin networks: from atomic and molecular physics to quantum computing and gravity

    Science.gov (United States)

    Aquilanti, Vincenzo; Bitencourt, Ana Carla P.; Ferreira, Cristiane da S.; Marzuoli, Annalisa; Ragni, Mirco

    2008-11-01

    The mathematical apparatus of quantum-mechanical angular momentum (re)coupling, developed originally to describe spectroscopic phenomena in atomic, molecular, optical and nuclear physics, is embedded in modern algebraic settings which emphasize the underlying combinatorial aspects. SU(2) recoupling theory, involving Wigner's 3nj symbols, as well as the related problems of their calculations, general properties, asymptotic limits for large entries, nowadays plays a prominent role also in quantum gravity and quantum computing applications. We refer to the ingredients of this theory—and of its extension to other Lie and quantum groups—by using the collective term of 'spin networks'. Recent progress is recorded about the already established connections with the mathematical theory of discrete orthogonal polynomials (the so-called Askey scheme), providing powerful tools based on asymptotic expansions, which correspond on the physical side to various levels of semi-classical limits. These results are useful not only in theoretical molecular physics but also in motivating algorithms for the computationally demanding problems of molecular dynamics and chemical reaction theory, where large angular momenta are typically involved. As for quantum chemistry, applications of these techniques include selection and classification of complete orthogonal basis sets in atomic and molecular problems, either in configuration space (Sturmian orbitals) or in momentum space. In this paper, we list and discuss some aspects of these developments—such as for instance the hyperquantization algorithm—as well as a few applications to quantum gravity and topology, thus providing evidence of a unifying background structure.

  11. On the nodal structure of atomic and molecular Wigner functions

    International Nuclear Information System (INIS)

    Dahl, J.P.; Schmider, H.

    1996-01-01

    In previous work on the phase-space representation of quantum mechanics, we have presented detailed pictures of the electronic one-particle reduced Wigner function for atoms and small molecules. In this communication, we focus upon the nodal structure of the function. On the basis of the simplest systems, we present an expression which relates the oscillatory decay of the Wigner function solely to the dot product of the position and momentum vector, if both arguments are large. We then demonstrate the regular behavior of nodal patterns for the larger systems. For the molecular systems, an argument analogous to the open-quotes bond-oscillatory principleclose quotes for momentum densities links the nuclear framework to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic nodes

  12. A molecular dynamics study of energetic particle bombardment on diamond

    International Nuclear Information System (INIS)

    Li Rongbin; Dai Yongbing; Hu Xiaojun; Shen Hesheng; He Xianchang

    2003-01-01

    Molecular dynamic simulations, utilizing the Tersoff many-body potential, are used to investigate the microscopic processes of a single boron atom with an energy of 500 eV implanted into the diamond (001) 2 x 1 reconstructed surface. By calculating the variation of the mean coordination number with time, the lifetime of a thermal spike created by B bombardment is about 0.18 ps. Formation of the split-interstitial composed of projectile and lattice atom (B-C) is observed. The total potential energy of the system decreases about 0.56 eV with a stable B split-interstitial existing in diamond. Lattice relaxations in the diamond (001) 2 x 1 reconstructed surface or near surface of the simulated have been discussed, and the results show that the outermost layer atoms tend to move inward and other atoms move outward, while the interplanar distance between the outermost layer and the second layer has been shortened by 15%, compared with its starting interplanar distance. Stress distribution in the calculated diamond configuration is inhomogeneous. After boron implanted into diamond with an energy of 500 eV, there is an excess of compressively stressed atoms in the lattice, which induces the total stress being compressive

  13. Nanojoining of crossed Ag nanowires: a molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Jianlei, E-mail: cjlxjtu@mail.xjtu.edu.cn; Wang, Xuewen; Barayavuga, Theogene; Mei, Xuesong; Wang, Wenjun [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); He, Xiaoqiao, E-mail: bcxqhe@cityu.edu.hk [City University of Hong Kong, Department of Architecture and Civil Engineering (Hong Kong)

    2016-07-15

    Ag nanowires are considered to be the promising candidates for future electronic circuit owing to the excellent electrical and thermal properties, with the miniaturization of electronics devices into nanometer scale. Though interconnect technology between Ag nanowires (Ag NWs) is essential for nanofunctional devices, it lacks sufficient experimental data. Besides, the determination of Ag NW interconnection configuration is experimentally difficult to do for lacking the sufficient investigation of atomic configuration evolution during nanojoining process. So the nanojoining between the crossed Ag NWs with the same diameter of 2 nm and different lengths was performed by molecular dynamics simulation to explain the unclear nanojoining mechanism based on thermal effect. As the simulation results present, when the nanojoining temperature is relatively high, though the Ag NWs are connected with the interpenetration effect of Ag atoms at the crossed nanojunction area, the nanostructures of Ag NWs have been seriously deformed with shorter length and larger diameter, showing relatively more obvious melting characteristics based on the chaotic atomic structures. If the temperature is reduced to 300 K as cold welding, the crossed Ag NWs can be partially contacted with the partial mixture of Ag atoms, and the interstices always exist between the Si surface and the upper Ag nanowire. In addition, the obvious dislocation phenomenon will appear and evolve as time goes on. Consequently, the dominant mechanism was revealed for providing a fundamental understanding of how ‘hot’ and ‘cold’ welding technology affects the atomic contact configuration, respectively.

  14. Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

    Science.gov (United States)

    2016-06-06

    2012): 0. doi: 10.1103/PhysRevLett.109.223002 Kuang Chen, Scott T. Sullivan, Wade G. Rellergert, Eric R. Hudson. Measurement of the Coulomb Logarithm...or fellowships for further studies in science, mathematics, engineering or technology fields: Student Metrics This section only applies to graduating...clouds of Ba+ ions and Ca atoms. Due to the strong Coulomb interaction, the Ba+ ions quickly cool the molecular ion translation motion, while the

  15. The Atom in a Molecule: Implications for Molecular Structure and Properties

    Science.gov (United States)

    2016-05-23

    Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

  16. International bulletin on atomic and molecular data for fusion. No. 64. October 2005

    International Nuclear Information System (INIS)

    Humbert, D.; Bannister, M.E.; Bretagne, J.; Fuhr, J.

    2005-10-01

    This bulletin comprises updated atomic and molecular data for fusion. It contains four parts. In part one the Atomic and Molecular Data Information System (AMDIS) of the IAEA is presented. In part two, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions. Part three contains the bibliographic data for both indexed and and non-indexed references. The author index (part four) refers to the bibliographic references contained in part three

  17. International bulletin on atomic and molecular data for fusion. No. 63

    International Nuclear Information System (INIS)

    Humbert, D.; Bannister, M.E.; Bretagne, J.; Fuhr, J.

    2004-10-01

    This bulletin comprises updated atomic and molecular data for fusion. It contains four parts. In part one the Atomic and Molecular Data Information System (AMDIS) of the IAEA is presented. In part two, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions. Part three contains the bibliographic data for both indexed and and non-indexed references. The author index (part four) refers to the bibliographic references contained in part three

  18. International bulletin on atomic and molecular data for fusion. No. 62. August 2003

    International Nuclear Information System (INIS)

    Humbert, D.; Bannister, M.E.; Delcroix, J.L.; Fuhr, J.

    2003-10-01

    This bulletin comprises updated atomic and molecular data for fusion. It contains four parts. In part one the Atomic and Molecular Data Information System (AMDIS) of the IAEA is presented. In part two, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions. Part three contains the bibliographic data for both indexed and and non-indexed references. The author index (part four) refers to the bibliographic references contained in part three

  19. International bulletin on atomic and molecular data for fusion. No. 65. July 2006

    International Nuclear Information System (INIS)

    Humbert, D.; Bannister, M.E.; Bretagne, J.; Fuhr, J.

    2006-08-01

    This bulletin comprises updated atomic and molecular data for fusion. It contains four parts. In part one the Atomic and Molecular Data Information System (AMDIS) of the IAEA is presented. In part two, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions. Part three contains the bibliographic data for both indexed and and non-indexed references. The author index (part four) refers to the bibliographic references contained in part three

  20. International bulletin on atomic and molecular data for fusion. No. 53

    International Nuclear Information System (INIS)

    Stephens, J.A.

    1997-11-01

    The International Bulletin on Atomic and Molecular Data for Fusion is presented in four parts: 1) The Atomic and Molecular Data Information System (AMDIS) of the IAEA; 2) the indexed papers listed separately for structure and spectra, atomic and molecular collisions, and surface interactions; 3) all bibliographic data for both the indexed and non-indexed references; 4) the Author Index refers to the bibliographic references contained in Part 3

  1. International bulletin on atomic and molecular data for fusion. No. 47

    International Nuclear Information System (INIS)

    Botero, J.

    1993-12-01

    This bulletin, published by the IAEA, provides atomic and molecular data references relevant to fusion research and technology. In part I the indexation of the papers is provided separately for (i) structure and spectra, (ii) atomic and molecular collisions, and (iii) surface interactions. Part II contains the bibliographic data for the above-listed topics and for high-energy laser and beam-matter interaction of atomic particles with fields. Also included are sections on atomic and molecular data needs for fusion research and on news about ALADDIN (A Labelled Atomic Data INterface) and evaluated data bases

  2. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    International Nuclear Information System (INIS)

    Mugnai, Mauro L.; Elber, Ron

    2015-01-01

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide

  3. Ti and Zr surfaces studied by molecular dynamics

    International Nuclear Information System (INIS)

    Pascuet, Maria I.; Passianot, Roberto C.; Monti, Ana M.

    2003-01-01

    The interaction between point defects technique and the (0001), (1-210), (10-10) surfaces in Ti and Zr is studied by the molecular dynamics technique. Both of metals are in the hexagonal structure and within a temperature range of 100 to 900 K. The atomic interactions are modeled by EAM-type many-body potentials, that were used previously in static simulations. New migration mechanisms are unraveled and others are verified with respect to those already proposed in the static studies. Also included is an analysis of the vacancy stability in the sub-surface layers of the prismatic surfaces. (author)

  4. Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals

    International Nuclear Information System (INIS)

    Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon

    2000-01-01

    We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the direction form intersecting stacking faults by slippage along {111} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society

  5. Structural, dynamical, and electronic properties of amorphous silicon: An ab initio molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Car, R.; Parrinello, M.

    1988-01-18

    An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.

  6. Molecular dynamics simulations of lysozyme in water/sugar solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2008-04-18

    Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.

  7. Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Smith, R.W.

    1991-01-01

    Molecular dynamics has been used with a Lenard-Jones (6-12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined as E=(E tot -E gnd )/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission. (orig.)

  8. Atomic and molecular photoelectron and Auger-electron-spectroscopy studies using synchrotron radiation

    International Nuclear Information System (INIS)

    Southworth, S.H.

    1982-01-01

    Electron spectroscopy, combined with synchrotron radiation, was used to measure the angular distributions of photoelectrons and Auger electrons from atoms and molecules as functions of photon energy. The branching ratios and partial cross sections were also measured in certain cases. By comparison with theoretical calculations, the experimental results are interpreted in terms of the characteristic electronic structure and ionization dynamics of the atomic or molecular sample. The time structure of the synchrotron radiation source was used to record time-of-flight (TOF) spectra of the ejected electrons. The double-angle-TOF method for the measurement of photoelectron angular distributions is discussed. This technique offers the advantages of increased electron collection efficiency and the elimination of certain systematic errors. An electron spectroscopy study of inner-shell photoexcitation and ionization of Xe, photoelectron angular distributions from H 2 and D 2 , and photoionization cross sections and photoelectron asymmetries of the valence orbitals of NO are reported

  9. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    Science.gov (United States)

    Shekhar, Adarsh

    Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

  10. Dynamical density functional theory for dense atomic liquids

    International Nuclear Information System (INIS)

    Archer, A J

    2006-01-01

    Starting from Newton's equations of motion, we derive a dynamical density functional theory (DDFT) applicable to atomic liquids. The theory has the feature that it requires as input the Helmholtz free energy functional from equilibrium density functional theory. This means that, given a reliable equilibrium free energy functional, the correct equilibrium fluid density profile is guaranteed. We show that when the isothermal compressibility is small, the DDFT generates the correct value for the speed of sound in a dense liquid. We also interpret the theory as a dynamical equation for a coarse grained fluid density and show that the theory can be used (making further approximations) to derive the standard mode coupling theory that is used to describe the glass transition. The present theory should provide a useful starting point for describing the dynamics of inhomogeneous atomic fluids

  11. Atomic dynamics with photon-dressed core states

    International Nuclear Information System (INIS)

    Robicheaux, F.

    1993-01-01

    This paper describes the atomic dynamics when a Rydberg atom is in a laser field which is resonant with a dipole-allowed core transition. The main approximation is to completely ignore the (short-range, direct) interaction of the outer electron with the resonant laser which is the same approximation used with great success in calculating the spectrum due to isolated core excitations (ICE). The atom autoionizes when the core absorbs a photon, because the electron can then inelastically scatter from the excited core state, gaining enough energy to escape the atom. Despite neglecting the direct interaction between the outermost electron and the laser, the laser profoundly affects the autoionization dynamics. This effect is incorporated through a frame transformation between the dressed and undressed core states which only utilizes the field free atomic scattering parameters. A two-color experiment is proposed which might be able to measure nonperturbative effects arising from the dressed core states. The usual ICE transition rate is obtained through a perturbative expansion. Generic effects are examined through a model problem. A calculation of the Mg spectrum when the driving laser is tuned to the 3s 1/2- 3p 1/2 or the 3s 1/2- 3p 3/2 transition is presented

  12. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

    Akahoshi, Y.; Schmauder, S.; Ludwig, M.

    1998-01-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  13. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  14. Molecular dynamics simulations of RNA motifs

    Czech Academy of Sciences Publication Activity Database

    Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

    2002-01-01

    Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

  15. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  16. Molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

  17. Catalysis and communication in dynamic molecular networks

    NARCIS (Netherlands)

    Fanlo Virgos, Hugo

    2015-01-01

    The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

  18. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  19. Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

    Science.gov (United States)

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

    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.

  20. 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.

  1. A hybrid algorithm for parallel molecular dynamics simulations

    Science.gov (United States)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  2. Molecular dynamics simulation of annealed ZnO surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Min, Tjun Kit; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

    2015-04-24

    The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.

  3. Lightweight computational steering of very large scale molecular dynamics simulations

    International Nuclear Information System (INIS)

    Beazley, D.M.

    1996-01-01

    We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages

  4. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

    Directory of Open Access Journals (Sweden)

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  5. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  6. Dynamics of entanglement between two atomic samples with spontaneous scattering

    International Nuclear Information System (INIS)

    Di Lisi, Antonio; De Siena, Silvio; Illuminati, Fabrizio

    2004-01-01

    We investigate the effects of spontaneous scattering on the evolution of entanglement of two atomic samples, probed by phase-shift measurements on optical beams interacting with both samples. We develop a formalism of conditional quantum evolutions and present a wave function analysis implemented in numerical simulations of the state vector dynamics. This method allows us to track the evolution of entanglement and to compare it with the predictions obtained when spontaneous scattering is neglected. We provide numerical evidence that the interferometric scheme to entangle atomic samples is only marginally affected by the presence of spontaneous scattering and should thus be robust even in more realistic situations

  7. Dynamic strain-induced transformation: An atomic scale investigation

    International Nuclear Information System (INIS)

    Zhang, H.; Pradeep, K.G.; Mandal, S.; Ponge, D.; Springer, H.; Raabe, D.

    2015-01-01

    Phase transformations provide the most versatile access to the design of complex nanostructured alloys in terms of grain size, morphology, local chemical constitution etc. Here we study a special case of deformation induced phase transformation. More specifically, we investigate the atomistic mechanisms associated with dynamic strain-induced transformation (DSIT) in a dual-phased multicomponent iron-based alloy at high temperatures. DSIT phenomena and the associated secondary phase nucleation were observed at atomic scale using atom probe tomography. The obtained local chemical composition was used for simulating the nucleation process which revealed that DSIT, occurring during load exertion, proceeds by a diffusion-controlled nucleation process

  8. Classical molecular dynamics simulation on the dynamical properties of H2 on silicene layer

    Directory of Open Access Journals (Sweden)

    Casuyac Miqueas

    2016-01-01

    Full Text Available This study investigates the diffusion of hydrogen molecule physisorbed on the surface of silicene nanoribbon (SiNRusing the classical molecular dynamic (MD simulation in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator. The interactions between silicon atoms are modeled using the modified Tersoff potential, the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO potential for hydrogen – hydrogen interaction and the Lennard – Jones potential for the physisorbed H2 on SiNR. By varying the temperatures (60 K Δ 130 K, we observed that the Δxdisplacement of H2 on the surface SiNR shows a Brownian motion on a Lennard-Jones potential and a Gaussian probability distribution can be plotted describing the diffusion of H2. The calculated mean square displacement (MSD was approximately increasing in time and the activation energy barrier for diffusion has been found to be 43.23meV.

  9. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  10. International bulletin on atomic and molecular data for fusion. No. 46

    International Nuclear Information System (INIS)

    Botero, J.

    1993-06-01

    The bulletin is published by the International Atomic Energy Agency to provide atomic and molecular data relevant to fusion research and technology. In Part I the indexed papers are listed separately for (i) structure and spectra (energy levels, wavelengths; transition probabilities, oscillator strengths; interatomic potentials); (ii) atomic and molecular collisions (photon collisions; electron collisions; heavy-particle collisions; homonuclear sequences; isoelectronic sequences), and (iii) surface interactions (sputtering; chemical reactions; trapping and detrapping; surface damage; blistering, flaking; secondary electron emission). Part II contains the bibliographic data for the above listed topics and for high energy laser- and beam-matter interaction; interaction of atomic particles with fields. The atomic and molecular data needs in fusion research, as identified during the IAEA Consultants' Meeting on 'Atomic and Molecular Database for Hydrogen Recycling and Helium Exhaust from Fusion Reactors', June 1992, Vienna, are listed, covering (i) atomic and molecular collision processes, (ii) particle-surface interaction processes, and (iii) the status of data bases on atomic and molecular data and plasma-surface interactions. News on the ALADDIN (A labelled Atomic Data INterface) system is provided. Finally, a list of evaluated atomic and molecular data bases is provided

  11. Dynamical quenching of tunneling in molecular magnets

    Energy Technology Data Exchange (ETDEWEB)

    José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

    2015-12-15

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

  12. Dynamical quenching of tunneling in molecular magnets

    International Nuclear Information System (INIS)

    José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

    2015-01-01

    It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation

  13. Capturing Chemistry in Action with Electrons: Realization of Atomically Resolved Reaction Dynamics.

    Science.gov (United States)

    Ischenko, Anatoly A; Weber, Peter M; Miller, R J Dwayne

    2017-08-23

    One of the grand challenges in chemistry has been to directly observe atomic motions during chemical processes. The depiction of the nuclear configurations in space-time to understand barrier crossing events has served as a unifying intellectual theme connecting the different disciplines of chemistry. This challenge has been cast as an imaging problem in which the technical issues reduce to achieving not only sufficient simultaneous space-time resolution but also brightness for sufficient image contrast to capture the atomic motions. This objective has been met with electrons as the imaging source. The review chronicles the first use of electron structural probes to study reactive intermediates, to the development of high bunch charge electron pulses with sufficient combined spatial-temporal resolution and intensity to literally light up atomic motions, as well as the means to characterize the electron pulses in terms of temporal brightness and image reconstruction. The use of femtosecond Rydberg spectroscopy as a novel means to use internal electron scattering within the molecular reference frame to obtain similar information on reaction dynamics is also discussed. The focus is on atomically resolved chemical reaction dynamics with pertinent references to work in other areas and forms of spectroscopy that provide additional information. Effectively, we can now directly observe the far-from-equilibrium atomic motions involved in barrier crossing and categorize chemistry in terms of a power spectrum of a few dominant reaction modes. It is this reduction in dimensionality that makes chemical reaction mechanisms transferrable to seemingly arbitrarily complex (large N) systems, up to molecules as large as biological macromolecules (N > 1000 atoms). We now have a new way to reformulate reaction mechanisms using an experimentally determined dynamic mode basis that in combination with recent theoretical advances has the potential to lead to a new conceptual basis for

  14. Selective vibrational pumping of molecular hydrogen via gas phase atomic recombination.

    Science.gov (United States)

    Esposito, Fabrizio; Capitelli, Mario

    2009-12-31

    Formation of rovibrational excited molecular hydrogen from atomic recombination has been computationally studied using three body dynamics and orbiting resonance theory. Each of the two methods in the frame of classical mechanics, that has been used for all of the calculations, appear complementary rather than complete, with similar values in the low temperature region, and predominance of three body dynamics for temperatures higher than about 1000 K. The sum of the two contributions appears in fairly good agreement with available data from the literature. Dependence of total recombination on the temperature over pressure ratio is stressed. Detailed recombination toward rovibrational states is presented, with large evidence of importance of rotation in final products. Comparison with gas-surface recombination implying only physiadsorbed molecules shows approximate similarities at T = 5000 K, being on the contrary different at lower temperature.

  15. Thermal conductivity of water: Molecular dynamics and generalized hydrodynamics results

    Science.gov (United States)

    Bertolini, Davide; Tani, Alessandro

    1997-10-01

    Equilibrium molecular dynamics simulations have been carried out in the microcanonical ensemble at 300 and 255 K on the extended simple point charge (SPC/E) model of water [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)]. In addition to a number of static and dynamic properties, thermal conductivity λ has been calculated via Green-Kubo integration of the heat current time correlation functions (CF's) in the atomic and molecular formalism, at wave number k=0. The calculated values (0.67+/-0.04 W/mK at 300 K and 0.52+/-0.03 W/mK at 255 K) are in good agreement with the experimental data (0.61 W/mK at 300 K and 0.49 W/mK at 255 K). A negative long-time tail of the heat current CF, more apparent at 255 K, is responsible for the anomalous decrease of λ with temperature. An analysis of the dynamical modes contributing to λ has shown that its value is due to two low-frequency exponential-like modes, a faster collisional mode, with positive contribution, and a slower one, which determines the negative long-time tail. A comparison of the molecular and atomic spectra of the heat current CF has suggested that higher-frequency modes should not contribute to λ in this temperature range. Generalized thermal diffusivity DT(k) decreases as a function of k, after an initial minor increase at k=kmin. The k dependence of the generalized thermodynamic properties has been calculated in the atomic and molecular formalisms. The observed differences have been traced back to intramolecular or intermolecular rotational effects and related to the partial structure functions. Finally, from the results we calculated it appears that the SPC/E model gives results in better agreement with experimental data than the transferable intermolecular potential with four points TIP4P water model [Jorgensen et al., J. Chem. Phys. 79, 926 (1983)], with a larger improvement for, e.g., diffusion, viscosities, and dielectric properties and a smaller one for thermal conductivity. The SPC/E model shares

  16. A new parallel molecular dynamics algorithm for organic systems

    International Nuclear Information System (INIS)

    Plimpton, S.; Hendrickson, B.; Heffelfinger, G.

    1993-01-01

    A new parallel algorithm for simulating bonded molecular systems such as polymers and proteins by molecular dynamics (MD) is presented. In contrast to methods that extract parallelism by breaking the spatial domain into sub-pieces, the new method does not require regular geometries or uniform particle densities to achieve high parallel efficiency. For very large, regular systems spatial methods are often the best choice, but in practice the new method is faster for systems with tens-of-thousands of atoms simulated on large numbers of processors. It is also several times faster than the techniques commonly used for parallelizing bonded MD that assign a subset of atoms to each processor and require all-to-all communication. Implementation of the algorithm in a CHARMm-like MD model with many body forces and constraint dynamics is discussed and timings on the Intel Delta and Paragon machines are given. Example calculations using the algorithm in simulations of polymers and liquid-crystal molecules will also be briefly discussed

  17. Parallel computing and molecular dynamics of biological membranes

    International Nuclear Information System (INIS)

    La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.

    1998-01-01

    In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)

  18. Rheology of liquid n-triacontane: Molecular dynamics simulation

    International Nuclear Information System (INIS)

    Kondratyuk, N D; Norman, G E; Stegailov, V V

    2016-01-01

    Molecular dynamics is applied to calculate diffusion coefficients of n-triacontane C 30 H 62 using Einstein-Smoluchowski and Green-Kubo relations. The displacement 〈Δr 2 〉( t ) has a subdiffusive part 〈Δr 2 〉 ∼ t α , caused by molecular crowding at low temperatures. Longtime asymptotes of 〈v(0)v(t)〉 are collated with the hydrodynamic tail t -3/2 demonstrated for atomic liquids. The influence of these asymptotes on the compliance of Einstein-Smoluchowski and Green-Kubo methods is analyzed. The effects of the force field parameters on the diffusion process are treated. The results are compared with experimental data. (paper)

  19. Quantum molecular dynamics simulations of thermophysical properties of fluid ethane.

    Science.gov (United States)

    Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

    2012-12-01

    We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.

  20. Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

    International Nuclear Information System (INIS)

    More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

    2012-01-01

    Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)

  1. Dynamics and Thermodynamics of Many Particle Cold Atom Systems

    Science.gov (United States)

    2016-05-05

    simulate their dynamics far from equilibrium . It is likely that these ideas will find many applications in many areas of physics, quantum chemistry and...focus of this proposal was theoretical research on various non- equilibrium phenomena in isolated quantum systems and applications to experimental setups...theoretical research on various non- equilibrium phenomena in isolated quantum systems and applications to experimental setups largely to cold atoms

  2. International bulletin on atomic and molecular data for fusion. No. 39

    International Nuclear Information System (INIS)

    Smith, J.J.

    1989-07-01

    The Bulletin provides information on atomic and molecular data relevant for fusion research. In part I the indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions. Part II contains all the bibliographic data for both the indexed and non-indexed references (514 references). An author index is included

  3. Proceedings of the 2. Latin American Meeting on Atomic, Molecular and Electronic Collisions

    International Nuclear Information System (INIS)

    Montenegro, E.C.; Pinho, A.G. de; Souza, G.G.B. de.

    1988-01-01

    Annals of the II Latin American Meeting on Atomic, Molecular and Electronic Collisions. Over than 50 people from Latin America participated on this meeting giving talks on different subjects (theoretical and experimental), related to atomic and molecular physics, as well as, nuclear physics. (A.C.A.S.) [pt

  4. International bulletin on atomic and molecular data for fusion. No. 35

    International Nuclear Information System (INIS)

    Smith, J.J.

    1987-05-01

    The bulletin provides information on atomic and molecular data for fusion research. In Part I the indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface effects. Part II contains all the bibliographic data for both indexed and non-indexed references (536 references). An author index is included

  5. International Bulletin on Atomic and Molecular Data for Fusion. No. 36

    International Nuclear Information System (INIS)

    Smith, J.J.

    1987-10-01

    The bulletin provides information on atomic and molecular data relevant for fusion research. In Part I the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part II contains all the bibliographic data for both the indexed and non-indexed references (555 references). An author index is included

  6. International bulletin on atomic and molecular data for fusion. No. 38

    International Nuclear Information System (INIS)

    Smith, J.J.

    1989-01-01

    The Bulletin provides information on atomic and molecular data relevant for fusion research. In Part I the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part II contains all the bibliographic data for both the indexed and non-indexed references (654 references). An author index is included

  7. Development of the atomic and molecular data markup language for internet data exchange

    International Nuclear Information System (INIS)

    Ralchenko, Yuri; Clark Robert E.H.; Humbert, Denis; Schultz, David R.; Kato, Takako; Rhee, Yong Joo

    2006-01-01

    Accelerated development of the Internet technologies, including those relevant to the atomic and molecular physics, poses new requirements for the proper communication between computers, users and applications. To this end, a new standard for atomic and molecular data exchange that would reflect the recent achievements in this field becomes a necessity. We report here on development of the Atomic and Molecular Data Markup Language (AMDML) that is based on eXtensible Markup Language (XML). The present version of the AMDML Schema covers atomic spectroscopic data as well as the electron-impact collisions. (author)

  8. Intrinsic localized modes in arrays of atomic-molecular Bose-Einstein condensates

    International Nuclear Information System (INIS)

    Abdullaev, F.Kh.; Konotop, V.V.

    2003-01-01

    The existence of strongly localized matter solitons, intrinsic localized modes (ILM's), in an array of atomic-molecular Bose-Einstein condensates (AMBEC's) is shown. The theory is based on the Wannier function expansion of the system order parameter and predicts the possibility of strong localization of the atomic and molecular components whose relative populations are determined by the Raman detuning parameter and by the atom-molecule conversion rate. ILM's can possess different symmetries and spatial distributions of the components. In this context AMBEC arrays can be viewed as potential compressors and separators of atomic and molecular condensates

  9. Crossed-molecular-beams reactive scattering of oxygen atoms

    International Nuclear Information System (INIS)

    Baseman, R.J.

    1982-11-01

    The reactions of O( 3 P) with six prototypical unsaturated hydrocarbons, and the reaction of O( 1 D) with HD, have been studied in high-resolution crossed-molecular-beams scattering experiments with mass-spectrometric detection. The observed laboratory-product angular and velocity distributions unambiguously identify parent-daughter ion pairs, distinguish different neutral sources of the same ion, and have been used to identify the primary products of the reactions. The derived center-of-mass product angular and translational energy distributions have been used to elucidate the detailed reaction dynamics. These results demonstrate that O( 3 P)-unsaturated hydrocarbon chemistry is dominated by single bond cleavages, leading to radical products exclusively

  10. Crossed-molecular-beams reactive scattering of oxygen atoms

    Energy Technology Data Exchange (ETDEWEB)

    Baseman, R.J.

    1982-11-01

    The reactions of O(/sup 3/P) with six prototypical unsaturated hydrocarbons, and the reaction of O(/sup 1/D) with HD, have been studied in high-resolution crossed-molecular-beams scattering experiments with mass-spectrometric detection. The observed laboratory-product angular and velocity distributions unambiguously identify parent-daughter ion pairs, distinguish different neutral sources of the same ion, and have been used to identify the primary products of the reactions. The derived center-of-mass product angular and translational energy distributions have been used to elucidate the detailed reaction dynamics. These results demonstrate that O(/sup 3/P)-unsaturated hydrocarbon chemistry is dominated by single bond cleavages, leading to radical products exclusively.

  11. Picosecond multiphoton ionization of atomic and molecular clusters

    International Nuclear Information System (INIS)

    Miller, J.C.; Smith, D.B.

    1990-01-01

    High peak-power picosecond laser pulses have been used for the first time to effect nonresonant or resonant multiphoton ionization (MPI) of clusters generated in a supersonic nozzle expansion. The resulting ions are subsequently detected and characterized by time-of-flight mass spectroscopy. Specifically, we present results involving MPI of clusters of xenon and nitric oxide. Previous MPI studies of many molecular clusters using nanosecond lasers have not been successful in observing the parent ion, presumably due to fast dissociation channels. It is proposed that the present technique is a new and rather general ionization source for cluster studies which is complementary to electron impact but may, in addition, provide unique spectroscopic or dynamical information. 23 refs., 5 figs

  12. Excited-state molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Pratt, S.T.

    1995-01-01

    This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

  13. Thermal relaxation of molecular oxygen in collisions with nitrogen atoms

    Energy Technology Data Exchange (ETDEWEB)

    Andrienko, Daniil A., E-mail: daniila@umich.edu; Boyd, Iain D. [Department of Aerospace Engineering, University of Michigan, 1320 Beal Ave., Ann Arbor, Michigan 48108 (United States)

    2016-07-07

    Investigation of O{sub 2}–N collisions is performed by means of the quasi-classical trajectory method on the two lowest ab initio potential energy surfaces at temperatures relevant to hypersonic flows. A complete set of bound–bound and bound–free transition rates is obtained for each precollisional rovibrational state. Special attention is paid to the vibrational and rotational relaxations of oxygen as a result of chemically non-reactive interaction with nitrogen atoms. The vibrational relaxation of oxygen partially occurs via the formation of an intermediate NO{sub 2} complex. The efficient energy randomization results in rapid vibrational relaxation at low temperatures, compared to other molecular systems with a purely repulsive potential. The vibrational relaxation time, computed by means of master equation studies, is nearly an order of magnitude lower than the relaxation time in N{sub 2}–O collisions. The rotational nonequilibrium starts to play a significant effect at translational temperatures above 8000 K. The present work provides convenient relations for the vibrational and rotational relaxation times as well as for the quasi-steady dissociation rate coefficient and thus fills a gap in data due to a lack of experimental measurements for this system.

  14. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  15. Molecular dynamics simulations of cluster fission and fusion processes

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...

  16. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    International Nuclear Information System (INIS)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-01-01

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies

  17. Deformation mechanisms in nanotwinned copper by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xing [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China); Lu, Cheng, E-mail: chenglu@uow.edu.au [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Tieu, Anh Kiet; Pei, Linqing; Zhang, Liang; Su, Lihong [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Zhan, Lihua [State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China)

    2017-02-27

    Nanotwinned materials exhibit simultaneous ultrahigh strength and high ductility which is attributed to the interactions between dislocations and twin boundaries but the specific deformation mechanisms are rarely seen in experiments at the atomic level. Here we use large scale molecular dynamics simulations to explore this intricate interplay during the plastic deformation of nanotwinned Cu. We demonstrate that the dominant deformation mechanism transits dynamically from slip transfer to twin boundary migration to slip-twin interactions as the twin boundary orientation changes from horizontal to slant, and then to a vertical direction. Building on the fundamental physics of dislocation processes from computer simulations and combining the available experimental investigations, we unravel the underlying deformation mechanisms for nanotwinned Cu, incorporating all three distinct dislocation processes. Our results give insights into systematically engineering the nanoscale twins to fabricate nanotwinned metals or alloys that have high strength and considerable ductility.

  18. Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts

    Directory of Open Access Journals (Sweden)

    Kazuaki Z. Takahashi

    2017-01-01

    Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.

  19. Molecular dynamics simulations of glycerol glass-forming liquid

    International Nuclear Information System (INIS)

    Blieck, J.; Affouard, F.; Bordat, P.; Lerbret, A.; Descamps, M.

    2005-01-01

    Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q ∼ 0.6 A -1 are observed. Our results are also found compatible with predictions of the Mode Coupling Theory

  20. ProtoMD: A prototyping toolkit for multiscale molecular dynamics

    Science.gov (United States)

    Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

    2016-05-01

    ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

  1. Towards the molecular bases of polymerase dynamics

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1991-03-01

    One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

  2. Methods to extract information on the atomic and molecular states from scientific abstracts

    International Nuclear Information System (INIS)

    Sasaki, Akira; Ueshima, Yutaka; Yamagiwa, Mitsuru; Murata, Masaki; Kanamaru, Toshiyuki; Shirado, Tamotsu; Isahara, Hitoshi

    2005-01-01

    We propose a new application of information technology to recognize and extract expressions of atomic and molecular states from electrical forms of scientific abstracts. Present results will help scientists to understand atomic states as well as the physics discussed in the articles. Combining with the internet search engines, it will make one possible to collect not only atomic and molecular data but broader scientific information over a wide range of research fields. (author)

  3. Molecular quantum dynamics. From theory to applications

    International Nuclear Information System (INIS)

    Gatti, Fabien

    2014-01-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

  4. Molecular quantum dynamics. From theory to applications

    Energy Technology Data Exchange (ETDEWEB)

    Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

    2014-09-01

    An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

  5. Molecular Dynamics with Helical Periodic Boundary Conditions

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Bouř, Petr

    2014-01-01

    Roč. 35, č. 21 (2014), s. 1552-1559 ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:GA AV ČR(CZ) M200551205; GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : periodic boundary conditions * helical symmetry * molecular dynamics * protein structure * amyloid fibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.589, year: 2014

  6. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  7. International bulletin on atomic and molecular data for fusion. No.2

    International Nuclear Information System (INIS)

    Beaty, E.C.; Katsonis, K.

    1977-10-01

    This bulletin deals with atomic and molecular data for fusion (spectroscopic data, atomic and molecular collisions, surface effects, ...). Particular emphasis is given to data applicable to Tokamak devices. A bibliography for the most recent data presented in the document is provided. A description of work in progress and ''Data Requests'' in the fusion field are also mentioned. Numerical data on light ion sputtering yields of first wall materials, electron capture and impact ionization for iron ions colliding with molecular hydrogen and charge exchange between multicharged ions and helium, argon, and, atomic or molecular hydrogen are given

  8. Extended Lagrangian Excited State Molecular Dynamics.

    Science.gov (United States)

    Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

    2018-02-13

    An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

  9. Coulomb interactions via local dynamics: a molecular-dynamics algorithm

    International Nuclear Information System (INIS)

    Pasichnyk, Igor; Duenweg, Burkhard

    2004-01-01

    We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

  10. The MOLDY short-range molecular dynamics package

    Science.gov (United States)

    Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

    2011-12-01

    We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as

  11. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.; Vashishta, P.

    1983-01-01

    Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

  12. Research briefing on selected opportunities in atomic, molecular, and optical sciences

    International Nuclear Information System (INIS)

    1991-01-01

    This report discusses research on the following topics: The Laser-Atom Revolution; Controlling Dynamical Pathways; Nonclassical States of Light; Transient States of Atomic Systems; New Light Generation and Handling; Clusters; Atomic Physics at User Facilities; and Impacts of AMO Sciences on Modern Technologies

  13. Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope

    International Nuclear Information System (INIS)

    Tang Deman; Li Aiqin; Attar, Peter; Dowell, Earl H.

    2004-01-01

    A dynamic analysis and numerical simulation has been conducted of a polysaccharides molecular structure (a ten (10) single-α-D-glucose molecule chain) connected to a moving atomic force microscope (AFM). Sinusoidal base excitation of the AFM cantilevered beam is considered. First a linearized perturbation model is constructed for the complex polysaccharides molecular structure. Then reduced order (dynamic) models based upon a proper orthogonal decomposition (POD) technique are constructed using global modes for both the linearized perturbation model and for the full nonlinear model. The agreement between the original and reduced order models (ROM/POD) is very good even when only a few global modes are included in the ROM for either the linear case or for the nonlinear case. The computational advantage of the reduced order model is clear from the results presented

  14. Conduction of molecular electronic devices: Qualitative insights through atom-atom polarizabilities

    International Nuclear Information System (INIS)

    Stuyver, T.; Fias, S.; De Proft, F.; Geerlings, P.; Fowler, P. W.

    2015-01-01

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability

  15. Conduction of molecular electronic devices: Qualitative insights through atom-atom polarizabilities

    Energy Technology Data Exchange (ETDEWEB)

    Stuyver, T.; Fias, S., E-mail: sfias@vub.ac.be; De Proft, F.; Geerlings, P. [ALGC, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel (Belgium); Fowler, P. W. [Department of Chemistry, University of Sheffield, Sheffield S3 7HF (United Kingdom)

    2015-03-07

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability.

  16. Conduction of molecular electronic devices: qualitative insights through atom-atom polarizabilities.

    Science.gov (United States)

    Stuyver, T; Fias, S; De Proft, F; Fowler, P W; Geerlings, P

    2015-03-07

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability.

  17. Dynamics of production of iodine atoms by dissociation of iodides in a pulsed self-sustained discharge

    International Nuclear Information System (INIS)

    Vagin, Nikolai P; Kochetov, Igor' V; Napartovich, A P; Yuryshev, Nikolai N

    2013-01-01

    Absorption at the laser transition has been used for the first time to assess the evolution of concentration of iodine atoms in a pulsed self-sustained discharge in mixtures of iodides with a buffer gas such as molecular nitrogen and helium. Dynamics of the iodine atom production is studied by the method of absorption spectroscopy. The dissociation of C n F 2n+1 I and CnH 2n+1 I (n = 1, 2) iodides is investigated. The energy required to produce atomic iodine is evaluated. The experimental data obtained for CF 3 I are compared with the results of numerical simulations, their reasonable agreement being demonstrated. (active media)

  18. Physical properties of Cu nanoparticles: A molecular dynamics study

    International Nuclear Information System (INIS)

    Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.

    2014-01-01

    Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index

  19. Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

    Science.gov (United States)

    Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

    2018-04-01

    Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.

  20. Machine learning molecular dynamics for the simulation of infrared spectra.

    Science.gov (United States)

    Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

    2017-10-01

    Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.

  1. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  2. Self-diffusion dynamic behavior of atomic clusters on Re(0 0 0 1) surface

    Energy Technology Data Exchange (ETDEWEB)

    Liu Fusheng [Department of Applied Physics, Hunan University, Changsha 410082 (China); Hu Wangyu, E-mail: wangyuhu2001cn@yahoo.com.cn [Department of Applied Physics, Hunan University, Changsha 410082 (China); Deng Huiqiu; Luo Wenhua; Xiao Shifang [Department of Applied Physics, Hunan University, Changsha 410082 (China); Yang Jianyu [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China)

    2009-08-15

    Using molecular dynamics simulations and a modified analytic embedded atom potential, the self-diffusion dynamics of rhenium atomic clusters up to seven atoms on Re(0 0 0 1) surface have been studied in the temperature ranges from 600 K to 1900 K. The simulation time varies from 20 ns to 200 ns according to the cluster sizes and the temperature. The heptamer and trimer are more stable comparing to other neighboring non-compact clusters. The diffusion coefficients of clusters are derived from the mean square displacement of cluster's mass-center, and diffusion prefactors D{sub 0} and activation energies E{sub a} are derived from the Arrhenius relation. It is found that the Arrhenius relation of the adatom can be divided into two parts at different temperature range. The activation energy of clusters increases with the increasing of the atom number in clusters. The prefactor of the heptamer is 2-3 orders of magnitude higher than a usual prefactor because of a large number of nonequivalent diffusion processes. The trimer and heptamer are the nuclei at different temperature range according to the nucleation theory.

  3. 2nd International Symposium "Atomic Cluster Collisions : Structure and Dynamics from the Nuclear to the Biological Scale"

    CERN Document Server

    Solov'yov, Andrey; ISACC 2007; Latest advances in atomic cluster collisions

    2008-01-01

    This book presents a 'snapshot' of the most recent and significant advances in the field of cluster physics. It is a comprehensive review based on contributions by the participants of the 2nd International Symposium on Atomic Cluster Collisions (ISACC 2007) held in July 19-23, 2007 at GSI, Darmstadt, Germany. The purpose of the Symposium is to promote the growth and exchange of scientific information on the structure and properties of nuclear, atomic, molecular, biological and complex cluster systems studied by means of photonic, electronic, heavy particle and atomic collisions. Particular attention is devoted to dynamic phenomena, many-body effects taking place in cluster systems of a different nature - these include problems of fusion and fission, fragmentation, collective electron excitations, phase transitions, etc.Both the experimental and theoretical aspects of cluster physics, uniquely placed between nuclear physics on the one hand and atomic, molecular and solid state physics on the other, are discuss...

  4. Quantum dynamics of hydrogen atoms on graphene. II. Sticking

    Science.gov (United States)

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene; Martinazzo, Rocco

    2015-09-01

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (˜0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  5. Quantum dynamics of hydrogen atoms on graphene. II. Sticking.

    Science.gov (United States)

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

    2015-09-28

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  6. Quantum dynamics of hydrogen atoms on graphene. II. Sticking

    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

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated.

  7. Quantum dynamics of hydrogen atoms on graphene. II. Sticking

    International Nuclear Information System (INIS)

    Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H.; Burghardt, Irene; Martinazzo, Rocco

    2015-01-01

    Following our recent system-bath modeling of the interaction between a hydrogen atom and a graphene surface [Bonfanti et al., J. Chem. Phys. 143, 124703 (2015)], we present the results of converged quantum scattering calculations on the activated sticking dynamics. The focus of this study is the collinear scattering on a surface at zero temperature, which is treated with high-dimensional wavepacket propagations with the multi-configuration time-dependent Hartree method. At low collision energies, barrier-crossing dominates the sticking and any projectile that overcomes the barrier gets trapped in the chemisorption well. However, at high collision energies, energy transfer to the surface is a limiting factor, and fast H atoms hardly dissipate their excess energy and stick on the surface. As a consequence, the sticking coefficient is maximum (∼0.65) at an energy which is about one and half larger than the barrier height. Comparison of the results with classical and quasi-classical calculations shows that quantum fluctuations of the lattice play a primary role in the dynamics. A simple impulsive model describing the collision of a classical projectile with a quantum surface is developed which reproduces the quantum results remarkably well for all but the lowest energies, thereby capturing the essential physics of the activated sticking dynamics investigated

  8. Dynamical localization in the 3-D kicked Rydberg atom

    International Nuclear Information System (INIS)

    Persson, E.; Yoshida, S.; Tong, X.-M.; Reinhold, C.; Burgdoerfer, J.

    2001-01-01

    Full text: The dynamical localization for the 3D periodically kicked Rydberg atom is analyzed. For the 1D kicked atom, earlier work shows dynamical localization as the quantum suppression of classically fast ionization associated with unbounded chaotic trajectories. The corresponding wave functions localize around unstable periodic orbits. For the experimental observation, the crucial question is the dependence of the dynamical localization on the dimension. As the first step, we simulate the full 3D evolution of an extreme parabolic initial state elongated in the direction of the unidirectional kicks. We compare this simulation with the 1D model and find signatures of localization also in 3D. We further examine the dependence of quantum localization on the parabolic quantum number of the initial state. In the limit of high kick frequencies, the origin of the localization can be understood in terms of Stark states in the average field. We discuss conditions for where an experimental observation of the localization is most likely. (author)

  9. Nanojets, Electrospray, and Ion Field Evaporation: Molecular Dynamics Simulations and Laboratory Experiments

    Science.gov (United States)

    2008-07-22

    Eft (d) (otherwise Coulomb fission occurs), and the solute residue diameter is less than the critical diameter at which E\\ = ER(</); i.e., in the...12 / tap " Figure 10. Atomic configurations taken from a molecular dynamics simulation of a 10 nm formamide droplet prior to and after the

  10. Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations

    DEFF Research Database (Denmark)

    Xiang, Ye; Du, Jincheng; Smedskjær, Morten Mattrup

    2013-01-01

    the recent Corning® Gorilla® Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al/Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role...

  11. Molecular-dynamics simulation of displacement cascades in Cu: analysis of replacement sequences

    International Nuclear Information System (INIS)

    King, W.E.; Benedek, R.

    1981-01-01

    Molecular-dynamics computer simulations of displacement cascades in copper have been performed for recoil energies up to 450 eV. Statistical analyses of the atomic replacements are presented. Linear replacement sequence lengths are extremely short on the average. The effect of the cooling phase of the cascade is discussed

  12. Molecular Dynamics Simulations of Phospholipid Membranes and Their Interaction with Phospholipase A2

    NARCIS (Netherlands)

    Berendsen, Herman; Egberts, Bert; Marrink, Siewert; Ahlstroem, Peter; Pullman, Alberte; Jortner, Joshua; Pullman, Bernhard

    1992-01-01

    Molecular Dynamics computer simulations have been carried out both on simplified model systems of biological membranes and on di(palmitoyl)lecithin/water multibilayers. The results, which agree with experimental data on chain order parameters, show a considerable disorder with atomic distributions

  13. Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

    Science.gov (United States)

    Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

    2018-04-01

    We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

  14. Bombardment of Ni(100) surface with low-energy argons: molecular dynamics simulations

    International Nuclear Information System (INIS)

    Guevenc, Ziya B.; Hippler, Rainer; Jackson, Bret

    2005-01-01

    Results of molecular dynamics simulations of the sputtering of Ni(100) by Ar atoms are reported. The solid is described by an embedded atom potential, and the interaction between the projectile and the metal atoms is modelled by a Morse-like function. Processes leading to Ni atom emissions from the lattice are analysed over the energy range of 70-80 eV. In this energy range cluster (larger than three atoms) emission is not observed. The maximum penetration depth of Ar, the kinetic energy and angular distributions of the reflected Ar, and the sputtered Ni atoms are evaluated as functions of the impact energy and sputtering time. The computed sputtering yield is compared with the available theoretical and experimental data

  15. International bulletin on atomic and molecular data for fusion. No. 54-55

    International Nuclear Information System (INIS)

    Stephens, J.A.

    1998-12-01

    This bulletin is published by the International Atomic Energy Agency to provide atomic and molecular data relevant to fusion research and technology. In the first part the indexed papers are listed separately for (i) structure and spectra (energy levels, wavelengths, transition probabilities, oscillator strengths, polarizabilities, electric moments, interatomic potentials), (ii) atomic and molecular collisions (photon collisions, electron collisions, heavy-particle collisions), and (iii) surface interactions (sputtering, chemical reactions, trapping and detrapping, adsorption, desorption, reflection, and secondary electron emission). There are also chapters with beam-matter interactions and data on interactions of atomic particles with fields. In the second Part contains the bibliographic data, essentially for the above listed topics

  16. Towards realistic molecular dynamics simulations of grain boundary mobility

    International Nuclear Information System (INIS)

    Zhou, J.; Mohles, V.

    2011-01-01

    In order to investigate grain boundary migration by molecular dynamics (MD) simulations a new approach involving a crystal orientation-dependent driving force has been developed by imposing an appropriate driving force on grain boundary atoms and enlarging the effective range of driving force. The new approach has been validated by the work of the driving force associated with the motion of grain boundaries. With the new approach the relation between boundary migration velocity and driving force is found to be nonlinear, as was expected from rate theory for large driving forces applied in MD simulations. By evaluating grain boundary mobility nonlinearly for a set of symmetrical tilt boundaries in aluminum at high temperature, high-angle grain boundaries were shown to move much faster than low-angle grain boundaries. This agrees well with experimental findings for recrystallization and grain growth. In comparison with the available data the simulated mobility of a 38.21 o Σ7 boundary was found to be significantly lower than other MD simulation results and comparable with the experimental values. Furthermore, the average volume involved during atomic jumps for boundary migration is determined in MD simulations for the first time. The large magnitude of the volume indicates that grain boundary migration is accomplished by the correlated motion of atom groups.

  17. Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

    Science.gov (United States)

    Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro

    2006-03-02

    We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to

  18. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Directory of Open Access Journals (Sweden)

    Rong Shen

    2015-10-01

    Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

  19. Coherent atomic and molecular spectroscopy in the far infrared

    International Nuclear Information System (INIS)

    Inguscio, M.

    1988-01-01

    Recent advances in far infrared spectroscopy of atoms (fine structure transitions) and molecules (rotational transitions) are reviewed. Results obtained by means of Laser Magnetic Resonance, using fixed frequency lasers, and Tunable Far Infrared spectrometers are illustrated. The importance of far infrared spectroscopy for several fields, including astrophysics, atmospheric physics, atomic structure and metology, is discussed. (orig.)

  20. Atomic dynamics of tin nanoparticles embedded into porous glass

    Energy Technology Data Exchange (ETDEWEB)

    Parshin, P. P.; Zemlyanov, M. G., E-mail: zeml@isssph.kiae.ru; Panova, G. Kh.; Shikov, A. A. [Russian Research Centre Kurchatov Institute (Russian Federation); Kumzerov, Yu. A.; Naberezhnov, A. A. [Russian Academy of Sciences, Ioffe Physicotechnical Institute (Russian Federation); Sergueev, I.; Crichton, W. [European Synchrotron Radiation Facility (France); Chumakov, A. I. [Russian Research Centre Kurchatov Institute (Russian Federation); Rueffer, R. [European Synchrotron Radiation Facility (France)

    2012-03-15

    The method of resonant nuclear inelastic absorption of synchrotron radiation has been used to study the phonon spectrum for tin nanoparticles (with a natural isotope mixture) embedded into a porous glassy (silica) matrix with an average pore diameter of 7 nm in comparison to the analogous spectrum of bulk tin enriched with {sup 119}Sn isotope. Differences between the spectra have been observed, which are related to both the dimensional effects and specific structural features of the porous glass-tin nanocomposite. Peculiarities in the dynamics of tin atoms embedded into nanopores of glass are interpreted in terms of a qualitative model of the nanocomposite structure.

  1. Atomic dynamics of tin nanoparticles embedded into porous glass

    International Nuclear Information System (INIS)

    Parshin, P. P.; Zemlyanov, M. G.; Panova, G. Kh.; Shikov, A. A.; Kumzerov, Yu. A.; Naberezhnov, A. A.; Sergueev, I.; Crichton, W.; Chumakov, A. I.; Rüffer, R.

    2012-01-01

    The method of resonant nuclear inelastic absorption of synchrotron radiation has been used to study the phonon spectrum for tin nanoparticles (with a natural isotope mixture) embedded into a porous glassy (silica) matrix with an average pore diameter of 7 nm in comparison to the analogous spectrum of bulk tin enriched with 119 Sn isotope. Differences between the spectra have been observed, which are related to both the dimensional effects and specific structural features of the porous glass-tin nanocomposite. Peculiarities in the dynamics of tin atoms embedded into nanopores of glass are interpreted in terms of a qualitative model of the nanocomposite structure.

  2. Molecular Dynamics: New Frontier in Personalized Medicine.

    Science.gov (United States)

    Sneha, P; Doss, C George Priya

    2016-01-01

    The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.

  3. Parallelization of quantum molecular dynamics simulation code

    International Nuclear Information System (INIS)

    Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu

    1998-02-01

    A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)

  4. Lipid Configurations from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek

    2018-01-01

    of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...

  5. Molecular dynamics studies of actinide nitrides

    International Nuclear Information System (INIS)

    Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo

    2004-01-01

    The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)

  6. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori

    2011-09-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

  7. Molecular dynamics of surfactant protein C

    DEFF Research Database (Denmark)

    Ramírez, Eunice; Santana, Alberto; Cruz, Anthony

    2006-01-01

    Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...

  8. Imaging modes of atomic force microscopy for application in molecular and cell biology.

    Science.gov (United States)

    Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

    2017-04-06

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  9. International bulletin on atomic and molecular data for fusion. No. 49

    International Nuclear Information System (INIS)

    Botero, J.

    1995-06-01

    This issue of the bulletin provides atomic and molecular data references relevant to fusion research and technology. In part 1 the indexation of the papers is provided separately for (i) structure and spectra, (ii) atomic and molecular collisions, and (iii) surface interactions. Part 2 contains the bibliographic data for the above-listed topics and brief bibliographic lists for the following topics: (a) fusion research of general interest, (b) high energy laser- and beam-matter interaction, (c) bibliographic and numerical data collections, and (d) interaction of atomic particles with fields. Moreover, the creation of the Atomic and Molecular Data Information System (AMDIS) is announced by the IAEA. AMDIS contains three main parts: the Atomic and Molecular Bibliographic Data System (AMBDAS), the numerical database of recommended and evaluated atomic, molecular and plasma-surface interaction data ALADDIN and an electronic bulletin board with information regarding data needs, meetings and programs of the IAEA Atomic and Molecular Data Unit. AMDIS may be reached via INTERNET. For information on how to access AMDIS, an electronic mail inquiry can be sent (address: ''pms'' followed by the usual ''at'' symbol followed by ''ripcrs01.iaea.or.at'')

  10. Probing molecular interactions in bone biomaterials: Through molecular dynamics and Fourier transform infrared spectroscopy

    International Nuclear Information System (INIS)

    Bhowmik, Rahul; Katti, Kalpana S.; Verma, Devendra; Katti, Dinesh R.

    2007-01-01

    Polymer-hydroxyapatite (HAP) composites are widely investigated for their potential use as bone replacement materials. The molecular interactions at mineral polymer interface are known to have significant role of mechanical response of the composite system. Modeling interactions between such dissimilar molecules using molecular dynamics (MD) is an area of current interest. Molecular dynamics studies require potential function or force field parameters. Some force fields are described in literature that represents the structure of hydroxyapatite reasonably well. Yet, the applicability of these force fields for studying the interaction between dissimilar materials (such as mineral and polymer) is limited, as there is no accurate representation of polymer in these force fields. We have obtained the parameters of consistent valence force field (CVFF) for monoclinic hydroxyapatite. Validation of parameters was done by comparing the computationally obtained unit cell parameters, vibrational spectra and atomic distances with XRD and FTIR experiments. Using the obtained parameters of HAP, and available parameters of polymer (polyacrylic acid), interaction study was performed with MD simulations. The MD simulations showed that several hydrogen bonds may form between HAP and polyacrylic acid depending upon the exposed surface of HAP. Also there are some favourable planes of HAP where polyacrylic acid is most likely to attach. We have also simulated the mineralization of HAP using a 'synthetic biomineralization'. These modeling studies are supported by photoacoustic spectroscopy experiments on both porous and non porous composite samples for potential joint replacement and bone tissue engineering applications

  11. Dynamical Disentangling and Cooling of Atoms in Bilayer Optical Lattices

    Science.gov (United States)

    Kantian, A.; Langer, S.; Daley, A. J.

    2018-02-01

    We show how experimentally available bilayer lattice systems can be used to prepare quantum many-body states with exceptionally low entropy in one layer, by dynamically disentangling the two layers. This disentangling operation moves one layer—subsystem A —into a regime where excitations in A develop a single-particle gap. As a result, this operation maps directly to cooling for subsystem A , with entropy being shuttled to the other layer. For both bosonic and fermionic atoms, we study the corresponding dynamics showing that disentangling can be realized cleanly in ongoing experiments. The corresponding entanglement entropies are directly measurable with quantum gas microscopes, and, as a tool for producing lower-entropy states, this technique opens a range of applications beginning with simplifying production of magnetically ordered states of bosons and fermions.

  12. The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

    Science.gov (United States)

    Chen, Jundong

    2018-03-01

    Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

  13. Dynamic molecular oxygen production in cometary comae

    Science.gov (United States)

    Yao, Yunxi; Giapis, Konstantinos P.

    2017-05-01

    Abundant molecular oxygen was discovered in the coma of comet 67P/Churyumov-Gerasimenko. Its origin was ascribed to primordial gaseous O2 incorporated into the nucleus during the comet's formation. This thesis was put forward after discounting several O2 production mechanisms in comets, including photolysis and radiolysis of water, solar wind-surface interactions and gas-phase collisions. Here we report an original Eley-Rideal reaction mechanism, which permits direct O2 formation in single collisions of energetic water ions with oxidized cometary surface analogues. The reaction proceeds by H2O+ abstracting a surface O-atom, then forming an excited precursor state, which dissociates to produce O2-. Subsequent photo-detachment leads to molecular O2, whose presence in the coma may thus be linked directly to water molecules and their interaction with the solar wind. This abiotic O2 production mechanism is consistent with reported trends in the 67P coma and raises awareness of the role of energetic negative ions in comets.

  14. Lithium atoms on helium nanodroplets: Rydberg series and ionization dynamics

    Science.gov (United States)

    Lackner, Florian; Krois, Günter; Ernst, Wolfgang E.

    2017-11-01

    The electronic excitation spectrum of lithium atoms residing on the surface of helium nanodroplets is presented and analyzed employing a Rydberg-Ritz approach. Utilizing resonant two-photon ionization spectroscopy, two different Rydberg series have been identified: one assigned to the nS(Σ) series and the other with predominantly nP(Π) character. For high Rydberg states, which have been resolved up to n = 13, the surrounding helium effectively screens the valence electron from the Li ion core, as indicated by the apparent red-shift of Li transitions and lowered quantum defects on the droplet with respect to their free atom counterparts. For low n states, the screening effect is weakened and the prevailing repulsive interaction gives rise to strongly broadened and blue-shifted transitions. The red-shifts originate from the polarization of nearby He atoms by the positive Li ion core. As a consequence of this effect, the ionization threshold is lowered by 116 ± 10 cm-1 for Li on helium droplets with a radius of about 40 Å. Upon single-photon ionization, heavy complexes corresponding to Li ions attached to intact helium droplets are detected. We conclude that ionization close to the on-droplet ionization threshold triggers a dynamic process in which the Li ion core undergoes a transition from a surface site into the droplet.

  15. Molecular dynamics in high electric fields

    International Nuclear Information System (INIS)

    Apostol, M.; Cune, L.C.

    2016-01-01

    Highlights: • New method for rotation molecular spectra in high electric fields. • Parametric resonances – new features in spectra. • New elementary excitations in polar solids from dipolar interaction (“dipolons”). • Discussion about a possible origin of the ferroelectricity from dipolar interactions. - Abstract: Molecular rotation spectra, generated by the coupling of the molecular electric-dipole moments to an external time-dependent electric field, are discussed in a few particular conditions which can be of some experimental interest. First, the spherical-pendulum molecular model is reviewed, with the aim of introducing an approximate method which consists in the separation of the azimuthal and zenithal motions. Second, rotation spectra are considered in the presence of a static electric field. Two particular cases are analyzed, corresponding to strong and weak fields. In both cases the classical motion of the dipoles consists of rotations and vibrations about equilibrium positions; this motion may exhibit parametric resonances. For strong fields a large macroscopic electric polarization may appear. This situation may be relevant for polar matter (like pyroelectrics, ferroelectrics), or for heavy impurities embedded in a polar solid. The dipolar interaction is analyzed in polar condensed matter, where it is shown that new polarization modes appear for a spontaneous macroscopic electric polarization (these modes are tentatively called “dipolons”); one of the polarization modes is related to parametric resonances. The extension of these considerations to magnetic dipoles is briefly discussed. The treatment is extended to strong electric fields which oscillate with a high frequency, as those provided by high-power lasers. It is shown that the effect of such fields on molecular dynamics is governed by a much weaker, effective, renormalized, static electric field.

  16. Molecular dynamics simulation of siderite-hematite-quartz flotation with sodium oleate

    Science.gov (United States)

    Li, Lixia; Hao, Haiqing; Yuan, Zhitao; Liu, Jiongtian

    2017-10-01

    Models of sodium oleate adsorption on siderite, hematite and quartz were investigated by molecular dynamic simulation, respectively. Surface energy was calculated to confirm the cleavage plan of hematite and quartz. Both natural cleavage plane of siderite and calculated plane were used to investigate the flotation of the three minerals. Based on the molecular simulation in solution with water as medium, adsorption quantity and interaction capability of oleate ions on the three minerals indicated that siderite could be collected efficiently by sodium oleate at neutral pH. Results of flotation experiments were further demonstrated by analysis of relative concentration of carbon atoms and oxygen atoms.

  17. The Art of Molecular Dynamics Simulation (by D. C. Rapaport)

    Science.gov (United States)

    Molner, Stephen P.

    1999-02-01

    Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95. This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a

  18. International bulletin on atomic and molecular data for fusion. No. 42-45

    International Nuclear Information System (INIS)

    Botero, J.

    1991-01-01

    The bulletin is published by the International Atomic Energy Agency to provide atomic and molecular data relevant to fusion research and technology. In Part I the indexed papers are listed separately for (i) structure and spectra (energy levels, wavelengths; transition probabilities, oscillator strengths; polarizabilities, electric moments; interatomic potentials); (ii) atomic and molecular collisions (photon collisions; electro collisions; heavy-particle collisions; homonuclear sequences), and (iii) surface interactions (sputtering; trapping, detrapping; adsorption, desorption; surface damage; blistering, flaking; chemical reactions). Part II contains the bibliographic data for the above listed topics and for plasma composition and impurities; plasma heating, cooling and fuelling; fusion research of general interest; high energy laser- and beam-matter interaction; interaction of atomic particles with fields. A list of evaluated data bases on atomic and molecular collisions and on particle-surface interactions is also given

  19. International bulletin on atomic and molecular data for fusion. No. 48

    International Nuclear Information System (INIS)

    1994-10-01

    This bulletin provides atomic and molecular data references relevant to thermonuclear fusion research and technology. In part I the indexing of the papers is given separately for (i) structure and spectra (energy levels, wavelengths; transition probabilities, oscillator strengths; interatomic potentials), (ii) atomic and molecular collisions (photon collisions, electron collisions, heavy particle collisions), and (iii) surface interactions (sputtering, surface damage, blistering, flaking, arcing, chemical reactions). Part II contains the bibliographic data for the above listed topics and for plasma composition and impurities, plasma heating, cooling and fuelling, high energy laser- and beam- matter interaction, bibliographic and numerical data collections, and on interaction of atomic particles with fields. Also included are sections on atomic and molecular data needs for fusion research and on news about ALADDIN (A Labelled Atomic Data Interface) and evaluated-data bases

  20. Molecular dynamics simulation of carbon nanostructures: The C60 buckminsterfullerene

    International Nuclear Information System (INIS)

    Laszlo, Istvan; Zsoldos, Ibolya

    2012-01-01

    Molecular dynamics calculations can reveal the physical and chemical properties of various carbon nanostructures or can help to devise the possible formation pathways. In our days the most well-known carbon nanostructures are the fullerenes, the nanotubes, and the graphene. The fullerenes and nanotubes can be thought of as being formed from graphene sheets, i.e., single layers of carbon atoms arranged in a honeycomb lattice. Usually the nature does not follow the mathematical constructions. Although the first time the C 60 and the C 70 were produced by laser irradiated graphite, the fullerene formation theories are based on various fragments of carbon chains and networks of pentagonal and hexagonal rings. In the present article various formation pathways for the buckminsterfullerene C 60 molecule will be presented. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  1. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    Science.gov (United States)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  2. Molecular dynamics characterization of as-implanted damage in silicon

    International Nuclear Information System (INIS)

    Santos, Ivan; Marques, Luis A.; Pelaz, Lourdes; Lopez, Pedro; Aboy, Maria; Barbolla, Juan

    2005-01-01

    We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions

  3. Molecular dynamics characterization of as-implanted damage in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Ivan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)]. E-mail: ivasan@ele.uva.es; Marques, Luis A. [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Pelaz, Lourdes [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Lopez, Pedro [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Aboy, Maria [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain); Barbolla, Juan [Dpto. de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicaciones, Campus Miguel Delibes s/n, 47011 Valladolid (Spain)

    2005-12-05

    We have analyzed the as-implanted damage produced in silicon by B, Si and Ge ions using molecular dynamics (MD) simulations. Implantations were carried out at 50 K to avoid damage migration and annealing. In order to make a statistical study of the damage features, we have simulated hundreds of independent cascades for each ion for the same nuclear deposited energy. We have obtained that the average number of displaced atoms (DA) from perfect lattice positions and the size of defect clusters formed increases with ion mass. This dependence has not been obtained from equivalent binary collisions simulations. This indicates that multiple interactions play an important role in the generation of damage. Amorphous regions are directly formed during the collisional phase of the cascade of Ge and Si ions.

  4. Molecular dynamics simulation of gold cluster growth during sputter deposition

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, J. W., E-mail: abraham@theo-physik.uni-kiel.de; Bonitz, M., E-mail: bonitz@theo-physik.uni-kiel.de [Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, Leibnizstraße 15, D-24098 Kiel (Germany); Strunskus, T.; Faupel, F. [Institut für Materialwissenschaft, Lehrstuhl für Materialverbunde, Christian-Albrechts-Universität zu Kiel, Kaiserstraße 2, D-24143 Kiel (Germany)

    2016-05-14

    We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

  5. Experimental comparison of the critical ionization velocity in atomic and molecular gases

    International Nuclear Information System (INIS)

    Axnaes, I.

    1978-08-01

    The critical ionization velocity usub(c) of Ne, Kr, Xe, Cl 2 , O 2 , CO, CO 2 , NH 3 and H 2 O is investigated experimentally in a coaxial plasma gun. Together with experimental data obtained in earlier experiments the present results make it possible to make a systematic comparison between the critical ionization velocity for atomic and molecular gases. It is found that atomic and molecular gases tend to have values of critical ionization velocity which are respectively smaller and larger than the theoretical values. The current dependence of usub(c) is found to be different for atomic and molecular gases. A number of atomic and molecular processes relevant to the experiment are discussed

  6. Study of atomic and molecular emission spectra of Sr by laser induced breakdown spectroscopy (LIBS).

    Science.gov (United States)

    Bhatt, Chet R; Alfarraj, Bader; Ayyalasomayajula, Krishna K; Ghany, Charles; Yueh, Fang Y; Singh, Jagdish P

    2015-12-01

    Laser Induced Breakdown Spectroscopy (LIBS) is an ideal analytical technique for in situ analysis of elemental composition. We have performed a comparative study of the quantitative and qualitative analysis of atomic and molecular emission from LIBS spectra. In our experiments, a mixture of SrCl2 and Al2O3 in powder form was used as a sample. The atomic emission from Sr and molecular emission from SrCl and SrO observed in LIBS spectra were analyzed. The optimum laser energies, gate delays, and gate widths for selected atomic lines and molecular bands were determined from spectra recorded at various experimental parameters. These optimum experimental conditions were used to collect calibration data, and the calibration curves were used to predict the Sr concentration. Limits of detection (LODs) for selected atomic and molecular emission spectra were determined.

  7. Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling

    International Nuclear Information System (INIS)

    Tawara, H.

    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.)

  8. Huge-scale molecular dynamics simulation of multibubble nuclei

    KAUST Repository

    Watanabe, Hiroshi

    2013-12-01

    We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.

  9. Energy-related atomic and molecular structure and scattering studies: Final report

    International Nuclear Information System (INIS)

    1987-01-01

    The general goals of the DOE research concerned the use of molecular beams techniques in the study of atomic and molecular polarizabilities and the study of the interactions between electrons and highly polar molecules. Both of these goals are directly relevant to the general problem of the role played by long-range forces in atomic and molecular physics. Details related to this motivation can be found in the published literature. Here we will describe in general terms the work performed under DOE sponsorship in the atomic beams laboratory at NYU. Our original intent was to exploit techniques developed at NYU, mainly in the study of simple atomic systems, to the more complex atomic and molecular systems that are related to DOE interests. These included the developing understanding of the structure of molecular systems, particularly of alkali halide molecules, and the study of the interactions of electrons with such molecules. The structure experiments would serve as critical experimental benchmarks for computational techniques on molecular properties, including both molecular wave functions and derivative properties of them, such as vibrational and rotational constants, but in particular of molecular electric dipole polarizabilities. We believe that we have at least to some extent fulfilled these goals. 16 refs., 1 fig

  10. First-Principles Molecular Dynamics Study on Helium- filled Carbon Nanotube

    International Nuclear Information System (INIS)

    Agusta, M K; Prasetiyo, I; Saputro, A G; Dipojono, H K; Maezono, R

    2016-01-01

    Investigation on carbon nanotube (CNT) filled by Helium (He) atoms is conducted using Density Functional Theory and Molecular Dynamics Simulation. It reveals that He atom is repelled by CNT's wall and find its stable position at the tube center. Vibrational analysis on modes corespond to radial inward and outward breathing movement of CNT shows that He filling tends to pull the CNT wall in inward direction. Furthermore, examination on C-C stretch mode reveals that the existence of He improve the stiffness of CNT's wall. Molecular dynamics calculations which are done on (3,3) and (5,5) nanotube with 0.25 gr/cm 3 and 0.5 gr/cm 3 He density at 300 K and 1500 K confirms the increase of stiffness of CNT wall by interaction with He atoms. Effects of variation of chirality, temperature and He density on CNT wall stiffness is also reported. (paper)

  11. Coordinated Research Projects of the IAEA Atomic and Molecular Data Unit

    Science.gov (United States)

    Braams, B. J.; Chung, H.-K.

    2011-05-01

    The IAEA Atomic and Molecular Data Unit is dedicated to the provision of databases for atomic, molecular and plasma-material interaction (AM/PMI) data that are relevant for nuclear fusion research. IAEA Coordinated Research Projects (CRPs) are the principal mechanism by which the Unit encourages data evaluation and the production of new data. Ongoing and planned CRPs on AM/PMI data are briefly described here.

  12. International bulletin on atomic and molecular data for fusion. No. 61

    International Nuclear Information System (INIS)

    Stephens, J.A.; Bannister, M.E.; Delcroix, J.L.; Fuhr, J.

    2002-01-01

    This bulletin is prepared by the IAEA to assist in the development of fusion research and technology. In part 1 the Atomic and Molecular Data Information System (AMDIS) of the IAEA is presented. In part 2, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part 3 contains all the bibliographic data for both indexed and non-indexed references

  13. Coordinated Research Projects of the IAEA Atomic and Molecular Data Unit

    International Nuclear Information System (INIS)

    Braams, B. J.; Chung, H.-K.

    2011-01-01

    The IAEA Atomic and Molecular Data Unit is dedicated to the provision of databases for atomic, molecular and plasma-material interaction (AM/PMI) data that are relevant for nuclear fusion research. IAEA Coordinated Research Projects (CRPs) are the principal mechanism by which the Unit encourages data evaluation and the production of new data. Ongoing and planned CRPs on AM/PMI data are briefly described here.

  14. Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.

    Science.gov (United States)

    Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei

    2018-06-05

    The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.

  15. Lattice dynamics of a crystal with a molecular impurity

    International Nuclear Information System (INIS)

    Sahoo, D.; Venkataraman, G.

    1975-01-01

    The dynamics of a crystal containing a molecular impurity is discussed with allowance for the effects of internal vibrations of the molecule. Cartesian coordinates are used to describe internal vibrations, angular oscillations and centre of mass translations of the impurity, and the displacement of atoms of the host lattice. Next the Hamiltonian is set up and the equations of motion derived. In this process, use is made of Dirac brackets when dealing with vibrational coordinates (of the molecule) which have redundancy and constraints. A method of solution of the normal modes of the system is indicated by using the defect space matrixpartitioning technique. The special case of a rigid molecular impurity is then discussed along with the relevance of the present formalism in the interpretation of a recent neutron scattering experiment. It is also shown how the results of crystal-field approximation model and those of the molecular model approximation are obtained as further special cases of the present formalism. A comparison of the present work with those of others has been made. (author)

  16. International bulletin on atomic and molecular data for fusion. No. 25

    International Nuclear Information System (INIS)

    Katsonis, K.

    1984-06-01

    This bulletin deals with atomic and molecular data for fusion. A bibliography for the most recent data presented in the document is provided. Work in progress is also briefly reported (Collision strengths and recombination coefficients for ions of C,N,O; Reactions between ions and atomic hydrogen; Cross sections for electron impact ionisation of Ne + , Ti + and Ni + ions)

  17. International bulletin on atomic and molecular data for fusion. No. 40

    International Nuclear Information System (INIS)

    Smith, J.J.

    1990-03-01

    Indexed papers relating to structure and spectra, atomic and molecular collisions, and surface interactions relevant to nuclear fusion are given. Included is the bibliography for all indexed papers. In addition, a list of evaluated numerical atomic databases stored in the IAEA data bank is given

  18. Systematic determination of extended atomic orbital basis sets and application to molecular SCF and MCSCF calculations

    Energy Technology Data Exchange (ETDEWEB)

    Feller, D.F.

    1979-01-01

    The behavior of the two exponential parameters in an even-tempered gaussian basis set is investigated as the set optimally approaches an integral transform representation of the radial portion of atomic and molecular orbitals. This approach permits a highly accurate assessment of the Hartree-Fock limit for atoms and molecules.

  19. International bulletin on atomic and molecular data for fusion. No. 18

    International Nuclear Information System (INIS)

    Katsonis, K.

    1982-02-01

    This bulletin deals with atomic and molecular data for fusion. A bibliography for the most recent data presented in the document is provided. Work in progress is briefly reported (electron impact excitation of hydrogen-like argon ions, excitation and charge transfer in collisions of Li atoms with alpha particles)

  20. Manipulation and analysis of atomic and molecular beams using transmission gratings and Fresnel zone plates

    Energy Technology Data Exchange (ETDEWEB)

    Grisenti, R.E.

    2000-06-01

    In this thesis experimental results on the diffraction of rare gas atoms (He, Ne, Ar, Kr) and molecular (D{sub 2}) beams by a 100 nm period transmission grating and on the focusing of a helium atom beam through a Fresnel zone plate have been reported. (orig.)