WorldWideScience

Sample records for atom molecular mechanics

  1. 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

  2. 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

  3. Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms.

    Science.gov (United States)

    Wu, Xin-Ping; Gagliardi, Laura; Truhlar, Donald G

    2018-05-30

    Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM-MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM-MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM-MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

  4. Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms

    Directory of Open Access Journals (Sweden)

    Xin-Ping Wu

    2018-05-01

    Full Text Available Combined quantum mechanical and molecular mechanical (QM/MM methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM−MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM−MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.

  5. 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.

  6. 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...

  7. Reaction mechanism of oxygen atoms with unsaturated hydrocarbons by the crossed molecular beams method

    Energy Technology Data Exchange (ETDEWEB)

    Buss, R.J.; Baseman, R.J.; Guozhong, H.; Lee, Y.T.

    1982-04-01

    From a series of studies of the reaction of oxygen atoms with unsaturated hydrocarbons using the crossed molecular beam method, the dominant reaction mechanisms were found to be the simple substitution reactions with oxygen atoms replacing H, Cl, Br atom or alkyl groups. Complication due to secondary reaction was avoided by carrying out experiments under single collisions and observing primary products directly. Primary products were identified by measuring the angular and velocity distributions of products at all the mass numbers which could be detected by the mass spectrometer, and from comparison of these distributions, applying the requirement of energy and momentum conservation.

  8. Reaction Mechanism of Oxygen Atoms with Unsaturated Hydrocarbons by the Crossed-Molecular-Beams Method

    Science.gov (United States)

    Buss, R. J.; Baseman, R. J.; Guozhong, H.; Lee, Y. T.

    1982-04-01

    From a series of studies of the reaction of oxygen atoms with unsaturated hydrocarbons using the crossed molecular beam method, the dominant reaction mechanisms were found to be the simple substitution reactions with oxygen atoms replacing H, Cl, Br atom or alkyl groups. Complication due to secondary reaction was avoided by carrying out experiments under single collisions and observing primary products directly. Primary products were identified by measuring the angular and velocity distributions of products at all the mass numbers which could be detected by the mass spectrometer, and from comparison of these distributions, applying the requirement of energy and momentum conservation.

  9. Perfect/complete scattering experiments. Probing quantum mechanics on atomic and molecular collisions and coincidences

    International Nuclear Information System (INIS)

    Lohmann, Bernd; Grum-Grzhimailo, Alexei N.; Kleinpoppen, Hans

    2013-01-01

    Derives parameters for electrons, photons, atoms, ions, molecules calculated from theory. Delivers the quantum mechanical knowledge of atomic and molecular physics. Presents state-of-the-art experiments in atomic and molecular physics and related theoretical approaches. The main goal of this book is to elucidate what kind of experiment must be performed in order to determine the full set of independent parameters which can be extracted and calculated from theory, where electrons, photons, atoms, ions, molecules, or molecular ions may serve as the interacting constituents of matter. The feasibility of such perfect' and-or 'complete' experiments, providing the complete quantum mechanical knowledge of the process, is associated with the enormous potential of modern research techniques, both, in experiment and theory. It is even difficult to overestimate the role of theory in setting of the complete experiment, starting with the fact that an experiment can be complete only within a certain theoretical framework, and ending with the direct prescription of what, and in what conditions should be measured to make the experiment 'complete'. The language of the related theory is the language of quantum mechanical amplitudes and their relative phases. This book captures the spirit of research in the direction of the complete experiment in atomic and molecular physics, considering some of the basic quantum processes: scattering, Auger decay and photo-ionization. It includes a description of the experimental methods used to realize, step by step, the complete experiment up to the level of the amplitudes and phases. The corresponding arsenal includes, beyond determining the total cross section, the observation of angle and spin resolved quantities, photon polarization and correlation parameters, measurements applying coincidence techniques, preparing initially polarized targets, and even more sophisticated methods. The 'complete' experiment is, until today, hardly to perform

  10. Perfect/complete scattering experiments. Probing quantum mechanics on atomic and molecular collisions and coincidences

    Energy Technology Data Exchange (ETDEWEB)

    Lohmann, Bernd [Muenster Univ. (Germany). Inst. fuer Theoretische Physik 1; Grum-Grzhimailo, Alexei N. [Moscow State Univ. (Russian Federation). Skobeltsyn Inst. of Nuclear Physics; Kleinpoppen, Hans

    2013-07-01

    Derives parameters for electrons, photons, atoms, ions, molecules calculated from theory. Delivers the quantum mechanical knowledge of atomic and molecular physics. Presents state-of-the-art experiments in atomic and molecular physics and related theoretical approaches. The main goal of this book is to elucidate what kind of experiment must be performed in order to determine the full set of independent parameters which can be extracted and calculated from theory, where electrons, photons, atoms, ions, molecules, or molecular ions may serve as the interacting constituents of matter. The feasibility of such perfect' and-or 'complete' experiments, providing the complete quantum mechanical knowledge of the process, is associated with the enormous potential of modern research techniques, both, in experiment and theory. It is even difficult to overestimate the role of theory in setting of the complete experiment, starting with the fact that an experiment can be complete only within a certain theoretical framework, and ending with the direct prescription of what, and in what conditions should be measured to make the experiment 'complete'. The language of the related theory is the language of quantum mechanical amplitudes and their relative phases. This book captures the spirit of research in the direction of the complete experiment in atomic and molecular physics, considering some of the basic quantum processes: scattering, Auger decay and photo-ionization. It includes a description of the experimental methods used to realize, step by step, the complete experiment up to the level of the amplitudes and phases. The corresponding arsenal includes, beyond determining the total cross section, the observation of angle and spin resolved quantities, photon polarization and correlation parameters, measurements applying coincidence techniques, preparing initially polarized targets, and even more sophisticated methods. The 'complete' experiment is

  11. 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

  12. Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations.

    Science.gov (United States)

    Álvarez-Barcia, Sonia; Kästner, Johannes

    2017-06-01

    Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe═O cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value.

  13. 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.

  14. 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.

  15. 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

  16. Mechanism and kinetics of Fe, Cr, Mo and Mn atom interaction with molecular oxygen

    International Nuclear Information System (INIS)

    Akhmadov, U.S.; Zaslonko, I.S.; Smirnov, V.N.

    1988-01-01

    Rate constants of atomic interaction of some transition metals (Fe, Cr, Mo, Mn) with molecular oxygen are measured in shock waves using the resonance atomic-absorption method. A new method for determination of the parameter γ in the modified Lambert-Beer law D=ε(lN)γ is suggested and applied. Bond strength in CrO and MoO molecules is estimated

  17. Perfect/complete scattering experiments probing quantum mechanics on atomic and molecular collisions and coincidences

    CERN Document Server

    Kleinpoppen, Hans; Grum-Grzhimailo, Alexei N

    2013-01-01

    The main goal of this book is to elucidate what kind of experiment must be performed in order to determine the full set of independent parameters which can be extracted and calculated from theory, where electrons, photons, atoms, ions, molecules, or molecular ions may serve as the interacting constituents of matter.  The feasibility of such perfect' and-or `complete' experiments, providing the complete quantum mechanical knowledge of the process, is associated with the enormous potential of modern research techniques, both, in experiment and theory.  It is even difficult to overestimate the role of theory in setting of the complete experiment, starting with the fact that an experiment can be complete only within a certain theoretical framework, and ending with the direct prescription of what, and in what conditions should be measured to make the experiment `complete'.  The language of the related theory is the language of quantum mechanical amplitudes and their relative phases.  This book captures the spi...

  18. 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

  19. 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

  20. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  1. 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

  2. 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.

  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. 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.

  5. 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

  6. 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

  7. 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...

  8. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations.

    Science.gov (United States)

    Song, Xudan; Lu, Jiarui; Lai, Wenzhen

    2017-08-02

    Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an Fe II /α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated Fe IV -oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated Fe IV -oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated Fe IV -oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated Fe IV -oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive Fe IV -oxo species.

  9. 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.)

  10. The molecular-scale arrangement and mechanical strength of phospholipid/cholesterol mixed bilayers investigated by frequency modulation atomic force microscopy in liquid

    International Nuclear Information System (INIS)

    Asakawa, Hitoshi; Fukuma, Takeshi

    2009-01-01

    Cholesterols play key roles in controlling molecular fluidity in a biological membrane, yet little is known about their molecular-scale arrangements in real space. In this study, we have directly imaged lipid-cholesterol complexes in a model biological membrane consisting of dipalmitoylphosphatidylcholine (DPPC) and cholesterols by frequency modulation atomic force microscopy (FM-AFM) in phosphate buffer solution. FM-AFM images of a DPPC/cholesterol bilayer in the liquid-ordered phase showed higher energy dissipation values compared to those measured on a nanoscale DPPC domain in the gel phase, reflecting the increased molecular fluidity due to the insertion of cholesterols. Molecular-resolution FM-AFM images of a DPPC/cholesterol bilayer revealed the existence of a rhombic molecular arrangement (lattice constants: a = 0.46 nm, b = 0.71 nm) consisting of alternating rows of DPPC and cholesterols as well as the increased defect density and reduced molecular ordering. The mechanical strength of a DPPC/cholesterol bilayer was quantitatively evaluated by measuring a loading force required to penetrate the membrane with an AFM tip. The result revealed the significant decrease of mechanical strength upon insertion of cholesterols. Based on the molecular-scale arrangement found in this study, we propose a model to explain the reduced mechanical strength in relation to the formation of lipid-ion networks.

  11. The molecular-scale arrangement and mechanical strength of phospholipid/cholesterol mixed bilayers investigated by frequency modulation atomic force microscopy in liquid

    Energy Technology Data Exchange (ETDEWEB)

    Asakawa, Hitoshi; Fukuma, Takeshi [Frontier Science Organization, Kanazawa University, Kakuma-machi, 920-1192 Kanazawa (Japan)], E-mail: hi_asa@staff.kanazawa-u.ac.jp, E-mail: fukuma@staff.kanazawa-u.ac.jp

    2009-07-01

    Cholesterols play key roles in controlling molecular fluidity in a biological membrane, yet little is known about their molecular-scale arrangements in real space. In this study, we have directly imaged lipid-cholesterol complexes in a model biological membrane consisting of dipalmitoylphosphatidylcholine (DPPC) and cholesterols by frequency modulation atomic force microscopy (FM-AFM) in phosphate buffer solution. FM-AFM images of a DPPC/cholesterol bilayer in the liquid-ordered phase showed higher energy dissipation values compared to those measured on a nanoscale DPPC domain in the gel phase, reflecting the increased molecular fluidity due to the insertion of cholesterols. Molecular-resolution FM-AFM images of a DPPC/cholesterol bilayer revealed the existence of a rhombic molecular arrangement (lattice constants: a = 0.46 nm, b = 0.71 nm) consisting of alternating rows of DPPC and cholesterols as well as the increased defect density and reduced molecular ordering. The mechanical strength of a DPPC/cholesterol bilayer was quantitatively evaluated by measuring a loading force required to penetrate the membrane with an AFM tip. The result revealed the significant decrease of mechanical strength upon insertion of cholesterols. Based on the molecular-scale arrangement found in this study, we propose a model to explain the reduced mechanical strength in relation to the formation of lipid-ion networks.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Atomic mechanics of solids

    CERN Document Server

    MacPherson, A K

    1990-01-01

    This volume brings together some of the presently available theoretical techniques which will be useful in the design of solid-state materials. At present, it is impossible to specify the atomic composition of a material and its macroscopic physical properties. However, the future possibilities for such a science are being laid today. This is coming about due to the development of fast, cheap computers which will be able to undertake the calculations which are necessary.Since this field of science is fairly new, it is not yet quite clear which direction of analysis will eventually prov

  17. 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)

  18. Mechanism of Intermittent Atomization

    Science.gov (United States)

    1993-06-01

    6] and Dolenc [7] that the dynamic pressure input to the nozzle is very important to engine efficiency. In their dis- cussion of optimizing fuel...Injection in Diesel Engines." Proceedings of the Institute of Mechanical Engineers, Vol. 199 No. D3, 1985, ppl6l-174. [7] Dolenc , A. "The Injection

  19. 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

  20. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  1. 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.

  2. 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

  3. 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

  4. Refresher Course in Applications of Quantum Mechanics to 'Atoms ...

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course in Applications of Quantum Mechanics to 'Atoms, Molecules and Radiation' will be held at the Indian Academy of Sciences, Bangalore from December 8 to 20. 2014. The Course is primarily aimed at teachers teaching quantum mechanics and/ or atomic and molecular physics at the UG / PG level.

  5. Quantum mechanical modeling of molecular properties of systems with heavy-atoms in condensed phases and on interfaces

    International Nuclear Information System (INIS)

    Olejniczak, M.; Gomes, A.S.P.; Bast, R.

    2015-07-01

    We report an implementation of the nuclear magnetic resonance (NMR) shielding tensor in the frozen density embedding (FDE) scheme - in which the total system is divided into interacting subsystems - using the four-component (4c) relativistic Dirac-Coulomb (DC) Hamiltonian and the non-collinear spin density functional theory (SDFT). The formalism takes into account the magnetic balance between the large and the small components of molecular spinors and assures the gauge-origin independence of results. This implementation has been applied to hydrogen-bonded H 2 X---H 2 O complexes (X = Se, Te, Po) and compared with the super-molecular calculations and with the approach based on the integration of the magnetically induced current density vector. (authors)

  6. Photocatalytic mechanism of high-activity anatase TiO2 with exposed (001) facets from molecular-atomic scale: HRTEM and Raman studies

    Science.gov (United States)

    Wu, Jun; Shi, Chentian; Zhang, Yupeng; Fu, Qiang; Pan, Chunxu

    2017-12-01

    Anatase TiO2 with a variant percentage of exposed (001) facets was prepared under hydrothermal processes by adjusting the volume of HF, and the photocatalytic mechanism was studied from atomic-molecular scale by HRTEM and Raman spectroscopy. It was revealed that: 1) From HRTEM observations, the surface of original TiO2 with exposed (001) facets was clean without impurity, and the crystal lattice was clear and completed; however, when mixed with methylene blue (MB) solution, there were many 1 nm molecular absorbed at the surface of TiO2; after the photocatalytic experiment, MB molecules disappeared and the TiO2 lattice image became fuzzy. 2) The broken path of the MB chemical bond was obtained by Raman spectroscopy, i.e., after the irradiation of the light, the vibrational mode of C-N-C disappeared due to the chemical bond breakage, and the groups containing C-N bond and carbon rings were gradually decomposed. Accordingly, we propose that the driving force for breaking the chemical bond and the disappearance of groups is from the surface lattice distortion of TiO2 during photocatalyzation.

  7. 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

  8. 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)

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. Molecular Mechanisms of Preeclampsia

    Directory of Open Access Journals (Sweden)

    N. Vitoratos

    2012-01-01

    Full Text Available Preeclampsia is one of the leading causes of maternal morbidity/mortality. The pathogenesis of preeclampsia is still under investigation. The aim of this paper is to present the molecular mechanisms implicating in the pathway leading to preeclampsia.

  2. 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

  3. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

    Science.gov (United States)

    Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

    2011-10-01

    Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

  4. 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.

  5. 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...

  6. 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....

  7. 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.

  8. Quantum mechanical determination of atomic polarizabilities of ionic liquids.

    Science.gov (United States)

    Heid, Esther; Szabadi, András; Schröder, Christian

    2018-04-25

    The distribution of a molecule's polarizability to individual atomic sites is inevitable to develop accurate polarizable force fields. We present the direct quantum mechanical calculation of atomic polarizabilities of 27 common ionic liquids. The method is superior to previously published distribution routines based on large databases of the molecular polarizability, and enables the correct description of any ionic liquid and its peculiarities within the quantum mechanical framework.

  9. 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)

  10. Mechanical properties and formation mechanisms of a wire of single gold atoms

    DEFF Research Database (Denmark)

    Rubio-Bollinger, G.; Bahn, Sune Rastad; Agrait, N.

    2001-01-01

    initio calculations of the force at chain fracture and compare quantitatively with experimental measurements. The observed mechanical failure and nanoelastic processes involved during atomic wire fabrication are investigated using molecular dynamics simulations, and we find that the total effective...

  11. Mechanical filter for alkali atoms

    CERN Document Server

    Toporkov, D K

    2000-01-01

    A device for separating gases of different mass is discussed. Such a device could be used in a laser-driven spin exchange source of polarized hydrogen atoms to reduce the contamination of alkali atoms. A Monte Carlo simulation has shown that the suggested apparatus based on a commercial turbo pump could reduce by a factor of 10-15 the concentration of the alkali-metal atoms in the hydrogen flow from a laser driven polarized source. This would greatly enhance the effective polarization in hydrogen targets.

  12. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  13. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Koffas, Telly Stelianos [Univ. of California, Berkeley, CA (United States)

    2004-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and other complementary surface-sensitive techniques have been used to study the surface molecular structure and surface mechanical behavior of biologically-relevant polymer systems. SFG and AFM have emerged as powerful analytical tools to deduce structure/property relationships, in situ, for polymers at air, liquid and solid interfaces. The experiments described in this dissertation have been performed to understand how polymer surface properties are linked to polymer bulk composition, substrate hydrophobicity, changes in the ambient environment (e.g., humidity and temperature), or the adsorption of macromolecules. The correlation of spectroscopic and mechanical data by SFG and AFM can become a powerful methodology to study and engineer materials with tailored surface properties. The overarching theme of this research is the interrogation of systems of increasing structural complexity, which allows us to extend conclusions made on simpler model systems. We begin by systematically describing the surface molecular composition and mechanical properties of polymers, copolymers, and blends having simple linear architectures. Subsequent chapters focus on networked hydrogel materials used as soft contact lenses and the adsorption of protein and surfactant at the polymer/liquid interface. The power of SFG is immediately demonstrated in experiments which identify the chemical parameters that influence the molecular composition and ordering of a polymer chain's side groups at the polymer/air and polymer/liquid interfaces. In general, side groups with increasingly greater hydrophobic character will be more surface active in air. Larger side groups impose steric restrictions, thus they will tend to be more randomly ordered than smaller hydrophobic groups. If exposed to a hydrophilic environment, such as water, the polymer chain will attempt to orient more of its hydrophilic groups to

  14. Mechanisms and energetics of surface atomic processes

    International Nuclear Information System (INIS)

    Tsong, T.T.

    1991-01-01

    The energies involved in various surface atomic processes such as surface diffusion, the binding of small atomic clusters on the surface, the interaction between two adsorbed atoms, the dissociation of an atom from a small cluster or from a surface layer, the binding of kink size atoms or atoms at different adsorption sites to the surface etc., can be derived from an analysis of atomically resolved field ion microscope images and a kinetic energy measurement of low temperature field desorbed ions using the time-of-flight atom-probe field ion microscope. These energies can be used to compare with theories and to understand the transport of atoms on the surface in atomic reconstructions, epitaxial growth of surface layers and crystal growth, adsorption layer superstructure formation, and also why an atomic ordering or atomic reconstruction at the surface is energetically favored. Mechanisms of some of the surface atomic processes are also clarified from these quantitative, atomic resolution studies. In this paper work in this area is bris briefly reviewed

  15. UNIQUAC interaction parameters for molecules with -OH groups on adjacent carbon atoms in aqueous solution determined by molecular mechanics - glycols, glycerol and glucose

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Klein, R. A.

    1997-01-01

    UNIQUAC interaction parameters have been determined, using molecular mechanics calculations, for 1,2-ethanediol, 1,2-propanediol, glycerol and glucose with water in aqueous solution. Conformational space for individual pairs of molecules was explored using a stochastic method, the Boltzmann Jump...

  16. 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

  17. Atomization mechanisms for barium in furnace atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Styris, D.L.

    1984-01-01

    Atomic absorption spectrometry and mass spectrometry are used simultaneously in order to elucidate atomization mechanisms of barium dichloride in pyrolytic graphite, vitreous carbon, and tantalum furnaces. Gas-phase barium dicarbide is observed to appear concurrently with the free barium. Barium oxide and barium dihydroxide precursors appear with the chlorides. Surface reactions involving species that are absorbed on the various furnaces are postulated to explain the appearances of the species that are observed in the gas phase. 49 references, 4 figures, 1 table

  18. Molecular mechanisms in gliomagenesis

    DEFF Research Database (Denmark)

    Hulleman, Esther; Helin, Kristian

    2005-01-01

    Glioma, and in particular high-grade astrocytoma termed glioblastoma multiforme (GBM), is the most common primary tumor of the brain. Primarily because of its diffuse nature, there is no effective treatment for GBM, and relatively little is known about the processes by which it develops. Therefore......, in order to design novel therapies and treatments for GBM, research has recently intensified to identify the cellular and molecular mechanisms leading to GBM formation. Modeling of astrocytomas by genetic manipulation of mice suggests that deregulation of the pathways that control gliogenesis during normal...... brain development, such as the differentiation of neural stem cells (NSCs) into astrocytes, might contribute to GBM formation. These pathways include growth factor-induced signal transduction routes and processes that control cell cycle progression, such as the p16-CDK4-RB and the ARF-MDM2-p53 pathways...

  19. 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.)

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Molecular mechanisms of cancer

    National Research Council Canada - National Science Library

    Weber, Georg F

    2007-01-01

    ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Section I. General Mechanisms of Transformation 1. Theories of Carcinogenesis...

  13. 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.

  14. 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

  15. 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.)

  16. 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.

  17. Molecular Mechanisms of Preeclampsia

    OpenAIRE

    N. Vitoratos; D. Hassiakos; C. Iavazzo

    2012-01-01

    Preeclampsia is a pregnancy-specific disease characterized by new onset hypertension and proteinuria after 20 wk of gestation. It is a leading cause of maternal and fetal morbidity and mortality worldwide. Exciting discoveries in the last decade have contributed to a better understanding of the molecular basis of this disease. Epidemiological, experimental, and therapeutic studies from several laboratories have provided compelling evidence that an antiangiogenic state owing to alterations in ...

  18. Topics in molecular mechanics

    International Nuclear Information System (INIS)

    Essen, H.

    1979-05-01

    This report is a personal review of theoretical research concerning molecules. Here one finds some mathematical background from tensor calculus and Lie group theory. The most general transformations of the 3N-dimensional Laplacian, including transformations to group operators, are also presented. I discuss kinematical questions, especially those behind the separations of electronic and nuclear and of vibrational and rotational motion. One also finds discussions of the dynamics of the former separation. Classical atom-diatomic molecule scattering and quasiclassical transition probabilities are touched upon. I present a general discussion of approximate separation schemes, especially adiabatic, and discuss predissociations with special reference to one in SiO. Finally, a simple model is presented which reveals what happens when inversion doubling is connected with decay. (author)

  19. Molecular Mechanisms of Preeclampsia.

    Science.gov (United States)

    Hod, Tammy; Cerdeira, Ana Sofia; Karumanchi, S Ananth

    2015-08-20

    Preeclampsia is a pregnancy-specific disease characterized by new onset hypertension and proteinuria after 20 wk of gestation. It is a leading cause of maternal and fetal morbidity and mortality worldwide. Exciting discoveries in the last decade have contributed to a better understanding of the molecular basis of this disease. Epidemiological, experimental, and therapeutic studies from several laboratories have provided compelling evidence that an antiangiogenic state owing to alterations in circulating angiogenic factors leads to preeclampsia. In this review, we highlight the role of key circulating antiangiogenic factors as pathogenic biomarkers and in the development of novel therapies for preeclampsia. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

  20. Molecular Mechanisms of Preeclampsia

    Science.gov (United States)

    Hod, Tammy; Cerdeira, Ana Sofia; Karumanchi, S. Ananth

    2015-01-01

    Preeclampsia is a pregnancy-specific disease characterized by new onset hypertension and proteinuria after 20 wk of gestation. It is a leading cause of maternal and fetal morbidity and mortality worldwide. Exciting discoveries in the last decade have contributed to a better understanding of the molecular basis of this disease. Epidemiological, experimental, and therapeutic studies from several laboratories have provided compelling evidence that an antiangiogenic state owing to alterations in circulating angiogenic factors leads to preeclampsia. In this review, we highlight the role of key circulating antiangiogenic factors as pathogenic biomarkers and in the development of novel therapies for preeclampsia. PMID:26292986

  1. Molecular mechanisms of carcinogenesis

    International Nuclear Information System (INIS)

    Hall, E.J.

    1997-01-01

    The possibility that chromosomal changes are responsible for neoplasia was proposed in the early years of this century. A combination of improved cytogenetics and the advent of recombinant technology has settled the issue. As recently as 20 years ago, however, the genetic and molecular basis of familiar predisposition to cancer were a mystery, and it is only in the last few years that light has been shed on a few specific types of malignancies. As the genetic basis of human cancer had been documented, a number of genes have been identified as functioning either as oncogenes which act in a dominant fashion to promote tumor growth when mutated, or as tumor suppressor genes which act in a recessive fashion

  2. Measuring the mechanical properties of molecular conformers

    Science.gov (United States)

    Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

    2015-09-01

    Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

  3. 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)

  4. 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.

  5. 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

  6. Quantum Mechanical Study of Atoms and Molecules

    Science.gov (United States)

    Sahni, R. C.

    1961-01-01

    This paper, following a brief introduction, is divided into five parts. Part I outlines the theory of the molecular orbital method for the ground, ionized and excited states of molecules. Part II gives a brief summary of the interaction integrals and their tabulation. Part III outlines an automatic program designed for the computation of various states of molecules. Part IV gives examples of the study of ground, ionized and excited states of CO, BH and N2 where the program of automatic computation and molecular integrals have been utilized. Part V enlists some special problems of Molecular Quantum Mechanics are being tackled at New York University.

  7. 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.

  8. 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.

  9. Mechanism of yttrium atom formation in electrothermal atomization from metallic and metal-carbide surfaces of a heated graphite atomizer in atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Wahab, H.S.; Chakrabarti, C.L.

    1981-01-01

    Mechanism of Y atom formation from pyrocoated graphite, tantalum and tungsten metal surfaces of a graphite tube atomizer has been studied and a mechanism for the formation for Y atoms is proposed for the first time. (author)

  10. 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)

  11. STATINS AND MYOPATHY: MOLECULAR MECHANISMS

    Directory of Open Access Journals (Sweden)

    O. M. Drapkina

    2012-01-01

    Full Text Available The safety of statin therapy is considered. In particular the reasons of a complication such as myopathy are discussed in detail. The molecular mechanisms of statin myopathy , as well as its risk factors are presented. The role of coenzyme Q10 in the myopathy development and coenzyme Q10 application for the prevention of this complication are considered. 

  12. 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

  13. 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.

  14. 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.

  15. Molecular mechanisms of crystal growth

    International Nuclear Information System (INIS)

    Pina, C. M.

    2000-01-01

    In this paper I present an example of the research that the Mineral Surface Group of the Munster University is conducting in the field of Crystal Growth. Atomic Force Microscopy (Am) in situ observations of different barite (BaSO4) faces growing from aqueous solutions, in combination with computer simulations of the surface attachment of growth units allows us to test crystal growth models. Our results demonstrate the strong structural control that a crystal can exert on its own growth, revealing also the limitation of the classical crystal growth theories (two dimensional nucleation and spiral growth models) in providing a complete explanation for the growth behaviour at a molecular scale. (Author) 6 refs

  16. Hyperinsulinemic Hypoglycemia ? The Molecular Mechanisms

    OpenAIRE

    Nessa, Azizun; Rahman, Sofia A.; Hussain, Khalid

    2016-01-01

    Under normal physiological conditions, pancreatic β-cells secrete insulin to maintain fasting blood glucose levels in the range 3.5–5.5 mmol/L. In hyperinsulinemic hypoglycemia (HH), this precise regulation of insulin secretion is perturbed so that insulin continues to be secreted in the presence of hypoglycemia. HH may be due to genetic causes (congenital) or secondary to certain risk factors. The molecular mechanisms leading to HH involve defects in the key genes regulating insulin secretio...

  17. 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

  18. 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.

  19. 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.

  20. 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)

  1. 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...

  2. 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.

  3. 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)

  4. 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

  5. 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.

  6. Mechanical deformation of atomic-scale metallic contacts: Structure and mechanisms

    DEFF Research Database (Denmark)

    Sørensen, Mads Reinholdt; Brandbyge, Mads; Jacobsen, Karsten Wedel

    1998-01-01

    We have simulated the mechanical deformation of atomic-scale metallic contacts under tensile strain using molecular dynamics and effective medium theory potentials. The evolution of the structure of the contacts and the underlying deformation mechanisms are described along with the calculated......, but vacancies can be permanently present. The transition states and energies for slip mechanisms have been determined using the nudged elastic band method, and we find a size-dependent crossover from a dislocation-mediated slip to a homogeneous slip when the contact diameter becomes less than a few nm. We show...

  7. Molecular mechanisms of fluoride toxicity.

    Science.gov (United States)

    Barbier, Olivier; Arreola-Mendoza, Laura; Del Razo, Luz María

    2010-11-05

    Halfway through the twentieth century, fluoride piqued the interest of toxicologists due to its deleterious effects at high concentrations in human populations suffering from fluorosis and in in vivo experimental models. Until the 1990s, the toxicity of fluoride was largely ignored due to its "good reputation" for preventing caries via topical application and in dental toothpastes. However, in the last decade, interest in its undesirable effects has resurfaced due to the awareness that this element interacts with cellular systems even at low doses. In recent years, several investigations demonstrated that fluoride can induce oxidative stress and modulate intracellular redox homeostasis, lipid peroxidation and protein carbonyl content, as well as alter gene expression and cause apoptosis. Genes modulated by fluoride include those related to the stress response, metabolic enzymes, the cell cycle, cell-cell communications and signal transduction. The primary purpose of this review is to examine recent findings from our group and others that focus on the molecular mechanisms of the action of inorganic fluoride in several cellular processes with respect to potential physiological and toxicological implications. This review presents an overview of the current research on the molecular aspects of fluoride exposure with emphasis on biological targets and their possible mechanisms of involvement in fluoride cytotoxicity. The goal of this review is to enhance understanding of the mechanisms by which fluoride affects cells, with an emphasis on tissue-specific events in humans. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  8. 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)

  9. 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.

  10. Multiresolution molecular mechanics: Implementation and efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Biyikli, Emre; To, Albert C., E-mail: albertto@pitt.edu

    2017-01-01

    Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3–8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

  11. Molecular mechanisms of renal aging.

    Science.gov (United States)

    Schmitt, Roland; Melk, Anette

    2017-09-01

    Epidemiologic, clinical, and molecular evidence suggest that aging is a major contributor to the increasing incidence of acute kidney injury and chronic kidney disease. The aging kidney undergoes complex changes that predispose to renal pathology. The underlying molecular mechanisms could be the target of therapeutic strategies in the future. Here, we summarize recent insight into cellular and molecular processes that have been shown to contribute to the renal aging phenotype.The main clinical finding of renal aging is the decrease in glomerular filtration rate, and its structural correlate is the loss of functioning nephrons. Mechanistically, this has been linked to different processes, such as podocyte hypertrophy, glomerulosclerosis, tubular atrophy, and gradual microvascular rarefaction. Renal functional recovery after an episode of acute kidney injury is significantly worse in elderly patients. This decreased regenerative potential, which is a hallmark of the aging process, may be caused by cellular senescence. Accumulation of senescent cells could explain insufficient repair and functional loss, a view that has been strengthened by recent studies showing that removal of senescent cells results in attenuation of renal aging. Other potential mechanisms are alterations in autophagy as an important component of a disturbed renal stress response and functional differences in the inflammatory system. Promising therapeutic measures to counteract these age-related problems include mimetics of caloric restriction, pharmacologic renin-angiotensin-aldosterone system inhibition, and novel strategies of senotherapy with the goal of reducing the number of senescent cells to decrease aging-related disease in the kidney. Copyright © 2017 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

  12. 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)

  13. 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.

  14. Molecular Mechanism of Somite Development

    Directory of Open Access Journals (Sweden)

    Gulfidan Coskun

    2013-06-01

    Full Text Available From third week of gestation, notochord and the neural folds begin to gather at the center of the embryo to form the paraxial mesoderm. Paraxial mesoderm separates into blocks of cells called somitomers at the lateral sides of the neural tube of the head region. At the beginning of the third week somitomeres take ring shapes and form blocks of somites from occipital region to caudal region. Although somites are transient structures, they are extremely important in organizing the segmental pattern of vertebrate embryos. Somites give rise to the cells that form the vertebrae and ribs, the dermis of the dorsal skin, the skeletal muscles of the back, and the skeletal muscles of the body wall and limbs. Somitogenesis are formed by a genetic mechanism that is regulated by cyclical expression of genes in the Notch, Wnt and fibroblast growth factor signaling pathways. The prevailing model of the mechanism governing somitogenesis is the “clock and wave front”. Somitogenesis has components of periodicity, separation, epithelialization and axial specification. According to this model, the clock causes cells to undergo repeated oscillations, with a particular phase of each oscillation defining the competency of cells in the presomitic mesoderm to form a somite. Any disruption in this mechanism can be cause of severe segmentation defects of the vertebrae and congenital anomalies. In this review, we discuss the molecular mechanisms underlying the somitogenesis which is an important part of morphogenesis. [Archives Medical Review Journal 2013; 22(3.000: 362-376

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. Molecular Mechanisms of Induced Pluripotency

    Science.gov (United States)

    Muchkaeva, I.A.; Dashinimaev, E.B.; Terskikh, V.V.; Sukhanov, Y.V.; Vasiliev, A.V.

    2012-01-01

    In this review the distinct aspects of somatic cell reprogramming are discussed. The molecular mechanisms of generation of induced pluripotent stem (iPS) cells from somatic cells via the introduction of transcription factors into adult somatic cells are considered. Particular attention is focused on the generation of iPS cells without genome modifications via the introduction of the mRNA of transcription factors or the use of small molecules. Furthermore, the strategy of direct reprogramming of somatic cells omitting the generation of iPS cells is considered. The data concerning the differences between ES and iPS cells and the problem of epigenetic memory are also discussed. In conclusion, the possibility of using iPS cells in regenerative medicine is considered. PMID:22708059

  20. 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

  1. 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)

  2. Mechanism of single atom switch on silicon

    DEFF Research Database (Denmark)

    Quaade, Ulrich; Stokbro, Kurt; Thirstrup, C.

    1998-01-01

    We demonstrate single atom switch on silicon which operates by displacement of a hydrogen atom on the silicon (100) surface at room temperature. We find two principal effects by which the switch is controlled: a pronounced maximum of the switching probability as function of sample bias...

  3. 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

  4. 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)

  5. 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

  6. 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)

  7. 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.

  8. Molecular Mechanisms of Bacterial Pathogenicity

    Science.gov (United States)

    Fuchs, Thilo Martin

    Cautious optimism has arisen over recent decades with respect to the long struggle against bacteria, viruses, and parasites. This has been offset, however, by a fatal complacency stemming from previous successes such as the development of antimicrobial drugs, the eradication of smallpox, and global immunization programs. Infectious diseases nevertheless remain the world's leading cause of death, killing at least 17 million persons annually [61]. Diarrheal diseases caused by Vibrio cholerae or Shigella dysenteriae kill about 3 million persons every year, most of them young children: Another 4 million die of tuberculosis or tetanus. Outbreaks of diphtheria in Eastern Europe threatens the population with a disease that had previously seemed to be overcome. Efforts to control infectious diseases more comprehensively are undermined not only by socioeconomic conditions but also by the nature of the pathogenic organisms itself; some isolates of Staphylococcus aureus and Enterobacter have become so resistant to drugs by horizontal gene transfer that they are almost untreatable. In addition, the mechanism of genetic variability helps pathogens to evade the human immune system, thus compromising the development of powerful vaccines. Therefore detailed knowledge of the molecular mechanisms of microbial pathogenicity is absolutely necessary to develop new strategies against infectious diseases and thus to lower their impact on human health and social development.

  9. 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 �...

  10. 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.

  11. Molecular toxicity mechanism of nanosilver

    Directory of Open Access Journals (Sweden)

    Danielle McShan

    2014-03-01

    Full Text Available Silver is an ancient antibiotic that has found many new uses due to its unique properties on the nanoscale. Due to its presence in many consumer products, the toxicity of nanosilver has become a hot topic. This review summarizes recent advances, particularly the molecular mechanism of nanosilver toxicity. The surface of nanosilver can easily be oxidized by O2 and other molecules in the environmental and biological systems leading to the release of Ag+, a known toxic ion. Therefore, nanosilver toxicity is closely related to the release of Ag+. In fact, it is difficult to determine what portion of the toxicity is from the nano-form and what is from the ionic form. The surface oxidation rate is closely related to the nanosilver surface coating, coexisting molecules, especially thiol-containing compounds, lighting conditions, and the interaction of nanosilver with nucleic acids, lipid molecules, and proteins in a biological system. Nanosilver has been shown to penetrate the cell and become internalized. Thus, nanosilver often acts as a source of Ag+ inside the cell. One of the main mechanisms of toxicity is that it causes oxidative stress through the generation of reactive oxygen species and causes damage to cellular components including DNA damage, activation of antioxidant enzymes, depletion of antioxidant molecules (e.g., glutathione, binding and disabling of proteins, and damage to the cell membrane. Several major questions remain to be answered: (1 the toxic contribution from the ionic form versus the nano-form; (2 key enzymes and signaling pathways responsible for the toxicity; and (3 effect of coexisting molecules on the toxicity and its relationship to surface coating.

  12. 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)

  13. 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.

  14. 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

  15. Quantum-mechanical transport equation for atomic systems.

    Science.gov (United States)

    Berman, P. R.

    1972-01-01

    A quantum-mechanical transport equation (QMTE) is derived which should be applicable to a wide range of problems involving the interaction of radiation with atoms or molecules which are also subject to collisions with perturber atoms. The equation follows the time evolution of the macroscopic atomic density matrix elements of atoms located at classical position R and moving with classical velocity v. It is quantum mechanical in the sense that all collision kernels or rates which appear have been obtained from a quantum-mechanical theory and, as such, properly take into account the energy-level variations and velocity changes of the active (emitting or absorbing) atom produced in collisions with perturber atoms. The present formulation is better suited to problems involving high-intensity external fields, such as those encountered in laser physics.

  16. 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

  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. Mechanism of formation and spatial distribution of lead atoms in quartz tube atomizers

    Science.gov (United States)

    Johansson, M.; Baxter, D. C.; Ohlsson, K. E. A.; Frech, W.

    1997-05-01

    The cross-sectional and longitudinal spatial distributions of lead atoms in a quartz tube (QT) atomizers coupled to a gas chromatograph have been investigated. A uniform analyte atom distribution over the cross-section was found in a QT having an inner diameter (i.d.) of 7 mm, whereas a 10 mm i.d. QT showed an inhomogeneous distribution. These results accentuate the importance of using QTs with i.d.s below 10 mm to fulfil the prerequirement of the Beer—Lambert law to avoid bent calibration curves. The influence of the make up gas on the formation of lead atoms from alkyllead compounds has been studied, and carbon monoxide was found equally efficient in promoting free atom formation as hydrogen. This suggests that hydrogen radicals are not essential for mediating the atomization of alkyllead in QT atomizers at ˜ 1200 K. Furthermore, thermodynamic equilibrium calculations describing the investigated system were performed supporting the experimental results. Based on the presented data, a mechanism for free lead atom formation in continuously heated QT atomizers is proposed; thermal atomization occurs under thermodynamic equilibrium conditions in a reducing gas. The longitudinal atom distribution has been further investigated applying other make up gases, N 2 and He. These results show the effect of the influx of atmospheric oxygen on the free lead atom formation. Calculations of the partial pressure of oxygen in the atomizer gas phase assuming thermodynamic equilibrium have been undertaken using a convective-diffusional model.

  19. Migration mechanisms of self-interstitial atoms and their clusters in Fe-Cr alloys

    International Nuclear Information System (INIS)

    Terentyev, D.; Malerba, L.

    2006-06-01

    The mobility of self-interstitial atoms (SIAs) and their clusters in pure iron and iron-chromium alloys was studied by atomic scale modelling techniques. Molecular dynamics (MD) was used to simulate thermally activated motion, i.e. diffusion, and its mechanisms whereas molecular statics was used to estimate energies of interactions of SIA and SIA clusters with Cr-impurities. It is shown that the presence of Cr atoms reduces the diffusivity of SIAs and their clusters in a non monotonic way with increasing Cr concentration. The main reason for this reduction is the presence of a long-range attractive interaction between self-interstitials in the crowdion configuration and Cr atoms. The migration mechanisms behind this effect are discussed relying on the results obtained from the MD simulations. (author)

  20. 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

  1. 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)

  2. 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

  3. 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

  4. 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.

  5. Molecular mechanics calculations on cobalt phthalocyanine dimers

    NARCIS (Netherlands)

    Heuts, J.P.A.; Schipper, E.T.W.M.; Piet, P.; German, A.L.

    1995-01-01

    In order to obtain insight into the structure of cobalt phthalocyanine dimers, molecular mechanics calculations were performed on dimeric cobalt phthalocyanine species. Molecular mechanics calculations are first presented on monomeric cobalt(II) phthalocyanine. Using the Tripos force field for the

  6. 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

  7. 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

  8. A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes.

    Science.gov (United States)

    Parks, Jerry M; Hu, Hao; Cohen, Aron J; Yang, Weitao

    2008-10-21

    The pseudobond method is used in quantum mechanical/molecular mechanical (QM/MM) simulations in which a covalent bond connects the quantum mechanical and classical subsystems. In this method, the molecular mechanical boundary atom is replaced by a special quantum mechanical atom with one free valence that forms a bond with the rest of the quantum mechanical subsystem. This boundary atom is modified through the use of a parametrized effective core potential and basis set. The pseudobond is designed to reproduce the properties of the covalent bond that it has replaced, while invoking as small a perturbation as possible on the system. Following the work of Zhang [J. Chem. Phys. 122, 024114 (2005)], we have developed new pseudobond parameters for use in the simulation of enzymatic systems. Our parameters yield improved electrostatics and deprotonation energies, while at the same time maintaining accurate geometries. We provide parameters for C(ps)(sp(3))-C(sp(3)), C(ps)(sp(3))-C(sp(2),carbonyl), and C(ps)(sp(3))-N(sp(3)) pseudobonds, which allow the interface between the quantum mechanical and molecular mechanical subsystems to be constructed at either the C(alpha)-C(beta) bond of a given amino acid residue or along the peptide backbone. In addition, we demonstrate the efficiency of our parametrization method by generating residue-specific pseudobond parameters for a single amino acid. Such an approach may enable higher accuracy than general purpose parameters for specific QM/MM applications.

  9. 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

  10. Mechanism of calcium oxide excitation by atom hydrogen

    International Nuclear Information System (INIS)

    Kharlamov, V.F.

    1991-01-01

    Heterogeneous recombination of hydrogen atoms on the surface of calcium oxide proceeds according to the Langmuir-Hinshelwood mechanism with participation of atoms in two different states, belonging to adsorption centres of the same type. CaO excitation is broughty about by vibration-electron transitions during associative desorption of H 2 molecules

  11. Study on orientation mechanisms of poly(vinylidenefluoride-trifluoroethylene) molecules aligned by atomic force microscopy

    International Nuclear Information System (INIS)

    Kimura, Kuniko; Kobayashi, Kei; Yamada, Hirofumi; Horiuchi, Toshihisa; Ishida, Kenji; Matsushige, Kazumi

    2006-01-01

    We have developed a molecular orientation control technique for polymers utilizing contact-mode atomic force microscopy (AFM). In this paper, we studied the molecular alignment mechanism of this technique by applying it to poly(vinylidenefluoride-trifluoroethylene) (P(VDF-TrFE)). The resultant alignment and formed crystal size were strongly dependent on the temperature during the modification. They also depended on the scan line spacing of the modification. These results made the alignment mechanism clear. The obtained molecular alignment was stable against the heat treatment even at the temperatures just below T m

  12. 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.

  13. Mechanical action of light of atoms

    National Research Council Canada - National Science Library

    Kazan︠t︡sev, A. P; Surdutovich, G. I; I︡Akovlev, V. P

    1990-01-01

    ... should be useful to both experts and beginners in laser physics and q u a n t u m optics.This page is intentionally left blankCONTENTS Preface v Introduction 1 C h a p t e r 1. C o h e r e n t I n t e r a c t i o n b e t w e e n A t o m s a n d F i e l d . 9 1. The Hamiltonian of Atom-Field Interaction 2. Light Pressure Force 2.1. Adiabatic states. Nonresonant pot...

  14. Atomic collision experiments at the border line between classical and quantum mechanics

    International Nuclear Information System (INIS)

    Aquilanti, V.

    1984-01-01

    In order to understand atomic and molecular interactions, one has to learn how to live with the wave-particle duality, considering classical nuclei and quantum electrons. A better way, illustrated by reference to experiments, is by quasiclassical (or semi-classical) mechanics, governing a world with a quasi-zero Planck's constant. One thus explains optical analogs (shadows, rainbows, glories) as interference effects in atomic collisions. Reference is also made to Wheeler's 'black bird' on the inversion problem from spectroscopy and scattering to molecular structure. The paper concludes outlining a journey in the hyperspace to escape from Einstein's torus and to find interferences and resonances in three body scattering and reactions. (Auth.)

  15. Molecular mechanisms of NCAM function

    DEFF Research Database (Denmark)

    Hinsby, Anders M; Berezin, Vladimir; Bock, Elisabeth

    2004-01-01

    receptor that responds to both homophilic and heterophilic cues, as well as a mediator of cell-cell adhesion. This review describes NCAM function at the molecular level. We discuss recent models for extracellular ligand-interactions of NCAM, and the intracellular signaling cascade that follows to define...

  16. Molecular mechanisms of insulin resistance

    African Journals Online (AJOL)

    Review Article. ,. Molecular ... This review discusses recent advances in understanding of the structure and ... insulin action from receptor to the alteration of blood glucose. Hence, in ... the first protein to have its amino acid sequence determined;2 ... an integral membrane glycoprotein composed of two subunits, a and 13 ...

  17. 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.

  18. Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

    Science.gov (United States)

    Wu, Jingheng; Shen, Lin; Yang, Weitao

    2017-10-28

    Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

  19. Polarization effects in molecular mechanical force fields

    Energy Technology Data Exchange (ETDEWEB)

    Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

    2009-08-19

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

  20. Molecular mechanism of insulin resistance

    Indian Academy of Sciences (India)

    Free fatty acids are known to play a key role in promoting loss of insulin sensitivity, thereby causing insulin resistance and type 2 diabetes. However, the underlying mechanism involved is still unclear. In searching for the cause of the mechanism, it has been found that palmitate inhibits insulin receptor (IR) gene expression, ...

  1. Localised quantum states of atomic and molecular particles physisorbed on carbon-based nanoparticles

    Czech Academy of Sciences Publication Activity Database

    Kaprálová-Žďánská, Petra Ruth; Trachta, Michal; Bludský, Ota; Špirko, Vladimír

    2014-01-01

    Roč. 141, č. 11 (2014), "114702-1"-"114702-10" ISSN 0021-9606 R&D Projects: GA ČR GAP205/11/0571; GA ČR GAP208/11/0436; GA ČR GAP208/10/0725 Institutional support: RVO:68378271 ; RVO:61388963 Keywords : periodic structure * carbon nanostructures * graphene * quantum mechanics * physisorbed Subject RIV: BG - Nuclear, Atomic and Molecular Physics , Colliders Impact factor: 2.952, year: 2014

  2. 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 ...).

  3. 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.

  4. 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)

  5. Semiclassical mechanics with molecular applications

    CERN Document Server

    Child, M S

    2014-01-01

    Semiclassical mechanics, which stems from the old quantum theory, has seen a remarkable revival in recent years as a physically intuitive and computationally accurate scheme for the interpretation of modern experiments. The main text concentrates less on the mathematical foundations than on the global influence of the classical phase space structures on the quantum mechanical observables. Further mathematical detail is contained in the appendices. Worked problem sets are included as an aid to the student.

  6. 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

  7. 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...

  8. 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.)

  9. 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

  10. Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations.

    Science.gov (United States)

    Moreira, Cátia; Ramos, Maria J; Fernandes, Pedro Alexandrino

    2016-06-27

    This paper is devoted to the understanding of the reaction mechanism of mycobacterium tuberculosis glutamine synthetase (mtGS) with atomic detail, using computational quantum mechanics/molecular mechanics (QM/MM) methods at the ONIOM M06-D3/6-311++G(2d,2p):ff99SB//B3LYP/6-31G(d):ff99SB level of theory. The complete reaction undergoes a three-step mechanism: the spontaneous transfer of phosphate from ATP to glutamate upon ammonium binding (ammonium quickly loses a proton to Asp54), the attack of ammonia on phosphorylated glutamate (yielding protonated glutamine), and the deprotonation of glutamine by the leaving phosphate. This exothermic reaction has an activation free energy of 21.5 kcal mol(-1) , which is consistent with that described for Escherichia coli glutamine synthetase (15-17 kcal mol(-1) ). The participating active site residues have been identified and their role and energy contributions clarified. This study provides an insightful atomic description of the biosynthetic reaction that takes place in this enzyme, opening doors for more accurate studies for developing new anti-tuberculosis therapies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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

  12. The general atomic and molecular electronic structure system HONDO: Version 7.0

    International Nuclear Information System (INIS)

    Dupuis, M.; Watts, J.D.; Villar, H.O.; Hurst, G.J.B.

    1989-01-01

    We describe a computer program for ab initio quantum mechanical calculations of atomic and molecular wavefunctions and energies. Capabilities for the calculation of energy gradients and second derivatives with respect to nuclear coordinates are provided for several types of wavefunctions. Calculations of many molecular properties based on the electron density are possible. The program contains automated algorithms for the determination of equilibrium structures, saddle points, reaction pathways, vibrational spectra including infrared and Raman intensities. We illustrate the capabilities of the program by highlighting research problems recently investigated with the present program. (orig.)

  13. Multiscale simulations in face-centered cubic metals: A method coupling quantum mechanics and molecular mechanics

    International Nuclear Information System (INIS)

    Yu Xiao-Xiang; Wang Chong-Yu

    2013-01-01

    An effective multiscale simulation which concurrently couples the quantum-mechanical and molecular-mechanical calculations based on the position continuity of atoms is presented. By an iterative procedure, the structure of the dislocation core in face-centered cubic metal is obtained by first-principles calculation and the long-range stress is released by molecular dynamics relaxation. Compared to earlier multiscale methods, the present work couples the long-range strain to the local displacements of the dislocation core in a simpler way with the same accuracy. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  14. 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...

  15. Molecular biological mechanism II. Molecular mechanisms of cell cycle regulation

    International Nuclear Information System (INIS)

    Jung, T.

    2000-01-01

    The cell cycle in eukaryotes is regulated by central cell cycle controlling protein kinase complexes. These protein kinase complexes consist of a catalytic subunit from the cyclin-dependent protein kinase family (CDK), and a regulatory subunit from the cyclin family. Cyclins are characterised by their periodic cell cycle related synthesis and destruction. Each cell cycle phase is characterised by a specific set of CDKs and cyclins. The activity of CDK/cyclin complexes is mainly regulated on four levels. It is controlled by specific phosphorylation steps, the synthesis and destruction of cyclins, the binding of specific inhibitor proteins, and by active control of their intracellular localisation. At several critical points within the cell cycle, named checkpoints, the integrity of the cellular genome is monitored. If damage to the genome or an unfinished prior cell cycle phase is detected, the cell cycle progression is stopped. These cell cycle blocks are of great importance to secure survival of cells. Their primary importance is to prevent the manifestation and heritable passage of a mutated genome to daughter cells. Damage sensing, DNA repair, cell cycle control and apoptosis are closely linked cellular defence mechanisms to secure genome integrity. Disregulation in one of these defence mechanisms are potentially correlated with an increased cancer risk and therefore in at least some cases with an increased radiation sensitivity. (orig.) [de

  16. Molecular mechanisms of induced pluripotency.

    Science.gov (United States)

    Kulcenty, Katarzyna; Wróblewska, Joanna; Mazurek, Sylwia; Liszewska, Ewa; Jaworski, Jacek

    2015-01-01

    Growing knowledge concerning transcriptional control of cellular pluripotency has led to the discovery that the fate of differentiated cells can be reversed, which has resulted in the generation, by means of genetic manipulation, of induced pluripotent stem cells. Overexpression of just four pluripotency-related transcription factors, namely Oct3/4, Sox2, Klf4, and c-Myc (Yamanaka factors, OKSM), in fibroblasts appears sufficient to produce this new cell type. Currently, we know that these factors induce several changes in genetic program of differentiated cells that can be divided in two general phases: the initial one is stochastic, and the subsequent one is highly hierarchical and organised. This review briefly discusses the molecular events leading to induction of pluripotency in response to forced presence of OKSM factors in somatic cells. We also discuss other reprogramming strategies used thus far as well as the advantages and disadvantages of laboratory approaches towards pluripotency induction in different cell types.

  17. Molecular pathogenesis and mechanisms of thyroid cancer

    Science.gov (United States)

    Xing, Mingzhao

    2013-01-01

    Thyroid cancer is a common endocrine malignancy. There has been exciting progress in understanding its molecular pathogenesis in recent years, as best exemplified by the elucidation of the fundamental role of several major signalling pathways and related molecular derangements. Central to these mechanisms are the genetic and epigenetic alterations in these pathways, such as mutation, gene copy-number gain and aberrant gene methylation. Many of these molecular alterations represent novel diagnostic and prognostic molecular markers and therapeutic targets for thyroid cancer, which provide unprecedented opportunities for further research and clinical development of novel treatment strategies for this cancer. PMID:23429735

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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)

  3. Description of ionization in the molecular approach to atomic collisions. II

    International Nuclear Information System (INIS)

    Errea, L.F.; Mendez, L.; Riera, A.; Sevila, I.; Harel, C.; Jouin, H.; Pons, B.

    2002-01-01

    We complement a previous article [Harel et al., Phys. Rev. A 55, 287 (1997)] that studied the characteristics of the description of ionization by the molecular approach to atomic collisions, by comparing the wave functions with accurate counterparts. We show how the failure of the basis to describe the phase of the ionizing wave function results in a trapping of the corresponding population in some molecular channels. The time evolution of the molecular wave function then departs from the exact one and the ionization and capture mechanisms appear as interlocked. We thus elucidate the question of the 'natural' boundary of the molecular approach and draw further consequences as to the choice of pseudostates and the use of translation factors

  4. 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

  5. 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

  6. 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.

  7. Molecular Mechanisms of Renal Ischemic Conditioning Strategies

    DEFF Research Database (Denmark)

    Kierulf-Lassen, Casper; Nieuwenhuijs-Moeke, Gertrude J; Krogstrup, Nicoline V

    2015-01-01

    summarizes research on the molecular mechanisms underlying both local and remote ischemic pre-, per- and postconditioning of the kidney. The different types of conditioning strategies in the kidney recruit similar powerful pro-survival mechanisms. Likewise, renal ischemic conditioning mobilizes many...

  8. Atom

    International Nuclear Information System (INIS)

    Auffray, J.P.

    1997-01-01

    The atom through centuries, has been imagined, described, explored, then accelerated, combined...But what happens truly inside the atom? And what are mechanisms who allow its stability? Physicist and historian of sciences, Jean-Paul Auffray explains that these questions are to the heart of the modern physics and it brings them a new lighting. (N.C.)

  9. Molecular mechanisms of thyroid tumorigenesis

    International Nuclear Information System (INIS)

    Krause, K.; Fuehrer, D.

    2008-01-01

    Thyroid nodules are the most frequent endocrine disorder and occur in approximately 30% of the German population. Thyroid nodular disease constitutes a very heterogeneous entity. A striking diversity of possible functional and morphological features of a thyroid tumour derived from the same thyroid ancestor cell, is a hallmark of thyroid tumorigenesis and is due to specific genetic alterations. Defects in known candidate genes can be found in up to 70% of differentiated thyroid carcinomas and determine the respective cancer phenotype. Papillary thyroid cancers (PTC) harbour BRAF (or much less frequently RAS) mutations in sporadically occurring tumours, while radiation-induced PTC display chromosomal rearrangements such as RET, TRK, APR9 / BRAF. These genetic events results in constitutive MAPKinase activation. Follicular thyroid cancers (FTC) harbour RAS mutations or PAX8/ PPARγ rearrangements, both of which, however have also been identified in follicular adenoma. In addition, recent studies show, that activation of PI3K/AKT signalling occurs with high frequency in follicular thyroid tumours. Undifferentiated (anaplastic) thyroid cancers (ATC) display genetic features of FTC or PTC, in addition to aberant activation of multiple tyrosinkinase pathways (overexpression or mutations in PI3K and MAPK pathways). This underscores the concept of a sequential evolution of ATC from differentiated thyroid cancer, a process widely conceived to be triggered by p53 inactivation. In contrast, the molecular pathogenesis of benign thyroid tumours, in particular cold thyroid nodules is less known, except for toxic thyroid nodules, which arise from constitutive activation of cAMP signalling, predominantly through TSHR mutations. (orig.)

  10. Molecular Mechanisms of Appetite Regulation

    Directory of Open Access Journals (Sweden)

    Ji Hee Yu

    2012-12-01

    Full Text Available The prevalence of obesity has been rapidly increasing worldwide over the last several decades and has become a major health problem in developed countries. The brain, especially the hypothalamus, plays a key role in the control of food intake by sensing metabolic signals from peripheral organs and modulating feeding behaviors. To accomplish these important roles, the hypothalamus communicates with other brain areas such as the brainstem and reward-related limbic pathways. The adipocyte-derived hormone leptin and pancreatic β-cell-derived insulin inform adiposity to the hypothalamus. Gut hormones such as cholecystokinin, peptide YY, pancreatic polypeptide, glucagon-like peptide 1, and oxyntomodulin transfer satiety signals to the brain and ghrelin relays hunger signals. The endocannabinoid system and nutrients are also involved in the physiological regulation of food intake. In this article, we briefly review physiological mechanisms of appetite regulation.

  11. 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.

  12. Molecular Mechanisms Underlying Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Christian Trepo

    2009-11-01

    Full Text Available Hepatocarcinogenesis is a complex process that remains still partly understood. That might be explained by the multiplicity of etiologic factors, the genetic/epigenetic heterogeneity of tumors bulks and the ignorance of the liver cell types that give rise to tumorigenic cells that have stem cell-like properties. The DNA stress induced by hepatocyte turnover, inflammation and maybe early oncogenic pathway activation and sometimes viral factors, leads to DNA damage response which activates the key tumor suppressive checkpoints p53/p21Cip1 and p16INK4a/pRb responsible of cell cycle arrest and cellular senescence as reflected by the cirrhosis stage. Still obscure mechanisms, but maybe involving the Wnt signaling and Twist proteins, would allow pre-senescent hepatocytes to bypass senescence, acquire immortality by telomerase reactivation and get the last genetic/epigenetic hits necessary for cancerous transformation. Among some of the oncogenic pathways that might play key driving roles in hepatocarcinogenesis, c-myc and the Wnt/β-catenin signaling seem of particular interest. Finally, antiproliferative and apoptosis deficiencies involving TGF-β, Akt/PTEN, IGF2 pathways for instance are prerequisite for cancerous transformation. Of evidence, not only the transformed liver cell per se but the facilitating microenvironment is of fundamental importance for tumor bulk growth and metastasis.

  13. 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

  14. Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study.

    Science.gov (United States)

    Ibrahim, Mahmoud A A

    2011-10-24

    The performance of semiempirical molecular-orbital methods--MNDO, MNDO-d, AM1, RM1, PM3 and PM6--in describing halogen bonding was evaluated, and the results were compared with molecular mechanical (MM) and quantum mechanical (QM) data. Three types of performance were assessed: (1) geometrical optimizations and binding energy calculations for 27 halogen-containing molecules complexed with various Lewis bases (Two of the tested methods, AM1 and RM1, gave results that agree with the QM data.); (2) charge distribution calculations for halobenzene molecules, determined by calculating the solvation free energies of the molecules relative to benzene in explicit and implicit generalized Born (GB) solvents (None of the methods gave results that agree with the experimental data.); and (3) appropriateness of the semiempirical methods in the hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme, investigated by studying the molecular inhibition of CK2 protein by eight halobenzimidazole and -benzotriazole derivatives using hybrid QM/MM molecular-dynamics (MD) simulations with the inhibitor described at the QM level by the AM1 method and the rest of the system described at the MM level. The pure MM approach with inclusion of an extra point of positive charge on the halogen atom approach gave better results than the hybrid QM/MM approach involving the AM1 method. Also, in comparison with the pure MM-GBSA (generalized Born surface area) binding energies and experimental data, the calculated QM/MM-GBSA binding energies of the inhibitors were improved by replacing the G(GB,QM/MM) solvation term with the corresponding G(GB,MM) term.

  15. 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)

  16. Molecular mechanisms of DNA photodamage

    Energy Technology Data Exchange (ETDEWEB)

    Starrs, S.M

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA){sub n} and (GA){sub n}, and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a

  17. Molecular mechanisms of DNA photodamage

    International Nuclear Information System (INIS)

    Starrs, S.M.

    2000-05-01

    Photodamage in DNA, caused by ultraviolet (UV) light, can occur by direct excitation of the nucleobases or indirectly via the action of photosensitisers. Such, DNA photodamage can be potentially mutagenic or lethal. Among the methods available for detecting UV-induced DNA damage, gel sequencing protocols, utilising synthetic oligodeoxyribonucleotides as targets for UV radiation, allow photolesions to be mapped at nucleotide resolution. This approach has been applied to investigate both DNA damage mechanisms. Following a general overview of DNA photoreactivity, and a description of the main experimental procedures, Chapter 3 identifies the origin of an anomalous mobility shift observed in purine chemical sequence ladders that can confuse the interpretation of DNA cleavage results; measures to abolish this shift are also described. Chapters 4 and 5 examine the alkali-labile DNA damage photosensitised by representative nonsteroidal antiinflammatory drugs (NSAIDs) and the fluoroquinolone antibiotics. Suprofen was the most photoactive NSAID studied, producing different patterns of guanine-specific damage in single-stranded and duplex DNA. Uniform modification of guanine bases, typifying attack by singlet oxygen, was observed in single-stranded oligodeoxyribonucleotides. In duplex molecules, modification was limited to the 5'-G of GG doublets, which is indicative of an electron transfer. The effect of quenchers and photoproduct analysis substantiated these findings. The quinolone, nalidixic acid, behaves similarly. The random base cleavage photosensitised by the fluoroquinolones, has been attributed to free radicals produced during their photodecomposition. Chapter 6 addresses the photoreactivity of purines within unusual DNA structures formed by the repeat sequences (GGA) n and (GA) n , and a minihairpin. There was no definitive evidence for enhanced purine reactivity caused by direct excitation. Finally, Chapter 7 investigates the mutagenic potential of a dimeric

  18. Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

    DEFF Research Database (Denmark)

    Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik

    2016-01-01

    )-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers......The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R...... indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site...

  19. Modeling the Mechanical Properties of Functionalized Carbon Nanotubes and Their Composites: Design at the Atomic Level

    Directory of Open Access Journals (Sweden)

    Qing-Sheng Yang

    2014-01-01

    Full Text Available This investigation focuses on the design of functionalization configuration at the atomic level to determine the influence of atomic structure on the mechanical properties of functionalized carbon nanotubes (F-CNTs and their composites. Tension and compressive buckling behaviors of different configurations of CNTs functionalized by H atoms are studied by a molecular dynamics (MD method. It is shown that H-atom functionalization reduces Young’s modulus of CNTs, but Young’s modulus is not sensitive to the functionalization configuration. The configuration does, however, affect the tensile strength and critical buckling stress of CNTs. Further, the stress-strain relations of composites reinforced by nonfunctionalized and various functionalized CNTs are analyzed.

  20. Molecular beam studies of oxide reduction by atomic hydrogen

    International Nuclear Information System (INIS)

    Olander, D.R.

    1978-01-01

    The graphite and oxide internals of a CTR are susceptible to chemical corrosion as well as to physical degradation by high-energy particles. Reactions of thermal atomic hydrogen with oxides are being studied. The hydrogen used is at thermal energy (0.22 eV). Typical data are reported for the H/UO 2 system. The reaction probability is plotted as a function of solid temperature at fixed beam intensity and moculation frequency. The reaction probability increases from low temperature to a high-temperature plateau at about 1300 0 C. Here the reaction rate is limited solely by the sticking probability of H on the surface; about one in seven of the incident atoms is chemisorbed by the surface and ultimately returns to the gas phase as water vapor. A reaction model comprising sticking, recombination to H 2 , solution and diffusion of H in the bulk of the UO 2 , surface reaction of adsorbed H with lattice oxygen atoms to produce the hydroxyl radical, and production of water is constructed. The rate constants for the elementary steps in the mechanism are tabulated. 2 figures, 2 tables

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Hybrid Systems: Cold Atoms Coupled to Micro Mechanical Oscillators =

    Science.gov (United States)

    Montoya Monge, Cris A.

    Micro mechanical oscillators can serve as probes in precision measurements, as transducers to mediate photon-phonon interactions, and when functionalized with magnetic material, as tools to manipulate spins in quantum systems. This dissertation includes two projects where the interactions between cold atoms and mechanical oscillators are studied. In one of the experiments, we have manipulated the Zeeman state of magnetically trapped Rubidium atoms with a magnetic micro cantilever. The results show a spatially localized effect produced by the cantilever that agrees with Landau-Zener theory. In the future, such a scalable system with highly localized interactions and the potential for single-spin sensitivity could be useful for applications in quantum information science or quantum simulation. In a second experiment, work is in progress to couple a sample of optically trapped Rubidium atoms to a levitated nanosphere via an optical lattice. This coupling enables the cooling of the center-of-mass motion of the nanosphere by laser cooling the atoms. In this system, the atoms are trapped in the optical lattice while the sphere is levitated in a separate vacuum chamber by a single-beam optical tweezer. Theoretical analysis of such a system has determined that cooling the center-of-mass motion of the sphere to its quantum ground state is possible, even when starting at room temperature, due to the excellent environmental decoupling achievable in this setup. Nanospheres cooled to the quantum regime can provide new tests of quantum behavior at mesoscopic scales and have novel applications in precision sensing.

  11. Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics.

    Science.gov (United States)

    Hudson, Nathan E; Ding, Feng; Bucay, Igal; O'Brien, E Timothy; Gorkun, Oleg V; Superfine, Richard; Lord, Susan T; Dokholyan, Nikolay V; Falvo, Michael R

    2013-06-18

    Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin's elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin's mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

    Science.gov (United States)

    Hudson, Nathan E.; Ding, Feng; Bucay, Igal; O’Brien, E. Timothy; Gorkun, Oleg V.; Superfine, Richard; Lord, Susan T.; Dokholyan, Nikolay V.; Falvo, Michael R.

    2013-01-01

    Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin’s elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin’s mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. PMID:23790375

  13. Molecular machines with bio-inspired mechanisms.

    Science.gov (United States)

    Zhang, Liang; Marcos, Vanesa; Leigh, David A

    2018-02-26

    The widespread use of molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular machines-which by and large function as switches-and the machines of the macroscopic world, which utilize the synchronized behavior of integrated components to perform more sophisticated tasks than is possible with any individual switch. Should we try to make molecular machines of greater complexity by trying to mimic machines from the macroscopic world or instead apply unfamiliar (and no doubt have to discover or invent currently unknown) mechanisms utilized by biological machines? Here we try to answer that question by exploring some of the advances made to date using bio-inspired machine mechanisms.

  14. Molecular mechanism of Endosulfan action in mammals

    Indian Academy of Sciences (India)

    Keywords. DNA damage; double-strand break; genomic instability; infertility; MMEJ; NHEJ; pesticides. Abstract. Endosulfan is a broad-spectrum organochlorine pesticide, speculated to be detrimental to human health in areas ofactive exposure. However, the molecular insights to its mechanism of action remain poorly ...

  15. Mixed 2D molecular systems: Mechanic, thermodynamic and dielectric properties

    Energy Technology Data Exchange (ETDEWEB)

    Beno, Juraj [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Weis, Martin [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)], E-mail: Martin.Weis@stuba.sk; Dobrocka, Edmund [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Institute of Electrical Engineering, Slovak Academy of Sciences, Dubravska cesta 9, 841 04-SK Bratislava (Slovakia); Hasko, Daniel [International Laser Centre, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)

    2008-08-15

    Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms ({pi}-A), the Maxwell displacement current (MDC) measurement, X-ray reflectivity (XRR) and atomic force microscopy (AFM) to investigate the selected mechanic, thermodynamic and dielectric properties based on orientational structure of monolayers. On the base of {pi}-A isotherms analysis we explain the creation of stable structures and found optimal monolayer composition. The dielectric properties represented by MDC generated monolayers were analyzed in terms of excess dipole moment, proposing the effect of dipole-dipole interaction. XRR and AFM results illustrate deposited film structure and molecular ordering.

  16. 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

  17. Nanostructure and molecular mechanics of spider dragline silk protein assemblies

    Science.gov (United States)

    Keten, Sinan; Buehler, Markus J.

    2010-01-01

    Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206

  18. 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.

  19. [Neonatal hyperbilirubinemia and molecular mechanisms of jaundice].

    Science.gov (United States)

    Jirsa, M; Sticová, E

    2013-07-01

    The introductory summarises the classical path of heme degradation and classification of jaundice. Subsequently, a description of neonatal types of jaundice is given, known as Crigler Najjar, Gilberts, DubinJohnson and Rotor syndromes, emphasising the explanation of the molecular mechanisms of these metabolic disorders. Special attention is given to a recently discovered molecular mechanism of the Rotor syndrome. The mechanism is based on the inability of the liver to retrospectively uptake the conjugated bilirubin fraction primarily excreted into the blood, not bile. A reduced ability of the liver to uptake the conjugated bilirubin contributes to the development of hyperbilirubinemia in common disorders of the liver and bile ducts and to the toxicity of xenobiotics and drugs using transport proteins for conjugated bilirubin.

  20. Electron, ion and atomic beams interaction with solid high-molecular dielectrics

    Energy Technology Data Exchange (ETDEWEB)

    Milyavskij, V V; Skvortsov, V A [Russian Academy of Sciences, Moscow (Russian Federation). High Energy Density Research Center

    1997-12-31

    A mathematical model was constructed and numerical investigation performed of the interaction between intense electron, ion and atomic beams and solid high-molecular dielectrics under various boundary conditions. The model is based on equations of the mechanics of continuum, electrodynamics and kinetics, describing the accumulation and relaxation of space charge and shock-wave processes, as well as the evolution of electric field in the sample. A semi-empirical procedure is proposed for the calculation of energy deposition by electron beam in a target in the presence of a non-uniform electric field. (author). 4 figs., 2 refs.

  1. Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

    Science.gov (United States)

    Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

    2016-09-13

    We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

  2. Molecular Mechanisms of Neuroplasticity: An Expanding Universe.

    Science.gov (United States)

    Gulyaeva, N V

    2017-03-01

    Biochemical processes in synapses and other neuronal compartments underlie neuroplasticity (functional and structural alterations in the brain enabling adaptation to the environment, learning, memory, as well as rehabilitation after brain injury). This basic molecular level of brain plasticity covers numerous specific proteins (enzymes, receptors, structural proteins, etc.) participating in many coordinated and interacting signal and metabolic processes, their modulation forming a molecular basis for brain plasticity. The articles in this issue are focused on different "hot points" in the research area of biochemical mechanisms supporting neuroplasticity.

  3. 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.

  4. Molecular mechanism of extreme mechanostability in a pathogen adhesin.

    Science.gov (United States)

    Milles, Lukas F; Schulten, Klaus; Gaub, Hermann E; Bernardi, Rafael C

    2018-03-30

    High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy-based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  5. 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.

  6. Understanding the mechanisms of amorphous creep through molecular simulation.

    Science.gov (United States)

    Cao, Penghui; Short, Michael P; Yip, Sidney

    2017-12-26

    Molecular processes of creep in metallic glass thin films are simulated at experimental timescales using a metadynamics-based atomistic method. Space-time evolutions of the atomic strains and nonaffine atom displacements are analyzed to reveal details of the atomic-level deformation and flow processes of amorphous creep in response to stress and thermal activations. From the simulation results, resolved spatially on the nanoscale and temporally over time increments of fractions of a second, we derive a mechanistic explanation of the well-known variation of creep rate with stress. We also construct a deformation map delineating the predominant regimes of diffusional creep at low stress and high temperature and deformational creep at high stress. Our findings validate the relevance of two original models of the mechanisms of amorphous plasticity: one focusing on atomic diffusion via free volume and the other focusing on stress-induced shear deformation. These processes are found to be nonlinearly coupled through dynamically heterogeneous fluctuations that characterize the slow dynamics of systems out of equilibrium.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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)

  13. 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

  14. Recent Data Generation Activities at the Atomic and Molecular Data Unit of the IAEA

    International Nuclear Information System (INIS)

    Clark, R.E.H.; Humbert, D.

    2005-01-01

    The main data generation mechanism of the Atomic and Molecular (A+M) Data Unit of the IAEA is the Co-ordinated Research Project (CRP). The International Fusion Research Council Subcommittee on Atomic and Molecular Data for Fusion recommends topics for new CRPs to be initiated by the A+M Unit. A typical CRP has a lifetime of three to five years. At the start of the CRP a Research Co-ordination Meeting (RCM) is held with the purpose of formulating a detailed work plan. At later RCMs progress on these work plans is reported and the studies debated and expanded. At the conclusion of the CRP the results are compiled in a volume of the journal Atomic and Plasma-Material Interaction Data for Fusion. Numerical results are also added to the electronic database as appropriate. Normally the Unit has three to four active CRPs, and also holds Technical Meetings and invites individual Consultants to IAEA Headquarters, Vienna for specific tasks. Such activities can result in providing advice on a particular topic, on data for a particular process, or a new capability to be made widely available. Recently, consultants to the Unit have provided extensive additions to the Unit databases, as well as interfaces to run several calculational tools through the Internet. Specific examples will be presented

  15. 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

  16. 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.

  17. Atomic-cascade photons and quantum-mechanical nonlocality

    International Nuclear Information System (INIS)

    Bell, J.S.

    1995-01-01

    In recent years there have been several experiments on polarization correlation between photons emitted in atomic cascades. They are supposed to bear on the notion that the consequences of events do not propagate faster than light. This notion is difficult to reconcile with quantum-mechanical predictions for idealized versions of the experiments in question. The present Comment offers a brief introduction to the situation. (author)

  18. 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)

  19. Molecular mechanisms of curcumin action: gene expression.

    Science.gov (United States)

    Shishodia, Shishir

    2013-01-01

    Curcumin derived from the tropical plant Curcuma longa has a long history of use as a dietary agent, food preservative, and in traditional Asian medicine. It has been used for centuries to treat biliary disorders, anorexia, cough, diabetic wounds, hepatic disorders, rheumatism, and sinusitis. The preventive and therapeutic properties of curcumin are associated with its antioxidant, anti-inflammatory, and anticancer properties. Extensive research over several decades has attempted to identify the molecular mechanisms of curcumin action. Curcumin modulates numerous molecular targets by altering their gene expression, signaling pathways, or through direct interaction. Curcumin regulates the expression of inflammatory cytokines (e.g., TNF, IL-1), growth factors (e.g., VEGF, EGF, FGF), growth factor receptors (e.g., EGFR, HER-2, AR), enzymes (e.g., COX-2, LOX, MMP9, MAPK, mTOR, Akt), adhesion molecules (e.g., ELAM-1, ICAM-1, VCAM-1), apoptosis related proteins (e.g., Bcl-2, caspases, DR, Fas), and cell cycle proteins (e.g., cyclin D1). Curcumin modulates the activity of several transcription factors (e.g., NF-κB, AP-1, STAT) and their signaling pathways. Based on its ability to affect multiple targets, curcumin has the potential for the prevention and treatment of various diseases including cancers, arthritis, allergies, atherosclerosis, aging, neurodegenerative disease, hepatic disorders, obesity, diabetes, psoriasis, and autoimmune diseases. This review summarizes the molecular mechanisms of modulation of gene expression by curcumin. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

  20. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    International Nuclear Information System (INIS)

    Alocci, Davide; Bernini, Andrea; Niccolai, Neri

    2013-01-01

    Highlights: •3D atom depth analysis is proposed to identify different layers in protein structures. •Amino acid contents for each layers have been analyzed for a large protein dataset. •Charged amino acids in the most external layer are present at very different extents. •Atom depth indexes of K residues reflect their side chains flexibility. •Mobile surface charges can be responsible for long range protein–protein recognition. -- Abstract: The systematic analysis of amino acid distribution, performed inside a large set of resolved protein structures, sheds light on possible mechanisms driving non random protein–protein approaches. Protein Data Bank entries have been selected using as filters a series of restrictions ensuring that the shape of protein surface is not modified by interactions with large or small ligands. 3D atom depth has been evaluated for all the atoms of the 2,410 selected structures. The amino acid relative population in each of the structural layers formed by grouping atoms on the basis of their calculated depths, has been evaluated. We have identified seven structural layers, the inner ones reproducing the core of proteins and the outer one incorporating their most protruding moieties. Quantitative analysis of amino acid contents of structural layers identified, as expected, different behaviors. Atoms of Q, R, K, N, D residues are increasingly more abundant in going from core to surfaces. An opposite trend is observed for V, I, L, A, C, and G. An intermediate behavior is exhibited by P, S, T, M, W, H, F and Y. The outer structural layer hosts predominantly E and K residues whose charged moieties, protruding from outer regions of the protein surface, reorient free from steric hindrances, determining specific electrodynamics maps. This feature may represent a protein signature for long distance effects, driving the formation of encounter complexes and the eventual short distance approaches that are required for protein

  1. 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

  2. Molecular mechanisms for protein-encoded inheritance

    Science.gov (United States)

    Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

    2013-01-01

    Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

  3. MOLECULAR MECHANISMS OF FEAR LEARNING AND MEMORY

    Science.gov (United States)

    Johansen, Joshua P.; Cain, Christopher K.; Ostroff, Linnaea E.; LeDoux, Joseph E.

    2011-01-01

    Pavlovian fear conditioning is a useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Together, this research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals, and potentially for understanding fear related disorders, such as PTSD and phobias. PMID:22036561

  4. Molecular mechanisms of fear learning and memory.

    Science.gov (United States)

    Johansen, Joshua P; Cain, Christopher K; Ostroff, Linnaea E; LeDoux, Joseph E

    2011-10-28

    Pavlovian fear conditioning is a particularly useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here, we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Collectively, this body of research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals and potentially for understanding fear-related disorders, such as PTSD and phobias. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Droplet Breakup Mechanisms in Air-blast Atomizers

    Science.gov (United States)

    Aliabadi, Amir Abbas; Taghavi, Seyed Mohammad; Lim, Kelly

    2011-11-01

    Atomization processes are encountered in many natural and man-made phenomena. Examples are pollen release by plants, human cough or sneeze, engine fuel injectors, spray paint and many more. The physics governing the atomization of liquids is important in understanding and utilizing atomization processes in both natural and industrial processes. We have observed the governing physics of droplet breakup in an air-blast water atomizer using a high magnification, high speed, and high resolution LASER imaging technique. The droplet breakup mechanisms are investigated in three major categories. First, the liquid drops are flattened to form an oblate ellipsoid (lenticular deformation). Subsequent deformation depends on the magnitude of the internal forces relative to external forces. The ellipsoid is converted into a torus that becomes stretched and disintegrates into smaller drops. Second, the drops become elongated to form a long cylindrical thread or ligament that break up into smaller drops (Cigar-shaped deformation). Third, local deformation on the drop surface creates bulges and protuberances that eventually detach themselves from the parent drop to form smaller drops.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. Molecular Mechanisms in Exercise-Induced Cardioprotection

    Directory of Open Access Journals (Sweden)

    Saeid Golbidi

    2011-01-01

    Full Text Available Physical inactivity is increasingly recognized as modifiable behavioral risk factor for cardiovascular diseases. A partial list of proposed mechanisms for exercise-induced cardioprotection include induction of heat shock proteins, increase in cardiac antioxidant capacity, expression of endoplasmic reticulum stress proteins, anatomical and physiological changes in the coronary arteries, changes in nitric oxide production, adaptational changes in cardiac mitochondria, increased autophagy, and improved function of sarcolemmal and/or mitochondrial ATP-sensitive potassium channels. It is currently unclear which of these protective mechanisms are essential for exercise-induced cardioprotection. However, most investigations focus on sarcolemmal KATP channels, NO production, and mitochondrial changes although it is very likely that other mechanisms may also exist. This paper discusses current information about these aforementioned topics and does not consider potentially important adaptations within blood or the autonomic nervous system. A better understanding of the molecular basis of exercise-induced cardioprotection will help to develop better therapeutic strategies.

  12. The self-breaking mechanism of atomic scale Au nanocontacts

    International Nuclear Information System (INIS)

    Nakazumi, Tomoka; Kiguchi, Manabu; Wada, Yasuo

    2012-01-01

    We have investigated the self-breaking mechanism of atomic scale Au nanocontacts at room temperature in air. In the conductance traces, we frequently observed traces showing both a 1G 0 (2e 2 /h) and 3G 0 plateaux, or only a 2G 0 plateau in the conductance regime below 3G 0 . The statistical analysis showed a negative correlation between the appearance of 1G 0 and 2G 0 peaks, and a positive correlation between 1G 0 and 3G 0 peaks. This conductance behavior suggested that the symmetric triple atomic rows changed into a symmetric single row, while the asymmetric double rows broke without changing into a symmetric single row. The regular self-breaking process can be explained by the breaking of the thermodynamically stable Au nanocontacts which were formed during the self-breaking of the contacts. (paper)

  13. Molecular mechanisms in compatibility and mechanical properties of Polyacrylamide/Polyvinyl alcohol blends.

    Science.gov (United States)

    Wei, Qinghua; Wang, Yanen; Che, Yu; Yang, Mingming; Li, Xinpei; Zhang, Yingfeng

    2017-01-01

    The objectives of this study were to develop a computational model based on molecular dynamics technique to investigate the compatibility and mechanical properties of Polyacrylamide (PAM)/Polyvinyl alcohol (PVA) blends. Five simulation models of PAM/PVA with different composition ratios (4/0, 3/1, 2/2, 1/3, 0/4) were constructed and simulated by using molecular dynamics (MD) simulation. The interaction mechanisms of molecular chains in PAM/PVA blend system were elaborated from the aspects of the compatibility, mechanical properties, binding energy and pair correlation function, respectively. The computed values of solubility parameters for PAM and PVA indicate PAM has a good miscibility with PVA. The results of the static mechanical analysis, based on the equilibrium structures of blends with differing component ratios, shows us that the elastic coefficient, engineering modulus, and ductility are increased with the addition of PVA content, which is 4/0 PAM/PVAPVAPVAPVAPVA. Moreover, binding energy results indicate that a stronger interaction exists among PVA molecular chains comparing with PAM molecular chains, which is why the mechanical properties of blend system increasing with the addition of PVA content. Finally, the results of pair correlation functions (PCFs) between polar functional groups and its surrounding hydrogen atoms, indicated they interact with each other mainly by hydrogen bonds, and the strength of three types of polar functional groups has the order of O(-OH)>O(-C=O)>N(-NH 2 ). This further elaborates the root reason why the mechanical properties of blend system increase with the addition of PVA content. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

    Directory of Open Access Journals (Sweden)

    Jiyoung Kang

    2012-01-01

    Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

  15. Molecular mechanism of Danshensu on platelet antiaggregation

    Science.gov (United States)

    Yu, Chen; Geng, Feng; Fan, Hua-Ying; Luan, Hai-Yun; Liu, Yue; Ji, Kai; Fu, Feng-Hua

    2018-04-01

    In this study, we detected the effect of Danshensu on PARs-PLCβsignaling pathway to elucidate molecular mechanism of Danshensu on platelet anti-aggregation. Our results demonstrate that Danshensu is able to decrease the levels of IP3, Ca2+ and AA secretion, which indicate that Danshensu may involve in PARs-PLCβ signaling pathways. Molecular docking study shows that Danshesu has similar polar interactions with PAR1 receptors as BMS200261 at the same position. The findings from our study enable a better understanding of Danshensu biological properties, which could ultimately lead to the development of multi-target antiplatelet natural medicine for the treatment and/or prevention of some thrombotic diseases.

  16. 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

  17. Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

    Science.gov (United States)

    Hu, Hao; Liu, Haiyan

    2013-05-30

    Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

  18. 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.)

  19. Mechanically induced atomic disorder and phase transformations. Doctoral thesis

    Energy Technology Data Exchange (ETDEWEB)

    Limei, D

    1992-11-30

    The study shows the possibilities of preparing alloys in various metastable configurations by the simple technique of ball milling. Firstly, chapter 2 gives the description of experimental techniques. In chapter 3, evidence of atomic anti-site disordering in A15-structure superconducting compounds Nb3Sn and Nb3Au during an early stage of milling is demonstrated. Chapter 4 represents the experimental results on the B2-structure magnetic compounds CoGa and CoAl upon mechanical impact. These compounds are well known for their particular type of atomic disorder, namely triple-defect disorder. Various examples of experimental evidence of phase transformations induced by mechanical grinding are presented in chapter 5. Section 5.2 gives an example of amorphization induced by mechanical attrition in the intermetallic compound Ni3Sn. Section 5.3 shows the milling experiment of the intermetallic compound V3 Ga. In section 5.4, for the first time, the observation of a phase transformation to a high-temperature phase with a complex structure will be demonstrated for the intermetallic compound Co3Sn2. In the last chapter, detailed studies on the intermetallic Nb-Au binary compounds for a variety of compositions are presented.

  20. Separating grain boundary migration mechanisms in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Ulomek, Felix; Mohles, Volker

    2016-01-01

    In molecular dynamics (MD) simulations of grain boundary (GB) migration it is quite common to find a temperature dependence of GB mobility that deviates strongly from an Arrhenius-type dependence. This usually indicates that more than one mechanism is actually active. With the goal to separate different GB migration mechanisms we investigate a Σ7 <111> 38.2° GB by MD using an EAM potential for aluminium. To drive the GB with a well-known and adjustable force, the energy conserving orientational driving force (ECO DF) is used that had been introduced recently. The magnitude of the DF and the temperature are varied. This yielded a high and a low temperature range for the GB velocity, with a transition temperature that depends on the magnitude of the DF. A method is introduced which allows both a visual and a statistical characterization of GB motion on a per atom basis. These analyses reveal that two mechanisms are active in this GB, a shuffling mechanism and its initiation. These mechanisms operate in a sequential, coupled manner. Based on this, a simple model is introduced that describes all simulated GB velocities (and hence the mobility) very well, including the transition between the dominating mechanisms.

  1. Mechanically controllable break junctions for molecular electronics.

    Science.gov (United States)

    Xiang, Dong; Jeong, Hyunhak; Lee, Takhee; Mayer, Dirk

    2013-09-20

    A mechanically controllable break junction (MCBJ) represents a fundamental technique for the investigation of molecular electronic junctions, especially for the study of the electronic properties of single molecules. With unique advantages, the MCBJ technique has provided substantial insight into charge transport processes in molecules. In this review, the techniques for sample fabrication, operation and the various applications of MCBJs are introduced and the history, challenges and future of MCBJs are discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Molecular mechanisms of action of bacterial exotoxins.

    Science.gov (United States)

    Balfanz, J; Rautenberg, P; Ullmann, U

    1996-07-01

    Toxins are one of the inventive strategies that bacteria have developed in order to survive. As virulence factors, they play a major role in the pathogenesis of infectious diseases. Recent discoveries have once more highlighted the effectiveness of these precisely adjusted bacterial weapons. Furthermore, toxins have become an invaluable tool in the investigation of fundamental cell processes, including regulation of cellular functions by various G proteins, cytoskeletal dynamics and neural transmission. In this review, the bacterial toxins are presented in a rational classification based on the molecular mechanisms of action.

  3. Molecular mechanics of silk nanostructures under varied mechanical loading.

    Science.gov (United States)

    Bratzel, Graham; Buehler, Markus J

    2012-06-01

    Spider dragline silk is a self-assembling tunable protein composite fiber that rivals many engineering fibers in tensile strength, extensibility, and toughness, making it one of the most versatile biocompatible materials and most inviting for synthetic mimicry. While experimental studies have shown that the peptide sequence and molecular structure of silk have a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies, in particular, under variations of genetic sequences have been reported. In this study, atomistic-level structures of wildtype as well as modified MaSp1 protein from the Nephila clavipes spider dragline silk sequences, obtained using an in silico approach based on replica exchange molecular dynamics and explicit water molecular dynamics, are subjected to simulated nanomechanical testing using different force-control loading conditions including stretch, pull-out, and peel. The authors have explored the effects of the poly-alanine length of the N. clavipes MaSp1 peptide sequence and identify differences in nanomechanical loading conditions on the behavior of a unit cell of 15 strands with 840-990 total residues used to represent a cross-linking β-sheet crystal node in the network within a fibril of the dragline silk thread. The specific loading condition used, representing concepts derived from the protein network connectivity at larger scales, have a significant effect on the mechanical behavior. Our analysis incorporates stretching, pull-out, and peel testing to connect biochemical features to mechanical behavior. The method used in this study could find broad applications in de novo design of silk-like tunable materials for an array of applications. Copyright © 2011 Wiley Periodicals, Inc.

  4. An overview of atomic and molecular processes in critical velocity ionization

    International Nuclear Information System (INIS)

    Lai, S.T.; Murad, E.; McNeil, W.J.

    1989-01-01

    Alfven's critical ionization velocity (CIV) is a multistep process involving plasma physics and plasma chemistry. The authors present an overview of the time development of some atomic and molecular processes in CIV. In the pre-onset stage, metastable states play an important role: They provide an energy pooling mechanism allowing low energy electrons to participate in the ionization processes; they may explain the low energy threshold as well as the fast time scale in the onset of CIV. For a sustaining CIV to occur, Townsend's criterion has to be satisfied. The kinetic energies of the neutrals are transformed to plasma wave energies via beam-plasma instabilities, and the plasma waves that heat the electrons result in a tail formation. Excitation of neutrals with subsequent radiation is an important energy loss mechanism. Finite beam size also limits the instability growth rate. In the propagation of CIV, ion-molecule reactions and molecular dissociative recombination are important. Ion-molecule reactions change the temporal chemical composition in a CIV process and help explain some results in CIV experiments. Molecular dissociative recombination reduces the plasma density, lowers the effective neutral mass, and loses energy via excitation and radiation; it tends to quench the propagation of CIV. Depending on various parameters, oscillatory behavior of CIV may occur

  5. Simulation with quantum mechanics/molecular mechanics for drug discovery.

    Science.gov (United States)

    Barbault, Florent; Maurel, François

    2015-10-01

    Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

  6. VAMDC - The Virtual Atomic and Molecular Data Centre: A New Era in Database Collaboration

    International Nuclear Information System (INIS)

    Mason, N.J.

    2011-01-01

    Atomic and molecular data (A and M) are of critical importance in developing models of radiation chemistry including track structures. Currently these vital and fundamental A and M data resources are highly fragmented and only available through a variety of often poorly documented interfaces. The Virtual Atomic and Molecular Data Centre (VAMDC) is an EU funded e-infrastructure (www.vamdc.eu) that aims to provide the scientific community with access to a comprehensive, federated set of Atomic and Molecular (A and M) data. These structures have been created by initiatives such as the Euro-VO (http://www.euro-vo.org) and EGEE (Enabling Grids for E-sciencE, (http://www.eu-egee.org/). VAMDC will be built upon existing A and M databases. It has the specific aim of creating an infrastructure that on the one hand can directly extract data from the existing depositories while on the other hand is sufficiently flexible to be tuned to the needs of a wide variety of users from academic, governmental, industrial communities or even the general public. Central to VAMDC is the task of overcoming the current fragmentation of the A and M database community. VAMDC will alleviate this by: - developing the largest and most comprehensive atomic and molecular e-infrastructure to be shared, fed and expanded by A and M scientists; - providing a major distributed infrastructure which can be accessed, referenced and exploited by the wider research community. In fulfilling these aims, the VAMDC project will organise a series of Networking Activities (NAs). NAs are specifically aimed at: Engaging data providers; Coordinating activities among existing database providers; Ascertaining and responding to the needs of different user communities; Providing training and awareness of the VAMDC across the international A and M community and other use communities such as the radiation chemistry community. In this talk I will therefore outline the aims, methodology and mechanisms of the VAMDC project

  7. 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'')

  8. Molecular mechanisms in radiation damage to DNA

    International Nuclear Information System (INIS)

    Osman, R.

    1991-01-01

    The objectives of this work are to elucidate the molecular mechanisms that are responsible for radiation-induced DNA damage. The overall goal is to understand the relationship between the chemical and structural changes produced by ionizing radiation in DNA and the resulting impairment of biological function expressed as carcinogenesis or cell death. The studies are based on theoretical explorations of possible mechanisms that link initial radiation damage in the form of base and sugar damage to conformational changes in DNA. These mechanistic explorations should lead to the formulation of testable hypothesis regarding the processes of impairment of regulation of gene expression, alternation in DNA repair, and damage to DNA structure involved in cell death or cancer

  9. Molecular mechanisms of glucocorticoid receptor signaling

    Directory of Open Access Journals (Sweden)

    Marta Labeur

    2010-10-01

    Full Text Available This review highlights the most recent findings on the molecular mechanisms of the glucocorticoid receptor (GR. Most effects of glucocorticoids are mediated by the intracellular GR which is present in almost every tissue and controls transcriptional activation via direct and indirect mechanisms. Nevertheless the glucocorticoid responses are tissue -and gene- specific. GR associates selectively with corticosteroid ligands produced in the adrenal gland in response to changes of humoral homeostasis. Ligand interaction with GR promotes either GR binding to genomic glucocorticoid response elements, in turn modulating gene transcription, or interaction of GR monomers with other transcription factors activated by other signalling pathways leading to transrepression. The GR regulates a broad spectrum of physiological functions, including cell differentiation, metabolism and inflammatory responses. Thus, disruption or dysregulation of GR function will result in severe impairments in the maintenance of homeostasis and the control of adaptation to stress.

  10. Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

    Science.gov (United States)

    Shen, Lin; Wu, Jingheng; Yang, Weitao

    2016-10-11

    Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

  11. 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.

  12. Programmed necrosis and necroptosis – molecular mechanisms

    Directory of Open Access Journals (Sweden)

    Agata Giżycka

    2015-12-01

    Full Text Available Programmed necrosis has been proven vital for organism development and homeostasis maintenance. Its regulatory effects on functional activity of the immune system, as well as on pathways regulating the death mechanisms in cells with diminished apoptotic activity, including malignant cells, have been confirmed. There is also increasing evidence indicating necrosis involvement in many human pathologies. Contrary to previous beliefs, necrosis is not only a passive, pathological, gene-independent process. However, the current knowledge regarding molecular regulation of programmed necrosis is scarce. In part this is due to the multiplicity and complexity of signaling pathways involved in programmed necrosis, as well as the absence of specific cellular markers identifying this process, but also the ambiguous and imprecise international terminology. This review presents the current state of the art on molecular mechanisms of programmed necrosis. In particular, its specific and frequent form, necroptosis, is discussed. The role of RIP1 and RIP3 kinases in this process is presented, as well as the diverse pathways induced by ligation of tumor necrosis factor α, to its receptor, TNFR1, i.e. cell survival, apoptosis or necroptosis.

  13. Understanding the molecular mechanisms of reprogramming

    Energy Technology Data Exchange (ETDEWEB)

    Krause, Marie N. [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States); University Hospital of Würzburg, Department of Pediatrics, 2 Josef-Schneiderstrasse, 97080 Würzburg (Germany); Sancho-Martinez, Ignacio [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States); Centre for Stem Cells and Regenerative Medicine, King' s College London, 28th Floor, Tower Wing, Guy' s Hospital, Great Maze Pond, London (United Kingdom); Izpisua Belmonte, Juan Carlos, E-mail: belmonte@salk.edu [Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla 92037, CA (United States)

    2016-05-06

    Despite the profound and rapid advancements in reprogramming technologies since the generation of the first induced pluripotent stem cells (iPSCs) in 2006[1], the molecular basics of the process and its implications are still not fully understood. Recent work has suggested that a subset of TFs, so called “Pioneer TFs”, play an important role during the stochastic phase of iPSC reprogramming [2–6]. Pioneer TFs activities differ from conventional transcription factors in their mechanism of action. They bind directly to condensed chromatin and elicit a series of chromatin remodeling events that lead to opening of the chromatin. Chromatin decondensation by pioneer factors progressively occurs during cell division and in turn exposes specific gene promoters in the DNA to which TFs can now directly bind to promoters that are readily accessible[2, 6]. Here, we will summarize recent advancements on our understanding of the molecular mechanisms underlying reprogramming to iPSC as well as the implications that pioneer Transcription Factor activities might play during different lineage conversion processes. - Highlights: • Pioneer transcription factor activity underlies the initial steps of iPSC generation. • Reprogramming can occur by cis- and/or trans- reprogramming events. • Cis-reprogramming implies remodeling of the chromatin for enabling TF accessibility. • Trans-reprogramming encompasses direct binding of Tfs to their target gene promoters.

  14. 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

  15. 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

  16. Committee on Atomic, Molecular, and Optical Sciences (CAMOS). Technical progress report ampersand continuation proposal, February 1, 1993--January 31, 1994

    International Nuclear Information System (INIS)

    Taylor, R.D.

    1997-01-01

    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, 1993 to January 31, 1994. The details of prior activities are discussed in earlier progress reports. 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). During the above period, CAMOS has continued to track and participate in, when requested, discussions on the health of the field. Much of the perspective of CAMOS has been presented in the recently-published report Research Briefing on Selected Opportunities in Atomic, Molecular, and Optical Sciences. That report has served as the basis for briefings to representatives of the federal government as well as the community-at-large. In keeping with its charge to monitor the health of the field, CAMOS launched a study designed to highlight future directions of the field

  17. 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

  18. 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.

  19. 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.)

  20. 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

  1. 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)

  2. 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

  3. 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)

  4. 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

  5. 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.

  6. 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)

  7. 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.)

  8. Atomic Force Microscopy in Characterizing Cell Mechanics for Biomedical Applications: A Review.

    Science.gov (United States)

    Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

    2017-09-01

    Cell mechanics is a novel label-free biomarker for indicating cell states and pathological changes. The advent of atomic force microscopy (AFM) provides a powerful tool for quantifying the mechanical properties of single living cells in aqueous conditions. The wide use of AFM in characterizing cell mechanics in the past two decades has yielded remarkable novel insights in understanding the development and progression of certain diseases, such as cancer, showing the huge potential of cell mechanics for practical applications in the field of biomedicine. In this paper, we reviewed the utilization of AFM to characterize cell mechanics. First, the principle and method of AFM single-cell mechanical analysis was presented, along with the mechanical responses of cells to representative external stimuli measured by AFM. Next, the unique changes of cell mechanics in two types of physiological processes (stem cell differentiation, cancer metastasis) revealed by AFM were summarized. After that, the molecular mechanisms guiding cell mechanics were analyzed. Finally the challenges and future directions were discussed.

  9. 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.

  10. Molecular Mechanisms of Mouse Skin Tumor Promotion

    International Nuclear Information System (INIS)

    Rundhaug, Joyce E.; Fischer, Susan M.

    2010-01-01

    Multiple molecular mechanisms are involved in the promotion of skin carcinogenesis. Induction of sustained proliferation and epidermal hyperplasia by direct activation of mitotic signaling pathways or indirectly in response to chronic wounding and/or inflammation, or due to a block in terminal differentiation or resistance to apoptosis is necessary to allow clonal expansion of initiated cells with DNA mutations to form skin tumors. The mitotic pathways include activation of epidermal growth factor receptor and Ras/Raf/mitogen-activated protein kinase signaling. Chronic inflammation results in inflammatory cell secretion of growth factors and cytokines such as tumor necrosis factor-α and interleukins, as well as production of reactive oxygen species, all of which can stimulate proliferation. Persistent activation of these pathways leads to tumor promotion

  11. Molecular Mechanisms of Neonatal Brain Injury

    Directory of Open Access Journals (Sweden)

    Claire Thornton

    2012-01-01

    Full Text Available Fetal/neonatal brain injury is an important cause of neurological disability. Hypoxia-ischemia and excitotoxicity are considered important insults, and, in spite of their acute nature, brain injury develops over a protracted time period during the primary, secondary, and tertiary phases. The concept that most of the injury develops with a delay after the insult makes it possible to provide effective neuroprotective treatment after the insult. Indeed, hypothermia applied within 6 hours after birth in neonatal encephalopathy reduces neurological disability in clinical trials. In order to develop the next generation of treatment, we need to know more about the pathophysiological mechanism during the secondary and tertiary phases of injury. We review some of the critical molecular events related to mitochondrial dysfunction and apoptosis during the secondary phase and report some recent evidence that intervention may be feasible also days-weeks after the insult.

  12. Molecular Mechanisms of DNA Replication Checkpoint Activation

    Directory of Open Access Journals (Sweden)

    Bénédicte Recolin

    2014-03-01

    Full Text Available The major challenge of the cell cycle is to deliver an intact, and fully duplicated, genetic material to the daughter cells. To this end, progression of DNA synthesis is monitored by a feedback mechanism known as replication checkpoint that is untimely linked to DNA replication. This signaling pathway ensures coordination of DNA synthesis with cell cycle progression. Failure to activate this checkpoint in response to perturbation of DNA synthesis (replication stress results in forced cell division leading to chromosome fragmentation, aneuploidy, and genomic instability. In this review, we will describe current knowledge of the molecular determinants of the DNA replication checkpoint in eukaryotic cells and discuss a model of activation of this signaling pathway crucial for maintenance of genomic stability.

  13. Molecular mechanism of the Syk activation switch.

    Science.gov (United States)

    Tsang, Emily; Giannetti, Anthony M; Shaw, David; Dinh, Marie; Tse, Joyce K Y; Gandhi, Shaan; Ho, Hoangdung; Wang, Sandra; Papp, Eva; Bradshaw, J Michael

    2008-11-21

    Many immune signaling pathways require activation of the Syk tyrosine kinase to link ligation of surface receptors to changes in gene expression. Despite the central role of Syk in these pathways, the Syk activation process remains poorly understood. In this work we quantitatively characterized the molecular mechanism of Syk activation in vitro using a real time fluorescence kinase assay, mutagenesis, and other biochemical techniques. We found that dephosphorylated full-length Syk demonstrates a low initial rate of substrate phosphorylation that increases during the kinase reaction due to autophosphorylation. The initial rate of Syk activity was strongly increased by either pre-autophosphorylation or binding of phosphorylated immune tyrosine activation motif peptides, and each of these factors independently fully activated Syk. Deletion mutagenesis was used to identify regions of Syk important for regulation, and residues 340-356 of the SH2 kinase linker region were identified to be important for suppression of activity before activation. Comparison of the activation processes of Syk and Zap-70 revealed that Syk is more readily activated by autophosphorylation than Zap-70, although both kinases are rapidly activated by Src family kinases. We also studied Syk activity in B cell lysates and found endogenous Syk is also activated by phosphorylation and immune tyrosine activation motif binding. Together these experiments show that Syk functions as an "OR-gate" type of molecular switch. This mechanism of switch-like activation helps explain how Syk is both rapidly activated after receptor binding but also sustains activity over time to facilitate longer term changes in gene expression.

  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. International bulletin on atomic and molecular data for fusion. No. 52

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, J A [ed.

    1997-08-01

    This bulletin is published by the International Atomic Energy Agency to provide atomic and molecular data relevant to fusion research and technology. In part 1 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); and (iii) surface interactions (sputtering, chemical reactions, trapping and detrapping, adsorption, desorption, reflection, and secondary electron emission). Part 2 contains the bibliographic data, essentially for the above listed topics.

  16. International bulletin on atomic and molecular data for fusion. Nos. 50-51

    International Nuclear Information System (INIS)

    Botero, J.; Stephens, J.A.

    1996-10-01

    This bulletin is published by the International Atomic Energy Agency to provide atomic and molecular data relevant to fusion research and technology. In part 1 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). Part 2 contains the bibliographic data, essentially for the above listed topics

  17. International bulletin on atomic and molecular data for fusion. No. 52

    International Nuclear Information System (INIS)

    Stephens, J.A.

    1997-08-01

    This bulletin is published by the International Atomic Energy Agency to provide atomic and molecular data relevant to fusion research and technology. In part 1 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); and (iii) surface interactions (sputtering, chemical reactions, trapping and detrapping, adsorption, desorption, reflection, and secondary electron emission). Part 2 contains the bibliographic data, essentially for the above listed topics

  18. Bibliography of atomic and molecular processes. Volume 1, 1978-1981

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Farmer, B.J. (comps.)

    1982-10-01

    This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. 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 county 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.

  19. Bibliography of atomic and molecular processes. Volume 1, 1978-1981

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Farmer, B.J.

    1982-10-01

    This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. 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 county 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

  20. Exact and Optimal Quantum Mechanics/Molecular Mechanics Boundaries.

    Science.gov (United States)

    Sun, Qiming; Chan, Garnet Kin-Lic

    2014-09-09

    Motivated by recent work in density matrix embedding theory, we define exact link orbitals that capture all quantum mechanical (QM) effects across arbitrary quantum mechanics/molecular mechanics (QM/MM) boundaries. Exact link orbitals are rigorously defined from the full QM solution, and their number is equal to the number of orbitals in the primary QM region. Truncating the exact set yields a smaller set of link orbitals optimal with respect to reproducing the primary region density matrix. We use the optimal link orbitals to obtain insight into the limits of QM/MM boundary treatments. We further analyze the popular general hybrid orbital (GHO) QM/MM boundary across a test suite of molecules. We find that GHOs are often good proxies for the most important optimal link orbital, although there is little detailed correlation between the detailed GHO composition and optimal link orbital valence weights. The optimal theory shows that anions and cations cannot be described by a single link orbital. However, expanding to include the second most important optimal link orbital in the boundary recovers an accurate description. The second optimal link orbital takes the chemically intuitive form of a donor or acceptor orbital for charge redistribution, suggesting that optimal link orbitals can be used as interpretative tools for electron transfer. We further find that two optimal link orbitals are also sufficient for boundaries that cut across double bonds. Finally, we suggest how to construct "approximately" optimal link orbitals for practical QM/MM calculations.

  1. Relativistic Green function for atomic and molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Gruzdev, P.F.; Sherstyuk, A.I.

    1981-12-01

    The problem on Green function construction of Dirac equation is solved for a wide class of single electron potentials in the atom and molecule theory. The solution is obtained in the form of a spectrum analysis according to the total system of eigenfuctions of the generalized Dirac problem for eigenvalues. The problem possesses a purely discrete spectrum.

  2. Stimulated Raman adiabatic passage from an atomic to a molecular Bose-Einstein condensate

    International Nuclear Information System (INIS)

    Drummond, P.D.; Kheruntsyan, K.V.; Heinzen, D.J.; Wynar, R.H.

    2002-01-01

    The process of stimulated Raman adiabatic passage (STIRAP) provides a possible route for the generation of a coherent molecular Bose-Einstein condensate (BEC) from an atomic BEC. We analyze this process in a three-dimensional mean-field theory, including atom-atom interactions and nonresonant intermediate levels. We find that the process is feasible, but at larger Rabi frequencies than anticipated from a crude single-mode lossless analysis, due to two-photon dephasing caused by the atomic interactions. We then identify optimal strategies in STIRAP allowing one to maintain high conversion efficiencies with smaller Rabi frequencies and under experimentally less demanding conditions

  3. Molecular and cellular mechanisms of aortic stenosis.

    Science.gov (United States)

    Yetkin, Ertan; Waltenberger, Johannes

    2009-06-12

    Calcific aortic stenosis is the most common cause of aortic valve replacement in developed countries, and this condition increases in prevalence with advancing age. The fibrotic thickening and calcification are common eventual endpoint in both non-rheumatic calcific and rheumatic aortic stenoses. New observations in human aortic valves support the hypothesis that degenerative valvular aortic stenosis is the result of active bone formation in the aortic valve, which may be mediated through a process of osteoblast-like differentiation in these tissues. Additionally histopathologic evidence suggests that early lesions in aortic valves are not just a disease process secondary to aging, but an active cellular process that follows the classical "response to injury hypothesis" similar to the situation in atherosclerosis. Although there are similarities with the risk factor and as well as with the process of atherogenesis, not all the patients with coronary artery disease or atherosclerosis have calcific aortic stenosis. This review mainly focuses on the potential vascular and molecular mechanisms involved in the pathogenesis of aortic valve stenosis. Namely extracellular matrix remodeling, angiogenesis, inflammation, and eventually osteoblast-like differentiation resulting in bone formation have been shown to play a role in the pathogenesis of calcific aortic stenosis. Several mediators related to underlying mechanisms, including growth factors especially transforming growth factor-beta1 and vascular endothelial growth factors, angiogenesis, cathepsin enzymes, adhesion molecules, bone regulatory proteins and matrix metalloproteinases have been demonstrated, however the target to be attacked is not defined yet.

  4. Molecular Mechanisms in the shock induced decomposition of FOX-7

    Science.gov (United States)

    Mishra, Ankit; Tiwari, Subodh C.; Nakano, Aiichiro; Vashishta, Priya; Kalia, Rajiv; CACS Team

    Experimental and first principle computational studies on FOX 7 have either involved a very small system consisting of a few atoms or they did not take into account the decomposition mechanisms under extreme conditions of temperature and pressure. We have performed a large-scale reactive MD simulation using ReaxFF-lg force field to study the shock decomposition of FOX 7. The chemical composition of the principal decomposition products correlates well with experimental observations. Furthermore, we observed that the production of N2 and H2O was inter molecular in nature and was through different chemical pathways. Moreover, the production of CO and CO2 was delayed due to production of large stable C,O atoms cluster. These critical insights into the initial processes involved in the shock induced decomposition of FOX-7 will greatly help in understanding the factors playing an important role in the insensitiveness of this high energy material. This research is supported by AFOSR Award No. FA9550-16-1-0042.

  5. Initiating Heavy-atom Based Phasing by Multi-Dimensional Molecular Replacement

    DEFF Research Database (Denmark)

    Pedersen, Bjørn Panyella; Gourdon, Pontus; Liu, Xiangyu

    2014-01-01

    -based approaches, which however may fail when only poorly diffracting derivative crystals are available, as often the case for e.g. membrane proteins. Here we present an approach for heavy atom site identification based on a Molecular Replacement Parameter Matrix (MRPM) search. It involves an n-dimensional search...... to test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied...... but correct molecular replacement solutions with maximum contrast to prime experimental phasing efforts....

  6. Molecular Mechanisms of Insulin Resistance Development

    Directory of Open Access Journals (Sweden)

    Vsevolod Arsen'evich Tkachuk

    2014-05-01

    Full Text Available Insulin resistance (IR is a phenomenon associated with an impaired ability of insulin to stimulate glucose uptake by target cells and to reduce the blood glucose level. A response increase in insulin secretion by the pancreas and hyperinsulinemia are compensatory reactions of the body. The development of IR leads to the inability of target cells to respond to insulin that results in developing type 2 diabetes mellitus (T2DM and metabolic syndrome. For this reason, the metabolic syndrome is defined in practice as a combination of IR with one or more pathologies such as T2DM, arterial hypertension, dyslipidemia, abdominal obesity, non-alcoholic fatty liver disease, and some others. However, a combination of high blood glucose and insulin levels always serves as its physiological criterion.IR should be considered as a systemic failure of the endocrine regulation in the body. Physiological causes of IR are diverse. The main ones are nutritional overload and accumulation of certain lipids and their metabolites in cells, low physical activity, chronic inflammation and stress of various nature, including oxidative and endoplasmic reticulum stress (impairment of damaged protein degradation in the cell. Recent studies have demonstrated that these physiological mechanisms likely act through a single intracellular scenario. This is the impairment of signal transduction from the insulin receptor to its targets via the negative feedback mechanism in intracellular insulin-dependent signaling cascades.This review describes the physiological and intracellular mechanisms of insulin action and focuses on their abnormalities upon IR development. Finally, feasible trends in early molecular diagnosis and therapy of IR are discussed.

  7. 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

  8. 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

  9. Atomic and molecular spectroscopy basic concepts and applications

    CERN Document Server

    Kakkar, Rita

    2015-01-01

    Spectroscopy is the study of electromagnetic radiation and its interaction with solid, liquid, gas and plasma. It is one of the widely used analytical techniques to study the structure of atoms and molecules. The technique is also employed to obtain information about atoms and molecules as a result of their distinctive spectra. The fast-spreading field of spectroscopic applications has made a noteworthy influence on many disciplines, including energy research, chemical processing, environmental protection and medicine. This book aims to introduce students to the topic of spectroscopy. The author has avoided the mathematical aspects of the subject as far as possible; they appear in the text only when inevitable. Including topics such as time-dependent perturbation theory, laser action and applications of Group Theory in interpretation of spectra, the book offers a detailed coverage of the basic concepts and applications of spectroscopy.

  10. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    Science.gov (United States)

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  11. Clean Nanotube Unzipping by Abrupt Thermal Expansion of Molecular Nitrogen: Graphene Nanoribbons with Atomically Smooth Edges

    Energy Technology Data Exchange (ETDEWEB)

    Sumpter, Bobby G [ORNL; Meunier, Vincent [ORNL; Terrones, M. [Universidad Carlos III, Madrid, Spain; Endo, M [Shinshu University; Munoz-Sandoval, Emilio [IPICyT; Kim, Y A [Shinshu University; Morelos-Bomez, Aaron [Shinshu University; Vega-Diaz, Sofia [Shinshu University

    2012-01-01

    We report a novel physicochemical route to produce highly crystalline nitrogen-doped graphene nanoribbons. The technique consists of an abrupt N2 gas expansion within the hollow core of nitrogen-doped multiwalled carbon nanotubes (CNx-MWNTs) when exposed to a fast thermal shock. The multiwalled nanotube unzipping mechanism is rationalized using molecular dynamics and density functional theory simulations, which highlight the importance of open-ended nanotubes in promoting the efficient introduction of N2 molecules by capillary action within tubes and surface defects, thus triggering an efficient and atomically smooth unzipping. The so-produced nanoribbons could be few-layered (from graphene bilayer onward) and could exhibit both crystalline zigzag and armchair edges. In contrast to methods developed previously, our technique presents various advantages: (1) the tubes are not heavily oxidized; (2) the method yields sharp atomic edges within the resulting nanoribbons; (3) the technique could be scaled up for the bulk production of crystalline nanoribbons from available MWNT sources; and (4) this route could eventually be used to unzip other types of carbon nanotubes or intercalated layered materials such as BN, MoS2, WS2, etc.

  12. Physics. Experimental and theoretical foundations. Pt. 3. Atomic, molecular, and quantum physics. 2. ed.

    International Nuclear Information System (INIS)

    Weber, Reinhart

    2012-01-01

    This textbook mediates in three volumes the matter of the first four semester of the bachelor respectively master course. The otherwise generally usual separate presentation of experimental and theoretical physics is canceled in favor of an integrated treatment. The advances are obvious: The studying is enabled to learn to understand knowledge gotten by means of experiments also immediately in a quantitative formulation. The can equally be used as textbook to an integrated course and to separated courses. Because the relevant theoretical concepts are developed without gap a special book of theoretical physics is unnecessary. Numerous exercise problems deepen the understanding and help directly in the preparation for examinations. The illustrations are mostly presented in two colours. Volume III treats atomic and molecular physics. After a semiclassical presentation the quantum-mechanical foundations are developed and in the following chapters applied to atomic systems and processes. An introduction in the foundations and application of the laser. The closure is formed by a chapter about entangled systems.

  13. Quantum mechanical force fields for condensed phase molecular simulations

    Science.gov (United States)

    Giese, Timothy J.; York, Darrin M.

    2017-09-01

    Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

  14. The Physics of Coupled Atomic-Molecular Condensate System

    Science.gov (United States)

    2010-10-09

    electric dipoles represents a novel state of matter with long-range and anisotropic dipole-dipole interactions, that are highly amenable to the...free-bound FC factor. Simultaneously, a series of laser �elds of (molecular) Rabi frequency i (i 2) are applied to move the molecules from the

  15. 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

  16. Molecular mechanisms of intrauterine growth restriction.

    Science.gov (United States)

    Gurugubelli Krishna, Rao; Vishnu Bhat, B

    2017-07-10

    Intrauterine growth restriction (IUGR) is a pregnancy specific disease characterized by decreased growth rate of fetus than the normal growth potential at particular gestational age. In the current scenario it is a leading cause of fetal and neonatal morbidity and mortality. In the last decade exhilarating experimental studies from several laboratories have provided fascinating proof for comprehension of molecular basis of IUGR. Atypical expression of enzymes governed by TGFβ causes the placental apoptosis and altered expression of TGFβ due to hyper alimentation causes impairment of lung function. Crosstalk of cAMP with protein kinases plays a prominent role in the regulation of cortisol levels. Increasing levels of NOD1 proteins leads to development of IUGR by increasing the levels of inflammatory mediators. Increase in leptin synthesis in placental trophoblast cells is associated with IUGR. In this review, we emphasize on the regulatory mechanisms of IUGR and its associated diseases. They may help improve the in-utero fetal growth and provide a better therapeutic intervention for prevention and treatment of IUGR.

  17. Molecular and genetic mechanisms of environmental mutagens

    International Nuclear Information System (INIS)

    Kubitschek, H.E.; Derstine, P.L.; Griego, V.M.; Matsushita, T.; Peak, J.G.; Peak, M.J.; Reynolds, P.R.; Webb, R.B.; Williams-Hill, D.

    1981-01-01

    This program is primarily concerned with elucidation of the nature of DNA lesions produced by environmental and energy related mutagens, their mechanisms of action, and their repair. The main focus is on actions of chemical mutagens and electromagnetic radiations. Synergistic interactions between mutagens and the mutational processes that lead to synergism are being investigated. Mutagens are chosen for study on the basis of their potential for analysis of mutation (as genetic probes), for development of procedures for reducing mutational damage, for their potential importance to risk assessment, and for development of improved mutagen testing systems. Bacterial cells are used because of the rapidity and clarity of scientific results that can be obtained, the detailed genetic maps, and the many well-defined mutand strains available. The conventional tools of microbial and molecular genetics are used, along with intercomparison of genetically related strains. Advantage is taken of tcollective dose commitment will result in more attention being paid to potential releases of radionuclides at relatively short times after disposal

  18. Molecular mechanism of radiosensitization by nitro compounds

    International Nuclear Information System (INIS)

    Kagiya, T.; Wada, T.; Nishimoto, S.I.

    1984-01-01

    In this chapter a molecular mechanism of radiosensitization by electron-affinic nitro compounds is discussed, mainly on the basis of the results of the radiation-induced chemical studies of DNA-related compounds in aqueous solutions. In Section II the general aspects of the radiation chemistry of organic compounds in the absence and presence of oxygen in aqueous solution are shown in order to demonstrate characteristic differences between radiation chemical reactions in hypoxic and oxic cells. The effects of nitro compounds on the radiolysis yields of DNA-related compounds in aqueous solutions are described in Section III. In Section IV the retardation effects of misonidazole on the radiation chemical processes of DNA-related compounds are shown along with the reaction characteristics of misonidazole with hydroxyl radical ( . OH) and hydrated electron (e/sub aq/-bar) produced by the radiolysis of water. The promotion of radiation-induced oxidation of thymine into thymine glycol (TG) by nitro radiosensitizers in deoxygenated solution and the relations between the activity of nitro compound for the thymine glycol formation and the enhancement activity measured in vitro are described in Section V. Finally, the protection against radiation-induced damage of thymine by a sulfhydryl compound of glutathione and the ability of electron-affinic compounds to decompose the intracellular radioprotector are described in Section VI

  19. Quantum mechanical study of molecular collisions at ultra-low energy: applications to alkali and alkaline-earth systems

    International Nuclear Information System (INIS)

    Quemener, G.

    2006-10-01

    In order to investigate the collisional processes which occur during the formation of molecular Bose-Einstein condensates, a time-independent quantum mechanical formalism, based on hyperspherical coordinates, has been applied to the study of atom-diatom dynamics at ultra-low energies. We present theoretical results for three alkali systems, each composed of lithium, sodium or potassium atoms, and for an alkaline-earth system composed of calcium atoms. We also study dynamics at large and positive atom-atom scattering length. Evidence for the suppression of inelastic processes in a fermionic system is given, as well as a linear relation between the atom-diatom scattering length and the atom-atom scattering length. (author)

  20. Spiers Memorial Lecture. Molecular mechanics and molecular electronics.

    Science.gov (United States)

    Beckman, Robert; Beverly, Kris; Boukai, Akram; Bunimovich, Yuri; Choi, Jang Wook; DeIonno, Erica; Green, Johnny; Johnston-Halperin, Ezekiel; Luo, Yi; Sheriff, Bonnie; Stoddart, Fraser; Heath, James R

    2006-01-01

    We describe our research into building integrated molecular electronics circuitry for a diverse set of functions, and with a focus on the fundamental scientific issues that surround this project. In particular, we discuss experiments aimed at understanding the function of bistable rotaxane molecular electronic switches by correlating the switching kinetics and ground state thermodynamic properties of those switches in various environments, ranging from the solution phase to a Langmuir monolayer of the switching molecules sandwiched between two electrodes. We discuss various devices, low bit-density memory circuits, and ultra-high density memory circuits that utilize the electrochemical switching characteristics of these molecules in conjunction with novel patterning methods. We also discuss interconnect schemes that are capable of bridging the micrometre to submicrometre length scales of conventional patterning approaches to the near-molecular length scales of the ultra-dense memory circuits. Finally, we discuss some of the challenges associated with fabricated ultra-dense molecular electronic integrated circuits.

  1. International Conference on the Frontiers in Atomic, Molecular, and Optical Physics (AMO2016)

    International Nuclear Information System (INIS)

    2016-01-01

    Atoms, molecules, and light have been at the forefront of understanding quantum mechanics, since its discovery over 100 years ago. Since then the field has progressed from understanding the most fundamental aspects of how particles behave under quantum mechanics to controlling individual atoms for creating new technologies. While matter and light are from ordinary experience rather different, with today's control of coherent quantum phenomena many of the ideas freely cross their respective boundaries. Some of the topics that will be covered at the conference include, but are not limited to, cold atoms and cold molecules, ultrafast and precision spectroscopy, quantum manipulation and precision measurement, quantum computing and quantum communication, and quantum metrology. In this conference we aim to bring together the leading experts working in the frontiers of atomic, molecular, and optical systems. Scientific Committee: Guoxiang Huang Director, NYU-ECNU Institute of Physics at NYU Shanghai; Professor of Physics Department of Physics and State Key Laboratory of Precision Spectroscopy East China Normal University Daniel L. Stein Director, NYU-ECNU Institute of Physics at NYU Shanghai; Professor of Physics and Mathematics Departments of Physics and Mathematics, NYU Jian Wu Director, Professor of Physics State Key Laboratory of Precision Spectroscopy East China Normal University E Wu Researcher State Key Laboratory of Precision Spectroscopy East China Normal University Haibin Wu Professor of Physics State Key Laboratory of Precision Spectroscopy East China Normal University Tim Byrnes Assistant Professor of Physics at NYU Shanghai Invited Speakers: Jurgen Appel (Copenhagen, Denmark) Luiz Davidovich (Universidade Federal Do Rio De Janeiro, Brazil) Jonathan Dowling (LSU, USA) Luming Duan (Michigan, USA) Claude Fabre (Universite Pierre Et Marie Curie, France) Elisabeth Giacobino (CNRS Laboratoire Kastler-Brossel, France) Rudolf Grimm (Innsbruck, Austria) Fedor

  2. The Russian effort in establishing large atomic and molecular databases

    Science.gov (United States)

    Presnyakov, Leonid P.

    1998-07-01

    The database activities in Russia have been developed in connection with UV and soft X-ray spectroscopic studies of extraterrestrial and laboratory (magnetically confined and laser-produced) plasmas. Two forms of database production are used: i) a set of computer programs to calculate radiative and collisional data for the general atom or ion, and ii) development of numeric database systems with the data stored in the computer. The first form is preferable for collisional data. At the Lebedev Physical Institute, an appropriate set of the codes has been developed. It includes all electronic processes at collision energies from the threshold up to the relativistic limit. The ion -atom (and -ion) collisional data are calculated with the methods developed recently. The program for the calculations of the level populations and line intensities is used for spectrical diagnostics of transparent plasmas. The second form of database production is widely used at the Institute of Physico-Technical Measurements (VNIIFTRI), and the Troitsk Center: the Institute of Spectroscopy and TRINITI. The main results obtained at the centers above are reviewed. Plans for future developments jointly with international collaborations are discussed.

  3. Multiresolution molecular mechanics: Surface effects in nanoscale materials

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Qingcheng, E-mail: qiy9@pitt.edu; To, Albert C., E-mail: albertto@pitt.edu

    2017-05-01

    Surface effects have been observed to contribute significantly to the mechanical response of nanoscale structures. The newly proposed energy-based coarse-grained atomistic method Multiresolution Molecular Mechanics (MMM) (Yang, To (2015), ) is applied to capture surface effect for nanosized structures by designing a surface summation rule SR{sup S} within the framework of MMM. Combined with previously proposed bulk summation rule SR{sup B}, the MMM summation rule SR{sup MMM} is completed. SR{sup S} and SR{sup B} are consistently formed within SR{sup MMM} for general finite element shape functions. Analogous to quadrature rules in finite element method (FEM), the key idea to the good performance of SR{sup MMM} lies in that the order or distribution of energy for coarse-grained atomistic model is mathematically derived such that the number, position and weight of quadrature-type (sampling) atoms can be determined. Mathematically, the derived energy distribution of surface area is different from that of bulk region. Physically, the difference is due to the fact that surface atoms lack neighboring bonding. As such, SR{sup S} and SR{sup B} are employed for surface and bulk domains, respectively. Two- and three-dimensional numerical examples using the respective 4-node bilinear quadrilateral, 8-node quadratic quadrilateral and 8-node hexahedral meshes are employed to verify and validate the proposed approach. It is shown that MMM with SR{sup MMM} accurately captures corner, edge and surface effects with less 0.3% degrees of freedom of the original atomistic system, compared against full atomistic simulation. The effectiveness of SR{sup MMM} with respect to high order element is also demonstrated by employing the 8-node quadratic quadrilateral to solve a beam bending problem considering surface effect. In addition, the introduced sampling error with SR{sup MMM} that is analogous to numerical integration error with quadrature rule in FEM is very small. - Highlights:

  4. Macro-mechanics controls quantum mechanics: mechanically controllable quantum conductance switching of an electrochemically fabricated atomic-scale point contact.

    Science.gov (United States)

    Staiger, Torben; Wertz, Florian; Xie, Fangqing; Heinze, Marcel; Schmieder, Philipp; Lutzweiler, Christian; Schimmel, Thomas

    2018-01-12

    Here, we present a silver atomic-scale device fabricated and operated by a combined technique of electrochemical control (EC) and mechanically controllable break junction (MCBJ). With this EC-MCBJ technique, we can perform mechanically controllable bistable quantum conductance switching of a silver quantum point contact (QPC) in an electrochemical environment at room temperature. Furthermore, the silver QPC of the device can be controlled both mechanically and electrochemically, and the operating mode can be changed from 'electrochemical' to 'mechanical', which expands the operating mode for controlling QPCs. These experimental results offer the perspective that a silver QPC may be used as a contact for a nanoelectromechanical relay.

  5. The importance of atomic and molecular correlation on the bonding in transition metal compounds

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Walch, Stephen P.

    1986-01-01

    The determination of accurate spectroscopic parameters for molecular systems containing transition metal atoms is shown to require extensive data sets and a high level correlation treatment, and techniques and their limitations are considered. Extensive results reported on the transition metal atoms, hydrides, oxides, and dimers makes possible the design of a calculation to correctly describe the mixing of different atomic asymptotes, and to give a correct balance between molecular bonding and exchange interactions. Examples considered include the dipole moment of the 2Delta state of NiH, which can help determine the mixture of 3d(8)4s(2) and 3d(9)4s(1) in the NiH wavefunction, and the bonding in CrO, where an equivalent description of the relative energies associated with the Cr 3d-3d atomic exchange and the Cr-O bond is important.

  6. ATOMIC AND MOLECULAR CARBON AS A TRACER OF TRANSLUCENT CLOUDS

    International Nuclear Information System (INIS)

    Burgh, Eric B.; France, Kevin; Jenkins, Edward B.

    2010-01-01

    Using archival, high-resolution far-ultraviolet Hubble Space Telescope/Space Telescope Imaging Spectrograph spectra of 34 Galactic O and B stars, we measure C I column densities and compare them with measurements from the literature of CO and H 2 with regard to understanding the presence of translucent clouds along the line of sight. We find that the CO/H 2 and CO/C I ratios provide good discriminators for the presence of translucent material, and both increase as a function of molecular fraction, f N = 2N(H 2 )/N(H). We suggest that sightlines with values below CO/H 2 ∼10 -6 and CO/C I ∼1 contain mostly diffuse molecular clouds, while those with values above sample clouds in the transition region between diffuse and dark. These discriminating values are also consistent with the change in slope of the CO versus H 2 correlation near the column density at which CO shielding becomes important, as evidenced by the change in photochemistry regime studied by Sheffer et al. Based on the lack of correlation of the presence of translucent material with traditional measures of extinction, we recommend defining 'translucent clouds' based on the molecular content rather than line-of-sight extinction properties.

  7. 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.

  8. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

    Science.gov (United States)

    Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

    2014-09-16

    Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine

  9. Hydrogen atom and the H+2 and HeH++ molecular ions inside prolate spheroidal boxes

    International Nuclear Information System (INIS)

    Ley-Koo, E.; Cruz, S.A.

    1981-01-01

    We formulate the exact solution of the Schroedinger equation for systems of one electron in the Coulomb field of one or two fixed nuclei at the foci inside prolate spheroidal boxes. Numerical results are obtained for the energy eigenvalues and eigenfunctions of the lowest states of the hydrogen atom and the H + 2 and HeH ++ molecular ions for boxes of different sizes and eccentricities. We also evaluate the hyperfine splitting of atomic hydrogen and of H + 2

  10. International bulletin on atomic and molecular data for fusion. No. 11

    International Nuclear Information System (INIS)

    Katsonis, K.; Rumble, J. Jr.

    1980-01-01

    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. The bulletin contains a list of references the publications on controlled fusion and plasma physics for 1979. It contains an index to the contributed papers presented at the 11th International Conference on the Physics of Electronics and Atomic Collision (ICPEAC) held in Kyoto (Japan) in summer 1979

  11. Atomic force microscope image contrast mechanisms on supported lipid bilayers.

    Science.gov (United States)

    Schneider, J; Dufrêne, Y F; Barger, W R; Lee, G U

    2000-08-01

    This work presents a methodology to measure and quantitatively interpret force curves on supported lipid bilayers in water. We then use this method to correlate topographic imaging contrast in atomic force microscopy (AFM) images of phase-separated Langmuir-Blodgett bilayers with imaging load. Force curves collected on pure monolayers of both distearoylphosphatidylethanolamine (DSPE) and monogalactosylethanolamine (MGDG) and dioleoylethanolamine (DOPE) deposited at similar surface pressures onto a monolayer of DSPE show an abrupt breakthrough event at a repeatable, material-dependent force. The breakthrough force for DSPE and MGDG is sizable, whereas the breakthrough force for DOPE is too small to measure accurately. Contact-mode AFM images on 1:1 mixed monolayers of DSPE/DOPE and MGDG/DOPE have a high topographic contrast at loads between the breakthrough force of each phase, and a low topographic contrast at loads above the breakthrough force of both phases. Frictional contrast is inverted and magnified at loads above the breakthrough force of both phases. These results emphasize the important role that surface forces and mechanics can play in imaging multicomponent biomembranes with AFM.

  12. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

    Science.gov (United States)

    Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

    2017-02-14

    In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

  13. PREFACE: 8th Asian International Seminar on Atomic and Molecular Physics (AISAMP)

    Science.gov (United States)

    Williams, Jim F.; Buckman, Steve; Bieske, Evan J.

    2009-09-01

    These proceedings arose from the 8th Asian International Seminar on Atomic and Molecular Physics (AISAMP) which was held at the University of Western Australia 24-28 November 2008. The history of AISAMP (Takayanagi and Matsuzawa 2002) recognizes its origin from the Japan-China meeting of 1985, and the first use of the name 'The First Asian International Seminar on Atomic and Molecular Physics (AISAMP)' in 1992. The initial attendees, Japan and China, were joined subsequently by scientists from Korea, Taiwan, India, Australia and recently by Malaysia, Thailand, Vietnam, Turkey Iran, UK and USA. The main purpose of the biennial AISAMP series is to create a wide forum for exchanging ideas and information among atomic and molecular scientists and to promote international collaboration. The scope of the AISAMP8 meeting included pure, strategic and applied research involving atomic and molecular structure and processes in all forms of matter and antimatter. For 2008 the AISAMP conference incorporated the Australian Atomic and Molecular Physics and Quantum Chemistry meeting. The topics for AISAMP8 embraced themes from earlier AISAMP meetings and reflected new interests, in atomic and molecular structures, spectroscopy and collisions; atomic and molecular physics with laser or synchrotron radiation; quantum information processing using atoms and molecules; atoms and molecules in surface physics, nanotechnology, biophysics, atmospheric physics and other interdisciplinary studies. The implementation of the AISAMP themes, as well as the international representation of research interests, is indicated both in the contents list of these published manuscripts as well as in the program for the meeting. Altogether, 184 presentations were made at the 8th AISAMP, including Invited Talks and Contributed Poster Presentations, of which 60 appear in the present Proceedings after review by expert referees in accordance with the usual practice of Journal of Physics: Conference Series of

  14. Dissecting molecular descriptors into atomic contributions in density functional reactivity theory

    Energy Technology Data Exchange (ETDEWEB)

    Rong, Chunying [Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081 (China); Lu, Tian [School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing (China); Liu, Shubin, E-mail: shubin@email.unc.edu [Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081 (China); Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420 (United States)

    2014-01-14

    Density functional reactivity theory (DFRT) employs the electron density of a molecule and its related quantities such as gradient and Laplacian to describe its structure and reactivity properties. Proper descriptions at both molecular (global) and atomic (local) levels are equally important and illuminating. In this work, we make use of Bader's zero-flux partition scheme and consider atomic contributions for a few global reactivity descriptors in DFRT, including the density-based quantification of steric effect and related indices. Earlier, we proved that these quantities are intrinsically correlated for atomic and molecular systems [S. B. Liu, J. Chem. Phys. 126, 191107 (2007); ibid. 126, 244103 (2007)]. In this work, a new basin-based integration algorithm has been implemented, whose reliability and effectiveness have been extensively examined. We also investigated a list of simple hydrocarbon systems and different scenarios of bonding processes, including stretching, bending, and rotating. Interesting changing patterns for the atomic and molecular values of these quantities have been revealed for different systems. This work not only confirms the strong correlation between these global reactivity descriptors for molecular systems, as theoretically proven earlier by us, it also provides new and unexpected changing patterns for their atomic values, which can be employed to understand the origin and nature of chemical phenomena.

  15. Dissecting molecular descriptors into atomic contributions in density functional reactivity theory

    International Nuclear Information System (INIS)

    Rong, Chunying; Lu, Tian; Liu, Shubin

    2014-01-01

    Density functional reactivity theory (DFRT) employs the electron density of a molecule and its related quantities such as gradient and Laplacian to describe its structure and reactivity properties. Proper descriptions at both molecular (global) and atomic (local) levels are equally important and illuminating. In this work, we make use of Bader's zero-flux partition scheme and consider atomic contributions for a few global reactivity descriptors in DFRT, including the density-based quantification of steric effect and related indices. Earlier, we proved that these quantities are intrinsically correlated for atomic and molecular systems [S. B. Liu, J. Chem. Phys. 126, 191107 (2007); ibid. 126, 244103 (2007)]. In this work, a new basin-based integration algorithm has been implemented, whose reliability and effectiveness have been extensively examined. We also investigated a list of simple hydrocarbon systems and different scenarios of bonding processes, including stretching, bending, and rotating. Interesting changing patterns for the atomic and molecular values of these quantities have been revealed for different systems. This work not only confirms the strong correlation between these global reactivity descriptors for molecular systems, as theoretically proven earlier by us, it also provides new and unexpected changing patterns for their atomic values, which can be employed to understand the origin and nature of chemical phenomena

  16. Molecular mechanisms in radiation carcinogenesis: introduction

    International Nuclear Information System (INIS)

    Setlow, R.B.

    1975-01-01

    Molecular studies of radiation carcinogenesis are discussed in relation to theories for extrapolating from cellular and animal models to man. Skin cancer is emphasized because of sunlight-induced photochemical damage to DNA. It is emphasized that cellular and animal models are needed as well as molecular theories for quantitative evaluation of hazardous environmental agents. (U.S.)

  17. Self-corrected sensors based on atomic absorption spectroscopy for atom flux measurements in molecular beam epitaxy

    International Nuclear Information System (INIS)

    Du, Y.; Liyu, A. V.; Droubay, T. C.; Chambers, S. A.; Li, G.

    2014-01-01

    A high sensitivity atom flux sensor based on atomic absorption spectroscopy has been designed and implemented to control electron beam evaporators and effusion cells in a molecular beam epitaxy system. Using a high-resolution spectrometer and a two-dimensional charge coupled device detector in a double-beam configuration, we employ either a non-resonant line or a resonant line with low cross section from the same hollow cathode lamp as the reference for nearly perfect background correction and baseline drift removal. This setup also significantly shortens the warm-up time needed compared to other sensor technologies and drastically reduces the noise coming from the surrounding environment. In addition, the high-resolution spectrometer allows the most sensitive resonant line to be isolated and used to provide excellent signal-to-noise ratio

  18. International bulletin on atomic and molecular data for fusion. No.6

    International Nuclear Information System (INIS)

    Katsonis, K.; Smith, F.J.

    1978-10-01

    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. Cross-sections for the electron impact excitation of 2sub(p1/2) and 2sub(p3/2) states of the lithium-line ions C 3+ , F 23+ , Mo 39+ and W 71+ calculated in the relativistic Coulomb-Born approximation are presented

  19. The cytotoxicity of organobismuth compounds with certain molecular structures can be diminished by replacing the bismuth atom with an antimony atom in the molecules.

    Science.gov (United States)

    Kohri, Kumiko; Yoshida, Eiko; Yasuike, Shuji; Fujie, Tomoya; Yamamoto, Chika; Kaji, Toshiyuki

    2015-06-01

    Organic-inorganic hybrid molecules, which are composed of an organic structure and metal(s), are indispensable for synthetic chemical reactions; however, their toxicity has been incompletely understood. In the present study, we discovered two cytotoxic organobismuth compounds whose cytotoxicity diminished upon replacement of the intramolecular bismuth atom with an antimony atom. The intracellular accumulation of the organobismuth compounds was much higher than that of the organoantimony compounds with the corresponding organic structures. We also showed that both the organic structure and bismuth atom are required for certain organobismuth compounds to exert their cytotoxic effect, suggesting that the cytotoxicity of such a compound is a result of an interaction between the organic structure and the bismuth atom. The present data suggest that organobismuth compounds with certain molecular structures exhibit cytotoxicity via an interaction between the molecular structure and the bismuth atom, and this cytotoxicity can be diminished by replacing the bismuth atom with an antimony atom, resulting in lower intracellular accumulation.

  20. A quantum-mechanics molecular-mechanics scheme for extended systems.

    Science.gov (United States)

    Hunt, Diego; Sanchez, Veronica M; Scherlis, Damián A

    2016-08-24

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.

  1. A quantum-mechanics molecular-mechanics scheme for extended systems

    International Nuclear Information System (INIS)

    Hunt, Diego; Scherlis, Damián A; Sanchez, Veronica M

    2016-01-01

    We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car–Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO 2 anatase (1 0 1) solid–liquid interface. This investigation suggests that the inclusion of a second monolayer of H 2 O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces. (paper)

  2. Nano Scale Mechanical Analysis of Biomaterials Using Atomic Force Microscopy

    Science.gov (United States)

    Dutta, Diganta

    The atomic force microscope (AFM) is a probe-based microscope that uses nanoscale and structural imaging where high resolution is desired. AFM has also been used in mechanical, electrical, and thermal engineering applications. This unique technique provides vital local material properties like the modulus of elasticity, hardness, surface potential, Hamaker constant, and the surface charge density from force versus displacement curve. Therefore, AFM was used to measure both the diameter and mechanical properties of the collagen nanostraws in human costal cartilage. Human costal cartilage forms a bridge between the sternum and bony ribs. The chest wall of some humans is deformed due to defective costal cartilage. However, costal cartilage is less studied compared to load bearing cartilage. Results show that there is a difference between chemical fixation and non-chemical fixation treatments. Our findings imply that the patients' chest wall is mechanically weak and protein deposition is abnormal. This may impact the nanostraws' ability to facilitate fluid flow between the ribs and the sternum. At present, AFM is the only tool for imaging cells' ultra-structure at the nanometer scale because cells are not homogeneous. The first layer of the cell is called the cell membrane, and the layer under it is made of the cytoskeleton. Cancerous cells are different from normal cells in term of cell growth, mechanical properties, and ultra-structure. Here, force is measured with very high sensitivity and this is accomplished with highly sensitive probes such as a nano-probe. We performed experiments to determine ultra-structural differences that emerge when such cancerous cells are subject to treatments such as with drugs and electric pulses. Jurkat cells are cancerous cells. These cells were pulsed at different conditions. Pulsed and non-pulsed Jurkat cell ultra-structures were investigated at the nano meter scale using AFM. Jurkat cell mechanical properties were measured under

  3. Atomic and molecular physics of plasma-based environmental technologies for abatement of volatile organic compounds

    International Nuclear Information System (INIS)

    Penetrante, B.M.; Hsiao, M.C.; Bardsley, J.N.; Merrit, B.T.; Vogtlin, G.E.; Kuthi, A.; Burkhart, C.P.; Bayless, J.R.

    1996-01-01

    Non-thermal plasma techniques represent a new generation of air emission control technology that potentially could treat large-volume emissions containing dilute concentrations of volatile organic compounds (VOCs). In order to apply non-thermal in an industrial scale, it is important to establish the electrical power requirements and byproducts of the process. There is a need for reliable data concerning the primary decomposition mechanisms and subsequent chemical kinetics associated with non-thermal plasma processing of VOCs. There are many basic atomic and molecular physics issues that are essential in evaluating the economic performance of non-thermal plasma reactor. These studies are important in understanding how the input electrical power is dissipated in the plasma and how efficiency it is converted to the production of the plasma species (radicals, ions or electrons) responsible for the decomposition of the VOCs. This paper presents results from basic experimental and theoretical studied aimed at identifying the reaction mechanisms responsible for the primary decomposition of various types of VOCs. (Authors)

  4. Atomic and molecular physics of plasma-based environmental technologies for abatement of volatile organic compounds

    International Nuclear Information System (INIS)

    Penetrante, B. M.; Hsiao, M. C.; Bardsley, J. N.; Merritt, B. T.; Vogtin, G. E.; Kuthi, A.; Burkhart, C. P.; Bayless, J. R.

    1997-01-01

    Non-thermal plasma techniques represent a new generation of air emission control technology that potentially could treat large-volume emissions containing dilute concentrations of volatile organic compounds. In order to apply non-thermal plasmas in an industrial scale, it is important to establish the electrical power requirements and byproducts of the process.There is a need for reliable data concerning the primary decomposition mechanisms and subsequent chemical kinetics associated with non- thermal plasma processing of volatile organic compounds. There are many basic atomic and molecular physics issues that are essential in evaluating the economic performance of non-thermal plasma reactors. These studies are important in understanding how the input electrical power is dissipated in the plasma and how efficiently it is converted to the production of the plasma species (radicals, ions or electrons) responsible for the decomposition of the volatile organic compounds. This paper will present results from basic experimental and theoretical studies aimed at identifying the reaction mechanisms responsible for the primary decomposition of various types of volatile organic compounds. (authors)

  5. Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach

    International Nuclear Information System (INIS)

    Yakubovich, Alexander V.; Solov'yov, Andrey V.; Surdutovich, Eugene

    2011-01-01

    We present a brief overview of the multiscale approach towards understanding of the processes responsible for the radiation damage caused by energetic ions. This knowledge is very important, because it can be utilized in the ion-beam cancer therapy, which is one of the most advanced modern techniques to cure certain type of cancer. The central element of the multiscale approach is the theoretical evaluation and quantification of the DNA damage within cell environment. To achieve this goal one needs a significant amount of data on various atomic and molecular processes involved into the cascade of events starting with the ion entering and propagation in the biological medium and resulting in the DNA damage. The discussion of the follow up biological processes are beyond the scope of this brief overview. We consider different paths of the DNA damage and focus on the the illustration of the thermo-mechanical effects caused by the propagation of ions through the biological environment and in particular on the possibility of the creation of the shock waves in the vicinity of the ion tracks. We demonstrate that at the initial stages after ion's passage the shock wave is so strong that it can contribute to the DNA damage due to large pressure gradients developed at the distances of a few nanometers from the ionic tracks. This novel mechanism of the DNA damage provides an important contribution to the cumulative biodamage caused by low-energy secondary electrons, holes and free radicals.

  6. 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.

  7. Atomic excitation and molecular dissociation by low energy electron collisions

    International Nuclear Information System (INIS)

    Weyland, Marvin

    2016-01-01

    In this work, momentum imaging experiments have been conducted for the electron impact excitation of metastable states in noble gases and for dissociative electron attachment (DEA) in polyatomic molecules. For the electron impact excitation study a new experimental technique has been developed which is able to measure the scattering angle distribution of the electrons by detection of the momentum transfer to the atoms. Momentum transfer images have been recorded for helium and neon at fixed electron impact energy close to the excitation threshold and good agreement with current R-matrix theory calculations was found. A new momentum imaging apparatus for negative ions has been built for the purpose of studying DEA in biologically relevant molecules. During this work, DEA was investigated in the molecules ammonia, water, formic acid, furan, pyridine and in two chlorofluorocarbons. Furthermore, the change of DEA resonance energies when molecules form clusters compared to monomers was investigated in ammonia and formic acid. The experimental results of most studied molecules could be compared to recent theoretical calculations and they support further development in the theoretical description of DEA. The new apparatus built in this work also delivered a superior momentum resolution compared to existing setups. This allows the momentum imaging of heavier fragments and fragments with lower kinetic energy.

  8. Atomic excitation and molecular dissociation by low energy electron collisions

    Energy Technology Data Exchange (ETDEWEB)

    Weyland, Marvin

    2016-11-16

    In this work, momentum imaging experiments have been conducted for the electron impact excitation of metastable states in noble gases and for dissociative electron attachment (DEA) in polyatomic molecules. For the electron impact excitation study a new experimental technique has been developed which is able to measure the scattering angle distribution of the electrons by detection of the momentum transfer to the atoms. Momentum transfer images have been recorded for helium and neon at fixed electron impact energy close to the excitation threshold and good agreement with current R-matrix theory calculations was found. A new momentum imaging apparatus for negative ions has been built for the purpose of studying DEA in biologically relevant molecules. During this work, DEA was investigated in the molecules ammonia, water, formic acid, furan, pyridine and in two chlorofluorocarbons. Furthermore, the change of DEA resonance energies when molecules form clusters compared to monomers was investigated in ammonia and formic acid. The experimental results of most studied molecules could be compared to recent theoretical calculations and they support further development in the theoretical description of DEA. The new apparatus built in this work also delivered a superior momentum resolution compared to existing setups. This allows the momentum imaging of heavier fragments and fragments with lower kinetic energy.

  9. Accelerator-based atomic and molecular collision physics

    International Nuclear Information System (INIS)

    Datz, S.

    1993-01-01

    Accelerators have been shown to have great utility in addressing a broad range of problems in experimental atomic physics. There are, of course, phenomena such as inner-shell MO promotion which can occur only at high collision energies. At much higher energies, large transient Coulomb fields can be generated which lead to copious production electron-positron pairs and to capture of electrons from the negative continuum. But in addition, many advantages can be gained by carrying out low-energy (center-of-mass) collisions at high laboratory energies, specifically in a single pass mode or in multi-pass modes in ion storage rings in which, e.g., collision in the milli-electron volt region can be achieved for electron-molecule reactions. Certain advantages also accrue using open-quotes reverse kinematicsclose quotes in which high velocity ions collide with almost open-quotes stationaryclose quotes electrons as in resonant transfer and excitation (RTE) and collisions of energetic ions in the dense open-quotes electron gasclose quotes found in crystal channels

  10. 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

  11. 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.

  12. 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

  13. Macro-mechanics controls quantum mechanics: mechanically controllable quantum conductance switching of an electrochemically fabricated atomic-scale point contact

    Science.gov (United States)

    Staiger, Torben; Wertz, Florian; Xie, Fangqing; Heinze, Marcel; Schmieder, Philipp; Lutzweiler, Christian; Schimmel, Thomas

    2018-01-01

    Here, we present a silver atomic-scale device fabricated and operated by a combined technique of electrochemical control (EC) and mechanically controllable break junction (MCBJ). With this EC-MCBJ technique, we can perform mechanically controllable bistable quantum conductance switching of a silver quantum point contact (QPC) in an electrochemical environment at room temperature. Furthermore, the silver QPC of the device can be controlled both mechanically and electrochemically, and the operating mode can be changed from ‘electrochemical’ to ‘mechanical’, which expands the operating mode for controlling QPCs. These experimental results offer the perspective that a silver QPC may be used as a contact for a nanoelectromechanical relay.

  14. 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

  15. Offsetting the difficulties of the molecular model of atomic collisions in the intermediate velocity range

    International Nuclear Information System (INIS)

    Errea, L.F.; Mendez, L.; Riera, A.

    1991-01-01

    To offset the defective behavior of the molecular method of atomic collisions at intermediate energies, we propose a method to approximate the probability flux towards continuum and discrete states not included in the molecular basis. We check the degree of accuracy and limitations of the method for a model case where transition probabilities can be calculated exactly. An application to the benchmark case of He + +H + collisions is also presented, and yields complementary information on the properties of this approach

  16. Quantum chemical approaches: semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques.

    Science.gov (United States)

    Bryce, Richard A; Hillier, Ian H

    2014-01-01

    The use of computational quantum chemical methods to aid drug discovery is surveyed. An overview of the various computational models spanning ab initio, density function theory, semiempirical molecular orbital (MO), and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods is given and their strengths and weaknesses are highlighted, focussing on the challenge of obtaining the accuracy essential for them to make a meaningful contribution to drug discovery. Particular attention is given to hybrid QM/MM and semiempirical MO methods which have the potential to yield the necessary accurate predictions of macromolecular structure and reactivity. These methods are shown to have advanced the study of many aspects of substrate-ligand interactions relevant to drug discovery. Thus, the successful parametrization of semiempirical MO methods and QM/MM methods can be used to model noncovalent substrate-protein interactions, and to lead to improved scoring functions. QM/MM methods can be used in crystal structure refinement and are particularly valuable for modelling covalent protein-ligand interactions and can thus aid the design of transition state analogues. An extensive collection of examples from the areas of metalloenzyme structure, enzyme inhibition, and ligand binding affinities and scoring functions are used to illustrate the power of these techniques.

  17. Initiating heavy-atom-based phasing by multi-dimensional molecular replacement.

    Science.gov (United States)

    Pedersen, Bjørn Panyella; Gourdon, Pontus; Liu, Xiangyu; Karlsen, Jesper Lykkegaard; Nissen, Poul

    2016-03-01

    To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts.

  18. Atomic and molecular data activities at JAERI, September 1999 - August 2001

    International Nuclear Information System (INIS)

    Shirai, T.

    2001-01-01

    Compilation and evaluation work has been carried out to make the 5th edition of Evaluated Atomic and Molecular (A+M) Data Library (JEAMDL-5) for fusion. The main objective of JEAMDL-5 is to evaluate A+M data relevant to divertor plasmas. Recent data activities and work in progress are briefly summarized. (author)

  19. International bulletin on atomic and molecular data for fusion. No. 24

    International Nuclear Information System (INIS)

    Katsonis, K.

    1984-01-01

    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: Transport on tokamak plasmas simulation, post collisions of gold ions in helium

  20. International bulletin on atomic and molecular data for fusion. No. 27

    International Nuclear Information System (INIS)

    Hughes, J.G.

    1984-12-01

    This bulletin deals with atomic and molecular data for fusion. A bibliography for the most recent relevent data, summarized in the document, is provided (373 literature pieces). Work in progress on the ionization by electron impact (theoretical results) is also briefly reported on

  1. International bulletin on atomic and molecular data for fusion. No. 16

    International Nuclear Information System (INIS)

    Katsonis, K.

    1981-06-01

    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 briefly reported. ''Data Request'' in the fusion field are also mentioned. The bulletin contains a list of references covering the years 1980 and 1981 for all the publications on controlled fusion and plasma physics

  2. International bulletin on atomic and molecular data for fusion. No. 14

    International Nuclear Information System (INIS)

    Katsonis, K.

    1980-11-01

    This bulletin deals with atomic and molecular data for fusion. A bibliography for the most recent data presented in the document is provided. The bulletin contains a list of references covering the year 1980 for all the publications on controlled fusion and plasma physics

  3. International bulletin on atomic and molecular data for fusion. No. 23

    International Nuclear Information System (INIS)

    Katsonis, K.

    1983-09-01

    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 (OIV in temperature and density diagnostics, measured cross section for electron impact ionization of Iron and Tungsten)

  4. International bulletin on atomic and molecular data for fusion. No. 22

    International Nuclear Information System (INIS)

    Katsonis, K.

    1983-05-01

    This bulletin deals with atomic and molecular data for fusion. Work in progress is briefly reported (charge exchange of slow ionized ions with neutral gases, cross section for electron impact ionization of Alt). The bulletin contains a list of references covering the years 1981, 1982 and 1983 for publications on controlled thermonuclear fusion and plasma physics

  5. International bulletin on atomic and molecular data for fusion. No. 9

    International Nuclear Information System (INIS)

    Katsonis, K.; Rumble, J. Jr.; Smith, F.J.

    1979-07-01

    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. The bulletin contains a list of references covering the years 1978 and 1979 for all the publications on controlled fusion and plasma physics

  6. International bulletin on atomic and molecular data for fusion. No. 15

    International Nuclear Information System (INIS)

    Katsonis, K.

    1981-03-01

    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. The bulletin contains a list of references covering the years 1980 and 1981 for all the publications on controlled fusion and plasma physics

  7. International bulletin on atomic and molecular data for fusion. No. 7

    International Nuclear Information System (INIS)

    Katsonis, K.; Smith, F.J.

    1979-01-01

    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. The bulletin contains an extensive list of references covering the years 1977 and 1978 for all the publications on control fusion and plasma physics

  8. International bulletin on atomic and molecular data for fusion. No. 8

    International Nuclear Information System (INIS)

    Katsonis, K.; Smith, F.J.

    1979-04-01

    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. The bulletin contains an extensive list of references covering the year 1978 and the beginning of 1979 for all the publications on control fusion and plasma physics

  9. International bulletin on atomic and molecular data for fusion. No. 19

    International Nuclear Information System (INIS)

    Katsonis, K.

    1982-06-01

    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 briefly reported. The bulletin contains a list of references covering the years 1981 and 1982 for all the publications on controlled fusion and plasma physics

  10. Distribution and kinematics of atomic and molecular gas inside the solar circle

    NARCIS (Netherlands)

    Marasco, A.; Fraternali, F.; van der Hulst, J. M.; Oosterloo, T.

    2017-01-01

    The detailed distribution and kinematics of the atomic and the CO-bright molecular hydrogen in the disc of the Milky Way inside the solar circle are derived under the assumptions of axisymmetry and pure circular motions. We divide the Galactic disc into a series of rings, and assume that the gas in

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

    International Nuclear Information System (INIS)

    Katsonis, K.

    1982-09-01

    This bulletin deals with atomic and molecular data for fusion. A bibliography for the most recent data presented in the document is provided. The bulletin contains a list of references covering the year 1982 for all the publications on controlled thermonuclear fusion and plasma physics

  12. Molecular structure of dipalmitoylphospatidylcholine Langmuir-Blodgett monolayers studied by atomic force microscopy.

    NARCIS (Netherlands)

    Zhai, X.; Kleijn, J.M.

    1997-01-01

    Monolayers of dipalmitoylphosphatidylcholine (DPPC) on the air-water interface have been transferred at various surface pressures onto quartz substrates using the Langmuir-Blodgett (LB) technique. The topography of these layers, on a molecular scale, has been examined by atomic force microscopy

  13. Evolution of the atomic and molecular gas content of galaxies in dark matter haloes

    NARCIS (Netherlands)

    Popping, Gergö; Behroozi, Peter S.; Peeples, Molly S.

    We present a semi-empirical model to infer the atomic and molecular hydrogen content of galaxies as a function of halo mass and time. Our model combines the star formation rate (SFR)-halo mass-redshift relation (constrained by galaxy abundances) with inverted SFR-surface density relations to infer

  14. Modeling inelastic phonon scattering in atomic- and molecular-wire junctions

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

    2005-01-01

    Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between the f...

  15. Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching

    Science.gov (United States)

    Engstrom, James R.; Kummel, Andrew C.

    2017-02-01

    Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.

  16. Atomic and molecular spectroscopy with optical-frequency-comb-referenced IR coherent sources

    International Nuclear Information System (INIS)

    Cancio, P.; Bartalini, S.; De Rosa, M.; Giusfredi, G.; Mazzotti, D.; Maddaloni, P.; Vitiello, M. S.; De Natale, P.

    2013-01-01

    We provide a review of progress in the development of metrological-grade measurements in atomic and molecular systems through the extension, in the mid-infrared and far-infrared range, of optical frequency combs (OFCs) and the introduction of new techniques and highly coherent sources. (authors)

  17. Interaction mechanisms between ceramic particles and atomized metallic droplets

    Science.gov (United States)

    Wu, Yue; Lavernia, Enrique J.

    1992-10-01

    The present study was undertaken to provide insight into the dynamic interactions that occur when ceramic particles are placed in intimate contact with a metallic matrix undergoing a phase change. To that effect, Al-4 wt pct Si/SiCp composite droplets were synthesized using a spray atomization and coinjection approach, and their solidification microstructures were studied both qualitatively and quantitatively. The present results show that SiC particles (SiCp) were incor- porated into the matrix and that the extent of incorporation depends on the solidification con- dition of the droplets at the moment of SiC particle injection. Two factors were found to affect the distribution and volume fraction of SiC particles in droplets: the penetration of particles into droplets and the entrapment and/or rejection of particles by the solidification front. First, during coinjection, particles collide with the atomized droplets with three possible results: they may penetrate the droplets, adhere to the droplet surface, or bounce back after impact. The extent of penetration of SiC particles into droplets was noted to depend on the kinetic energy of the particles and the magnitude of the surface energy change in the droplets that occurs upon impact. In liquid droplets, the extent of penetration of SiC particles was shown to depend on the changes in surface energy, ΔEs, experienced by the droplets. Accordingly, large SiC particles encoun- tered more resistance to penetration relative to small ones. In solid droplets, the penetration of SiC particles was correlated with the dynamic pressure exerted by the SiC particles on the droplets during impact and the depth of the ensuing crater. The results showed that no pene- tration was possible in such droplets. Second, once SiC particles have penetrated droplets, their final location in the microstructure is governed by their interactions with the solidification front. As a result of these interactions, both entrapment and rejection of

  18. Cytogenetic and molecular genetic analysis of leukemias found in atomic bomb survivors

    International Nuclear Information System (INIS)

    Kamada, Nanao; Tanaka, Kimio; Eguchi, Mariko

    1994-01-01

    Seventy five radiation-related leukemia patients in Hiroshima including 16 patients exposed to more than one Gray were cytogenetically examined. Statistical analysis of data on the frequencies of chromosomal aberrations in the survivor groups according to bone marrow doses by DS86 estimation revealed that the heavily exposed group tended to have significantly higher aberration rates compared to the non-exposed group. Furthermore, the chromosomal aberrations in the survivors were observed to be of a more complex nature and had the characteristic findings of secondary leukemia. These observations therefore suggest that patients with a history of heavy exposure to atomic bomb radiation had leukemic cells originating from a stem cell which had been damaged by irradiation at the time of the bombing as well as cells involved in complex chromosome abnormalities. A higher incidence(p=0.06) of 11q23 abnormality was found in acute leukemia patients who had a history of exposure to A-bomb and developed from 1986 to 1993. However, we could not detect rearrangement of MLL gene in these patients. Break point region on 11q23 of radiation induced leukemias may be different from the common 8.5 kb region. Molecular biologic studies on RAS genes in acute and chronic leukemias and the BCR gene in chronic myelocytic leukemia were performed in exposed and non-exposed groups. So far, no distinctive differences have been observed in the frequency and sites of point mutations in N and K-RAS genes or in the rearrangement of the BCR gene. Further, retrospective analysis using DNA from leukemia patients who developed the disease in the early period from atomic bomb radiation exposure would be useful for elucidation of the mechanisms of radiation-induced leukemia. (author)

  19. The cognitive life of mechanical molecular models.

    Science.gov (United States)

    Charbonneau, Mathieu

    2013-12-01

    The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler's cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models' materiality contributing to the solving of the molecule's structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Interplay of intra-atomic and interatomic effects: An investigation of the 2p core level spectra of atomic Fe and molecular FeCl2

    International Nuclear Information System (INIS)

    Richter, T.; Wolff, T.; Zimmermann, P.; Godehusen, K.; Martins, M.

    2004-01-01

    The 2p photoabsorption and photoelectron spectra of atomic Fe and molecular FeCl 2 were studied by photoion and photoelectron spectroscopy using monochromatized synchrotron radiation and atomic or molecular beam technique. The atomic spectra were analyzed with configuration interaction calculations yielding excellent agreement between experiment and theory. For the analysis of the molecular photoelectron spectrum which shows pronounced interatomic effects, a charge transfer model was used, introducing an additional 3d 7 configuration. The resulting good agreement between the experimental and theoretical spectrum and the remarkable similarity of the molecular with the corresponding spectrum in the solid phase opens a way to a better understanding of the interplay of the interatomic and intra-atomic interactions in the 2p core level spectra of the 3d metal compounds

  1. Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

    Science.gov (United States)

    Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao

    2013-09-10

    Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

  2. 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.

  3. Quantum mechanics of molecular rate processes

    CERN Document Server

    Levine, Raphael D

    1999-01-01

    This survey of applications of the theory of collisions and rate processes to molecular problems explores collisions of molecules with internal structure, generalized Ehrenfest theorem, theory of reactive collisions, and role of symmetry. It also reviews partitioning technique, equivalent potentials and quasibound states, theory of direct reactions, more. 1969 edition.

  4. Oligodendroglioma: pathology, molecular mechanisms and markers

    NARCIS (Netherlands)

    Wesseling, P.; Bent, M. van den; Perry, A.

    2015-01-01

    For nearly a century, the diagnosis and grading of oligodendrogliomas and oligoastrocytomas has been based on histopathology alone. Roughly 20 years ago, the first glioma-associated molecular signature was found with complete chromosome 1p and 19q codeletion being particularly common in

  5. Secondary electron emission from Au by medium energy atomic and molecular ions

    CERN Document Server

    Itoh, A; Obata, F; Hamamoto, Y; Yogo, A

    2002-01-01

    Number distributions of secondary electrons emitted from a Au metal surface have been measured for atomic and molecular ions of H sup + , He sup + , C sup + , N sup + , O sup + , H sup + sub 2 , H sup + sub 3 , HeH sup + , CO sup + and O sup + sub 2 in the energy range 0.3-2.0 MeV. The emission statistics obtained are described fairly well by a Polya function. The Polya parameter b, determining the distribution shape, is found to decrease monotonously with increasing emission yield gamma, revealing a surprising relationship of b gamma approx 1 over the different projectile species and impact energies. This finding supports certainly the electron cascading model. Also we find a strong negative molecular effect for heavier molecular ions, showing a significant reduction of gamma compared to the estimated values using constituent atomic projectile data.

  6. Atomic and molecular hydrogen gas temperatures in a low-pressure helicon plasma

    Science.gov (United States)

    Samuell, Cameron M.; Corr, Cormac S.

    2015-08-01

    Neutral gas temperatures in hydrogen plasmas are important for experimental and modelling efforts in fusion technology, plasma processing, and surface modification applications. To provide values relevant to these application areas, neutral gas temperatures were measured in a low pressure (radiofrequency helicon discharge using spectroscopic techniques. The atomic and molecular species were not found to be in thermal equilibrium with the atomic temperature being mostly larger then the molecular temperature. In low power operation (measurements near a graphite target demonstrated localised cooling near the sample surface. The temporal evolution of the molecular gas temperature during a high power 1.1 ms plasma pulse was also investigated and found to vary considerably as a function of pressure.

  7. 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

  8. Description of card input data and formats for the International Bulletin on Atomic and Molecular Data for Fusion

    International Nuclear Information System (INIS)

    Katsonis, K.; Smith, F.J.

    1979-05-01

    This document describes the input data and the corresponding format of the computer programme which is used by the Atomic and Molecular Unit of the IAEA for storing, compiling and retrieving numerical data and/or bibliographic information for publishing the International Bulletin on Atomic and Molecular Data for Fusion

  9. Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

    Science.gov (United States)

    Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

    2014-01-01

    A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions

  10. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation.

  11. Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism.

    Science.gov (United States)

    Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

    2016-10-11

    The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S N 1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

  12. Investigating the properties and interaction mechanism of nano-silica in polyvinyl alcohol/polyacrylamide blends at an atomic level.

    Science.gov (United States)

    Wei, Qinghua; Wang, Yanen; Wang, Shuzhi; Zhang, Yingfeng; Chen, Xiongbiao

    2017-11-01

    The nano-silica can be incorporated into polymers for improved mechanical properties. Notably, the interaction between nano-silica and polymer is of a microscopic phenomenon and thus, hard to observe and study by using experimental methods. Based on molecular dynamics, this paper presents a study on the properties and the interaction mechanism of nano-silica in the polyvinyl alcohol (PVA)/polyacrylamide (PAM) blends at an atomic level. Specifically, six blends of PVA/PAM with varying concentrations of nano-silica (0-13wt%) and two interfacial interaction models of polymers on the silica surface were designed and analyzed at an atomic level in terms of concentration profile, mechanical properties, fractional free volume (FFV), dynamic properties of polymers and X-ray diffraction patterns. The concentration profile results and micromorphologies of equilibrium models suggest PAM molecular chains are easier to be adsorbed on the silica surface than PVA molecular chains in blends. The incorporation of nano-silica into the PVA/PAM blends can increase the blend mechanical properties, densities, and semicrystalline character. Meanwhile, the FFV and the mobility of polymer chain decrease with the silica concentration, which agrees with the results of mechanical properties, densities, and semicrystalline character. Our results also illustrate that an analysis of binding energies and pair correlation functions (PCF) allows for the discovery of the interaction mechanism of nano-silica in PVA/PAM blends; and that hydrogen bond interactions between polar functional groups of polymer molecular chains and the hydroxyl groups of the silica surface are involved in adsorption of the polymers on the silica surface, thus affecting the interaction mechanism of nano-silica in PVA/PAM blend systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Molecular mechanisms involved in convergent crop domestication.

    Science.gov (United States)

    Lenser, Teresa; Theißen, Günter

    2013-12-01

    Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. International bulletin on atomic and molecular data for fusion. No. 66, August 2007

    International Nuclear Information System (INIS)

    Humbert, D.; Bannister, M.E.; Fuhr, J.; Gilbody, H.B.

    2007-08-01

    Information in this Bulletin is presented in four parts. The Atomic and Molecular Data Information System (AMDIS) of the International Atomic Energy Agency is presented in Part 1. The indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions in Part 2. The structure and spectra indexation lines are grouped by process. The first column gives the process, the second one the reactants and then the character of the data contained (Th for theoretical, Ex for experimental, and E/T for both experimental and theoretical). The number in the last column is the reference number in Part 3 of the Bulletin. The atomic and molecular indexation lines are grouped by one collision partner (photon, electron or heavy particle). The first column gives the reactants, the second column gives the process, the third column gives the energy range with the appropriate units, and the last two columns are the same as in the structure and spectra indexation lines. The particle-surface interactions indexation lines are grouped by process. The first column gives the reactants, the second the energy range with the appropriate units, and the last two columns are the same as in the previous cases. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Those references which are indexed in Part 1 are identified by the repeated indexation lines. The Author Index (Part 4) refers to the bibliographic references contained in Part 3

  15. Report of the workshop on accelerator-based atomic and molecular science

    International Nuclear Information System (INIS)

    Meyerhof, W.E.

    1981-01-01

    This Workshop, held in New London, NH on July 27-30, 1980, had a registration of 43, representing an estimated one-third of all principal investigators in the United States in this research subfield. The workshop was organized into 5 working groups for the purpose of (1) identifying some vital physics problems which experimental and theoretical atomic and molecular science can address with current and projected techniques; (2) establishing facilities and equipment needs required to realize solutions to these problems; (3) formulating suggestions for a coherent national policy concerning this discipline; (4) assessing and projecting the manpower situation; and (5) evaluating the relations of this interdisciplinary science to other fields. Recommedations deal with equipment and operating costs for small accelerator laboratories, especially at universities; instrumentation of ion beam lines dedicated to atomic and molecular science at some large accelerators; development of low-velocity, high charge-state ion sources; synchrotron light sources; improvement or replacement of tandem van de Graaff accelerators; high-energy beam lines for atomic physics; the needs for postdoctoral support in this subfield; new accelerator development; need for representatives from atomic and molecular science on program committees for large national accelerator facilities; and the contributions the field can make to applied physics problems

  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. International bulletin on atomic and molecular data for fusion. No. 68, December 2009

    International Nuclear Information System (INIS)

    Chung, H.K.; Humbert, D.

    2009-12-01

    Information in this Bulletin is presented in four parts. The Atomic and Molecular Data Information System (AMDIS) of the International Atomic Energy Agency is presented in Part 1. The indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions in Part 2. The structure and spectra index lines are grouped by process. The first column gives the reactants, the second one the process and then the character of the data contained (Th for theoretical, Ex for experimental, and E/T for both experimental and theoretical). The number in the last column is the reference number in Part 3 of the Bulletin. The atomic and molecular index lines are grouped by one collision partner (photon, electron or heavy particle). The first column gives the reactants, the second column gives the process, the third column gives the energy range with the appropriate units, and the last two columns are the same as in the structure and spectra index lines. The particle-surface interactions index lines are grouped by process. The first column gives the reactants, the second the energy range with the appropriate units, and the last two columns are the same as in the previous cases. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Those references which are indexed in Part 1 are identified by the repeated index lines. The Author Index (Part 4) refers to the bibliographic references contained in Part 3

  18. International Bulletin on Atomic and Molecular Data for Fusion. No. 67, December 2008

    International Nuclear Information System (INIS)

    Humbert, D.

    2008-12-01

    Information in this Bulletin is presented in four parts. The Atomic and Molecular Data Information System (AMDIS) of the International Atomic Energy Agency is presented in Part 1. The indexed papers are listed separately for structure and spectra, atomic and molecular collisions, and surface interactions in Part 2. The structure and spectra indexation lines are grouped by process. The first column gives the process, the second one the reactants and then the character of the data contained (Th for theoretical, Ex for experimental, and E/T for both experimental and theoretical). The number in the last column is the reference number in Part 3 of the Bulletin. The atomic and molecular indexation lines are grouped by one collision partner (photon, electron or heavy particle). The first column gives the reactants, the second column gives the process, the third column gives the energy range with the appropriate units, and the last two columns are the same as in the structure and spectra indexation lines. The particle-surface interactions indexation lines are grouped by process. The first column gives the reactants, the second the energy range with the appropriate units, and the last two columns are the same as in the previous cases. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Those references which are indexed in Part 1 are identified by the repeated indexation lines. The Author Index (Part 4) refers to the bibliographic references contained in Part 3.

  19. Molecular mechanisms of induced-mutations

    International Nuclear Information System (INIS)

    Kato, Takeshi

    1985-01-01

    The outcome of recent studies on mechanisms of induced-mutations is outlined with particular emphasis on the dependence of recA gene function in Escherichia coli. Genes involved in spontaneous mutation and x-ray- and chemical-induced mutation and genes involved in adaptive response are presented. As for SOS mutagenesis, SOS-induced regulation mechanisms and mutagenic routes are described. Furthermore, specificity of mutagens themselves are discussed in relation to mechanisms of base substitution, frameshift, and deletion mutagenesis. (Namekawa, K.)

  20. Scattering of atomic and molecular ions from single crystal surfaces of Cu, Ag and Fe

    International Nuclear Information System (INIS)

    Zoest, J.M. van.

    1986-01-01

    This thesis deals with analysis of crystal surfaces of Cu, Ag and Fe with Low Energy Ion scattering Spectroscopy (LEIS). Different atomic and molecular ions with fixed energies below 7 keV are scattered by a metal single crystal (with adsorbates). The energy and direction of the scattered particles are analysed for different selected charge states. In that way information can be obtained concerning the composition and atomic and electronic structure of the single crystal surface. Energy spectra contain information on the composition of the surface, while structural atomic information is obtained by direction measurements (photograms). In Ch.1 a description is given of the experimental equipment, in Ch.2 a characterization of the LEIS method. Ch.3 deals with the neutralization of keV-ions in surface scattering. Two different ways of data interpretation are presented. First a model is treated in which the observed directional dependence of neutralization action of the first atom layer of the surface is presented by a laterally varying thickness of the neutralizing layer. Secondly it is shown that the data can be reproduced by a more realistic, physical model based on atomic transition matrix elements. In Ch.4 the low energy hydrogen scattering is described. The study of the dissociation of H 2 + at an Ag surface r0230ted in a model based on electronic dissociation, initialized by electron capture into a repulsive (molecular) state. In Ch.5 finally the method is applied to the investigation of the surface structure of oxidized Fe. (Auth.)

  1. Molecular Mechanisms of Bacterial Superantigen Function

    National Research Council Canada - National Science Library

    Sadegh-Nasseri, Scheherazade

    2004-01-01

    ...) Vb domains and can result in systemic shock and death. Rational design of strategies for prevention or treatments of such diseases may only be possible if we have insights into the mechanisms of T cell activation by SEs...

  2. Molecular mechanisms of HIV-1 associated neurodegeneration

    Indian Academy of Sciences (India)

    Unknown

    progressive multiple symptoms of motor, cognitive dys- function and behavioural ..... using different types of neurons such as rodent cortical, hippocampal and ..... in the neocortex of rat via a mechanism involving CXCR4 chemokine receptor ...

  3. Mechanically magnified imaging of molecular interferograms

    International Nuclear Information System (INIS)

    Stibor, A.; Stefanov, A.; Goldfarb, F.; Reiger, E.; Arndt, M.

    2005-01-01

    Full text: Imaging of surface adsorbed molecules is presented as a valuable detection method for matter interferometry with fluorescent particles. A mechanical magnification scheme is implemented to circumvent the optical resolution limit. Mechanically magnified fluorescence imaging turns out to be an excellent tool for recording quantum interference patterns with high visibility. A unique advantage of this technique is its scalability: for certain classes of nanosized objects, the detection sensitivity will even increase significantly with increasing size of the particle. (author)

  4. Molecular biological mechanisms I. DNA repair

    International Nuclear Information System (INIS)

    Friedl, A.A.

    2000-01-01

    Cells of all living systems possess a variety of mechanisms that allow to repair spontaneous and exogeneously induced DNA damage. DNA repair deficiencies may invoke enhanced sensitivity towards DNA-damaging agents such as ionizing radiation. They may also enhance the risk of cancer development, both spontaneously or after induction. This article reviews several DNA repair mechanisms, especially those dealing with DNA double-strand breaks, and describes hereditary diseases associated with DNA repair defects. (orig.) [de

  5. 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.

  6. 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.

  7. The Advanced Light Source: A new tool for research in atomic and molecular physics

    International Nuclear Information System (INIS)

    Schlachter, F.; Robinson, A.

    1991-04-01

    The Advanced Light Source at the Lawrence Berkeley Laboratory will be the world's brightest synchrotron radiation source in the extreme ultraviolet and soft x-ray regions of the spectrum when it begins operation in 1993. It will be available as a national user facility to researchers in a broad range of disciplines, including materials science, atomic and molecular physics, chemistry, biology, imaging, and technology. The high brightness of the ALS will be particularly well suited to high-resolution studies of tenuous targets, such as excited atoms, ions, and clusters. 13 figs., 4 tabs

  8. 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

  9. The molecular mechanism of gene-radiotherapy of tumor

    International Nuclear Information System (INIS)

    Zhu Xian

    2004-01-01

    Gene-radiotherapy of tumor is a new method which is induced by ionizing radiation. The molecular mechanism is to activate various molecular target by many ways and induce the apoptosis of tumor cell. It is a gene therapy based on the radiation-inducible property of the Egr-1 gene. It has good application prospect in therapy of tumor

  10. Molecular mechanisms of canalization: Hsp90 and beyond

    Indian Academy of Sciences (India)

    Madhu Sudhan

    2007-03-26

    Mar 26, 2007 ... clients are essential nodes in signal transduction pathways and regulatory circuits, accounting for the .... respective contributions of genetics versus epigenetics ... authors succeeded in elucidating the molecular mechanism.

  11. Symposium on molecular and cellular mechanisms of mutagenesis

    International Nuclear Information System (INIS)

    1981-01-01

    These proceedings contain abstracts only of the 21 papers presented at the Sympsoium. The papers dealt with molecular mechanisms of mutagenesis and cellular responses to chemical and physical mutagenic agents

  12. What molecular mechanism is adapted by plants during salt stress ...

    African Journals Online (AJOL)

    What molecular mechanism is adapted by plants during salt stress tolerance? ... Salt stress harmfully shocks agricultural yield throughout the world affecting production whether it is for subsistence or economic outcomes. ... from 32 Countries:.

  13. Symposium on molecular and cellular mechanisms of mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    1981-01-01

    These proceedings contain abstracts only of the 21 papers presented at the Sympsoium. The papers dealt with molecular mechanisms of mutagenesis and cellular responses to chemical and physical mutagenic agents. (ERB)

  14. Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2018-03-13

    Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

  15. A coupled channel study on a binding mechanism of positronic alkali atoms

    International Nuclear Information System (INIS)

    Kubota, Yoshihiro; Kino, Yasushi

    2008-01-01

    In order to investigate the binding mechanism of weakly bound states of positronic alkali atoms, we calculate the energies and wavefunctions using the Gaussian expansion method (GEM) where a positronium (Ps)-alkali ion channel and a positron-alkali atom channel are explicitly introduced. The energies of the bound states are updated using a model potential that reproduces well the observed energy levels of alkali atoms. The binding mechanism of the positronic alkali atom is analyzed by the wavefunctions obtained. The structure of the positronic alkali atom has been regarded as a Ps cluster orbiting the alkali ion, which is described by the Ps-alkali ion channel. We point out that the fraction having the positron-alkali atom configuration is small but plays an indispensable role for the weakly bound system

  16. Atomic motions in the αβ-region of glass-forming polymers: molecular versus mode coupling theory approach

    International Nuclear Information System (INIS)

    Colmenero, Juan; Narros, Arturo; Alvarez, Fernando; Arbe, Arantxa; Moreno, Angel J

    2007-01-01

    We present fully atomistic molecular dynamics simulation results on a main-chain polymer, 1,4-polybutadiene, in the merging region of the α- and β-relaxations. A real-space analysis reveals the occurrence of localized motions ('β-like') in addition to the diffusive structural relaxation. A molecular approach provides a direct connection between the local conformational changes reflected in the atomic motions and the secondary relaxations in this polymer. Such local processes occur just in the time window where the β-process of the mode coupling theory is expected. We show that the application of this theory is still possible and yields an unusually large value of the exponent parameter. This result might originate from the competition between two mechanisms for dynamic arrest: intermolecular packing and intramolecular barriers for local conformational changes ('β-like')

  17. Atomic-level characterization of the activation mechanism of SERCA by calcium.

    Directory of Open Access Journals (Sweden)

    L Michel Espinoza-Fonseca

    Full Text Available We have performed molecular dynamics (MD simulations to elucidate, in atomic detail, the mechanism by which the sarcoplasmic reticulum Ca(2+-ATPase (SERCA is activated by Ca(2+. Crystal structures suggest that activation of SERCA occurs when the cytoplasmic head-piece, in an open (E1 conformation stabilized by Ca(2+, undergoes a large-scale open-to-closed (E1 to E2 transition that is induced by ATP binding. However, spectroscopic measurements in solution suggest that these structural states (E1 and E2 are not tightly coupled to biochemical states (defined by bound ligands; the closed E2 state predominates even in the absence of ATP, in both the presence and absence of Ca(2+. How is this loose coupling consistent with the high efficiency of energy transduction in the Ca(2+-ATPase? To provide insight into this question, we performed long (500 ns all-atom MD simulations starting from the open crystal structure, including a lipid bilayer and water. In both the presence and absence of Ca(2+, we observed a large-scale open-to-closed conformational transition within 400 ns, supporting the weak coupling between structural and biochemical states. However, upon closer inspection, it is clear that Ca(2+ is necessary and sufficient for SERCA to reach the precise geometrical arrangement necessary for activation of ATP hydrolysis. Contrary to suggestions from crystal structures, but in agreement with solution spectroscopy, the presence of ATP is not required for this activating transition. Principal component analysis showed that Ca(2+ reshapes the free energy landscape of SERCA to create a path between the open conformation and the activated closed conformation. Thus the malleability of the free energy landscape is essential for SERCA efficiency, ensuring that ATP hydrolysis is tightly coupled to Ca(2+ transport. These results demonstrate the importance of real-time dynamics in the formation of catalytically competent conformations of SERCA, with broad

  18. Molecular dynamics and Monte Carlo calculations in statistical mechanics

    International Nuclear Information System (INIS)

    Wood, W.W.; Erpenbeck, J.J.

    1976-01-01

    Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

  19. Molecular mechanics and quantum mechanical modeling of hexane soot structure and interactions with pyrene

    Directory of Open Access Journals (Sweden)

    Kubicki JD

    2000-09-01

    Full Text Available Molecular simulations (energy minimizations and molecular dynamics of an n-hexane soot model developed by Smith and co-workers (M. S. Akhter, A. R. Chughtai and D. M. Smith, Appl. Spectrosc., 1985, 39, 143; ref. 1 were performed. The MM+ (N. L. Allinger, J. Am. Chem. Soc., 1977, 395, 157; ref. 2 and COMPASS (H. Sun, J. Phys. Chem., 1998, 102, 7338; ref. 3 force fields were tested for their ability to produce realistic soot nanoparticle structure. The interaction of pyrene with the model soot was simulated. Quantum mechanical calculations on smaller soot fragments were carried out. Starting from an initial 2D structure, energy minimizations are not able to produce the observed layering within soot with either force field. Results of molecular dynamics simulations indicate that the COMPASS force field does a reasonably accurate job of reproducing observations of soot structure. Increasing the system size from a 683 to a 2732 atom soot model does not have a significant effect on predicted structures. Neither does the addition of water molecules surrounding the soot model. Pyrene fits within the soot structure without disrupting the interlayer spacing. Polycyclic aromatic hydrocarbons (PAH, such as pyrene, may strongly partition into soot and have slow desorption kinetics because the PAH-soot bonding is similar to soot–soot interactions. Diffusion of PAH into soot micropores may allow the PAH to be irreversibly adsorbed and sequestered so that they partition slowly back into an aqueous phase causing dis-equilibrium between soil organic matter and porewater.

  20. Molecular and cellular mechanisms of pulmonary fibrosis

    Science.gov (United States)

    2012-01-01

    Pulmonary fibrosis is a chronic lung disease characterized by excessive accumulation of extracellular matrix (ECM) and remodeling of the lung architecture. Idiopathic pulmonary fibrosis is considered the most common and severe form of the disease, with a median survival of approximately three years and no proven effective therapy. Despite the fact that effective treatments are absent and the precise mechanisms that drive fibrosis in most patients remain incompletely understood, an extensive body of scientific literature regarding pulmonary fibrosis has accumulated over the past 35 years. In this review, we discuss three broad areas which have been explored that may be responsible for the combination of altered lung fibroblasts, loss of alveolar epithelial cells, and excessive accumulation of ECM: inflammation and immune mechanisms, oxidative stress and oxidative signaling, and procoagulant mechanisms. We discuss each of these processes separately to facilitate clarity, but certainly significant interplay will occur amongst these pathways in patients with this disease. PMID:22824096

  1. Challenging the Science Curriculum Paradigm: Teaching Primary Children Atomic-Molecular Theory

    Science.gov (United States)

    Haeusler, Carole; Donovan, Jennifer

    2017-11-01

    Solutions to global issues demand the involvement of scientists, yet concern exists about retention rates in science as students pass through school into University. Young children are curious about science, yet are considered incapable of grappling with abstract and microscopic concepts such as atoms, sub-atomic particles, molecules and DNA. School curricula for primary (elementary) aged children reflect this by their limitation to examining only what phenomena are without providing any explanatory frameworks for how or why they occur. This research challenges the assumption that atomic-molecular theory is too difficult for young children, examining new ways of introducing atomic theory to 9 year olds and seeks to verify their efficacy in producing genuine learning in the participants. Early results in three cases in different schools indicate these novel methods fostered further interest in science, allowed diverse children to engage and learn aspects of atomic theory, and satisfied the children's desire for intellectual challenge. Learning exceeded expectations as demonstrated in the post-interview findings. Learning was also remarkably robust, as demonstrated in two schools 8 weeks after the intervention and, in one school, 1 year after their first exposure to ideas about atoms, elements and molecules.

  2. Molecular and cellular mechanisms of cadmium carcinogenesis

    International Nuclear Information System (INIS)

    Waisberg, Michael; Joseph, Pius; Hale, Beverley; Beyersmann, Detmar

    2003-01-01

    Cadmium is a heavy metal, which is widely used in industry, affecting human health through occupational and environmental exposure. In mammals, it exerts multiple toxic effects and has been classified as a human carcinogen by the International Agency for Research on Cancer. Cadmium affects cell proliferation, differentiation, apoptosis and other cellular activities. Cd 2+ does not catalyze Fenton-type reactions because it does not accept or donate electrons under physiological conditions, and it is only weakly genotoxic. Hence, indirect mechanisms are implicated in the carcinogenicity of cadmium. In this review multiple mechanisms are discussed, such as modulation of gene expression and signal transduction, interference with enzymes of the cellular antioxidant system and generation of reactive oxygen species (ROS), inhibition of DNA repair and DNA methylation, role in apoptosis and disruption of E-cadherin-mediated cell-cell adhesion. Cadmium affects both gene transcription and translation. The major mechanisms of gene induction by cadmium known so far are modulation of cellular signal transduction pathways by enhancement of protein phosphorylation and activation of transcription and translation factors. Cadmium interferes with antioxidant defense mechanisms and stimulates the production of reactive oxygen species, which may act as signaling molecules in the induction of gene expression and apoptosis. The inhibition of DNA repair processes by cadmium represents a mechanism by which cadmium enhances the genotoxicity of other agents and may contribute to the tumor initiation by this metal. The disruption of E-cadherin-mediated cell-cell adhesion by cadmium probably further stimulates the development of tumors. It becomes clear that there exist multiple mechanisms which contribute to the carcinogenicity of cadmium, although the relative weights of these contributions are difficult to estimate

  3. Atomic Force Microscope Image Contrast Mechanisms on Supported Lipid Bilayers

    OpenAIRE

    Schneider, James; Dufrêne, Yves F.; Barger Jr., William R.; Lee, Gil U.

    2000-01-01

    This work presents a methodology to measure and quantitatively interpret force curves on supported lipid bilayers in water. We then use this method to correlate topographic imaging contrast in atomic force microscopy (AFM) images of phase-separated Langmuir-Blodgett bilayers with imaging load. Force curves collected on pure monolayers of both distearoylphosphatidylethanolamine (DSPE) and monogalactosylethanolamine (MGDG) and dioleoylethanolamine (DOPE) deposited at similar surface pressures o...

  4. Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl- + CH3I Reaction in Water.

    Science.gov (United States)

    Liu, Peng; Li, Chen; Wang, Dunyou

    2017-10-19

    The Cl - + CH 3 I → CH 3 Cl + I - reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.

  5. Molecular mechanisms of synaptic remodeling in alcoholism.

    Science.gov (United States)

    Kyzar, Evan J; Pandey, Subhash C

    2015-08-05

    Alcohol use and alcohol addiction represent dysfunctional brain circuits resulting from neuroadaptive changes during protracted alcohol exposure and its withdrawal. Alcohol exerts a potent effect on synaptic plasticity and dendritic spine formation in specific brain regions, providing a neuroanatomical substrate for the pathophysiology of alcoholism. Epigenetics has recently emerged as a critical regulator of gene expression and synaptic plasticity-related events in the brain. Alcohol exposure and withdrawal induce changes in crucial epigenetic processes in the emotional brain circuitry (amygdala) that may be relevant to the negative affective state defined as the "dark side" of addiction. Here, we review the literature concerning synaptic plasticity and epigenetics, with a particular focus on molecular events related to dendritic remodeling during alcohol abuse and alcoholism. Targeting epigenetic processes that modulate synaptic plasticity may yield novel treatments for alcoholism. Published by Elsevier Ireland Ltd.

  6. Atom economy, molecular engeneering and biphasic organometallic catalysis: molecular concepts for the generation of "green" technologies

    OpenAIRE

    Dupont, Jairton

    2000-01-01

    For economical and ecological reasons, synthetic chemists are confronted with the increasing obligation of optimizing their synthetic methods. Maximizing efficiency and minimizing costs in the production of molecules and macromolecules constitutes, therefore, one of the most exciting challenges of synthetic chemistry. The ideal synthesis should produce the desired product in 100% yield and selectivity, in a safe and environmentally acceptable process. In this highlight the concepts of atom ec...

  7. Constructing oxide interfaces and heterostructures by atomic layer-by-layer laser molecular beam epitaxy

    OpenAIRE

    Lei, Qingyu; Golalikhani, Maryam; Davidson, Bruce A.; Liu, Guozhen; Schlom, D. G.; Qiao, Qiao; Zhu, Yimei; Chandrasena, Ravini U.; Yang, Weibing; Gray, Alexander X.; Arenholz, Elke; Farrar, Andrew K.; Tenne, Dmitri A.; Hu, Minhui; Guo, Jiandong

    2016-01-01

    Advancements in nanoscale engineering of oxide interfaces and heterostructures have led to discoveries of emergent phenomena and new artificial materials. Combining the strengths of reactive molecular-beam epitaxy and pulsed-laser deposition, we show here, with examples of Sr1+xTi1-xO3+delta, Ruddlesden-Popper phase Lan+1NinO3n+1 (n = 4), and LaAl1+yO3(1+0.5y)/SrTiO3 interfaces, that atomic layer-by-layer laser molecular-beam epitaxy (ALL-Laser MBE) significantly advances the state of the art...

  8. 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...

  9. The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Ferguson, Ken R. [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Department of Applied Physics, Stanford University, 348 Via Pueblo, Stanford, CA 94305 (United States); Bucher, Maximilian; Bozek, John D.; Carron, Sebastian; Castagna, Jean-Charles [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Coffee, Ryan [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Curiel, G. Ivan; Holmes, Michael; Krzywinski, Jacek; Messerschmidt, Marc; Minitti, Michael; Mitra, Ankush; Moeller, Stefan; Noonan, Peter; Osipov, Timur; Schorb, Sebastian; Swiggers, Michele; Wallace, Alexander; Yin, Jing [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Bostedt, Christoph, E-mail: bostedt@slac.stanford.edu [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States)

    2015-04-17

    A description of the Atomic, Molecular and Optical Sciences (AMO) instrument at the Linac Coherent Light Source is presented. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument. The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump–probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.

  10. Implementation of exterior complex scaling in B-splines to solve atomic and molecular collision problems

    International Nuclear Information System (INIS)

    McCurdy, C William; MartIn, Fernando

    2004-01-01

    B-spline methods are now well established as widely applicable tools for the evaluation of atomic and molecular continuum states. The mathematical technique of exterior complex scaling has been shown, in a variety of other implementations, to be a powerful method with which to solve atomic and molecular scattering problems, because it allows the correct imposition of continuum boundary conditions without their explicit analytic application. In this paper, an implementation of exterior complex scaling in B-splines is described that can bring the well-developed technology of B-splines to bear on new problems, including multiple ionization and breakup problems, in a straightforward way. The approach is demonstrated for examples involving the continuum motion of nuclei in diatomic molecules as well as electronic continua. For problems involving electrons, a method based on Poisson's equation is presented for computing two-electron integrals over B-splines under exterior complex scaling

  11. Xenon preconditioning: molecular mechanisms and biological effects

    Directory of Open Access Journals (Sweden)

    Liu Wenwu

    2013-01-01

    Full Text Available Abstract Xenon is one of noble gases and has been recognized as an anesthetic for more than 50 years. Xenon possesses many of the characteristics of an ideal anesthetic, but it is not widely applied in clinical practice mainly because of its high cost. In recent years, numerous studies have demonstrated that xenon as an anesthetic can exert neuroprotective and cardioprotective effects in different models. Moreover, xenon has been applied in the preconditioning, and the neuroprotective and cardioprotective effects of xenon preconditioning have been investigated in a lot of studies in which some mechanisms related to these protections are proposed. In this review, we summarized these mechanisms and the biological effects of xenon preconditioning.

  12. Vancomycin Molecular Interactions: Antibiotic and Enantioselective Mechanisms

    Science.gov (United States)

    Ward, Timothy J.; Gilmore, Aprile; Ward, Karen; Vowell, Courtney

    Medical studies established that vancomycin and other related macrocyclic antibiotics have an enhanced antimicrobial activity when they are associated as dimers. The carbohydrate units attached to the vancomycin basket have an essential role in the dimerization reaction. Covalently synthesized dimers were found active against vancomycin-resistant bacterial strains. A great similarity between antibiotic potential and enantioselectivity was established. A covalent vancomycin dimer was studied in capillary electrophoresis producing excellent chiral separation of dansyl amino acids. Balhimycin is a macrocyclic glycopeptide structurally similar to vancomycin. The small differences are, however, responsible for drastic differences in enantioselectivity in the same experimental conditions. Contributions from studies examining vancomycin's mechanism for antimicrobial activity have substantially aided our understanding of its mechanism in chiral recognition.

  13. Physical mechanisms of biological molecular motors

    Energy Technology Data Exchange (ETDEWEB)

    Miller, John H. Jr. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States)], E-mail: jhmiller@uh.edu; Vajrala, Vijayanand; Infante, Hans L. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States); Claycomb, James R. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States); Department of Mathematics and Physics, Houston Baptist University, 7502 Fondren Road, Houston, TX 77074-3298 (United States); Palanisami, Akilan; Fang Jie; Mercier, George T. [Department of Physics and Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Ste. 617 SR1 Houston, TX 77204-5005 (United States)

    2009-03-01

    Biological motors generally fall into two categories: (1) those that convert chemical into mechanical energy via hydrolysis of a nucleoside triphosphate, usually adenosine triphosphate, regarded as life's chemical currency of energy and (2) membrane bound motors driven directly by an ion gradient and/or membrane potential. Here we argue that electrostatic interactions play a vital role for both types of motors and, therefore, the tools of physics can greatly contribute to understanding biological motors.

  14. Physical mechanisms of biological molecular motors

    International Nuclear Information System (INIS)

    Miller, John H. Jr.; Vajrala, Vijayanand; Infante, Hans L.; Claycomb, James R.; Palanisami, Akilan; Fang Jie; Mercier, George T.

    2009-01-01

    Biological motors generally fall into two categories: (1) those that convert chemical into mechanical energy via hydrolysis of a nucleoside triphosphate, usually adenosine triphosphate, regarded as life's chemical currency of energy and (2) membrane bound motors driven directly by an ion gradient and/or membrane potential. Here we argue that electrostatic interactions play a vital role for both types of motors and, therefore, the tools of physics can greatly contribute to understanding biological motors

  15. Cellular and molecular mechanisms of muscle atrophy

    Directory of Open Access Journals (Sweden)

    Paolo Bonaldo

    2013-01-01

    Full Text Available Skeletal muscle is a plastic organ that is maintained by multiple pathways regulating cell and protein turnover. During muscle atrophy, proteolytic systems are activated, and contractile proteins and organelles are removed, resulting in the shrinkage of muscle fibers. Excessive loss of muscle mass is associated with poor prognosis in several diseases, including myopathies and muscular dystrophies, as well as in systemic disorders such as cancer, diabetes, sepsis and heart failure. Muscle loss also occurs during aging. In this paper, we review the key mechanisms that regulate the turnover of contractile proteins and organelles in muscle tissue, and discuss how impairments in these mechanisms can contribute to muscle atrophy. We also discuss how protein synthesis and degradation are coordinately regulated by signaling pathways that are influenced by mechanical stress, physical activity, and the availability of nutrients and growth factors. Understanding how these pathways regulate muscle mass will provide new therapeutic targets for the prevention and treatment of muscle atrophy in metabolic and neuromuscular diseases.

  16. Destruction of fast H(2S) atoms in collisions with neon, krypton, xenon, and molecular hydrogen

    International Nuclear Information System (INIS)

    Roussel, F.; Pradel, P.; Spiess, G.

    1977-01-01

    Measurements are reported for the total quenching of metastable hydrogen atoms by neon, krypton, xenon, and molecular hydrogen, in the energy range 0.052--3 keV. The cross sections are found to be on the order of 5 x 10 -15 cm 2 at the lowest energies, and decrease to approximately 2 x 10 -15 cm 2 at the highest energies. The data at low energy are analyzed using a simple theoretical model

  17. IAEA technical meeting on 'Technical aspects of atomic and molecular data processing and exchange'. Summary report

    International Nuclear Information System (INIS)

    Humbert, Denis

    2004-03-01

    The proceedings of the IAEA Advisory Group Meeting on 'Technical Aspects of Atomic and Molecular Data Processing and Exchange' (17th Meeting of A+M Data Centres and ALADDIN Network), held on 6-7 October, 2003 in Vienna, Austria are briefly described. The meeting conclusions and recommendations on the priorities in A+M data compilation and evaluation, and on the technical aspects of data processing, exchange, and distribution are also presented. (author)

  18. Bibliography of atomic and molecular excitation in heavy particle collisions, 1950--1975

    International Nuclear Information System (INIS)

    Hawthorne, S.W.; Thomas, E.W.; Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Kirkpatrick, M.I.; McDaniel, E.W.; Phaneuf, R.A.

    1979-02-01

    This annotated bibliography lists published work on atomic and molecular excitation in heavy particle collisions for the period 1950 to 1975. Sources include scientific journals, abstract compilations, conference proceedings, books, and reports. The bibliography is arranged alphabetically by author. Each entry indicates whether the work was experimental or theoretical, what energy range was covered, and what reactants were investigated. Following the bibliographical listing are indexes of reactions and authors

  19. Archives of Astronomical Spectral Observations and Atomic/Molecular Databases for their Analysis

    Directory of Open Access Journals (Sweden)

    Ryabchikova T.

    2015-12-01

    Full Text Available We present a review of open-source data for stellar spectroscopy investigations. It includes lists of the main archives of medium-to-high resolution spectroscopic observations, with brief characteristics of the archive data (spectral range, resolving power, flux units. We also review atomic and molecular databases that contain parameters of spectral lines, cross-sections and reaction rates needed for a detailed analysis of high resolution, high signal-to-noise ratio stellar spectra.

  20. Molecular Dynamics Simulation of Nanoindentation-induced Mechanical Deformation and Phase Transformation in Monocrystalline Silicon

    Directory of Open Access Journals (Sweden)

    Jian Sheng-Rui

    2008-01-01

    Full Text Available AbstractThis work presents the molecular dynamics approach toward mechanical deformation and phase transformation mechanisms of monocrystalline Si(100 subjected to nanoindentation. We demonstrate phase distributions during loading and unloading stages of both spherical and Berkovich nanoindentations. By searching the presence of the fifth neighboring atom within a non-bonding length, Si-III and Si-XII have been successfully distinguished from Si-I. Crystallinity of this mixed-phase was further identified by radial distribution functions.

  1. 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.

  2. Physics. Experimental and theoretical foundations. Pt. 3. Atomic, molecular, and quantum physics. 2. ed.; Physik. Experimentelle und theoretische Grundlagen. T. 3. Atom-, Molekuel- und Quantenphysik

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Reinhart [Konstanz Univ. (Germany). Fachbereich Physik

    2012-07-01

    This textbook mediates in three volumes the matter of the first four semester of the bachelor respectively master course. The otherwise generally usual separate presentation of experimental and theoretical physics is canceled in favor of an integrated treatment. The advances are obvious: The studying is enabled to learn to understand knowledge gotten by means of experiments also immediately in a quantitative formulation. The can equally be used as textbook to an integrated course and to separated courses. Because the relevant theoretical concepts are developed without gap a special book of theoretical physics is unnecessary. Numerous exercise problems deepen the understanding and help directly in the preparation for examinations. The illustrations are mostly presented in two colours. Volume III treats atomic and molecular physics. After a semiclassical presentation the quantum-mechanical foundations are developed and in the following chapters applied to atomic systems and processes. An introduction in the foundations and application of the laser. The closure is formed by a chapter about entangled systems.

  3. 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.

  4. Nonlinear effects in defect production by atomic and molecular ion implantation

    International Nuclear Information System (INIS)

    David, C.; Dholakia, Manan; Chandra, Sharat; Nair, K. G. M.; Panigrahi, B. K.; Amirthapandian, S.; Amarendra, G.; Varghese Anto, C.; Santhana Raman, P.; Kennedy, John

    2015-01-01

    This report deals with studies concerning vacancy related defects created in silicon due to implantation of 200 keV per atom aluminium and its molecular ions up to a plurality of 4. The depth profiles of vacancy defects in samples in their as implanted condition are carried out by Doppler broadening spectroscopy using low energy positron beams. In contrast to studies in the literature reporting a progressive increase in damage with plurality, implantation of aluminium atomic and molecular ions up to Al 3 , resulted in production of similar concentration of vacancy defects. However, a drastic increase in vacancy defects is observed due to Al 4 implantation. The observed behavioural trend with respect to plurality has even translated to the number of vacancies locked in vacancy clusters, as determined through gold labelling experiments. The impact of aluminium atomic and molecular ions simulated using MD showed a monotonic increase in production of vacancy defects for cluster sizes up to 4. The trend in damage production with plurality has been explained on the basis of a defect evolution scheme in which for medium defect concentrations, there is a saturation of the as-implanted damage and an increase for higher defect concentrations

  5. Molecular Ions in Ion Upflows and their Effects on Hot Atomic Oxygen Production

    Science.gov (United States)

    Foss, V.; Yau, A. W.; Shizgal, B.

    2017-12-01

    We present new direct ion composition observations of molecular ions in auroral ion upflows from the CASSIOPE Enhanced Polar Outflow Probe (e-POP). These observed molecular ions are N2+, NO+, and possibly O2+, and are found to occur at all e-POP altitudes starting at about 400 km, during auroral substorms and the different phases of magnetic storms, sometimes with upflow velocities exceeding a few hundred meters per second and abundances of 5-10%. The dissociative recombination of both O2+ and NO+ was previously proposed as an important source of hot oxygen atoms in the topside thermosphere [Hickey et al., 1995]. We investigate the possible effect of the observed molecular ions on the production of hot oxygen atoms in the storm and substorm-time auroral thermosphere. We present numerical solutions of the Boltzmann equation for the steady-state oxygen energy distribution function, taking into account both the production of the hot atoms and their subsequent collisional relaxation. Our result suggests the formation of a hot oxygen population with a characteristic temperature on the order of 0.3 eV and constituting 1-5% of the oxygen density near the exobase. We discuss the implication of this result in the context of magnetosphere-ionosphere-thermosphere coupling.

  6. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    International Nuclear Information System (INIS)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

  7. Conversion of a Degenerate Fermi Gas of 6Li Atoms to a Molecular BEC

    International Nuclear Information System (INIS)

    Strecker, K.E.; Partridge, G.B.; Kamar, R.I.; Jack, M.W.; Hulet, R.G.

    2005-01-01

    Atomic Feshbach resonances have recently been used to produce a strongly interacting Fermi gas, where the BCS/BEC crossover can be explored. We have used both narrow and broad Feshbach resonances to convert a quantum degenerate Fermi gas of 6Li atoms into an ultracold gas of Li2 molecules. For the narrow resonances, the molecules are formed by coherent adiabatic passage through the resonance. We find that 50% of the atoms are converted to molecules. Furthermore, the lifetime of these molecules was measured to be surprisingly long, 1 s. We will discuss these measurements in the context of the present theoretical understanding. Molecules can also be formed using static fields near the broad Feshbach resonance. The lifetime of these molecules is again long, and sufficient to enable their evaporation to a Bose-Einstein condensate. Phase contrast images of the molecular condensate are presented. The BCS/BEC crossover may be explored by starting with a pure molecular condensate on the low-field side of the Feshbach resonance, and adiabatically changing the field to any final value around resonance. We combine this ability with optical spectroscopy on a bound-bound molecular transition to probe the nature of the many-body wavefunction in the crossover regime

  8. Differences between application of some basic principles of quantum mechanics on atomic and mesoscopic levels

    OpenAIRE

    Nikulov, Alexey

    2005-01-01

    Formalism of the quantum mechanics developed for microscopic (atomic) level comes into collision with some logical difficulties on mesoscopic level. Some fundamental differences between application of its basic principles on microscopic and mesoscopic levels are accentuated.

  9. Molecular mechanisms in radiation damage to DNA: Final report

    International Nuclear Information System (INIS)

    Osman, R.

    1996-01-01

    The objectives of this work were to elucidate the molecular mechanisms that were responsible for radiation-induced DNA damage. The studies were based on theoretical explorations of possible mechanisms that link initial radiation damage in the form of base and sugar damage to conformational changes in DNA

  10. Diagnostics of the molecular component of photon-dominated regions with mechanical heating. II. Line intensities and ratios

    NARCIS (Netherlands)

    Kazandjian, M.; Meijerink, R.; Pelupessy, F.I.; Israel, F.P.; Spaans, M.

    2015-01-01

    CO observations in active galactic nuclei and starbursts reveal high kinetic temperatures. Those environments are thought to be very turbulent due to dynamic phenomena, such as outflows and high supernova rates. We investigate the effect of mechanical heating on atomic fine-structure and molecular

  11. IAEA advisory group meeting on atomic and molecular data for fusion, Culham Laboratory, UK, 1 - 5 November 1976

    International Nuclear Information System (INIS)

    Lorenz, A.

    1977-02-01

    The IAEA Nuclear Data Section convened an Advisory Group Meeting on Atomic and Molecular Data for Fusion at the UKAEA Laboratory at Culham, from 1-5 November 1976. Three detailed working group reports identifying requirements and availability of atomic collision data, atomic structure data, and surface interaction data in fusion research are presented. The meeting recommended the formation of an international network of data centres for the compilation and dissemination of atomic and molecular data required for fusion, and recommended that the IAEA Nuclear Data Section be given the responsibility to establish and coordinate this network

  12. Molecular Mechanisms of Circadian Regulation During Spaceflight

    Science.gov (United States)

    Zanello, S. B.; Boyle, R.

    2012-01-01

    The physiology of both vertebrates and invertebrates follows internal rhythms coordinated in phase with the 24-hour daily light cycle. This circadian clock is governed by a central pacemaker, the suprachiasmatic nucleus (SCN) in the brain. However, peripheral circadian clocks or oscillators have been identified in most tissues. How the central and peripheral oscillators are synchronized is still being elucidated. Light is the main environmental cue that entrains the circadian clock. Under the absence of a light stimulus, the clock continues its oscillation in a free-running condition. In general, three functional compartments of the circadian clock are defined. The vertebrate retina contains endogenous clocks that control many aspects of retinal physiology, including retinal sensitivity to light, neurohormone synthesis (melatonin and dopamine), rod disk shedding, signalling pathways and gene expression. Neurons with putative local circadian rhythm generation are found among all the major neuron populations in the mammalian retina. In the mouse, clock genes and function are more localized to the inner retinal and ganglion cell layers. The photoreceptor, however, secrete melatonin which may still serve a an important circadian signal. The reception and transmission of the non-visual photic stimulus resides in a small subpopulation (1-3%) or retinal ganglion cells (RGC) that express the pigment melanopsin (Opn4) and are called intrisically photoreceptive RGC (ipRGC). Melanopsin peak absorption is at 420 nm and all the axons of the ipRGC reach the SCN. A common countermeasure for circadian re-entrainment utilizes blue-green light to entrain the circadian clock and mitigate the risk of fatigue and health and performance decrement due to circadian rhythm disruption. However, an effective countermeasure targeting the photoreceptor system requires that the basic circadian molecular machinery remains intact during spaceflight. We hypothesize that spaceflight may affect ip

  13. The Scales of Time, Length, Mass, Energy, and Other Fundamental Physical Quantities in the Atomic World and the Use of Atomic Units in Quantum Mechanical Calculations

    Science.gov (United States)

    Teo, Boon K.; Li, Wai-Kee

    2011-01-01

    This article is divided into two parts. In the first part, the atomic unit (au) system is introduced and the scales of time, space (length), and speed, as well as those of mass and energy, in the atomic world are discussed. In the second part, the utility of atomic units in quantum mechanical and spectroscopic calculations is illustrated with…

  14. NARROW Na AND K ABSORPTION LINES TOWARD T TAURI STARS: TRACING THE ATOMIC ENVELOPE OF MOLECULAR CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Pascucci, I.; Simon, M. N. [Lunar and Planetary Laboratory, The University of Arizona, Tucson, AZ 85721 (United States); Edwards, S. [Five College Astronomy Department, Smith College, Northampton, MA 01063 (United States); Heyer, M. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003-9305 (United States); Rigliaco, E. [Institute for Astronomy, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich (Switzerland); Hillenbrand, L. [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Gorti, U.; Hollenbach, D., E-mail: pascucci@lpl.arizona.edu [SETI Institute, Mountain View, CA 94043 (United States)

    2015-11-20

    We present a detailed analysis of narrow Na i and K i absorption resonance lines toward nearly 40 T Tauri stars in Taurus with the goal of clarifying their origin. The Na i λ5889.95 line is detected toward all but one source, while the weaker K i λ7698.96 line is detected in about two-thirds of the sample. The similarity in their peak centroids and the significant positive correlation between their equivalent widths demonstrate that these transitions trace the same atomic gas. The absorption lines are present toward both disk and diskless young stellar objects, which excludes cold gas within the circumstellar disk as the absorbing material. A comparison of Na i and CO detections and peak centroids demonstrates that the atomic gas and molecular gas are not co-located, the atomic gas being more extended than the molecular gas. The width of the atomic lines corroborates this finding and points to atomic gas about an order of magnitude warmer than the molecular gas. The distribution of Na i radial velocities shows a clear spatial gradient along the length of the Taurus molecular cloud filaments. This suggests that absorption is associated with the Taurus molecular cloud. Assuming that the gradient is due to cloud rotation, the rotation of the atomic gas is consistent with differential galactic rotation, whereas the rotation of the molecular gas, although with the same rotation axis, is retrograde. Our analysis shows that narrow Na i and K i absorption resonance lines are useful tracers of the atomic envelope of molecular clouds. In line with recent findings from giant molecular clouds, our results demonstrate that the velocity fields of the atomic and molecular gas are misaligned. The angular momentum of a molecular cloud is not simply inherited from the rotating Galactic disk from which it formed but may be redistributed by cloud–cloud interactions.

  15. NARROW Na AND K ABSORPTION LINES TOWARD T TAURI STARS: TRACING THE ATOMIC ENVELOPE OF MOLECULAR CLOUDS

    International Nuclear Information System (INIS)

    Pascucci, I.; Simon, M. N.; Edwards, S.; Heyer, M.; Rigliaco, E.; Hillenbrand, L.; Gorti, U.; Hollenbach, D.

    2015-01-01

    We present a detailed analysis of narrow Na i and K i absorption resonance lines toward nearly 40 T Tauri stars in Taurus with the goal of clarifying their origin. The Na i λ5889.95 line is detected toward all but one source, while the weaker K i λ7698.96 line is detected in about two-thirds of the sample. The similarity in their peak centroids and the significant positive correlation between their equivalent widths demonstrate that these transitions trace the same atomic gas. The absorption lines are present toward both disk and diskless young stellar objects, which excludes cold gas within the circumstellar disk as the absorbing material. A comparison of Na i and CO detections and peak centroids demonstrates that the atomic gas and molecular gas are not co-located, the atomic gas being more extended than the molecular gas. The width of the atomic lines corroborates this finding and points to atomic gas about an order of magnitude warmer than the molecular gas. The distribution of Na i radial velocities shows a clear spatial gradient along the length of the Taurus molecular cloud filaments. This suggests that absorption is associated with the Taurus molecular cloud. Assuming that the gradient is due to cloud rotation, the rotation of the atomic gas is consistent with differential galactic rotation, whereas the rotation of the molecular gas, although with the same rotation axis, is retrograde. Our analysis shows that narrow Na i and K i absorption resonance lines are useful tracers of the atomic envelope of molecular clouds. In line with recent findings from giant molecular clouds, our results demonstrate that the velocity fields of the atomic and molecular gas are misaligned. The angular momentum of a molecular cloud is not simply inherited from the rotating Galactic disk from which it formed but may be redistributed by cloud–cloud interactions

  16. Uncertainty Assessment for Theoretical Atomic and Molecular Scattering Data. Summary Report of a Joint IAEA-ITAMP Technical Meeting

    International Nuclear Information System (INIS)

    Chung, Hyun-Kyung; Bartschat, Klaus; Tennyson, Jonathan; Schultz, David R.

    2014-10-01

    This report summarizes the proceedings of the Joint IAEA-ITAMP Technical Meeting on “Uncertainty Assessment for Theoretical Atomic and Molecular Scattering Data” on 7-9 July 2014. Twenty-five participants from ten Member States and one from the IAEA attended the three-day meeting held at the Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts, USA and hosted by the Institute of Theoretical Atomic, Molecular and Optical Physics (ITAMP). The report includes discussions on the issues of uncertainty estimates for theoretical atomic and molecular scattering data. The abstracts of presentations presented in the meeting are attached in the Appendix. (author)

  17. 14th meeting of the IFRC Subcommittee on Atomic and Molecular Data for Fusion. Summary report of IAEA technical meeting

    International Nuclear Information System (INIS)

    Clark, R.E.H.; Peacock, N.J.

    2006-01-01

    The 14th Meeting of the Subcommittee on Atomic and Molecular Data for Fusion of the International Fusion Research Council was held on 24-25 June 2004, at the IAEA Headquarters in Vienna, Austria. Subcommittee members reviewed the work of the Atomic and Molecular Data Unit over the two-year period from June 2002 to June 2004, and made recommendations that covered the 2005-2006 budget cycle. The proceedings, conclusions and recommendations of the meeting are briefly described in this report, along with a short summary of the activities of the IAEA Atomic and Molecular Data Unit of the Nuclear Data Section from June 2002 to June 2004. (author)

  18. Summary report of IAEA technical meeting: 15. meeting of the IFRC Subcommittee on Atomic and Molecular Data for Fusion

    International Nuclear Information System (INIS)

    Clark, R.E.H.; Peacock, N.J.

    2007-02-01

    The 15th Meeting of the Subcommittee on Atomic and Molecular Data for Fusion of the International Fusion Research Council was held on 20-21 April 2006, at the IAEA Headquarters in Vienna, Austria. Work of the Atomic and Molecular Data Unit for the period 2004-2006 was reviewed, and recommendations were made for the 2008-2009 budget cycle. The proceedings, conclusions and recommendations of the Subcommittee meeting are briefly described in this report. Specific recommendations of the Subcommittee from this meeting, as well as the report on the activities of the IAEA Atomic and Molecular Data Unit for the period June 2004 - March 2006, are also included. (author)

  19. Mechanical torques generated by optically pumped atomic spin relaxation at surfaces

    International Nuclear Information System (INIS)

    Herman, R.M.

    1982-01-01

    It is argued that a valuable method of observing certain types of surface-atom interactions may lie in mechanical torques generated through the spin-orbit relaxation of valence electronic spins of optically pumped atoms at surfaces. The unusual feature of this phenomenon is that the less probable spin-orbit relaxation becomes highly visible as compared with the much more rapid paramagnetic relaxation, because of an enhancement, typically by as much as a factor 10 9 , in the torques delivered to mechanical structures, by virtue of a very large effective moment arm. Spin-orbit relaxation operates through an exchange of translational momentum which, in turn, can be identified with the delivery of a gigantic angular momentum (in units of h) relative to a distant axis about which mechanical motion is referred. The spin-orbit relaxation strongly depends upon the atomic number of the surface atoms and the strength of interaction with the optically pumped atoms. Being dominated by high-atomic-number surface atoms, spin-orbit relaxation rates may not be too strongly influenced by minor surface contamination of lighter-weight optically active atoms

  20. Mechanical torques generated by optically pumped atomic spin relaxation at surfaces

    Science.gov (United States)

    Herman, R. M.

    1982-03-01

    It is argued that a valuable method of observing certain types of surface-atom interactions may lie in mechanical torques generated through the spin-orbit relaxation of valence electronic spins of optically pumped atoms at surfaces. The unusual feature of this phenomenon is that the less probable spin-orbit relaxation becomes highly visible as compared with the much more rapid paramagnetic relaxation, because of an enhancement, typically by as much as a factor 109, in the torques delivered to mechanical structures, by virtue of a very large effective moment arm. Spin-orbit relaxation operates through an exchange of translational momentum which, in turn, can be identified with the delivery of a gigantic angular momentum (in units of ℏ) relative to a distant axis about which mechanical motion is referred. The spin-orbit relaxation strongly depends upon the atomic number of the surface atoms and the strength of interaction with the optically pumped atoms. Being dominated by high-atomic-number surface atoms, spin-orbit-relaxation rates may not be too strongly influenced by minor surface contamination of lighter-weight optically active atoms.

  1. Molecular cytotoxic mechanisms of anticancer hydroxychalcones.

    Science.gov (United States)

    Sabzevari, Omid; Galati, Giuseppe; Moridani, Majid Y; Siraki, Arno; O'Brien, Peter J

    2004-06-30

    Chalcones are being considered as anticancer agents as they are natural compounds that are particularly cytotoxic towards K562 leukemia or melanoma cells. In this study, we have investigated phloretin, isoliquiritigenin, and 10 other hydroxylated chalcones for their cytotoxic mechanisms towards isolated rat hepatocytes. All hydroxychalcones partly depleted hepatocyte GSH and oxidized GSH to GSSG. These chalcones also caused a collapse of mitochondrial membrane potential and increased oxygen uptake. Furthermore, glycolytic or citric acid cycle substrates prevented cytotoxicity and mitochondrial membrane potential collapse. The highest pKa chalcones were the most effective at collapsing the mitochondrial membrane potential which suggests that the cytotoxic activity of hydroxychalcones are likely because of their ability to uncouple mitochondria.

  2. [Molecular mechanisms of skeletal muscle hypertrophy].

    Science.gov (United States)

    Astratenkova, I V; Rogozkin, V A

    2014-06-01

    Enzymes Akt, AMPK, mTOR, S6K and PGC-1a coactivator take part in skeletal muscles in the regulation of synthesis of proteins. The expression of these proteins is regulated by growth factors, hormones, nutrients, mechanical loading and leads to an increase in muscle mass and skeletal muscle hypertrophy. The review presents the results of studies published in the past four years, which expand knowledge on the effects of various factors on protein synthesis in skeletal muscle. The attention is focused on the achievements that reveal and clarify the signaling pathways involved in the regulation of protein synthesis in skeletal muscle. The central place is taken by mTOR enzyme which controls and regulates the main stages of the cascade of reactions of muscle proteins providing synthesis in the conditions of human life. coactivator PGC-1a.

  3. Molecular and neuroendocrine mechanisms of cancer cachexia.

    Science.gov (United States)

    Mendes, Maria Carolina S; Pimentel, Gustavo D; Costa, Felipe O; Carvalheira, José B C

    2015-09-01

    Cancer and its morbidities, such as cancer cachexia, constitute a major public health problem. Although cancer cachexia has afflicted humanity for centuries, its underlying multifactorial and complex physiopathology has hindered the understanding of its mechanism. During the last few decades we have witnessed a dramatic increase in the understanding of cancer cachexia pathophysiology. Anorexia and muscle and adipose tissue wasting are the main features of cancer cachexia. These apparently independent symptoms have humoral factors secreted by the tumor as a common cause. Importantly, the hypothalamus has emerged as an organ that senses the peripheral signals emanating from the tumoral environment, and not only elicits anorexia but also contributes to the development of muscle and adipose tissue loss. Herein, we review the roles of factors secreted by the tumor and its effects on the hypothalamus, muscle and adipose tissue, as well as highlighting the key targets that are being exploited for cancer cachexia treatment. © 2015 Society for Endocrinology.

  4. Neurotrophin Propeptides: Biological Functions and Molecular Mechanisms.

    Science.gov (United States)

    Rafieva, Lola M; Gasanov, Eugene V

    2016-01-01

    Neurotrophins constitute a family of growth factors that play a key role in the regulation of the development and function of the central and peripheral nervous systems. A common feature of all the neurotrophins is their synthesis in cells as long precursors (pre-pro-neurotrophins) that contain an N-terminal signal peptide, a following propeptide and the mature neurotrophin. Although the signal peptide functions have been well studied, the role of neurotrophin propeptides is not so clear. Here, we briefly summarize the biochemistry of neurotrophin propeptides, including their role as folding-assistants for the mature factor and their role in processing and in secretion of neurotrophins. In the main part of the review we summarize our current state of knowledge of the biological activity of neurotrophin propeptides, their possible mechanisms of action, and their potential influence on the activity of the mature neurotrophins.

  5. Cellular and molecular mechanisms coordinating pancreas development.

    Science.gov (United States)

    Bastidas-Ponce, Aimée; Scheibner, Katharina; Lickert, Heiko; Bakhti, Mostafa

    2017-08-15

    The pancreas is an endoderm-derived glandular organ that participates in the regulation of systemic glucose metabolism and food digestion through the function of its endocrine and exocrine compartments, respectively. While intensive research has explored the signaling pathways and transcriptional programs that govern pancreas development, much remains to be discovered regarding the cellular processes that orchestrate pancreas morphogenesis. Here, we discuss the developmental mechanisms and principles that are known to underlie pancreas development, from induction and lineage formation to morphogenesis and organogenesis. Elucidating such principles will help to identify novel candidate disease genes and unravel the pathogenesis of pancreas-related diseases, such as diabetes, pancreatitis and cancer. © 2017. Published by The Company of Biologists Ltd.

  6. Lys169 of human glucokinase is a determinant for glucose phosphorylation: implication for the atomic mechanism of glucokinase catalysis.

    Directory of Open Access Journals (Sweden)

    Jian Zhang

    Full Text Available Glucokinase (GK, a glucose sensor, maintains plasma glucose homeostasis via phosphorylation of glucose and is a potential therapeutic target for treating maturity-onset diabetes of the young (MODY and persistent hyperinsulinemic hypoglycemia of infancy (PHHI. To characterize the catalytic mechanism of glucose phosphorylation by GK, we combined molecular modeling, molecular dynamics (MD simulations, quantum mechanics/molecular mechanics (QM/MM calculations, experimental mutagenesis and enzymatic kinetic analysis on both wild-type and mutated GK. Our three-dimensional (3D model of the GK-Mg(2+-ATP-glucose (GMAG complex, is in agreement with a large number of mutagenesis data, and elucidates atomic information of the catalytic site in GK for glucose phosphorylation. A 10-ns MD simulation of the GMAG complex revealed that Lys169 plays a dominant role in glucose phosphorylation. This prediction was verified by experimental mutagenesis of GK (K169A and enzymatic kinetic analyses of glucose phosphorylation. QM/MM calculations were further used to study the role of Lys169 in the catalytic mechanism of the glucose phosphorylation and we found that Lys169 enhances the binding of GK with both ATP and glucose by serving as a bridge between ATP and glucose. More importantly, Lys169 directly participates in the glucose phosphorylation as a general acid catalyst. Our findings provide mechanistic details of glucose phorphorylation catalyzed by GK, and are important for understanding the pathogenic mechanism of MODY.

  7. A molecular-mechanics based finite element model for strength prediction of single wall carbon nanotubes

    International Nuclear Information System (INIS)

    Meo, M.; Rossi, M.

    2007-01-01

    The aim of this work was to develop a finite element model based on molecular mechanics to predict the ultimate strength and strain of single wallet carbon nanotubes (SWCNT). The interactions between atoms was modelled by combining the use of non-linear elastic and torsional elastic spring. In particular, with this approach, it was tried to combine the molecular mechanics approach with finite element method without providing any not-physical data on the interactions between the carbon atoms, i.e. the CC-bond inertia moment or Young's modulus definition. Mechanical properties as Young's modulus, ultimate strength and strain for several CNTs were calculated. Further, a stress-strain curve for large deformation (up to 70%) is reported for a nanotube Zig-Zag (9,0). The results showed that good agreement with the experimental and numerical results of several authors was obtained. A comparison of the mechanical properties of nanotubes with same diameter and different chirality was carried out. Finally, the influence of the presence of defects on the strength and strain of a SWNT was also evaluated. In particular, the stress-strain curve a nanotube with one-vacancy defect was evaluated and compared with the curve of a pristine one, showing a reduction of the ultimate strength and strain for the defected nanotube. The FE model proposed demonstrate to be a reliable tool to simulate mechanical behaviour of carbon nanotubes both in the linear elastic field and the non-linear elastic field

  8. Mechanical properties of pillared-graphene nanostructures using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Wang, Chih-Hao; Fang, Te-Hua; Sun, Wei-Li

    2014-01-01

    The deformation behaviour and mechanical properties of three-dimensional (3D) pillared graphene are investigated using molecular dynamics simulations. The Tersoff–Brenner many-body potential model is employed to evaluate the interactions between 3D pillared-graphene carbon atoms and nanotube carbons. The Lennard-Jones potential model is used to compute the interactions between a conical indenter and 3D pillared-graphene carbon atoms. The effects of the size and geometric structure of 3D pillared-graphene are evaluated in terms of the indentation force and contact stiffness. The simulation results for an armchair nanotube of 3D pillared graphene show that the contact stiffness increases with increasing chiral vector of the 3D-pillared graphene. However, the adhesive force sharply decreases with increasing chiral vector of the 3D-pillared graphene. A zigzag nanotube of 3D-pillared graphene exhibits better mechanical properties compared with those of the armchair nanotube. (paper)

  9. Molecular mechanism for generation of antibody memory.

    Science.gov (United States)

    Shivarov, Velizar; Shinkura, Reiko; Doi, Tomomitsu; Begum, Nasim A; Nagaoka, Hitoshi; Okazaki, Il-Mi; Ito, Satomi; Nonaka, Taichiro; Kinoshita, Kazuo; Honjo, Tasuku

    2009-03-12

    Activation-induced cytidine deaminase (AID) is the essential enzyme inducing the DNA cleavage required for both somatic hypermutation and class switch recombination (CSR) of the immunoglobulin gene. We originally proposed the RNA-editing model for the mechanism of DNA cleavage by AID. We obtained evidence that fulfils three requirements for CSR by this model, namely (i) AID shuttling between nucleus and cytoplasm, (ii) de novo protein synthesis for CSR, and (iii) AID-RNA complex formation. The alternative hypothesis, designated as the DNA-deamination model, assumes that the in vitro DNA deamination activity of AID is representative of its physiological function in vivo. Furthermore, the resulting dU was removed by uracil DNA glycosylase (UNG) to generate a basic site, followed by phosphodiester bond cleavage by AP endonuclease. We critically examined each of these provisional steps. We identified a cluster of mutants (H48A, L49A, R50A and N51A) that had particularly higher CSR activities than expected from their DNA deamination activities. The most striking was the N51A mutant that had no ability to deaminate DNA in vitro but retained approximately 50 per cent of the wild-type level of CSR activity. We also provide further evidence that UNG plays a non-canonical role in CSR, namely in the repair step of the DNA breaks. Taking these results together, we favour the RNA-editing model for the function of AID in CSR.

  10. Molecular mechanics work station for protein conformational studies

    International Nuclear Information System (INIS)

    Fine, R.; Levinthal, C.; Schoenborn, B.; Dimmier, G.; Rankowitz, C.

    1984-01-01

    Interest in computational problems in Biology has intensified over the last few years, partly due to the development of techniques for the rapid cloning, sequencing, and mutagenesis of genes from organisims ranging from E. coli to Man. The central dogma of molecular biology; that DNA codes for mRNA which codes for protein, has been understood in a linear programming sense since the genetic code was cracked. But what is not understood at present is how a protein, once assembled as a long sequence of amino acids, folds back on itself to produce a three-dimensional structure which is unique to that protein and which dictates its chemical and biological activity. This folding process is purely physics, and involves the time evolution of a system of several thousand atoms which interact with each other and with atoms from the surrounding solvent. Molecular dynamics simulations on smaller molecules suggest that approaches which treat the protein as a classical ensemble of atoms interacting with each other via an empirical Hamiltonian can yield the kind of predictive results one would like when applied to proteins

  11. Atomic and molecular physics - Ions in solids - Laser systems. Courses, corrected exercises and problems Level M1/M2

    International Nuclear Information System (INIS)

    Cremer, Georgette-Laura; Moncorge, Richard; Chesnel, Jean-Yves; Adoui, Lamri; Lelievre, Gerard

    2010-01-01

    This document proposes the table of contents and a brief presentation of a course book for students in atomic and molecular physics. After some generalities on energy quantification and on photon momentum / Compton Effect, the different chapters address topics like hydrogen and helium atoms, alkalis, alkaline-earth, atoms with several valence electrons, the atom-radiation interaction, molecule and ion spectroscopy in solids, and the most significant laser systems using an active media based on atoms, ions or molecules in a diluted environment. Each chapter contains exercises and problems

  12. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    Energy Technology Data Exchange (ETDEWEB)

    López-Moreno, S., E-mail: sinlopez@uacam.mx [Centro de Investigación en Corrosión, Universidad Autónoma de Campeche, Av. Héroe de Nacozari 480, Campeche, Campeche 24029 (Mexico); Romero, A. H. [Physics Department, West Virginia University, Morgantown, West Virginia 26506-6315 (United States)

    2015-04-21

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O{sub 2} molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

  13. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    Science.gov (United States)

    López-Moreno, S.; Romero, A. H.

    2015-04-01

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered.

  14. Atomic and molecular oxygen adsorbed on (111) transition metal surfaces: Cu and Ni

    International Nuclear Information System (INIS)

    López-Moreno, S.; Romero, A. H.

    2015-01-01

    Density functional theory is used to investigate the reaction of oxygen with clean copper and nickel [111]-surfaces. We study several alternative adsorption sites for atomic and molecular oxygen on both surfaces. The minimal energy geometries and adsorption energies are in good agreement with previous theoretical studies and experimental data. From all considered adsorption sites, we found a new O 2 molecular precursor with two possible dissociation paths on the Cu(111) surface. Cross barrier energies for the molecular oxygen dissociation have been calculated by using the climbing image nudge elastic band method, and direct comparison with experimental results is performed. Finally, the structural changes and adsorption energies of oxygen adsorbed on surface when there is a vacancy nearby the adsorption site are also considered

  15. Molecular Theory of the Living Cell Concepts, Molecular Mechanisms, and Biomedical Applications

    CERN Document Server

    Ji, Sungchul

    2012-01-01

    This book presents a comprehensive molecular theory of the living cell based on over thirty concepts, principles and laws imported from thermodynamics, statistical mechanics, quantum mechanics, chemical kinetics, informatics, computer science, linguistics, semiotics, and philosophy. The author formulates physically, chemically and enzymologically realistic molecular mechanisms to account for the basic living processes such as ligand-receptor interactions, protein folding, single-molecule enzymic catalysis, force-generating mechanisms in molecular motors, signal transduction, regulation of the genome-wide RNA metabolism, morphogenesis, the micro-macro coupling in coordination dynamics, the origin of life, and the mechanisms of biological evolution itself. Possible solutions to basic and practical problems facing contemporary biology and biomedical sciences have been suggested, including pharmacotheragnostics and personalized medicine.

  16. Mini-review: Molecular mechanisms of antifouling compounds

    KAUST Repository

    Qian, Pei-Yuan

    2013-04-01

    Various antifouling (AF) coatings have been developed to protect submerged surfaces by deterring the settlement of the colonizing stages of fouling organisms. A review of the literature shows that effective AF compounds with specific targets are ones often considered non-toxic. Such compounds act variously on ion channels, quorum sensing systems, neurotransmitters, production/release of adhesive, and specific enzymes that regulate energy production or primary metabolism. In contrast, AF compounds with general targets may or may not act through toxic mechanisms. These compounds affect a variety of biological activities including algal photosynthesis, energy production, stress responses, genotoxic damage, immunosuppressed protein expression, oxidation, neurotransmission, surface chemistry, the formation of biofilms, and adhesive production/release. Among all the targets, adhesive production/release is the most common, possibly due to a more extensive research effort in this area. Overall, the specific molecular targets and the molecular mechanisms of most AF compounds have not been identified. Thus, the information available is insufficient to draw firm conclusions about the types of molecular targets to be used as sensitive biomarkers for future design and screening of compounds with AF potential. In this review, the relevant advantages and disadvantages of the molecular tools available for studying the molecular targets of AF compounds are highlighted briefly and the molecular mechanisms of the AF compounds, which are largely a source of speculation in the literature, are discussed. © 2013 Copyright Taylor and Francis Group, LLC.

  17. Graph-drawing algorithms geometries versus molecular mechanics in fullereness

    Science.gov (United States)

    Kaufman, M.; Pisanski, T.; Lukman, D.; Borštnik, B.; Graovac, A.

    1996-09-01

    The algorithms of Kamada-Kawai (KK) and Fruchterman-Reingold (FR) have been recently generalized (Pisanski et al., Croat. Chem. Acta 68 (1995) 283) in order to draw molecular graphs in three-dimensional space. The quality of KK and FR geometries is studied here by comparing them with the molecular mechanics (MM) and the adjacency matrix eigenvectors (AME) algorithm geometries. In order to compare different layouts of the same molecule, an appropriate method has been developed. Its application to a series of experimentally detected fullerenes indicates that the KK, FR and AME algorithms are able to reproduce plausible molecular geometries.

  18. Spring meeting of the scientific associations for atomic physics, high speed physics, mass spectrometry, molecular physics, plasma physics

    International Nuclear Information System (INIS)

    1996-01-01

    The volume contains the abstracts of the contributions to the Spring Meeting in Rostock with aspects of atomic physics, molecular physics, high speed physics, plasma physics and mass spectrometry. (MM)

  19. Protein Nano-Object Integrator: Generating atomic-style objects for use in molecular biophysics

    Science.gov (United States)

    Smith, Nicholas David Fenimore

    As researchers obtain access to greater and greater amounts of computational power, focus has shifted towards modeling macroscopic objects while still maintaining atomic-level details. The Protein Nano-Object Integrator (ProNOI) presented here has been designed to provide a streamlined solution for creating and designing macro-scale objects with atomic-level details to be used in molecular simulations and tools. To accomplish this, two different interfaces were developed: a Protein Data Bank (PDB), PDB-focused interface for generating regularly-shaped three-dimensional atomic objects and a 2D image-based interface for tracing images with irregularly shaped objects and then extracting three-dimensional models from these images. Each interface is dependent upon the C++ backend utility for generating the objects and ensures that the output is consistent across each program. The objects are exported in a standard PDB format which allows for the visualization and manipulation of the objects via standard tools available in Molecular Computational Biophysics.

  20. IAEA activities on atomic, molecular and plasma-material interaction data for fusion

    Science.gov (United States)

    Braams, Bastiaan J.; Chung, Hyun-Kyung

    2013-09-01

    The IAEA Atomic and Molecular Data Unit (http://www-amdis.iaea.org/) aims to provide internationally evaluated and recommended data for atomic, molecular and plasma-material interaction (A+M+PMI) processes in fusion research. The Unit organizes technical meetings and coordinates an A+M Data Centre Network (DCN) and a Code Centre Network (CCN). In addition the Unit organizes Coordinated Research Projects (CRPs), for which the objectives are mixed between development of new data and evaluation and recommendation of existing data. In the area of A+M data we are placing new emphasis in our meeting schedule on data evaluation and especially on uncertainties in calculated cross section data and the propagation of uncertainties through structure data and fundamental cross sections to effective rate coefficients. Following a recent meeting of the CCN it is intended to use electron scattering on Be, Ne and N2 as exemplars for study of uncertainties and uncertainty propagation in calculated data; this will be discussed further at the presentation. Please see http://www-amdis.iaea.org/CRP/ for more on our active and planned CRPs, which are concerned with atomic processes in core and edge plasma and with plasma interaction with beryllium-based surfaces and with irradiated tungsten.