WorldWideScience

Sample records for atom molecular mechanics

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

    OpenAIRE

    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 ...

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

    OpenAIRE

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

    2011-01-01

    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 ...

  3. 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. PMID:22022236

  4. Dynamics of the molecular and atomic mechanisms for the hydrogen-iodine exchange reaction.

    Science.gov (United States)

    Raff, L. M.; Thompson, D. L.; Sims, L. B.; Porter, R. N.

    1972-01-01

    The molecular and atomic mechanisms for the hydrogen-iodine exchange reaction are treated theoretically by means of extensive classical trajectories calculated on a reasonable potential energy surface on which the single adjustable parameter is the iodine-core effective charge. The analysis shows the molecular mechanism to be dynamically forbidden, but gives an over-all rate constant for the atomic mechanism that is in agreement with the experimental values. It is indicated that the formation of a weak H2I complex plays an important dynamical role if the atomic mechanism is limited to reactions with collision complexes involving no more than two hydrogen atoms and two iodine atoms. Excellent agreement with experiment is obtained for the rate constant for the recombination I+I+H2 yields I2+H2 and its negative temperature coefficient.

  5. 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...

  6. The role of the atomic force function in molecular mechanics simulations for carbon nanostructures

    International Nuclear Information System (INIS)

    Molecular mechanics studies were performed on structures consisting of Y junctions of carbon nanotubes. Tensile simulations were run on the same structure, wherein atomic force functions of various shape were used. According to the numerical test results the behavior of the structure, the failure site and the failure process could be determined irrespective of the shape of the force function

  7. 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.

  8. 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

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

    International Nuclear Information System (INIS)

    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. Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.

    Science.gov (United States)

    Pepłowski, Lukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-28

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids. PMID:21361557

  11. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    Science.gov (United States)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  12. 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...

  13. Atomic and molecular structure

    International Nuclear Information System (INIS)

    This book is a textbook for an introductory course of atomic physics for students of chemistry. After an introduction to the mathematical and physical foundations the quantum mechanical theory of atoms is described starting from simple examples of quantum mechanics. Then the atomic structure and the chemical bending are extensively discussed. This book is also suited for physicists who are especially interested in the atomic structure and the theory of chemical reactions. (HSI)

  14. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

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

  15. Quantum Mechanical and Molecular Dynamics Studies of the Reaction Mechanism of the Nucleophilic Substitution at the Si Atom.

    Science.gov (United States)

    Matsubara, Toshiaki; Ito, Tomoyoshi

    2016-05-01

    The mechanism of the nucleophilic substitution at the Si atom, SiH3Cl + Cl*(-) → SiH3Cl* + Cl(-), is examined by both quantum mechanical (QM) and molecular dynamics (MD) methods. This reaction proceeds by two steps with the inversion or retention of the configuration passing through an intermediate with the trigonal bipyramid (TBP) structure, although the conventional SN2 reaction at the C atom proceeds by one step with the inversion of the configuration passing through a transition state with the TBP structure. We followed by the QM calculations all the possible paths of the substitution reaction that undergo the TBP intermediates with the cis and trans forms produced by the frontside and backside attacks of Cl(-). As a result, it was thought that TBPcis1 produced with a high probability is readily transformed to the energetically more stable TBPtrans. This fact was also shown by the MD simulations. In order to obtain more information concerning the trajectory of Cl(-) on the dissociation from TBPtrans, which we cannot clarify on the basis of the energy profile determined by the QM method, the MD simulations with and without the water solvent were conducted and analyzed in detail. The QM-MD simulations without the water solvent revealed that the dissociation of Cl(-) from TBPtrans occurs without passing through TBPcis1'. The ONIOM-MD simulations with the water solvent further suggested that the thermal fluctuation of the water solvent significantly affects the oscillation of the kinetic and potential energies of the substrate to facilitate the isomerization of the TBP intermediate from the cis form to the trans form and the subsequent dissociation of Cl(-) from TBPtrans. PMID:27046773

  16. 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. PMID:26930454

  17. Molecular jamming - the cystine slipknot mechanical clamp in all-atom simulations

    OpenAIRE

    Peplowski, Lukasz; Sikora, Mateusz; Nowak, Wieslaw; Cieplak, Marek

    2011-01-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force-peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e. by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement w...

  18. Molecular Mechanics

    OpenAIRE

    Vanommeslaeghe, Kenno; Guvench, Olgun; Alexander D MacKerell

    2014-01-01

    Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and wea...

  19. 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.

  20. Atomic and molecular theory

    International Nuclear Information System (INIS)

    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

  1. Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability.

    Science.gov (United States)

    Wang, Junmei; Cieplak, Piotr; Li, Jie; Hou, Tingjun; Luo, Ray; Duan, Yong

    2011-03-31

    In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, that is, whether the interactions of two atoms that form the bond, bond angle, and dihedral angle are turned off or scaled down. When 1-2 (bonded) and 1-3 (separated by two bonds) interactions are turned off, 1-4 (separated by three bonds) interactions are scaled down, or both, all models including the Applequist model achieved similar performance: the average percentage error (APE) ranges from 1.15 to 1.23%, and the average unsigned error (AUE) ranges from 0.143 to 0.158 Å(3). When the short-range 1-2, 1-3, and full 1-4 terms are taken into account (set D models), the APE ranges from 1.30 to 1.58% for the three Thole models, whereas the Applequist model (DA) has a significantly larger APE (3.82%). The AUE ranges from 0.166 to 0.196 Å(3) for the three Thole models, compared with 0.446 Å(3) for the Applequist model. Further assessment using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact have smaller errors than the models developed using this particular data set (set E models). The fact that A, B, and C model sets are notably more accurate than both D and E model sets strongly suggests that the inclusion of 1-2 and 1-3 interactions reduces the transferability and accuracy. PMID:21391553

  2. Probing intra-molecular mechanics of single circularly permuted green fluorescent protein with atomic force microscopy

    International Nuclear Information System (INIS)

    We investigated the mechanical unfolding of single circularly permuted green fluorescent protein (cpGFP) with atomic force microscopy (AFM). The molecule was stretched from its N- and C-termini by an external force causing an elongation of the polypeptide chain up to its full length. The features of the force-extension (F-E) curves were found to depend on the stretching speed. At fast speeds, we detected one peak in the F-E curves before final rupture of the extended molecule, which we interpreted as the unfolding of two terminal halves within cpGFP. We observed several more force peaks in a sawtooth pattern at much slower speeds, and explained the appearance of such force peaks as cooperative unfolding of the hidden sub-structures inside each terminal half

  3. Atomic and molecular science with synchrotron radiation

    International Nuclear Information System (INIS)

    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. Construction of a single-axis molecular puller for measuring polysaccharide and protein mechanics by atomic force microscopy.

    Science.gov (United States)

    Rabbi, Mahir; Marszalek, Piotr E

    2007-01-01

    INTRODUCTIONPolysaccharides and proteins are frequently subjected to mechanical forces in vivo. Because these forces affect a wide range of biological activities, it is important to develop methods that directly investigate the mechanical properties of these molecules. Recent progress in techniques that allow the mechanical manipulation of biopolymers at a single-molecule level has revealed the complex nature of the elasticity of proteins and polysaccharides. The atomic force microscope (AFM) is an excellent force spectrometer for probing the mechanical properties (e.g., length and tension) of individual polysaccharides and proteins. The following protocol describes the basic design and construction of an AFM (a single-axis molecular puller) that has four parts: a head, a base, electronics, and software. Those with a background in mechanical engineering, basic knowledge of electronics and data acquisition techniques, and some computer programming skills (e.g., with LabView, Matlab, or Igor) should be able to construct this instrument. It is advisable to inspect commercial AFMs before constructing one from scratch. PMID:21357001

  5. Atomic and Molecular Physics

    OpenAIRE

    Cohen-Tannoudji, Claude

    2015-01-01

    When physicists began to explore the world of atoms more precisely, as they endeavoured to understand its structure and the laws governing its behaviour, they soon encountered serious difficulties. Our intuitive concepts, based on our daily experience of the macroscopic world around us, proved to be completely erroneous on the atomic scale; the atom was incomprehensible within the framework of classical physics. In order to uncover these new mysteries, after a great deal of trial and error, e...

  6. Molecular invariants: atomic group valence

    International Nuclear Information System (INIS)

    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)

  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. Molecular dynamics study on the atomic mechanisms of coupling motion of [0 0 1] symmetric tilt grain boundaries in copper bicrystal

    International Nuclear Information System (INIS)

    Recent research has revealed that some grain boundaries (GBs) can migrate coupled to applied shear stress. In this paper, molecular dynamics (MD) simulations were performed on sixteen [0 0 1] symmetric tilt GBs of bicrystal Cu to identify atomic-scale GB migration mechanisms and investigate their dependence on GB structure. The misorientation angles (θ) of the sixteen GBs cover the interval from 0° to 90° and a wide range of Σ values. A general method was proposed to explore the possible GB structures for each misorientation angle. Molecular statics simulation at a temperature of 0 K was carried out first to determine the equilibrium and some possible metastable structures of the sixteen investigated [0 0 1] GBs. MD simulations were then conducted on the bicrystal models at equilibrium by applying a shear strain parallel to the GB plane. Shear deformation caused the tangential translation of the grain and induced normal motion of the GBs. This boundary coupling motion was present in the entire range of misorientation angles. Different mechanisms of coupled boundary motion at atomic scale were carefully examined in this work. The common feature of these mechanisms can be regarded as the displacement of local atoms and rotation of certain structure unit. Structure phase transformation of GB was found during the migration of Σ17 (4 1 0) and Σ73 (8 3 0) GBs. (papers)

  9. 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

  10. 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.

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

    International Nuclear Information System (INIS)

    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

  12. Uncertainty Estimates for Theoretical Atomic and Molecular Data

    CERN Document Server

    Chung, H -K; Bartschat, K; Csaszar, 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 structure 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.

  13. Atomic and molecular collision processes

    International Nuclear Information System (INIS)

    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 H2

  14. Discrete atomic layers at the molecular level

    International Nuclear Information System (INIS)

    In this review, we deal with the syntheses of large discrete atomic layers at the molecular level. Spectroscopic measurements as well as X-ray crystallographic analyses lead to unambiguous characterizations of these layers. The molecular atomic layers can be considered to be parts of graphenes and related atomic layers, thereby helping to understand such indefinitely huge atomic layers or serving as seeds for the controlled synthesis of nanocarbons. (author)

  15. Molecular Mechanisms of Preeclampsia

    OpenAIRE

    Vitoratos, N.; Hassiakos, D.; C. Iavazzo

    2012-01-01

    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.

  16. 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.

  17. Virtual atomic and molecular data centre

    International Nuclear Information System (INIS)

    The Virtual Atomic and Molecular Data Centre (VAMDC, (http://www.vamdc.eu)) is a European Union funded collaboration between groups involved in the generation, evaluation, and use of atomic and molecular data. VAMDC aims to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data. The project will cover establishing the core consortium, the development and deployment of the infrastructure and the development of interfaces to the existing atomic and molecular databases. It will also provide a forum for training potential users and dissemination of expertise worldwide. This review describes the scope of the VAMDC project; it provides a survey of the atomic and molecular data sets that will be included plus a discussion of how they will be integrated. Some applications of these data are also discussed.

  18. Experimental atomic and molecular physics research

    International Nuclear Information System (INIS)

    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

  19. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

    OpenAIRE

    Huang, Yu-ming M; Chang, Chia-en A.

    2011-01-01

    Abstract Background Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusive...

  20. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

    OpenAIRE

    Huang Yu-ming M; Chang Chia-en A

    2011-01-01

    Abstract Background Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusively chooses...

  1. Perspectives and Current the Development of Non-Born-Oppenheimer Atomic and Molecular Quantum Mechanical Variational Calculations using Explicitly Correlated Gaussian Basis Functions

    Science.gov (United States)

    Sharkey, Keeper L.; Adamowicz Team

    2014-03-01

    The development of highly accurate theoretical quantum mechanics models for atomic and molecular calculations is crucial for the verification of the results of high-resolution experimental spectroscopy. High accuracy in the calculations can be achieved by not assuming the Born-Oppenheimer approximation (non-BO) and by using the variational principle. The non-relativistic Hamiltonian describing the internal state of the considered system used in the approach is obtained by separating out the center-of-mass motion from the laboratory frame Hamiltonian. The wave functions used in the calculations are expanded in terms of explicitly correlated Gaussian (ECG) functions. The optimization of the Gaussian non-linear parameters is aided by the analytical energy gradient determined with respect to these parameters. Examples of some very accurate calculations of small atoms and diatomic molecules will be presented. The presentation will also include a discussion of the extension of the approach to perform non-BO calculations of bound states of small triatomic molecules (e.g. H 3 +). Acknowledgements go to Ludwik Adamowicz for guidance and NSF for funding (DGE1-1143953).

  2. Molecular mechanisms of cholangiocarcinoma.

    Science.gov (United States)

    Fava, Giammarco

    2010-04-15

    Cholangiocarcinoma (CC), the malignant tumor of the epithelial cells lining the biliary ducts, has undergone a worldwide increase in incidence and mortality. The malignant transformation of the biliary cells originates from a multistep process evolving through chronic inflammation of the biliary tract to CC. In the last few years several advances have been towards understanding and clarifying the molecular mechanisms implicated in the cholangiocarcinogenesis process. However, many pathophysiologic aspects governing the growth of CC are still undefined. The poor prognosis of this tumor underlines the urgent need to codify the underlying molecular mechanisms involved in the growth and progression of CC in order to design effective preventive measures and valid treatment regimens. This review reports on progresses made in the last few years in clarifying the molecular pathways involved in the process of cholangiocarcinogenesis. PMID:21607138

  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. Molecular mechanisms in gliomagenesis

    DEFF Research Database (Denmark)

    Hulleman, Esther; Helin, Kristian

    2005-01-01

    , 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...... pathways. The expression of several of the components of these signaling cascades has been found altered in GBM, and recent data indicate that combinations of mutations in these pathways may contribute to GBM formation, although the exact mechanisms are still to be uncovered. Use of novel techniques...... including large-scale genomics and proteomics in combination with relevant mouse models will most likely provide novel insights into the molecular mechanisms underlying glioma formation and will hopefully lead to development of treatment modalities for GBM....

  5. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Huang Yu-ming M

    2011-05-01

    Full Text Available Abstract Background Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA domain. The first two recognize both phosphothreonine (pThr and phosphoserine (pSer residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions. Results Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA or in combination with α-helix (BRCT repeats or β-sheet (WW domain fail to differentiate pThr/pSer. Conclusions Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors.

  6. Wave mechanics of the hydrogen atom

    CERN Document Server

    Ogilvie, J F

    2016-01-01

    The hydrogen atom is a system amenable to an exact treatment within Schroedinger's formulation of quantum mechanics according to coordinates in four systems -- spherical polar, paraboloidal, ellipsoidal and spheroconical coordinates; the latter solution is reported for the first time. Applications of these solutions include angular momenta, a quantitative calculation of the absorption spectrum and accurate plots of surfaces of amplitude functions. The shape of an amplitude function, and even the quantum numbers in a particular set to specify such an individual function, depend on the coordinates in a particular chosen system, and are therefore artefacts of that particular coordinate representation within wave mechanics. All discussion of atomic or molecular properties based on such shapes or quantum numbers therefore lacks general significance

  7. 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)

  8. Atomic and molecular data for radiotherapy

    International Nuclear Information System (INIS)

    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

  9. Molecular mechanisms of cholangiocarcinoma

    OpenAIRE

    Fava, Giammarco

    2010-01-01

    Cholangiocarcinoma (CC), the malignant tumor of the epithelial cells lining the biliary ducts, has undergone a worldwide increase in incidence and mortality. The malignant transformation of the biliary cells originates from a multistep process evolving through chronic inflammation of the biliary tract to CC. In the last few years several advances have been towards understanding and clarifying the molecular mechanisms implicated in the cholangiocarcinogenesis process. However, many pathophysio...

  10. 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.

  11. 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.

  12. 1984 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.; Howard, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    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.

  13. 1985 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    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

  14. 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.

  15. Bibliography of atomic and molecular processes, 1983

    International Nuclear Information System (INIS)

    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

  16. 1982 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    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

  17. 1978 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    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

  18. 1980 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    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

  19. 1979 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    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

  20. 1984 Bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    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

  1. The atomic and molecular reaction statics

    Institute of Scientific and Technical Information of China (English)

    ZHU; ZhengHe

    2007-01-01

    This work presents a new science called atomic and molecular reaction statics (AMRS). There are four parts for AMRS, i.e. the group theoretical derivation of molecular electronic states, the principle of microscopic reversibility, the principle of microscopic transitivity and the optimum energy process rule. AMRS has been developed for about twenty years.

  2. Molecular dynamics simulation by atomic mass weighting

    OpenAIRE

    Mao, Boryeu; Friedman, Alan R.

    1990-01-01

    A molecular dynamics-based simulation method in which atomic masses are weighted is described. Results from this method showed that the capability for conformation search in molecular dynamics simulation of a short peptide (FMRF-amide) is significantly increased by mass weighting.

  3. Creating large area molecular electronic junctions using atomic layer deposition

    International Nuclear Information System (INIS)

    We demonstrate a technique for creating large area, electrically stable molecular junctions. We use atomic layer deposition to create nanometer thick passivating layers of aluminum oxide on top of self-assembled organic monolayers with hydrophilic terminal groups. This layer acts as a protective barrier and allows simple vapor deposition of the top electrode without short circuits or molecular damage. This method allows nonshorting molecular junctions of up to 9 mm2 to be easily and reliably fabricated. The effect of passivation on molecular monolayers is studied with Auger and x-ray spectroscopy, while electronic transport measurements confirm molecular tunneling as the transport mechanism for these devices

  4. Interfacing ultracold atoms and mechanical oscillators on an atom chip

    Science.gov (United States)

    Treutlein, Philipp

    2010-03-01

    Ultracold atoms can be trapped and coherently manipulated close to a chip surface using atom chip technology. This opens the exciting possibility of studying interactions between atoms and on-chip solid-state systems such as micro- and nanostructured mechanical oscillators. One goal is to form hybrid quantum systems, in which atoms are used to read out, cool, and coherently manipulate the oscillators' state. In our work, we investigate different coupling mechanisms between ultracold atoms and mechanical oscillators. In a first experiment, we use atom-surface forces to couple the vibrations of a mechanical cantilever to the motion of a Bose-Einstein condensate in a magnetic microtrap on an atom chip. The atoms are trapped at about one micrometer distance from the cantilever surface. We make use of the coupling to read out the cantilever vibrations with the atoms and observe resonant coupling to several well-resolved mechanical modes of the condensate. In a second experiment, we investigate coupling via a 1D optical lattice that is formed by a laser beam retroreflected from a SiN membrane oscillator. The optical lattice serves as a `transfer rod' that couples vibrations of the membrane to the atoms and vice versa. We point out that the strong coupling regime can be reached in coupled atom-oscillator systems by placing both the atoms and the oscillator in a high-finesse optical cavity.

  5. Theoretical atomic and molecular physics: Progress report

    International Nuclear Information System (INIS)

    The theoretical atomic and molecular physics program at Rice University addresses basic problems on the structure and collision dynamics of electrons, atoms, ions and molecules, emphasizing processes related to possible new energy technologies and other applications. The program focuses on collision processes under ''disturbed'' conditions, i.e., high levels of excitation, ionization, energy transfer, and external influences. Research projects include: collision processes in ICF plasmas; excitation and charge-transfer processes; Rydberg atom collisions; Penning ionization of atoms; excitation in electron-molecule collisions; and related topics. 48 refs

  6. 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

  7. Experimental study of the collision mechanisms involved in one-electron capture by slow N5+ ions in atomic and molecular hydrogen

    International Nuclear Information System (INIS)

    Translational energy spectroscopy (TES) in the range 214-857 eV amu-1 has been used to study the collision mechanisms involved in one-electron capture by slow helium-like N5+ in both atomic and molecular hydrogen. In the case of N5+-H2 collisions, our measurements show that non-dissociative electron capture leading to the N4+ (n=3) states is the main product channel at the higher impact energies with smaller contributions to the N4+ (n=4) states. While this has also been observed in previous studies based on photon emission spectroscopy (PES), there are substantial differences in both magnitude and energy dependence between the TES and PES results. Theoretical predictions for n=3 formation are also in poor accord with experiment. Unlike previous PES measurements, the present TES study has been able to identify the presence of dissociative one-electron capture channels and two-electron autoionizing capture channels, both leading to N4+ (n=2) formation. Two-electron autoionizing electron capture is found to be the main collision mechanism leading to N4+ ions at the lowest energies considered. Our measurements of one-electron capture in N5+ + H(1s) are in excellent accord with previous higher measurements based on PES and now provide a useful extension to energies below 1 keV amu-1. In this case, only the N4+ (n=4) and N4+ (n=3) product channels are observed, with contributions from the latter becoming insignificant at our lowest energies

  8. Atomic and molecular data for radiotherapy

    International Nuclear Information System (INIS)

    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

  9. Wave Mechanics of a Two Wire Atomic Beamsplitter

    OpenAIRE

    Bortolotti, Daniele C. E.; Bohn, John L.

    2003-01-01

    We consider the problem of an atomic beam propagating quantum mechanically through an atom beam splitter. Casting the problem in an adiabatic representation (in the spirit of the Born-Oppenheimer approximation in molecular physics) sheds light on explicit effects due to non-adiabatic passage of the atoms through the splitter region. We are thus able to probe the fully three dimensional structure of the beam splitter, gathering quantitative information about mode-mixing, splitting ratios,and r...

  10. Wave Mechanics of a Two Wire Atomic Beamsplitter

    CERN Document Server

    Bortolotti, D C E; Bortolotti, Daniele C. E.; Bohn, John L.

    2004-01-01

    We consider the problem of an atomic beam propagating quantum mechanically through an atom beam splitter. Casting the problem in an adiabatic representation (in the spirit of the Born-Oppenheimer approximation in molecular physics) sheds light on explicit effects due to non-adiabatic passage of the atoms through the splitter region. We are thus able to probe the fully three dimensional structure of the beam splitter, gathering quantitative information about mode-mixing, splitting ratios,and reflection and transmission probabilities.

  11. Wave mechanics of a two-wire atomic beam splitter

    International Nuclear Information System (INIS)

    We consider the problem of an atomic beam propagating quantum mechanically through an atom beam splitter. Casting the problem in an adiabatic representation (in the spirit of the Born-Oppenheimer approximation in molecular physics) sheds light on explicit effects due to nonadiabatic passage of the atoms through the splitter region. We are thus able to probe the fully three-dimensional structure of the beam splitter, gathering quantitative information about mode mixing, splitting ratios, and reflection and transmission probabilities

  12. Committee on Atomic, Molecular and Optical Sciences

    Energy Technology Data Exchange (ETDEWEB)

    Lancaster, James [National Academy of Sciences, Washington, DC (United States)

    2015-06-30

    The Committee on Atomic, Molecular, and Optical Sciences (CAMOS) is a standing activity of the National Research Council (NRC) that operates under the auspices of the Board on Physics and Astronomy. CAMOS is one of five standing committees of the BPA that are charged with assisting it in achieving its goals—monitoring the health of physics and astronomy, identifying important new developments at the scientific forefronts, fostering interactions with other fields, strengthening connections to technology, facilitating effective service to the nation, and enhancing education in physics. CAMOS provides these capabilities for the atomic, molecular and optical (AMO) sciences.

  13. Atomic and molecular database activities at NIFS

    International Nuclear Information System (INIS)

    Recent activities on atomic and molecular data research and database development in NIFS are summarized. Comprehensive collision data set for Fe ions were compiled for electron-density diagnostics of laboratory and solar plasmas. Spectroscopic studies on atomic processes of highly charged impurity ions are performed by means of Electron-Beam-Ion-Trap (EBIT) and Large-Helical-Device (LHD). New database for photo-absorption cross sections is under development upon data demands in radiation transport studies for magnetic fusion devices. Importance of acquiring atomic collision data for tritium and knowledge on hydrogen isotopic effects in edge plasmas is pointed out. (author)

  14. 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...

  15. 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

    2004-05-15

    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

  16. Stout: Cloudy's Atomic and Molecular Database

    CERN Document Server

    Lykins, M L; Kisielius, R; Chatzikos, M; Porter, R L; van Hoof, P A M; Williams, R J R; Keenan, F P; Stancil, P C

    2015-01-01

    We describe a new atomic and molecular database we developed for use in the spectral synthesis code Cloudy. The design of Stout is driven by the data needs of Cloudy, which simulates molecular, atomic, and ionized gas with kinetic temperatures 2.8 K < T < 1e10 K and densities spanning the low to high-density limits. The radiation field between photon energies $10^{-8}$ Ry and 100 MeV is considered, along with all atoms and ions of the lightest 30 elements, and ~100 molecules. For ease of maintenance, the data are stored in a format as close as possible to the original data sources. Few data sources include the full range of data we need. We describe how we fill in the gaps in the data or extrapolate rates beyond their tabulated range. We tabulate data sources both for the atomic spectroscopic parameters and for collision data for the next release of Cloudy. This is not intended as a review of the current status of atomic data, but rather a description of the features of the database which we will build ...

  17. Molecular dynamics investigation of mechanical mixing in mechanical alloying

    International Nuclear Information System (INIS)

    Molecular dynamic simulation is exploited to obtain a deep insight of atomic scale mixing and amorphization mechanisms happening during mechanical mixing. Impact-relaxation cycles are performed to simulate the mechanical alloying process. The results obtained by structural analysis shows that the final structure obtained through simulation of mechanical alloying is in an amorphous state. This analysis reveals that amorphization occurs concurrently with the attainment of a perfectly mixed alloy. The results indicate diffusion and deformation are two important mechanisms for mixing during mechanical alloying. The rate of diffusion is controlled by the temperature and by the density of defects in the structure. Deformation enhances mixing directly by sliding atomic layers on each other and increases the number of defects in the structure. The results agree with mechanical alloying experiments described in the literature

  18. Molecular dynamics investigation of mechanical mixing in mechanical alloying

    Energy Technology Data Exchange (ETDEWEB)

    Ali Nematollahi, Gh. [Department of Ceramic, Materials and Energy Research Center, Karaj, Tehran (Iran, Islamic Republic of)], E-mail: ali61gh@yahoo.com; Marzbanrad, E.; Aghaei, A.R. [Department of Ceramic, Materials and Energy Research Center, Karaj, Tehran (Iran, Islamic Republic of)

    2008-09-25

    Molecular dynamic simulation is exploited to obtain a deep insight of atomic scale mixing and amorphization mechanisms happening during mechanical mixing. Impact-relaxation cycles are performed to simulate the mechanical alloying process. The results obtained by structural analysis shows that the final structure obtained through simulation of mechanical alloying is in an amorphous state. This analysis reveals that amorphization occurs concurrently with the attainment of a perfectly mixed alloy. The results indicate diffusion and deformation are two important mechanisms for mixing during mechanical alloying. The rate of diffusion is controlled by the temperature and by the density of defects in the structure. Deformation enhances mixing directly by sliding atomic layers on each other and increases the number of defects in the structure. The results agree with mechanical alloying experiments described in the literature.

  19. Atomic and molecular database for fusion

    International Nuclear Information System (INIS)

    Workshop on 'Atomic and Molecular Database for Fusion' was held at the Institute of Plasma Physics on 20th January 1989 under a callaborating research program of Research Information Center at the Institute of Plasma Physics, Nagoya University. This joint program aims to construct a database which is easy to manipulate for plasma physicist. The database will consists of the evaluated data for rata coefficients for various collisional processes. (author)

  20. 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...... difficulties in sampling conformational space in a statistically acceptable manner. As the parameters representinteractions per unit molecular surface area and all of the molecules consist of -CH2OH or -CH2O- units, the values obtained for thewater/1,2-ethanediol system were used to predict VLE data for the......,2-ethanediol, 1,2-propanediol and glycerol, surrounded by different numbers of water molecules. The interaction energy was observed to be linearly dependent on the number of water molecules present. This constant increment means that the additional interaction energy for each water molecule added is the same...

  1. Coupling cold atoms with mechanical oscillators

    Science.gov (United States)

    Montoya, Cris; Valencia, Jose; Geraci, Andrew; Eardley, Matthew; Kitching, John

    2014-05-01

    Macroscopic systems, coupled to quantum systems with well understood coherence properties, can enable the study of the boundary between quantum microscopic phenomena and macroscopic systems. Ultra-cold atoms can be probed and manipulated with micro-mechanical resonators that provide single-spin sensitivity and sub-micron spatial resolution, facilitating studies of decoherence and quantum control. In the future, hybrid quantum systems consisting of cold atoms interfaced with mechanical devices may have applications in quantum information science. We describe our experiment to couple laser-cooled Rb atoms to a magnetic cantilever tip. This cantilever is precisely defined on the surface of a chip with lithography and the atoms are trapped at micron-scale distances from this chip. To match cantilever mechanical resonances, atomic magnetic resonances are tuned with a magnetic field.

  2. 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.

  3. Atomic and molecular phases through attosecond streaking

    DEFF Research Database (Denmark)

    Baggesen, Jan Conrad; Madsen, Lars Bojer

    2011-01-01

    In attosecond streaking, an electron is released by a short xuv pulse into a strong near infrared laser field. If the laser couples two states in the target, the streaking technique, which allows for a complete determination of the driving field, also gives an accurate measurement of the relative...... 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...

  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 and molecular data needs for fusion

    International Nuclear Information System (INIS)

    Atomic and molecular processes in plasmas play a crucial role in the development of net energy producing magnetic fusion devices. In light of this fact, presented here is a survey of the broad needs of fusion energy research and a review of the status of the existing database. Emphasis is placed on the relatively new needs for data as novel materials are evaluated for use in the next devices, and as components such as the divertor take on more significance for demonstration and practical reactors. Also, examples are given of recent or ongoing data evaluation efforts, the role of national and international data centers is discussed, and some summarizing comments are given

  6. The Atomic-scale Finite Element Method for Analyzing Mechanical Behavior of Carbon Nanotube and Quartz

    OpenAIRE

    Kim, Kyusang

    2006-01-01

    The mechanical behavior of discrete atoms has been studied with molecular dynamics whose computational time is proportional to the square of the number of atoms, O(N2). Recently, a faster algorithm, Atomic-scale Finite Element Method (AFEM) with computational time proportional to the number of atoms, O(N), had been developed. The main idea of AFEM, compared with conventional finite element method is to replace nodes with atoms and elements with electric forces between atoms. When interpreting...

  7. International bulletin on atomic and molecular data for fusion

    International Nuclear Information System (INIS)

    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

  8. Tunneling Dynamics Between Atomic and Molecular Bose-Einstein Condensates

    Institute of Scientific and Technical Information of China (English)

    CHEN Chang-Yong

    2004-01-01

    Tunneling dynamics of multi-atomic molecules between atomic and multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated.It is indicated that the tunneling in the two Bose-Einstein condensates depends on not only the inter-atomic-molecular nonlinear interactions and the initial number of atoms in these condensates,but also the tunneling coupling between the atomic condensate and the multi-atomic molecular condensate.It is discovered that besides oscillating tunneling current between the atomic condensate and the multi-atomic molecular condensate,the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance:a macroscopic quantum self-trapping effect.The influence of de-coherence caused by non-condensate atoms on the tunneling dynamics is studied.It is shown that de-coherence suppresses the multi-atomic molecular tunneling.Moreover,the conception of the molecular Bose-Einstein condensate,which is different from the conventional single-atomic Bose-Einstein condensate,is specially emphasized in this paper.

  9. Systemic structural modular generalization of the crystallography of bound water applied to study the mechanisms of processes in biosystems at the atomic and molecular level

    International Nuclear Information System (INIS)

    The main reasons of the modern scientific revolution, one of the consequences of which are nanotechnologies and the development of interdisciplinary overall natural science (which can build potentially possible atomic structures and study the mechanisms of the processes occurring in them), are considered. The unifying role of crystallography in the accumulation of interdisciplinary knowledge is demonstrated. This generalization of crystallography requires the introduction of a new concept: a module which reflects the universal condition for stability of all real and potential and equilibrium and nonequilibrium structures of matter (their connectivity). A modular generalization of crystallography covers all forms of solids, including the structure of bound water (a system-forming matrix for the self-organization and morphogenesis of hierarchical biosystems which determines the metric selection of all other structural components of these systems). A dynamic model of the water surface layer, which serves as a matrix in the formation of Langmuir monolayers and plays a key role in the occurrence of life on the Earth, is developed.

  10. Molecular mechanisms of rosacea pathogenesis

    Directory of Open Access Journals (Sweden)

    Davydova A.M.

    2013-09-01

    Full Text Available The article presents possible molecular mechanisms for rosacea pathogenesis from current domestic and foreign clinical observations and laboratory research: regulation and expression defects of antimicrobial peptides, vascular endothelial growth factor, the effect of serine proteases, oxidative stress, reactive oxygen species and ferritin on the occurrence and course of rosacea. New developments in molecular biology and genetics are advanced for researching the interaction of multiple factors involved in rosacea pathogenesis, as well as providing the bases for potentially new therapies.

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

    International Nuclear Information System (INIS)

    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

  12. 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

    A scanning tunneling microscope supplemented with a force sensor is used to study the mechanical properties of a novel metallic nanostructure: a freely suspended chain of single gold atoms. We find that the bond strength of the nanowire is about twice that of a bulk metallic bond. We perform ab...... 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...... stiffness of the nanostructure is strongly affected by the detailed local atomic arrangement at the chain bases....

  13. Collective mechanisms for atomic processes in plasmas

    International Nuclear Information System (INIS)

    New mechanisms for atomic processes in plasmas induced by the collective behavior of the system are proposed, the collective behavior being a consequence of the long range of the Coulomb forces between the (charged) particles. These new mechanisms are hydrogen recombination with plasmon emission, ionization by plasmon absorption, and bound-bound and free-free atomic transitions with emission or absorption of plasmons. The Bohm-Pines Fock-Tani Hamiltonian for a proton at rest immersed in a finite temperature plasma (in the electron gas model), is obtained from first principles by a sequence of canonical transformations. This Hamiltonian shows explicitly the new proposed reaction and scattering mechanisms, in which, the emission or absorption of plasmons allow the process to occur. Expressions for plasmonic recombination matrix elements in the orthogonalized Born approximation (OBA) and the distorted wave Born approximation (DWBA) are given in terms of 6- or 12-dimensional integrals which are reduced analytically to 2-dimensional integrals. Explicit evaluations of the cross section for the plasmonic and radiative recombination in the (OBA) are obtained. The results indicate that the radiative mechanism is negligible compared to the plasmonic mode for the value of the parameters and quantum numbers indicated above. Finally by using a generalized Schroedinger equation for composite particles in a medium he recalculates the energy shift of a hydrogen atom produced by the exchange between a free electron and the bound atomic electron. The result shows that the shifts are important for the highly excited states of atoms in plasmas

  14. Reaction of tungsten anion clusters with molecular and atomic nitrogen

    OpenAIRE

    Kim, Young Dok; Stolcic, Davor; Fischer, Matthias; Ganteför, Gerd

    2003-01-01

    Ultraviolet photoelectron spectra for WnN-2 (n=1 8) clusters produced by addition of atomic and molecular nitrogen on W anion clusters are presented. Evidence is provided that molecular chemisorption of N2 is more stable than the dissociative one on tungsten anion clusters consisting of eight atoms or less, which is completely different from the results on tungsten bulk surfaces. A general tendency toward molecular chemisorption for small clusters can be explained by reduced charge transfer f...

  15. Atomic and Molecular Phases of the Interstellar Medium

    CERN Document Server

    Mac Low, Mordecai-Mark

    2016-01-01

    This review covers four current questions in the behavior of the atomic and molecular interstellar medium. These include whether the atomic gas originates primarily in cold streams or hot flows onto galaxies; what the filling factor of cold gas actually is in galactic regions observationally determined to be completely molecular; whether molecular hydrogen determines or merely traces star formation; and whether gravity or turbulence drives the dynamical motions observed in interstellar clouds, with implications on their star formation properties.

  16. Atomic mechanisms of unalloyed iron vitrification

    International Nuclear Information System (INIS)

    It is shown within the frames of the molecular dynamic method on the iron model with the pair potential of the Pak-Doyama interatomic interaction that the structural stabilization of the pure iron amorphous phase in the process of hardening from the melt is based on the percolation cluster formation from the interpenetrating and mutually contacting icosahedrons, in the tops and centers whereof the atoms are positioned. The revealed regularities of the icosahedral substructure self-organization by vitrification correlated well with the temperature dependences of the basic thermodynamic characteristics

  17. Mechanics at the molecular scale: Insight into the physical mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Neucheva, Olga A.; Temirov, Ruslan; Tautz, Stefan [Institut fuer Bio- und Nanosysteme (IBN-3) and JARA - Fundamental of Future Information Technology, Forschungszentrum Juelich, 52425 Juelich (Germany)

    2010-07-01

    The manipulation of atoms and molecules is one of the problems under investigation in a surface science. The first successful attempt to transfer an atom from a surface with use of a scanning tunneling microscope has been realized by Eigler et al. An interest to understand the underlying physical mechanism from both experimental and theoretical points of view has led to investigations of many systems which can be used as atomic and molecular switches. In our work the behaviour of a single PTCDA molecule on Ag(111) has been investigated with a LT-STM. Two level fluctuations of the conductance of the junction have been observed within a narrow range of the tip heights and bias voltages. The bistability is related to reversible switching of one of the carboxylic oxygen atoms between the surface and the STM-tip. The current passing through the junction induces vibrations of the molecule leading to weakening and breaking of a chemical bond with the surface and establishing a new one with the tip and vice versa. The switching frequency strongly depends on the bias voltages and tip heights, following a non-linear dependence on the current.

  18. Screened Electrostatic Interactions in Molecular Mechanics.

    Science.gov (United States)

    Wang, Bo; Truhlar, Donald G

    2014-10-14

    In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal

  19. Molecular Mechanisms Underlying Bacterial Persisters

    DEFF Research Database (Denmark)

    Maisonneuve, Etienne; Gerdes, Kenn

    2014-01-01

    All bacteria form persisters, cells that are multidrug tolerant and therefore able to survive antibiotic treatment. Due to the low frequencies of persisters in growing bacterial cultures and the complex underlying molecular mechanisms, the phenomenon has been challenging to study. However, recent...... technological advances in microfluidics and reporter genes have improved this scenario. Here, we summarize recent progress in the field, revealing the ubiquitous bacterial stress alarmone ppGpp as an emerging central regulator of multidrug tolerance and persistence, both in stochastically and environmentally...

  20. Atomic vacancies significantly degrade the mechanical properties of phosphorene

    Science.gov (United States)

    Sha, Zhen-Dong; Pei, Qing-Xiang; Zhang, Ying-Yan; Zhang, Yong-Wei

    2016-08-01

    Due to low formation energies, it is very easy to create atomic defects in phosphorene during its fabrication process. How these atomic defects affect its mechanical behavior, however, remain unknown. Here, we report on a systematic study of the effect of atomic vacancies on the mechanical properties and failure behavior of phosphorene using molecular dynamics simulations. It is found that atomic vacancies induce local stress concentration and cause early bond-breaking, leading to a significant degradation of the mechanical properties of the material. More specifically, a 2% concentration of randomly distributed mono-vacancies is able to reduce the fracture strength by ∼40%. An increase in temperature from 10 to 400 K can further deteriorate the fracture strength by ∼60%. The fracture strength of defective phosphorene is also found to be affected by defect distribution. When the defects are patterned in a line, the reduction in fracture strength greatly depends on the tilt angle and the loading direction. Furthermore, we find that di-vacancies cause an even larger reduction in fracture strength than mono-vacancies when the loading is in an armchair direction. These findings provide important guidelines for the structural design of phosphorene in future applications.

  1. Atomic vacancies significantly degrade the mechanical properties of phosphorene.

    Science.gov (United States)

    Sha, Zhen-Dong; Pei, Qing-Xiang; Zhang, Ying-Yan; Zhang, Yong-Wei

    2016-08-01

    Due to low formation energies, it is very easy to create atomic defects in phosphorene during its fabrication process. How these atomic defects affect its mechanical behavior, however, remain unknown. Here, we report on a systematic study of the effect of atomic vacancies on the mechanical properties and failure behavior of phosphorene using molecular dynamics simulations. It is found that atomic vacancies induce local stress concentration and cause early bond-breaking, leading to a significant degradation of the mechanical properties of the material. More specifically, a 2% concentration of randomly distributed mono-vacancies is able to reduce the fracture strength by ∼40%. An increase in temperature from 10 to 400 K can further deteriorate the fracture strength by ∼60%. The fracture strength of defective phosphorene is also found to be affected by defect distribution. When the defects are patterned in a line, the reduction in fracture strength greatly depends on the tilt angle and the loading direction. Furthermore, we find that di-vacancies cause an even larger reduction in fracture strength than mono-vacancies when the loading is in an armchair direction. These findings provide important guidelines for the structural design of phosphorene in future applications. PMID:27345189

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

    International Nuclear Information System (INIS)

    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+ [Phys. Rev. A, 81, 043428 (2010)]. Limits of the method and potential applications for molecular spectroscopy are discussed

  3. Anticancer Molecular Mechanisms of Resveratrol

    Science.gov (United States)

    Varoni, Elena M.; Lo Faro, Alfredo Fabrizio; Sharifi-Rad, Javad; Iriti, Marcello

    2016-01-01

    Resveratrol is a pleiotropic phytochemical belonging to the stilbene family. Though it is only significantly present in grape products, a huge amount of preclinical studies investigated its anticancer properties in a plethora of cellular and animal models. Molecular mechanisms of resveratrol involved signaling pathways related to extracellular growth factors and receptor tyrosine kinases; formation of multiprotein complexes and cell metabolism; cell proliferation and genome instability; cytoplasmic tyrosine kinase signaling (cytokine, integrin, and developmental pathways); signal transduction by the transforming growth factor-β super-family; apoptosis and inflammation; and immune surveillance and hormone signaling. Resveratrol also showed a promising role to counteract multidrug resistance: in adjuvant therapy, associated with 5-fluoruracyl and cisplatin, resveratrol had additive and/or synergistic effects increasing the chemosensitization of cancer cells. Resveratrol, by acting on diverse mechanisms simultaneously, has been emphasized as a promising, multi-target, anticancer agent, relevant in both cancer prevention and treatment.

  4. Atomic and Molecular Aspects of Astronomical Spectra

    OpenAIRE

    Sochi, T.

    2012-01-01

    In the first section of this thesis, we present the atomic part of our investigation. A C2+ atomic target was prepared and used to generate theoretical data required in the investigation of recombination lines that arise from collisions between electrons and ions in thin plasma found in planetary nebulae and other astrophysical objects. The R-matrix method of electron scattering theory was used to describe the C2+ plus electron system. Theoretical data concerning bound and autoionizing states...

  5. Cell mechanics measured with Atomic force microscopy

    International Nuclear Information System (INIS)

    Full text: In this contribution, I would like to present recent results about cell mechanics obtained with atomic force microscopy and its relation with basic soft matter science. We will present a novel way to obtain viscoelastic properties (Young modulus, relaxation time and viscosity) of breast cancer cells based on stress relaxation and creep measurements. Additionally we will show the influence of applied stress on red blood cell shape. The importance of such type of measurements on soft matter physics, cell biology, and biomedical science. (author)

  6. Recent progress of atomic and molecular database in IAPCM

    International Nuclear Information System (INIS)

    Our recent work and progress on atomic and molecular database will be introduce in detail in the present report, which includes constructing the website with versions of homepages in Chinese and English, data collecting, compiling, and evaluation, data calculation and assessment, discussing and framing the data structure and format, and so on. Now our atomic and molecular database can be freely accessed through the website http://www.camdb.ac.cn. Details of our database website will also be introduced. (author)

  7. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

    Science.gov (United States)

    Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna

    2016-01-01

    Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations. PMID:26733483

  8. Molecular Mechanisms of Cardiovascular Aging

    Directory of Open Access Journals (Sweden)

    Anna Meiliana

    2013-12-01

    Full Text Available BACKGROUND: The average lifespan of humans is increasing, and with it the percentage of people entering the 65 and older age group is growing rapidly and will continue to do so in the next 20 years. Within this age group, cardiovascular disease will remain the leading cause of death, and the cost associated with treatment will continue to increase. Aging is an inevitable part of life and unfortunately poses the largest risk factor for cardiovascular disease. CONTENT: We provide an overview of some of the molecular mechanisms involved in regulating lifespan and health, including mitochondria, telomeres, stem cells, sirtuins, Adenosine Monophosphate-activated Protein Kinase, Mammalian Target of Rapamycin and Insulin-like Growth Factor 1. We also provide future perspectives of lifespan and health, which are intimately linked fields. SUMMARY: Aging remains the biggest non-modifiable risk factor for cardiovascular disease. The biological, structural and mechanical changes in senescent cardiovascular system are thought to contribute in increasing incidence of cardiovascular disease in aging. Understanding the mechanisms contributing to such changes is therefore crucial for both prevention and development of treatment for cardiovascular diseases. KEYWORDS: cardiovascular aging, mitochondria, telomeres, sirtuin, stem cells.

  9. Investigating cell mechanics with atomic force microscopy.

    Science.gov (United States)

    Haase, Kristina; Pelling, Andrew E

    2015-03-01

    Transmission of mechanical force is crucial for normal cell development and functioning. However, the process of mechanotransduction cannot be studied in isolation from cell mechanics. Thus, in order to understand how cells 'feel', we must first understand how they deform and recover from physical perturbations. Owing to its versatility, atomic force microscopy (AFM) has become a popular tool to study intrinsic cellular mechanical properties. Used to directly manipulate and examine whole and subcellular reactions, AFM allows for top-down and reconstitutive approaches to mechanical characterization. These studies show that the responses of cells and their components are complex, and largely depend on the magnitude and time scale of loading. In this review, we generally describe the mechanotransductive process through discussion of well-known mechanosensors. We then focus on discussion of recent examples where AFM is used to specifically probe the elastic and inelastic responses of single cells undergoing deformation. We present a brief overview of classical and current models often used to characterize observed cellular phenomena in response to force. Both simple mechanistic models and complex nonlinear models have been used to describe the observed cellular behaviours, however a unifying description of cell mechanics has not yet been resolved. PMID:25589563

  10. 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.

  11. 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.

  12. Atomic and molecular manipulation with the scanning tunneling microscope.

    Science.gov (United States)

    Stroscio, J A; Eigler, D M

    1991-11-29

    The prospect of manipulating matter on the atomic scale has fascinated scientists for decades. This fascination may be motivated by scientific and technological opportunities, or from a curiosity about the consequences of being able to place atoms in a particular location. Advances in scanning tunneling microscopy have made this prospect a reality; single atoms can be placed at selected positions and structures can be built to a particular design atom-by-atom. Atoms and molecules may be manipulated in a variety of ways by using the interactions present in the tunnel junction of a scanning tunneling microscope. Some of these recent developments and some of the possible uses of atomic and molecular manipulation as a tool for science are discussed. PMID:17773601

  13. 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.

  14. 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...

  15. Partitioning of the molecular density matrix over atoms and bonds

    CERN Document Server

    Vanfleteren, Diederik; Bultinck, Patrick; Ayers, Paul W; Waroquier, Michel; 10.1063/1.3394018

    2011-01-01

    A double-index atomic partitioning of the molecular first-order density matrix is proposed. Contributions diagonal in the atomic indices correspond to atomic density matrices, whereas off-diagonal contributions carry information about the bonds. The resulting matrices have good localization properties, in contrast to single-index atomic partitioning schemes of the molecular density matrix. It is shown that the electron density assigned to individual atoms, when derived from the density matrix partitioning, can be made con- sistent with well-known partitions of the electron density over AIM basins, either with sharp or with fuzzy boundaries. The method is applied to a test set of about 50 molecules, representative for various types of chemical binding. A close correlation is observed between the trace of the bond matrices and the SEDI (shared electron density index) bond index.

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

    International Nuclear Information System (INIS)

    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)

  17. Atomic and Molecular Aspects of Astronomical Spectra

    CERN Document Server

    Sochi, Taha

    2012-01-01

    In the first section we present the atomic part where a C2+ atomic target was prepared and used to generate theoretical data to investigate recombination lines arising from electron-ion collisions in thin plasma. R-matrix method was used to describe the C2+ plus electron system. Theoretical data concerning bound and autoionizing states were generated in the intermediate-coupling approximation. The data were used to generate dielectronic recombination data for C+ which include transition lines, oscillator strengths, radiative transition probabilities, emissivities and dielectronic recombination coefficients. The data were cast in a line list containing 6187 optically-allowed transitions which include many C II lines observed in astronomical spectra. This line list was used to analyze the spectra from a number of astronomical objects, mainly planetary nebulae, and identify their electron temperature. The electron temperature investigation was also extended to include free electron energy analysis to investigate...

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

    Science.gov (United States)

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

    1989-02-01

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

  19. Lecture notes on atomic and molecular physics

    CERN Document Server

    Erkoc, Sakir

    1996-01-01

    This book aims to present a unified account of the physics of atoms and molecules from a modern viewpoint. It is based on courses given by the authors at Middle East Technical University, Ankara and Georgia Institute of Technology, Atlanta, and is suitable for study at third and fourth year levels of an undergraduate course.Students should be able to read this volume and understand its contents without the need to supplement it by referring to more detailed discussions. The whole subject covered in this volume is expected to be finished in one semester.

  20. The virtual atomic and molecular data centre (VAMDC) consortium

    Science.gov (United States)

    Dubernet, M. L.; Antony, B. K.; Ba, Y. A.; Babikov, Yu L.; Bartschat, K.; Boudon, V.; Braams, B. J.; Chung, H.-K.; Daniel, F.; Delahaye, F.; Del Zanna, G.; de Urquijo, J.; Dimitrijević, M. S.; Domaracka, A.; Doronin, M.; Drouin, B. J.; Endres, C. P.; Fazliev, A. Z.; Gagarin, S. V.; Gordon, I. E.; Gratier, P.; Heiter, U.; Hill, C.; Jevremović, D.; Joblin, C.; Kasprzak, A.; Krishnakumar, E.; Leto, G.; Loboda, P. A.; Louge, T.; Maclot, S.; Marinković, B. P.; Markwick, A.; Marquart, T.; Mason, H. E.; Mason, N. J.; Mendoza, C.; Mihajlov, A. A.; Millar, T. J.; Moreau, N.; Mulas, G.; Pakhomov, Yu; Palmeri, P.; Pancheshnyi, S.; Perevalov, V. I.; Piskunov, N.; Postler, J.; Quinet, P.; Quintas-Sánchez, E.; Ralchenko, Yu; Rhee, Y.-J.; Rixon, G.; Rothman, L. S.; Roueff, E.; Ryabchikova, T.; Sahal-Bréchot, S.; Scheier, P.; Schlemmer, S.; Schmitt, B.; Stempels, E.; Tashkun, S.; Tennyson, J.; Tyuterev, Vl G.; Vujčić, V.; Wakelam, V.; Walton, N. A.; Zatsarinny, O.; Zeippen, C. J.; Zwölf, C. M.

    2016-04-01

    The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium is a worldwide consortium which federates atomic and molecular databases through an e-science infrastructure and an organisation to support this activity. About 90% of the inter-connected databases handle data that are used for the interpretation of astronomical spectra and for modelling in many fields of astrophysics. Recently the VAMDC Consortium has connected databases from the radiation damage and the plasma communities, as well as promoting the publication of data from Indian institutes. This paper describes how the VAMDC Consortium is organised for the optimal distribution of atomic and molecular data for scientific research. It is noted that the VAMDC Consortium strongly advocates that authors of research papers using data cite the original experimental and theoretical papers as well as the relevant databases. .

  1. Early Atomic Models - From Mechanical to Quantum (1904-1913)

    OpenAIRE

    Baily, Charles

    2012-01-01

    A complete history of early atomic models would fill volumes, but a reasonably coherent tale of the path from mechanical atoms to the quantum can be told by focusing on the relevant work of three great contributors to atomic physics, in the critically important years between 1904 and 1913: J.J. Thomson, Ernest Rutherford and Niels Bohr. We first examine the origins of Thomson’s mechanical atomic models, from his ethereal vortex atoms in the early 1880’s, to the myriad “corpuscular” atoms he p...

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

    International Nuclear Information System (INIS)

    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.

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

    International Nuclear Information System (INIS)

    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

  4. Line emission processes in atomic and molecular shocks

    International Nuclear Information System (INIS)

    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

  5. Atoms

    International Nuclear Information System (INIS)

    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)

  6. Molecular deformation mechanisms in polyethylene.

    OpenAIRE

    Coutry, Sandry

    2001-01-01

    This work is concerned with details of the molecular changes caused by deformation and also establishes any conformational differences between linear and branched polyethylene before, during and after deformation. Four blends of isotopically labelled polymers of different types, rapidly quenched from the melt, have been studied by Mixed Crystal Infra-red Spectroscopy and Small Angle Neutron Scattering (SANS), in order to clarify any differences in the molecular basis of drawing...

  7. Theory of quantum and classical connections in modeling atomic, molecular and electrodynamical systems

    CERN Document Server

    Popa, Alexandru

    2013-01-01

    Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamic Systems is intended for scientists and graduate students interested in the foundations of quantum mechanics and applied scientists interested in accurate atomic and molecular models. This is a reference to those working in the new field of relativistic optics, in topics related to relativistic interactions between very intense laser beams and particles, and is based on 30 years of research. The novelty of this work consists of accurate connections between the properties of quantum equations and correspon

  8. Atomic and Molecular Data and Their Applications. Proceedings

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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)

  11. Multimillion atom molecular dynamics simulations of glasses and ceramic materials

    International Nuclear Information System (INIS)

    Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed. (c) 1999 American Institute of Physics

  12. 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 and a...

  13. From the warm magnetized atomic medium to molecular clouds

    CERN Document Server

    Hennebelle, P; Vázquez-Semadeni, E; Klessen, R; Audit, E

    2008-01-01

    {It has recently been proposed that giant molecular complexes form at the sites where streams of diffuse warm atomic gas collide at transonic velocities.} {We study the global statistics of molecular clouds formed by large scale colliding flows of warm neutral atomic interstellar gas under ideal MHD conditions. The flows deliver material as well as kinetic energy and trigger thermal instability leading eventually to gravitational collapse.} {We perform adaptive mesh refinement MHD simulations which, for the first time in this context, treat self-consistently cooling and self-gravity.} {The clouds formed in the simulations develop a highly inhomogeneous density and temperature structure, with cold dense filaments and clumps condensing from converging flows of warm atomic gas. In the clouds, the column density probability density distribution (PDF) peaks at $\\sim 2 \\times 10^{21} \\psc$ and decays rapidly at higher values; the magnetic intensity correlates weakly with density from $n \\sim 0.1$ to $10^4 \\pcc$, an...

  14. Atomic and molecular spectroscopy of transition metals in condensed helium

    International Nuclear Information System (INIS)

    Full text: We investigated laser induced fluorescence spectra of copper and gold atoms and dimers thereof isolated in solid and liquid 4He. Among the atomic spectral lines the most interesting ones are forbidden transitions that involve electrons from inner d-shells which are screened from the surrounding He atoms by the outer s-shell and are therefore much less affected by the interaction with the He matrix. Indeed, the observed spectral lineshapes are much narrower than those of transitions involving outer shell electrons. Another important result is the observation of well resolved vibrational structures in five molecular bands of the Au2 and Cu2 dimers. We expect that the analysis of those spectra will significantly advance our understanding of impurity atoms and molecules in condensed He. (author)

  15. Normal Mode Analysis with Molecular Geometry Restraints: Bridging Molecular Mechanics and Elastic Models

    OpenAIRE

    Lu, Mingyang; Ma, Jianpeng

    2011-01-01

    A new method for normal mode analysis is reported for all-atom structures using molecular geometry restraints (MGR). Similar to common molecular mechanics force fields, the MGR potential contains short- and long-range terms. The short-range terms are defined by molecular geometry, i.e. bond lengths, angles and dihedrals; the long-range term is similar to that in elastic network models. Each interaction term uses a single force constant parameter, and is determined by fitting against a set of ...

  16. The Atomic and Molecular Gas Around Evolved Stars

    Science.gov (United States)

    Fong, D.; Meixner, M.; Sutton, E. C.; Castro-Carrizo, A.; Bujarrabal, V.; Latter, W. B.; Tielens, A. G. G. M.; Kelly, D. M.; Welch, W. J.

    2001-12-01

    We present ISO LWS and SWS observations of far-infrared atomic fine structure lines of 24 evolved stars including asymptotic giant branch (AGB) stars, proto-planetary nebulae (PPNe) and planetary nebulae (PNe). The spectra include grating and Fabry-Perot measurements of the line emission from [OI], [CII], [SiI], [SiII], [SI], [FeI], [FeII], [NeII] and [NII] which trace the low-excitation atomic gas. Atomic emission was only found in those sources where Teff >= 10000 K. Above this cutoff, the number of detectable lines and the intensity of the line emission increase as Teff increases. These trends suggest that the atomic lines originate from photodissociation regions (PDRs). In general, the kinematics of the atomic gas, derived from line fits to the Fabry-Perot data, are comparable to the molecular expansion velocities. These kinematics are expected for atomic cooling lines associated with circumstellar PDRs. A new PDR code which properly treats enhanced carbon abundances was used to model the observations. The predicted line intensities agree reasonably well with the observations. Shock models, however, do not compare well with the observed line intensities. PDR mass estimates ranging from ~0.01-0.2 Msun were derived from the [CII] 158 μ m line emission. The atomic gas only occupies a small fraction of the total mass for young planetary nebulae, but grows significantly as they evolve. To compliment our atomic gas study we also present CO J=1-0 observations of 7 objects in our ISO sample to investigate the evolution of the molecular envelope. By combining data from the Berkeley-Illinois-Maryland-Association (BIMA) Millimeter Array and the NRAO 12m, we have constructed full synthesis data cubes for MIRA, IRC +10216, IRAS 17436+5003 (HD 161796), AFGL 2688, IRAS 22272+5435 (HD 235858), AFGL 2343 (IRAS 19114+0002) and NGC 7027. The history of the circumstellar gas is imprinted on the circumstellar envelope itself, such as the record of its molecular mass loss, and its

  17. 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)

  18. Polarization effects in molecular mechanical force fields.

    Science.gov (United States)

    Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei

    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. PMID:21828594

  19. Atomic mechanics and reversibility of failure in nanoscale

    International Nuclear Information System (INIS)

    Full text: Mechanics of nanotubes serves as a benchmark in atomically-precise modeling of elasticity, buckling, yield and failure mechanisms. The molecular simplicity combined with the hollow morphology, permit synergism of continuum elasticity, shell stability, classical and quantum molecular dynamics and kinetic rate theory. Recent quantum ab initio calculations of structures and moduli for C, BN and CFx shells are connected with their persistence length and vibrations. Further, a comparative ab initio density functional analysis of yield thermodynamics for carbon (C, purely covalent) and boron nitride (BN, covalent-ionic) structures will be presented and their strengths compared. Consistent approach to strength evaluation based on the rate equations and transition state theory, adapted from chemical kinetics, is outlined. Its implementation with classical potentials and more recent density functional realization permits obtaining the realistic strength estimates. Finally we will discuss in detail a novel phenomenon in nanoscale: coalescence or 'welding' of nanostructures. These processes are opposite to yield relaxation and failure. We have identified the exact paths-trajectories for chemical bond rearrangements that lead to complete and seamless fusion of the generic types, e.g. (10,10) + (10,10) → (10,10), or (15,0) + (15,0) → (15,0), etc. This is important for engineering of new nanostructures through stretching or 'welding', as well as for improvement of bulk material properties due to increased connectivity of the tubules. Same class of processes includes incorporation of a C60-ball into a tubule, an important step in the growth mechanism. Bond rotation (Stone-Wales transformation in chemistry) plays the key role in these molecular 'beam-and-truss' constructions. A lateral fusion of adjacent cylinders is analyzed, and the SW-sequence is shown to lead to complete merging and diameter doubling. We will finally discuss an intriguing physics of possible

  20. Quantum mechanics of molecular structures

    CERN Document Server

    Yamanouchi, Kaoru

    2012-01-01

    At a level accessible to advanced undergraduates, this textbook explains the fundamental role of quantum mechanics in determining the structure, dynamics, and other properties of molecules. Readers will come to understand the quantum-mechanical basis for harmonic oscillators, angular momenta and scattering processes. Exercises are provided to help readers deepen their grasp of the essential phenomena.

  1. Unveiling atomic-scale features of inherent heterogeneity in metallic glass by molecular dynamics simulations

    Science.gov (United States)

    Hu, Y. C.; Guan, P. F.; Li, M. Z.; Liu, C. T.; Yang, Y.; Bai, H. Y.; Wang, W. H.

    2016-06-01

    Heterogeneity is commonly believed to be intrinsic to metallic glasses (MGs). Nevertheless, how to distinguish and characterize the heterogeneity at the atomic level is still debated. Based on the extensive molecular dynamics simulations that combine isoconfigurational ensemble and atomic pinning methods, we directly reveal that MG contains flow units and the elastic matrix which can be well distinguished by their distinctive atomic-level responsiveness and mechanical performance. The microscopic features of the flow units, such as the shape, spatial distribution dimensionality, and correlation length, are characterized from atomic position analyses. Furthermore, the correlation between the flow units and the landscape of energy state, free volume, atomic-level stress, and especially the local bond orientational order parameter is discussed.

  2. Atomic mechanism and prediction of hydrogen embrittlement in iron.

    Science.gov (United States)

    Song, Jun; Curtin, W A

    2013-02-01

    Hydrogen embrittlement in metals has posed a serious obstacle to designing strong and reliable structural materials for many decades, and predictive physical mechanisms still do not exist. Here, a new H embrittlement mechanism operating at the atomic scale in α-iron is demonstrated. Direct molecular dynamics simulations reveal a ductile-to-brittle transition caused by the suppression of dislocation emission at the crack tip due to aggregation of H, which then permits brittle-cleavage failure followed by slow crack growth. The atomistic embrittlement mechanism is then connected to material states and loading conditions through a kinetic model for H delivery to the crack-tip region. Parameter-free predictions of embrittlement thresholds in Fe-based steels over a range of H concentrations, mechanical loading rates and H diffusion rates are found to be in excellent agreement with experiments. This work provides a mechanistic, predictive framework for interpreting experiments, designing structural components and guiding the design of embrittlement-resistant materials. PMID:23142843

  3. Non-trivial length dependence of the conductance and negative differential resistance in atomic molecular wires

    International Nuclear Information System (INIS)

    We study the electronic and transport properties of two novel molecular wires made of atomic chains of carbon atoms (polyynes) capped with either benzene-thiols or pyridines. While both molecules are structurally similar, the electrical conductance of benzene-thiol-capped chains attached to gold electrodes is found to be much higher than that of pyridine-capped chains. We predict that the conductance is almost independent of molecular length, which suggests that these molecules could be ideal molecular wires for sub-10 nm circuitry. Both systems exhibit negative differential resistance (NDR) but its origin and characteristics depend on the type of molecule. We find a novel type of NDR mechanism produced by the movement of the lowest unoccupied molecular orbital (LUMO) resonance with bias. We also show that by gating the pyridine-capped molecules it is possible to make the NDR disappear and dramatically modify the I-V characteristics and the length dependence.

  4. Molecular deformation mechanisms in polyethylene

    CERN Document Server

    Coutry, S

    2001-01-01

    adjacent labelled stems is significantly larger when the DPE guest is a copolymer molecule. Our comparative studies on various types of polyethylene lead to the conclusion that their deformation behaviour under drawing has the same basis, with additional effects imputed to the presence of tie-molecules and branches. Three major points were identified in this thesis. The changes produced by drawing imply (1) the crystallisation of some of the amorphous polymer and the subsequent orientation of the newly formed crystals, (2) the re-orientation of the crystalline ribbons and (3) the beginning of crystallite break-up. However, additional effects were observed for the high molecular weight linear sample and the copolymer sample and were attributed, respectively, to the presence of tie-molecules and of branches. It was concluded that both the tie-molecules and the branches are restricting the molecular movement during deformation, and that the branches may be acting as 'anchors'. This work is concerned with details...

  5. Harmful molecular mechanisms in sepsis

    OpenAIRE

    Rittirsch, Daniel; Flierl, Michael A; Ward, Peter A.

    2008-01-01

    Sepsis and sepsis-associated multi-organ failure are major challenges for scientists and clinicians and are a tremendous burden for health-care systems. Despite extensive basic research and clinical studies, the pathophysiology of sepsis is still poorly understood. We are now beginning to understand that sepsis is a heterogeneous, dynamic syndrome caused by imbalances in the ‘inflammatory network’. In this Review, we highlight recent insights into the molecular interactions that occur during ...

  6. Atomic and molecular physics in the gas phase

    International Nuclear Information System (INIS)

    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

  7. Molecular quantum mechanical observers, symmetry, and string theory

    OpenAIRE

    Dance, M.

    2010-01-01

    The paper \\cite{Dance0601} tentatively suggested a physical picture that might underlie string theories. The string parameters $\\tau $ and $\\sigma_i $ were interpreted as spacetime dimensions which a simple quantum mechanical observer can observe, while symmetries of the relevant observer states could limit the observability of other dimensions. An atomic observer was the focus of the discussion. The present paper extends the discussion of\\cite{Dance0601} to molecular observers, including the...

  8. 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)

  9. Understanding the Atomic-Scale World with the Molecular Workbench

    Science.gov (United States)

    Tinker, Robert F.

    2006-12-01

    The Molecular Workbench (MW) is a sophisticated system for developing and delivering interactive learning activities to teach basic concepts that govern atomic and nanoscale phenomena. The system is based on a molecular dynamics model that calculates the motion of atoms, molecules, and other objects in real time as a result of the applicable forces, including Lennard-Jones potentials, electrostatic potentials, elastic bonds, and external fields. Light-atom interactions are modeled with photons of selectable energy that interact with the excited states of atoms. The built-in authoring functions can be used to create or modify learning activities. The ease of creating MW materials has led to over 200 activities contributed by staff and collaborators. Many are housed in a database with fields that include an overview, learning objectives, a description of the central concepts addressed, textbook references, and extensions. MW has been used extensively in classrooms in grades 7-14. In several settings student learning gains have been measured using a pre-posttest design. Research results will be reported that show Overall increases in understanding of atomic scale phenomena at high school and community college levels. The ability to transfer understanding of atomic-scale phenomena to new situations and to reason about macroscopic phenomena on the basis of atomic-scale interactions. Better understanding of difficult questions that required immersive visualization and prediction MW is written in Java, so it runs under all common operating systems, including Mac OSX, Windows, and Linux. It is open source, so it can be shared and copied by any user.

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

    International Nuclear Information System (INIS)

    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)

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

    International Nuclear Information System (INIS)

    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.)

  12. Molecular mechanism of insulin resistance

    Indian Academy of Sciences (India)

    Samir Bhattacharya; Debleena Dey; Sib Sankar Roy

    2007-03-01

    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, leading to a reduced amount of IR protein in insulin target cells. PDK1-independent phosphorylation of PKCε causes this reduction in insulin receptor gene expression. One of the pathways through which fatty acid can induce insulin resistance in insulin target cells is suggested by these studies. We provide an overview of this important area, emphasizing the current status.

  13. Molecular Mechanisms Underlying Pituitary Pathogenesis.

    Science.gov (United States)

    Sapochnik, Melanie; Nieto, Leandro Eduardo; Fuertes, Mariana; Arzt, Eduardo

    2016-04-01

    During the last years, progress has been made on the identification of mechanisms involved in anterior pituitary cell transformation and tumorigenesis. Oncogene activation, tumor suppressor gene inactivation, epigenetic changes, and microRNAs deregulation contribute to the initiation of pituitary tumors. Despite the high prevalence of pituitary adenomas, they are mostly benign, indicating that intrinsic mechanisms may regulate pituitary cell expansion. Senescence is characterized by an irreversible cell cycle arrest and represents an important protective mechanism against malignancy. Pituitary tumor transforming gene (PTTG) is an oncogene involved in early stages of pituitary tumor development, and also triggers a senescence response by activating DNA-damage signaling pathway. Cytokines, as well as many other factors, play an important role in pituitary physiology, affecting not only cell proliferation but also hormone secretion. Special interest is focused on interleukin-6 (IL-6) because its dual function of stimulating pituitary tumor cell growth but inhibiting normal pituitary cells proliferation. It has been demonstrated that IL-6 has a key role in promoting and maintenance of the senescence program in tumors. Senescence, triggered by PTTG activation and mediated by IL-6, may be a mechanism for explaining the benign nature of pituitary tumors. PMID:26718581

  14. Cellular and molecular mechanisms in kidney fibrosis

    Science.gov (United States)

    Duffield, Jeremy S.

    2014-01-01

    Fibrosis is a characteristic feature of all forms of chronic kidney disease. Deposition of pathological matrix in the interstitial space and within the walls of glomerular capillaries as well as the cellular processes resulting in this deposition are increasingly recognized as important factors amplifying kidney injury and accelerating nephron demise. Recent insights into the cellular and molecular mechanisms of fibrogenesis herald the promise of new therapies to slow kidney disease progression. This review focuses on new findings that enhance understanding of cellular and molecular mechanisms of fibrosis, the characteristics of myofibroblasts, their progenitors, and molecular pathways regulating both fibrogenesis and its resolution. PMID:24892703

  15. Molecular hydrogen formation by excited atom radiative association

    Science.gov (United States)

    Latter, William B.; Black, John H.

    1991-01-01

    The results from a semiclassical calculation of the thermal rate coefficient for the radiative association process H(n = 2) + H(n = 1) - H2 + hv are presented (n is the principal quantum number of the separated hydrogen atoms). The relative importance of this reaction in various environments is briefly discussed. Models of the early universe around the epoch of recombination and protostellar winds have been calculated which include the excited atom process. Not surprisingly, it is shown that the excited atom process will not be important in the general interstellar medium, except possibly in environments where the amount of Ly-alpha photon trapping is large. Examples may be the material surrounding quasars, active galactic nuclei, and bright H II regions. The most likely application of this process might be within rapidly evolving systems where a large transient n = 2 population of neutral hydrogen could result in a burst of molecular hydrogen formation.

  16. Electron transport properties of single molecular junctions under mechanical modulations

    International Nuclear Information System (INIS)

    Electron transport behaviors of single molecular junctions are very sensitive to the atomic scale molecule-metal electrode contact interfaces, which have been difficult to control. We used a modified scanning probe microscope-break junction technique (SPM-BJT) to control the dynamics of the contacts and simultaneously monitor both the conductance and force. First, by fitting the measured data into a modified multiple tunneling barrier model, the static contact resistances, corresponding to the different contact conformations of single alkanedithiol and alkanediamine molecular junctions, were identified. Second, the changes of contact decay constant were measured under mechanical extensions of the molecular junctions, which helped to classify the different single molecular conductance sets into specific microscopic conformations of the molecule-electrode contacts. Third, by monitoring the changes of force and contact decay constant with the mechanical extensions, the changes of conductance were found to be caused by the changes of contact bond length and by the atomic reorganizations near the contact bond. This study provides a new insight into the understanding of the influences of contact conformations, especially the effect of changes of dynamic contact conformation on electron transport through single molecular junctions. (paper)

  17. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    OpenAIRE

    Jahn, S.; P. A. Madden

    2008-01-01

    The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q) from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω) from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the ...

  18. Atomic and molecular physics at INDUS-1: plans and prospects

    International Nuclear Information System (INIS)

    This paper will give a brief description of the INDUS-1 source, details of the proposed beam lines, the present status of the beam lines and atomic and molecular physics experiments planned to be carried out on these beam lines. It will also include some of the future plans for utilisation of INDUS-1 and INDUS-2, a higher energy (2 GeV) machine

  19. PAMOP: Petascale Atomic, Molecular and Optical Collision Calculations

    OpenAIRE

    McLaughlin, Brendan M.; Ballance, Connor P.; Pindzola, Michael S.; Müller, Alfred

    2015-01-01

    Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\\"odinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. In this report, various examples are shown from our theoretical results compared with exper...

  20. Petascale computations for Large-scale Atomic and Molecular collisions

    OpenAIRE

    McLaughlin, Brendan M.; Ballance, Connor P.

    2014-01-01

    Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schroedinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. Various examples are shown of our theoretical results compared with those obtained from Sync...

  1. 2004 Atomic and Molecular Interactions Gordon Research Conference

    International Nuclear Information System (INIS)

    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

  2. Dynamics of excess electrons in atomic and molecular clusters

    OpenAIRE

    Young, Ryan Michael

    2011-01-01

    Femtosecond time-resolved photoelectron imaging (TRPEI) is applied to the study of excess electrons in clusters as well as to microsolvated anion species. This technique can be used to perform explicit time-resolved as well as one-color (single- or multiphoton) studies on gas phase species. The first part of this dissertation details time-resolved studies done on atomic clusters with an excess electron, the excited-state dynamics of solvated molecular anions, and charge-transfer dynamics to...

  3. Early atomic models - from mechanical to quantum (1904-1913)

    Science.gov (United States)

    Baily, C.

    2013-01-01

    A complete history of early atomic models would fill volumes, but a reasonably coherent tale of the path from mechanical atoms to the quantum can be told by focusing on the relevant work of three great contributors to atomic physics, in the critically important years between 1904 and 1913: J.J. Thomson, Ernest Rutherford and Niels Bohr. We first examine the origins of Thomson's mechanical atomic models, from his ethereal vortex atoms in the early 1880's, to the myriad "corpuscular" atoms he proposed following the discovery of the electron in 1897. Beyond qualitative predictions for the periodicity of the elements, the application of Thomson's atoms to problems in scattering and absorption led to quantitative predictions that were confirmed by experiments with high-velocity electrons traversing thin sheets of metal. Still, the much more massive and energetic α-particles being studied by Rutherford were better suited for exploring the interior of the atom, and careful measurements on the angular dependence of their scattering eventually allowed him to infer the existence of an atomic nucleus. Niels Bohr was particularly troubled by the radiative instability inherent to any mechanical atom, and succeeded in 1913 where others had failed in the prediction of emission spectra, by making two bold hypotheses that were in contradiction to the laws of classical physics, but necessary in order to account for experimental facts.

  4. 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. PMID:27225077

  5. Molecular mechanisms of cryptococcal meningitis

    OpenAIRE

    Liu, Tong-Bao; Perlin, David; Xue, Chaoyang

    2012-01-01

    Fungal meningitis is a serious disease caused by a fungal infection of the central nervous system (CNS) mostly in individuals with immune system deficiencies. Fungal meningitis is often fatal without proper treatment, and the mortality rate remains unacceptably high even with antifungal drug interventions. Currently, cryptococcal meningitis is the most common fungal meningitis in HIV-1/AIDS, and its disease mechanism has been extensively studied. The key steps for fungi to infect brain and ca...

  6. Molecular mechanisms of manganese mutagenesis.

    OpenAIRE

    el-Deiry, W S; Downey, K M; So, A G

    1984-01-01

    The mechanism by which DNA polymerase discriminates between complementary and noncomplementary nucleotides for insertion into a primer terminus has been investigated. Apparent kinetic constants for the insertion of dGTP and dATP into the hook polymer d(C)194-d(G)12 with Escherichia coli DNA polymerase I (large fragment) were determined. The results suggest that the high specificity of base selection by DNA polymerase I is achieved by utilization of both Km and Vmax differences between complem...

  7. Hyperpolarizabilities of extended molecular mechanical systems.

    Science.gov (United States)

    Harczuk, Ignat; Vahtras, Olav; Ågren, Hans

    2016-03-16

    We propose and evaluate algorithms for the calculation of molecular polarizabilities and hyperpolarizabilities of extended chemical systems. These algorithms are generalizations of the Silberstein-Applequist procedure involving interacting induced classical dipoles through the localized polarizabilities and hyperpolarizabilities. The models are evaluated in terms of interacting molecular units as well as interacting atomic units that result from the atomic decomposition scheme known as the LoProp transformation. We introduce a generalized LoProp scheme which applies to hyperpolarizabilities as well as to polarizabilities. The accuracy of the second-order Applequist method is tested for the first hyperpolarizability for the TIP3P water model using both Hartree-Fock and density functional theory evaluated with different basis sets. Possible applications and ramifications of the scheme are discussed. PMID:26954519

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

  10. Enhancing coherence in molecular spin qubits via atomic clock transitions

    Science.gov (United States)

    Shiddiq, Muhandis; Komijani, Dorsa; Duan, Yan; Gaita-Ariño, Alejandro; Coronado, Eugenio; Hill, Stephen

    2016-03-01

    Quantum computing is an emerging area within the information sciences revolving around the concept of quantum bits (qubits). A major obstacle is the extreme fragility of these qubits due to interactions with their environment that destroy their quantumness. This phenomenon, known as decoherence, is of fundamental interest. There are many competing candidates for qubits, including superconducting circuits, quantum optical cavities, ultracold atoms and spin qubits, and each has its strengths and weaknesses. When dealing with spin qubits, the strongest source of decoherence is the magnetic dipolar interaction. To minimize it, spins are typically diluted in a diamagnetic matrix. For example, this dilution can be taken to the extreme of a single phosphorus atom in silicon, whereas in molecular matrices a typical ratio is one magnetic molecule per 10,000 matrix molecules. However, there is a fundamental contradiction between reducing decoherence by dilution and allowing quantum operations via the interaction between spin qubits. To resolve this contradiction, the design and engineering of quantum hardware can benefit from a ‘bottom-up’ approach whereby the electronic structure of magnetic molecules is chemically tailored to give the desired physical behaviour. Here we present a way of enhancing coherence in solid-state molecular spin qubits without resorting to extreme dilution. It is based on the design of molecular structures with crystal field ground states possessing large tunnelling gaps that give rise to optimal operating points, or atomic clock transitions, at which the quantum spin dynamics become protected against dipolar decoherence. This approach is illustrated with a holmium molecular nanomagnet in which long coherence times (up to 8.4 microseconds at 5 kelvin) are obtained at unusually high concentrations. This finding opens new avenues for quantum computing based on molecular spin qubits.

  11. Enhancing coherence in molecular spin qubits via atomic clock transitions.

    Science.gov (United States)

    Shiddiq, Muhandis; Komijani, Dorsa; Duan, Yan; Gaita-Ariño, Alejandro; Coronado, Eugenio; Hill, Stephen

    2016-03-17

    Quantum computing is an emerging area within the information sciences revolving around the concept of quantum bits (qubits). A major obstacle is the extreme fragility of these qubits due to interactions with their environment that destroy their quantumness. This phenomenon, known as decoherence, is of fundamental interest. There are many competing candidates for qubits, including superconducting circuits, quantum optical cavities, ultracold atoms and spin qubits, and each has its strengths and weaknesses. When dealing with spin qubits, the strongest source of decoherence is the magnetic dipolar interaction. To minimize it, spins are typically diluted in a diamagnetic matrix. For example, this dilution can be taken to the extreme of a single phosphorus atom in silicon, whereas in molecular matrices a typical ratio is one magnetic molecule per 10,000 matrix molecules. However, there is a fundamental contradiction between reducing decoherence by dilution and allowing quantum operations via the interaction between spin qubits. To resolve this contradiction, the design and engineering of quantum hardware can benefit from a 'bottom-up' approach whereby the electronic structure of magnetic molecules is chemically tailored to give the desired physical behaviour. Here we present a way of enhancing coherence in solid-state molecular spin qubits without resorting to extreme dilution. It is based on the design of molecular structures with crystal field ground states possessing large tunnelling gaps that give rise to optimal operating points, or atomic clock transitions, at which the quantum spin dynamics become protected against dipolar decoherence. This approach is illustrated with a holmium molecular nanomagnet in which long coherence times (up to 8.4 microseconds at 5 kelvin) are obtained at unusually high concentrations. This finding opens new avenues for quantum computing based on molecular spin qubits. PMID:26983539

  12. Molecular mechanism of sweetness sensation.

    Science.gov (United States)

    DuBois, Grant E

    2016-10-01

    The current understanding of peripheral molecular events involved in sweet taste sensation in humans is reviewed. Included are discussions of the sweetener receptor T1R2/T1R3, its agonists, antagonists, positive allosteric modulators, the transduction of its activation in taste bud cells and the coding of its signaling to the CNS. Areas of incomplete understanding include 1) signal communication with afferent nerve fibers, 2) contrasting concentration/response (C/R) functions for high-potency (HP) sweeteners (hyperbolic) and carbohydrate (CHO) sweeteners (linear), 3) contrasting temporal profiles for HP sweeteners (delayed onset and extinction) and CHO sweeteners (rapid onset and extinction) and 4) contrasting adaptation behaviors for HP sweeteners (moderate to strong adaptation) and CHO sweeteners (low adaptation). Evidence based on the sweet water aftertastes of several novel sweetness inhibitors is presented providing new support for constitutive activity in T1R2/T1R3. And a model is developed to rationalize the linear C/R functions of CHO sweeteners and hyperbolic C/R functions of HP sweeteners, where the former may activate T1R2/T1R3 by both binding and constitutive activity modulation (i.e., without binding) and the latter activate T1R2/T1R3 only by binding. PMID:26992959

  13. Molecular mechanism of cholangiocarcinoma carcinogenesis.

    Science.gov (United States)

    Maemura, Kosei; Natsugoe, Shoji; Takao, Sonshin

    2014-10-01

    Cholangiocarcinoma (CCA) is a highly malignant cancer of the biliary tract with a poor prognosis, which often arises from conditions causing long-term inflammation, injury, and reparative biliary epithelial cell proliferation. Several conditions are known to be major risk factors for cancer in the biliary tract or gallbladder, including primary sclerosing cholangitis, liver fluke infection, pancreaticobiliary maljunction, and chemical exposure in proof-printing workers. Abnormalities in various signaling cascades, molecules, and genetic mutations are involved in the pathogenesis of CCA. CCA is characterized by a series of highly recurrent mutations in genes, including KRAS, BRF, TP53, Smad, and p16(INK4a) . Cytokines that are affected by inflammatory environmental conditions, such as interleukin-6 (IL-6), transforming growth factor-β (TGF-β), tumor necrosis factor-α (TNF-α), and platelet-derived growth factor (PDGF), play an important role in cancer pathogenesis. Prominent signaling pathways important in carcinogenesis include TGF-β/Smad, IL-6/STAT-3, PI3K/AKT, Wnt, RAF/MEK/MAPK, and Notch. Additionally, some microRNAs regulate targets in critical pathways of CCA development and progression. This review article provides the understanding of the genetic and epigenetic mechanism(s) of carcinogenesis in CCA, which leads to the development of new therapeutic targets for the prevention and treatment of this devastating cancer. PMID:24895231

  14. Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

    OpenAIRE

    Chiappori, Federica; Merelli, Ivan; Colombo, Giorgio; Milanesi, Luciano; Morra, Giulia

    2012-01-01

    Author Summary Allostery, or the capability of proteins to respond to ligand binding events with a variation in structure or dynamics at a distant site, is a common feature for biomolecular function and regulation in a large number of proteins. Intra-protein connections and inter-residue coordinations underlie allosteric mechanisms and react to binding primarily through a finely tuned modulation of motions and structures at the microscopic scale. Hence, all-atom molecular dynamics simulations...

  15. Atomic and molecular layer deposition for surface modification

    International Nuclear Information System (INIS)

    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 Al2O3 due to e.g. complex formation. • Same effect on cellulosic fabrics observed with low temperature deposited TiO2. • Different film growth and oxidation potential with different precursors. • Hybrid layer on inorganic layer can be used to improve adhesion of polymer melt

  16. 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.

  17. Molecular self-assembly on two-dimensional atomic crystals: insights from molecular dynamics simulations.

    Science.gov (United States)

    Zhao, Yinghe; Wu, Qisheng; Chen, Qian; Wang, Jinlan

    2015-11-19

    van der Waals (vdW) epitaxy of ultrathin organic films on two-dimensional (2D) atomic crystals has become a sovereign area because of their unique advantages in organic electronic devices. However, the dynamic mechanism of the self-assembly remains elusive. Here, we visualize the nanoscale self-assembly of organic molecules on graphene and boron nitride monolayer from a disordered state to a 2D lattice via molecular dynamics simulation for the first time. It is revealed that the assembly toward 2D ordered structures is essentially the minimization of the molecule-molecule interaction, that is, the vdW interaction in nonpolar systems and the vdW and Coulomb interactions in polar systems that are the decisive factors for the formation of the 2D ordering. The role of the substrate is mainly governing the array orientation of the adsorbates. The mechanisms unveiled here are generally applicable to a broad class of organic thin films via vdW epitaxy. PMID:26523464

  18. A Modiifed Molecular Structure Mechanics Method for Analysis of Graphene

    Institute of Scientific and Technical Information of China (English)

    HUA Jun; LI Dongbo; ZHAO Dong; LIANG Shengwei; LIU Qinlong; JIA Ruiyan

    2015-01-01

    Based on molecular mechanics and the deformation characteristics of the atomic lattice structure of graphene, a modiifed molecular structure mechanics method was developed to improve the original one, that is, the semi-rigid connections were used to model the bond angle variations between the C-C bonds in graphene. The simulated results show that the equivalent space frame model with semi-rigid connections for graphene proposed in this article is a simple, efifcient, and accurate model to evaluate the equivalent elastic properties of graphene. Though the present computational model of the semi-rigid connected space frame is only applied to characterize the mechanical behaviors of the space lattices of graphene, it has more potential applications in the static and dynamic analyses of graphene and other nanomaterials.

  19. 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.

  20. Molecular mechanisms of induced mutagenesis

    International Nuclear Information System (INIS)

    Genetic analysis has revealed that radiation and many chemical mutagens induce in bacteria an error-prone DNA repair process which is responsible for their mutagenic effect. The biochemical mechanism of this inducible error-prone repair has been studied by analysis of the first round of DNA synthesis on ultraviolet light-irradiated phiX174 DNA in both intact and ultraviolet light-irradiated host cells. Intracellular phiX174 DNA was extracted, subjected to isopycnic CsCl density-gradient analysis, hydroxylapatite chromatography and digestion by single-strand-specific endonuclease S1. Ultraviolet light-induced photolesions in viral DNA cause a permanent blockage of DNA synthesis in intact Escherichia coli cells. However, when host cells were irradiated and incubated to induce fully the error-prone repair system, a significant fraction of irradiated phiX174 DNA molecules can be fully replicated. Thus, inducible error-prone repair in E.coli is manifested by an increased capacity for DNA synthesis on damaged phiX174 DNA. Chloramphenicol (100 μ g/ml), which is an inhibitor of the inducible error-prone DNA repair, is also an inhibitor of this particular inducible DNA synthesis. (author)

  1. 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

  2. Molecular mechanisms of DNA photodamage

    International Nuclear Information System (INIS)

    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 adenine

  3. Molecular mechanism of the sweet taste enhancers

    OpenAIRE

    Feng ZHANG; Klebansky, Boris; Fine, Richard M.; Liu, Haitian; Xu, Hong; Servant, Guy; Zoller, Mark; Tachdjian, Catherine; Li, Xiaodong

    2010-01-01

    Positive allosteric modulators of the human sweet taste receptor have been developed as a new way of reducing dietary sugar intake. Besides their potential health benefit, the sweet taste enhancers are also valuable tool molecules to study the general mechanism of positive allosteric modulations of T1R taste receptors. Using chimeric receptors, mutagenesis, and molecular modeling, we reveal how these sweet enhancers work at the molecular level. Our data argue that the sweet enhancers follow a...

  4. Machine Learning for Quantum Mechanical Properties of Atoms in Molecules

    CERN Document Server

    Rupp, Matthias; von Lilienfeld, O Anatole

    2015-01-01

    We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach accuracies on par with density functional theory reference. Locality is exploited within non-linear regression via local atom-centered coordinate systems. The approach is validated on a diverse set of 9k small organic molecules. Linear scaling is demonstrated for saturated polymers with up to sub-mesoscale lengths.

  5. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    OpenAIRE

    Sha, Wei

    2008-01-01

    In this seminar, I will talk about the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscopy (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics simulations were then carried out to investigate the ...

  6. 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

  7. Foil dissociation of fast molecular ions into atomic excited states

    International Nuclear Information System (INIS)

    The intensity and polarizations of light emitted from atomic excited states of dissociated molecular ions were measured. The dissociations are induced when fast molecular ions (50 to 500 keV/amu) are transmitted through thin carbon foils. A calculation of multiple scattering and the Coulomb explosion gives the average internuclear separation of the projectile at the foil surface. Experimentally, the foil thickness is varied to give varying internuclear separations at the foil surface and observe the consequent variation in light yield and optical polarization. Using HeH+ projectiles, factors of 1 to 5 enhancements of the light yields from n = 3, 13P,D states of He I and some He II and H I emissions were observed. The results can be explained in terms of molecular level crossings which provide mixings of the various final states during dissociation of the molecular ions at the exit surface. They suggest a short range surface interaction of the electron pick-up followed by a slow molecular dissociation. Alignment measurements confirm the essential features of the model. Observations of Lyman α emission after dissociation of H2+ amd H3+ show rapid variations in light yield for small internuclear separations at the foil surface

  8. 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...... was found to be icosahedral in the 55-atom system and face centered cubic for the two larger systems. ©1974 American Institute of Physics...

  9. Atomic and Molecular Data for Optical Stellar Spectroscopy

    CERN Document Server

    Heiter, U; Asplund, M; Barklem, P S; 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- to 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 ...

  10. Atomic and Molecular Data: Division B / Commission 14

    CERN Document Server

    Mashonkina, Lyudmila; Wahlgren, Glenn M; Allard, France; Barklem, Paul; Beiersdorfer, Peter; Fraser, Helen; Nave, Gillian; Nilsson, Hampus

    2015-01-01

    Commission 14 has been operating for almost a century. It was one of the 32 Standing IAU Commissions and established in 1919. The main purpose of Commission 14 is to foster interactions between the astronomical community and those conducting research on atoms, molecules, and solid state particles to provide data vital to reducing and analysing astronomical observations and performing theoretical investigations. Although Commission 14 terminated at the Honolulu General Assembly, the field Atomic and Molecular Data remains with the IAU. By call of the IAU, the Commission 14 OC initiated a proposal for a new Commission on Laboratory Astrophysics that was approved. Commission on Laboratory Astrophysics will be a natural evolution of Commission 14.

  11. 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 ...).

  12. 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

  13. Hydrated electron production by reaction of hydrogen atoms with hydroxide ions: A first-principles molecular dynamics study

    International Nuclear Information System (INIS)

    The solvated electron production by reaction between the H atom and the hydroxide anion was studied using Density Functional Theory based first-principles molecular dynamics. The simulation reveals a complex mechanism, controlled by proton transfers in the coordination sphere of the hydroxide and by the diffusion of the H atom in its solvent cavity. We formulate the hypothesis, based on a coupling between classical and first-principles molecular dynamics, that these two processes give rise to a lag time for the reaction that would explain the H atom extremely small reactivity compared to other radical species. Furthermore, the reaction observed gives an original insight in excess electron solvation. (authors)

  14. Hydrogen atom mechanism of residuum conversion

    International Nuclear Information System (INIS)

    The mechanism of converting Athabaska bitumen to crude oil by heating it in an inert atmosphere (coking), or with hydrogen (hydrocracking), was described. The differences between the two processes were explained, with emphasis on the hydrocracking, a process which prevents coke formation.'Capping' of the carbon radicals and preventing them from undergoing a series of complex reactions which result in the production of coke, is the conventional explanation for the mechanism of hydrocracking. An alternative mechanism, involving the aromatic radicals interacting with the hydrogen to form a cyclohexadienyl radical intermediate, and thereby providing the pathway by which the large condensed aromatic centers can decompose to form gases and distillable liquids, was proposed as a more complete explanation for this complex process. An improved understanding of the mechanism should result in improvements to the process, either in the form of increased yield of desirable products, higher overall process conversion, lower severity or lower pressure. All of these would lead to better process economics. 6 refs., 4 figs

  15. Reactive atomization and deposition process: Fundamental mechanisms

    Science.gov (United States)

    Lin, Yaojun

    A modification of spray forming process, namely reactive atomization and deposition (RAD) process, where a reactive gas or gas mixture (e.g., O 2-N2) is used to replace an inert gas, was investigated. First, oxidation behavior during RAD process was numerically analyzed. It is shown that, the overall volume fraction of oxides in the RAD material increases with increasing the atomization pressure, the pouring temperature and the O2 concentration and decreasing the melt flow rate. Second, the influence of in-situ reactions on grain size during RAD process was investigated. By analyzing the influence of in-situ reactions on nucleation behavior during flight and deposition (numerically), as well as on grain coarsening during slow solidification of the remaining liquid phase and grain growth during the solid phase cooling (experimentally), it is predicted that, under the same processing conditions, average grain size in the RAD material is slightly smaller than that in the material processed by spray deposition using N 2 (SDN). Third, size, distribution and morphology of oxides in as-sprayed RAD materials were experimentally studied. It is shown that, oxides exhibit a thin-plate morphology and are distributed at the three typical spatial locations with a dimension scale on an order from tenths of micrometers to micrometers. Fourth, an analytical model was established to describe the oxide fragmentation in the deposition stage during RAD process. With an assumption of disc-shaped oxide dispersoids, the following dimension scales of oxide dispersoids in as-sprayed materials are predicted: on an order from tenths of micrometers to micrometers in diameter and tens of nanometers in thickness. Fifth, an analytical model was established to describe the oxide fragmentation during working processes in a RAD material. It is predicted that, in the worked RAD materials, oxide dispersoid discs exhibit a size scale on an order of tens of nanometers for both diameter and thickness

  16. Atomic and molecular hydrogen from Titan in the Kronian magnetosphere

    Science.gov (United States)

    Eviatar, Aharon; Podolak, Morris; Richardson, John D.

    1990-01-01

    The question of the neutral gas and plasma population in the region of the Kronian magnetosphere, outside the plasma mantle and inside the magnetopause, dominated by the efflux of Titan's atmosphere is considered. A model that has been used successfully to describe the inner magnetosphere is applied to this region under constraints derived from the plasma science and ultraviolet spectrometer experiments on Voyager. It is shown that it is not possible to reconcile the results of these two experiments simultaneously with the values of the atomic and molecular source strengths of the atmosphere of Titan extant in the literature. The possible sources of the discrepancy are delineated.

  17. PAMOP: Petascale Atomic, Molecular and Optical Collision Calculations

    CERN Document Server

    McLaughlin, Brendan M; Pindzola, Michael S; Müller, Alfred

    2015-01-01

    Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\\"odinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. In this report, various examples are shown from our theoretical results compared with experimental results obtained from Synchrotron Radiation facilities where the Cray architecture at HLRS is playing an integral part in our computational projects.

  18. Correlation of spiral arm molecular clouds with cold atomic hydrogen

    International Nuclear Information System (INIS)

    The relationship between molecular clouds and the cold atomic hydrogen gas seen in self-absorption has been examined in the longitude range 36-40 deg. The results confirm what the authors found previously in another region of the Galaxy. By reanalyzing both sets of data, the authors show that those cold clouds which are detected both in H I self-absorption at 21 cm against a hotter background and in CO emission at 2.6 mm are confined to the Sagittarius spiral arm feature in velocity-longitude space. Outside of this arm feature, clouds which show both H I absorption and CO emission are very rare. 14 references

  19. Petascale computations for Large-scale Atomic and Molecular collisions

    CERN Document Server

    McLaughlin, Brendan M

    2014-01-01

    Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schroedinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. Various examples are shown of our theoretical results compared with those obtained from Synchrotron Radiation facilities and from Satellite observations. We also indicate future directions and implementation of the R-matrix codes on emerging GPU architectures.

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

    International Nuclear Information System (INIS)

    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)

  1. 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 of the...... hydrogen bonding network in the two bilayers. The second part deals with binary mixtures of sterols with either SM or PC. The results show how the membrane properties may vary substantially depending on the sterol and SM type available, the membrane order and interdigitation being just two of the many...

  2. Super-atom molecular orbital excited states of fullerenes.

    Science.gov (United States)

    Johansson, J Olof; Bohl, Elvira; Campbell, Eleanor E B

    2016-09-13

    Super-atom molecular orbitals are orbitals that form diffuse hydrogenic excited electronic states of fullerenes with their electron density centred at the centre of the hollow carbon cage and a significant electron density inside the cage. This is a consequence of the high symmetry and hollow structure of the molecules and distinguishes them from typical low-lying molecular Rydberg states. This review summarizes the current experimental and theoretical studies related to these exotic excited electronic states with emphasis on femtosecond photoelectron spectroscopy experiments on gas-phase fullerenes.This article is part of the themed issue 'Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene'. PMID:27501970

  3. Atomic mechanism of homogeneous melting of bcc Fe at the limit of superheating

    International Nuclear Information System (INIS)

    Atomic mechanism of homogeneous melting of bcc Fe is studied via monitoring spatiotemporal arrangements of the liquid-like atoms, which are detected by the Lindemann criterion of melting, during the heating process. Calculations are performed by molecular dynamics (MD) simulations. Calculations show that liquid-like atoms occur randomly in the crystalline matrix at temperature far below the melting point due to local instability of the crystalline lattice. Number of liquid-like atoms increases with increasing temperature and they have a tendency to form clusters. Subsequently, a single percolated liquid-like cluster is formed in the crystalline model and at the melting point 99% atoms in the model become liquid-like to form a liquid phase. Melting is also accompanied by the sudden changes in various static and thermodynamic quantities. However, total melting is reached just at the point above the melting one. Three characteristic temperatures of the homogeneous melting of bcc Fe are determined.

  4. The Cologne Database for Molecular Spectroscopy, CDMS, in the Virtual Atomic and Molecular Data Centre, VAMDC

    CERN Document Server

    Endres, Christian P; Schilke, Peter; Stutzki, Jürgen; Müller, Holger S P

    2016-01-01

    The CDMS was founded 1998 to provide in its catalog section line lists of molecular species which may be observed in various astronomical sources using radio astronomy. The line lists contain transition frequencies with qualified accuracies, intensities, quantum numbers, as well as further auxilary information. They have been generated from critically evaluated experimental line lists, mostly from laboratory experiments, employing established Hamiltonian models. Seperate entries exist for different isotopic species and usually also for different vibrational states. As of December 2015, the number of entries is 792. They are available online as ascii tables with additional files documenting information on the entries. The Virtual Atomic and Molecular Data Centre was founded more than 5 years ago as a common platform for atomic and molecular data. This platform facilitates exchange not only between spectroscopic databases related to astrophysics or astrochemistry, but also with collisional and kinetic databases...

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

    International Nuclear Information System (INIS)

    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 CH3I and C6H6 perturbed by H2 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 CH3I have also been measured as a function of perturber pressure in 11 different binary gas mixtures consisting of CH3I 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 (H2, CH4, N2, C2H6, C3H8). 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

  6. Photochemistry of molecular and atomic oxygen in the terrestrial nightglow

    Science.gov (United States)

    Lednyts'kyy, Olexandr; Von Savigny, Christian; Sinnhuber, Miriam

    2016-07-01

    The electronic states of molecular oxygen ({O}_2) are in constant communication through collisions in high vibrational levels of {O}_2 in the MLT (Mesosphere/Lower Thermosphere) region. We assume that the Herzberg {O}_2 electronic states transfer energy to O-atoms to generate the green line. Our Multiple Nightglow Chemistry model is based on more than 80 (odd oxygen and odd hydrogen) aeronomical reactions to implement this concept. We retrieved atomic oxygen concentration ([O]) profiles in the MLT region with help of SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) and SABER (Sounding of the Atmosphere using Broadband Emission Radiometry) infrared radiometer observations of the nightglow. Particularly, we obtained volume emission rate (VER) profiles (due to the infrared atmospheric {O}_2(a^1Δ_g) nightglow at 1.27 μm) from SABER to retrieve [O] profiles. We discussed quenching profiles that correspond to retrieved [O] profiles to reflect complex molecularity of infrared atmospheric and green line nightglow emissions.

  7. United polarizable multipole water model for molecular mechanics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu [Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Wang, Lee-Ping; Pande, Vijay S. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  8. United polarizable multipole water model for molecular mechanics simulation

    International Nuclear Information System (INIS)

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water

  9. Ocular diseases: immunological and molecular mechanisms

    Science.gov (United States)

    Song, Jing; Huang, Yi-Fei; Zhang, Wen-Jing; Chen, Xiao-Fei; Guo, Yu-Mian

    2016-01-01

    Many factors, such as environmental, microbial and endogenous stress, antigen localization, can trigger the immunological events that affect the ending of the diverse spectrum of ocular disorders. Significant advances in understanding of immunological and molecular mechanisms have been researched to improve the diagnosis and therapy for patients with ocular inflammatory diseases. Some kinds of ocular diseases are inadequately responsive to current medications; therefore, immunotherapy may be a potential choice as an alternative or adjunctive treatment, even in the prophylactic setting. This article first provides an overview of the immunological and molecular mechanisms concerning several typical and common ocular diseases; second, the functions of immunological roles in some of systemic autoimmunity will be discussed; third, we will provide a summary of the mechanisms that dictate immune cell trafficking to ocular local microenvironment in response to inflammation.

  10. Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy

    Science.gov (United States)

    Klocke, Michael

    2016-01-01

    Summary A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively. PMID:27335760

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

    International Nuclear Information System (INIS)

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

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

    Beňo, Juraj; Weis, Martin; Dobročka, Edmund; Haško, Daniel

    2008-08-01

    Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms ( π- 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 π- 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.

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

    International Nuclear Information System (INIS)

    Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms (π-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 π-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

  15. Molecular mechanism for the umami taste synergism

    OpenAIRE

    Feng ZHANG; Klebansky, Boris; Fine, Richard M.; Xu, Hong; Pronin, Alexey; Liu, Haitian; Tachdjian, Catherine; Li, Xiaodong

    2008-01-01

    Umami is one of the 5 basic taste qualities. The umami taste of L-glutamate can be drastically enhanced by 5′ ribonucleotides and the synergy is a hallmark of this taste quality. The umami taste receptor is a heteromeric complex of 2 class C G-protein-coupled receptors, T1R1 and T1R3. Here we elucidate the molecular mechanism of the synergy using chimeric T1R receptors, site-directed mutagenesis, and molecular modeling. We propose a cooperative ligand-binding model involving the Venus flytrap...

  16. Prediction of organic molecular crystal geometries from MP2-level fragment quantum mechanical/molecular mechanical calculations

    Science.gov (United States)

    Nanda, Kaushik D.; Beran, Gregory J. O.

    2012-11-01

    The fragment-based hybrid many-body interaction (HMBI) model provides a computationally affordable means of applying electronic structure wavefunction methods to molecular crystals. It combines a quantum mechanical treatment of individual molecules in the unit cell and their short-range pairwise interactions with a polarizable molecular mechanics force-field treatment of long-range and many-body interactions. Here, we report the implementation of analytic nuclear gradients for the periodic model to enable full relaxation of both the atomic positions and crystal lattice parameters. Using a set of five, chemically diverse molecular crystals, we compare the quality of the HMBI MP2/aug-cc-pVDZ-level structures with those obtained from dispersion-corrected periodic density functional theory, B3LYP-D*, and from the Amoeba polarizable force field. The MP2-level structures largely agree with the experimental lattice parameters to within 2%, and the root-mean-square deviations in the atomic coordinates are less than 0.2 Å. These MP2 structures are almost as good as those predicted from periodic B3LYP-D*/TZP and are significantly better than those obtained with B3LYP-D*/6-31G(d,p) or with the Amoeba force field.

  17. Nonstationary structure of atomic and molecular layers in electrothermal. Atomic absorption spectrometry: formation of atomic and molecular absorbing layers of gallium and indium

    International Nuclear Information System (INIS)

    The dynamics of the formation of absorbing layers of gallium and indium atoms and their compounds in a graphite tubular atomizer was investigated by the shadow spectral filming method. These compounds are localozed in the central part of the furnace over the platform and dissapear ay the hotter walls. It the case of gallium and indium atomization, the effects of chemical reactions between the vapor and the walls of the furnace on the formation of absorbing layers are stronger than that of diffusion and convective mass-transfer processes, which are common to all of the elements. Atom propagation from the center to the stomizer ends proceeds through the cascade mechanism because of its relatively low rate of warming up and strong longitudinal anisothermicity

  18. Estimation of mechanical properties of single wall carbon nanotubes using molecular mechanics approach

    Indian Academy of Sciences (India)

    P Subba Rao; Sunil Anandatheertha; G Narayana Naik; G Gopalakrishnan

    2015-06-01

    Molecular mechanics based finite element analysis is adopted in the current work to evaluate the mechanical properties of Zigzag, Armchair and Chiral Single wall Carbon Nanotubes (SWCNT) of different diameters and chiralities. Three different types of atomic bonds, that is Carbon–Carbon covalent bond and two types of Carbon–Carbon van der Waals bonds are considered in the carbon nanotube system. The stiffness values of these bonds are calculated using the molecular potentials, namely Morse potential function and Lennard-Jones interaction potential function respectively and these stiffness’s are assigned to spring elements in the finite element model of the CNT. The geometry of CNT is built using a macro that is developed for the finite element analysis software. The finite element model of the CNT is constructed, appropriate boundary conditions are applied and the behavior of mechanical properties of CNT is studied.

  19. Molecular mechanism and regulation of autophagy

    Institute of Scientific and Technical Information of China (English)

    Ya-ping YANG; Zhong-qin LIANG; Zhen-lun GU; Zheng-hong QIN

    2005-01-01

    Autophagy is a major cellular pathway for the degradation of long-lived proteins and cytoplasmic organelles in eukaryotic cells. A large number of intracellular/extracellular stimuli, including amino acid starvation and invasion of microorganisms, are able to induce the autophagic response in cells. The discovery of the ATG genes in yeast has greatly advanced our understanding of the molecular mechanisms participating in autophagy and the genes involved in regulating the autophagic pathway. Many yeast genes have mammalian homologs,suggesting that the basic machinery for autophagy has been evolutionarily conserved along the eukaryotic phylum. The regulation of autophagy is a very complex process. Many signaling pathways, including target of rapamycin (TOR) or mammalian target of rapamycin (mTOR), phosphatidylinositol 3-kinase-I (PI3K-I)/PKB, GTPases, calcium and protein synthesis all play important roles in regulating autophagy. The molecular mechanisms and regulation of autophagy are discussed in this review.

  20. Modeling molecular crystals formed by spin-active metal complexes by atom-atom potentials

    CERN Document Server

    Sinitskiy, Anton V; Tokmachev, Andrei M; Dronskowski, Richard

    2009-01-01

    We apply the atom-atom potentials to molecular crystals of iron (II) complexes with bulky organic ligands. The crystals under study are formed by low-spin or high-spin molecules of Fe(phen)$_{2}$(NCS)$_{2}$ (phen = 1,10-phenanthroline), Fe(btz)$_{2}$(NCS)$_{2}$ (btz = 5,5$^{\\prime }$,6,6$^{\\prime}$-tetrahydro-4\\textit{H},4$^{\\prime}$\\textit{H}-2,2$^{\\prime }$-bi-1,3-thiazine), and Fe(bpz)$_{2}$(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2$^{\\prime}$-bipyridine). All molecular geometries are taken from the X-ray experimental data and assumed to be frozen. The unit cell dimensions and angles, positions of the centers of masses of molecules, and the orientations of molecules corresponding to the minimum energy at 1 atm and 1 GPa are calculated. The optimized crystal structures are in a good agreement with the experimental data. Sources of the residual discrepancies between the calculated and experimental structures are discussed. The intermolecular contributions to the enthalpy of the spin transiti...

  1. Molecular mechanisms of metastasis in prostate cancer

    Institute of Scientific and Technical Information of China (English)

    Noel W.Clarke; Claire A.Hart; Mick D.Brown

    2009-01-01

    Prostate cancer (PCa) preferentially metastasizes to the bone marrow stroma of the axial skeleton.This activity is the principal cause of PCa morbidity and mortality.The exact mechanism of PCa metastasis is currently unknown,although considerable progress has been made in determining the key players in this process.In this review,we present the current understanding of the molecular processes driving PCa metastasis to the bone.

  2. Molecular mechanisms of amyloid self-regulation

    OpenAIRE

    Landreh, Michael

    2012-01-01

    Amyloid is associated with both pathological protein deposits and the formation of functional protein structures. Therefore, several strategies have evolved to control the formation or inhibition of amyloid in vivo. In this thesis, three separate systems were investigated in which amyloidogenic protein segments are coupled to regulatory elements that prevent or promote fibrillation. We describe the molecular mechanism for how (a) a propeptide segment prevents the uncontrolled a...

  3. Cellular and molecular mechanisms in kidney fibrosis

    OpenAIRE

    Duffield, Jeremy S.

    2014-01-01

    Fibrosis is a characteristic feature of all forms of chronic kidney disease. Deposition of pathological matrix in the interstitial space and within the walls of glomerular capillaries as well as the cellular processes resulting in this deposition are increasingly recognized as important factors amplifying kidney injury and accelerating nephron demise. Recent insights into the cellular and molecular mechanisms of fibrogenesis herald the promise of new therapies to slow kidney disease progressi...

  4. Molecular Mechanism of Biological Proton Transport

    Energy Technology Data Exchange (ETDEWEB)

    Pomes, R.

    1998-09-01

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  5. Molecular mechanism of magnet formation in bacteria.

    Science.gov (United States)

    Matsunaga, T; Sakaguchi, T

    2000-01-01

    Magnetic bacteria have an ability to synthesize intracellular ferromagnetic crystalline particles consisting of magnetite (Fe3O4) or greigite (Fe3S4) which occur within a specific size range (50-100 nm). Bacterial magnetic particles (BMPs) can be distinguished by the regular morphology and the presence of an thin organic membrane enveloping crystals from abiologically formed magnetite. The particle is the smallest magnetic crystal that has a regular morphology within the single domain size. Therefore, BMPs have an unfathomable amount of potential value for various technological applications not only scientific interests. However, the molecular and genetic mechanism of magnetite biomineralization is hardly understood although iron oxide formation occurs widely in many higher animals as well as microorganisms. In order to elucidate the molecular and genetic mechanisms of magnetite biomineralization, a magnetic bacterium Magnetospirillum sp. AMB-1, for which gene transfer and transposon mutagenesis techniques had been recently developed, has been used as a model organism. Several findings and information on the BMPs formation process have been obtained within this decade by means of studies with this model organism and its related one. Biomineralization mechanism and potential availability in biotechnology of bacterial magnets have been elucidated through molecular and genetic approach. PMID:16232810

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

    International Nuclear Information System (INIS)

    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)

  7. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    S.Jahn

    2008-03-01

    Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.

  8. CRYRING - a facility for atomic, molecular and nuclear physics

    International Nuclear Information System (INIS)

    The CRYRING project was put forward by the Research Institute of Physics (AFI), Stockholm, Sweden, as a proposal in October 1983 under the heading A facility with CRYSIS and other ion sources connected to a synchrotron ring intended for studies of atomic, molecular and nuclear collisions, in particular in experiments with interacting beams of ions, molecules, electrons and laser photons. In September 1985 funding was granted for the last subproject, comprising the actual ring structure to be completed by 1989-90. Thus started the third Swedish storage ring project, the first being the synchrotron radiation electron ring MAX at Lund and the second the nuclear and particle physics light ion ring CELSIUS at Uppsala. The present short contribution aims at a pedagogical (though necessarily somewhat superficial) presentation of CRYRING and its modes of operation. 21 references, 5 figures

  9. Molecular beam studies of oxide reduction by atomic hydrogen

    International Nuclear Information System (INIS)

    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/UO2 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 13000C. 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 H2, solution and diffusion of H in the bulk of the UO2, 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

  10. 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.

  11. Collisions near threshold in atomic and molecular physics

    International Nuclear Information System (INIS)

    We review topics of current interest in the physics of electronic, atomic and molecular scattering in the vicinity of thresholds. Starting from phase space arguments, we discuss the modifications of the Wigner law that are required to deal with scattering by Coulomb, dipolar and dispersion potentials, as well as aspects of threshold behaviour observed in ultracold atomic collisions. We employ the tools of quantum defect and semiclassical theories to bring out the rich variety of threshold behaviours. The discussion is then turned to recent progress in understanding threshold behaviour of many-body break-ups into both charged and neutral species, including both Wannier double ionization and three-body recombination in ultracold gases. We emphasize the dominant role that hyperspherical coordinate methods have played in understanding these problems. We assess the effects of external fields on scattering, and the corresponding modification of phase space that alters the Wigner law. Threshold laws in low dimensions and examples of their applications to specific collision processes are discussed. (author)

  12. Three-dimensional solitons in coupled atomic-molecular Bose-Einstein condensates

    OpenAIRE

    Vaughan, T. G.; Kheruntsyan, K. V.; Drummond, P. D.

    2004-01-01

    We present a theoretical analysis of three-dimensional (3D) matter-wave solitons and their stability properties in coupled atomic and molecular Bose-Einstein condensates (BEC). The soliton solutions to the mean-field equations are obtained in an approximate analytical form by means of a variational approach. We investigate soliton stability within the parameter space described by the atom-molecule conversion coupling, atom-atom s-wave scattering, and the bare formation energy of the molecular...

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

    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

  19. A Quantum-Mechanics Molecular-Mechanics scheme for extended systems

    CERN Document Server

    Hunt, Diego; Scherlis, Damian A

    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 throu...

  20. Mechanically induced luminescence changes in molecular assemblies.

    Science.gov (United States)

    Sagara, Yoshimitsu; Kato, Takashi

    2009-11-01

    Altering the shape and properties of a material through external factors such as heat, light, pressure, pH, electric or magnetic fields, or the introduction of a guest molecule, is an attractive prospect. In this Perspective, piezochromic luminescent materials - which change the colour of their luminescence in response to mechanical stimuli - are described. Such piezochromism has been observed for a few molecular materials that contain luminescent cores in liquid-crystalline and crystalline solid states, as well as for polymeric materials doped with dyes. These changes in photoluminescent colour can be activated by various types of mechanical pressure such as shearing, grinding or elongation, which can trigger different mechanisms of producing the colour. Such stimuli-responsive materials have potential for various applications, including sensors, memory and displays. PMID:21378953

  1. Molecular Mechanisms of Renal Ischemic Conditioning Strategies.

    Science.gov (United States)

    Kierulf-Lassen, Casper; Nieuwenhuijs-Moeke, Gertrude J; Krogstrup, Nicoline V; Oltean, Mihai; Jespersen, Bente; Dor, Frank J M F

    2015-01-01

    Ischemia-reperfusion injury is the leading cause of acute kidney injury in a variety of clinical settings such as renal transplantation and hypovolemic and/or septic shock. Strategies to reduce ischemia-reperfusion injury are obviously clinically relevant. Ischemic conditioning is an inherent part of the renal defense mechanism against ischemia and can be triggered by short periods of intermittent ischemia and reperfusion. Understanding the signaling transduction pathways of renal ischemic conditioning can promote further clinical translation and pharmacological advancements in this era. This review 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 of the same protective signaling pathways as in other organs, but differences are recognized. PMID:26330099

  2. Molecular mechanisms for protein-encoded inheritance

    Energy Technology Data Exchange (ETDEWEB)

    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; (Cornell); (HHMI)

    2009-12-01

    In prion inheritance and transmission, strains are phenotypic variants encoded by protein 'conformations'. However, it is unclear how a protein conformation can be stable enough to endure transmission between cells or organisms. Here we describe new polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of {beta}-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct {beta}-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 protein-encoded information into prion strains share features with the familiar mechanism for transfer of nucleic acid-encoded information into microbial strains, including sequence specificity and recognition by noncovalent bonds.

  3. 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.

  4. 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. PMID:22996381

  5. A density-based adaptive quantum mechanical/molecular mechanical method.

    Science.gov (United States)

    Waller, Mark P; Kumbhar, Sadhana; Yang, Jack

    2014-10-20

    We present a density-based adaptive quantum mechanical/molecular mechanical (DBA-QM/MM) method, whereby molecules can switch layers from the QM to the MM region and vice versa. The adaptive partitioning of the molecular system ensures that the layer assignment can change during the optimization procedure, that is, on the fly. The switch from a QM molecule to a MM molecule is determined if there is an absence of noncovalent interactions to any atom of the QM core region. The presence/absence of noncovalent interactions is determined by analysis of the reduced density gradient. Therefore, the location of the QM/MM boundary is based on physical arguments, and this neatly removes some empiricism inherent in previous adaptive QM/MM partitioning schemes. The DBA-QM/MM method is validated by using a water-in-water setup and an explicitly solvated L-alanyl-L-alanine dipeptide. PMID:24954803

  6. Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R

    2005-02-02

    Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.

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

    International Nuclear Information System (INIS)

    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

  8. Recent Progress in Molecular Recognition Imaging Using Atomic Force Microscopy.

    Science.gov (United States)

    Senapati, Subhadip; Lindsay, Stuart

    2016-03-15

    Atomic force microscopy (AFM) is an extremely powerful tool in the field of bionanotechnology because of its ability to image single molecules and make measurements of molecular interaction forces with piconewton sensitivity. It works in aqueous media, enabling studies of molecular phenomenon taking place under physiological conditions. Samples can be imaged in their near-native state without any further modifications such as staining or tagging. The combination of AFM imaging with the force measurement added a new feature to the AFM technique, that is, molecular recognition imaging. Molecular recognition imaging enables mapping of specific interactions between two molecules (one attached to the AFM tip and the other to the imaging substrate) by generating simultaneous topography and recognition images (TREC). Since its discovery, the recognition imaging technique has been successfully applied to different systems such as antibody-protein, aptamer-protein, peptide-protein, chromatin, antigen-antibody, cells, and so forth. Because the technique is based on specific binding between the ligand and receptor, it has the ability to detect a particular protein in a mixture of proteins or monitor a biological phenomenon in the native physiological state. One key step for recognition imaging technique is the functionalization of the AFM tips (generally, silicon, silicon nitrides, gold, etc.). Several different functionalization methods have been reported in the literature depending on the molecules of interest and the material of the tip. Polyethylene glycol is routinely used to provide flexibility needed for proper binding as a part of the linker that carries the affinity molecule. Recently, a heterofunctional triarm linker has been synthesized and successfully attached with two different affinity molecules. This novel linker, when attached to AFM tip, helped to detect two different proteins simultaneously from a mixture of proteins using a so-called "two

  9. Radioadaptive response and its molecular mechanism

    International Nuclear Information System (INIS)

    Radioadaptive response is a biological defense of which low dose ionizing radiation induces cellular resistance to the genotoxic effects of subsequent challenge irradiation. However, so for molecular mechanism of radioadaptive response remains obscure. Research is mainly involved in activation of the intracellular repair system, cell cycle regulation system, antioxidative stress system and stress-response protein. Signaling factors involved in cell response to radiation include protein kinase C, mitogen-activated protein kinase, p53 tumor suppressor' protein, ataxia-telansiectasia mutated, and DNA-dependent protein kinase. (authors)

  10. Thymic Output: Influence Factors and Molecular Mechanism

    Institute of Scientific and Technical Information of China (English)

    Rong Jin; Jun Zhang; Weifeng Chen

    2006-01-01

    Thymus is a primary lymphoid organ, able to generate mature T cells that eventually colonize secondary lymphoid organs, and is therefore essential for peripheral T cell renewal. Recent data showed that normal thymocyte export can be altered by several influence factors including several chemokines,sphingosinel-phosphate (S1P),transcription factors such as Foxjl, Kruppel-like transcription factor 2 (KLF2) and antigen stimulation, etc. In this review, we summarized the recent reports about study strategies, influence factors and possible molecular mechanisms in thymic output.

  11. Atomic and molecular effects on spherically convergent ion flow. II. Multiple molecular species

    Science.gov (United States)

    Emmert, Gilbert A.; Santarius, John F.

    2010-01-01

    A theoretical model for the effect of molecular interactions on the flow of molecular ions in spherically convergent geometry where the inner grid (cathode) is at a large negative potential and the outer grid (anode) is grounded has been developed. The model assumes a weakly ionized deuterium plasma composed of D+, D2+, and D3+ ions that interact with the dominant background gas (D2). The interactions included are charge exchange, ionization, and dissociative processes. The formalism developed includes the bouncing motion of the ions in the electrostatic well and sums over all generations of subsequent ions produced by atomic and molecular processes. This leads to a set of two coupled Volterra integral equations, which are solved numerically. From the solution of the Volterra equations, one can obtain quantities of interest, such as the energy spectra of the ions and fast neutral atoms and molecules, and the fusion reaction rate. To provide an experimental test, the model is applied to inertial electrostatic devices and the calculated neutron production rate is compared to previously reported measurements for one University of Wisconsin inertial electrostatic confinement device [D. C. Donovan et al., Fusion Sci. Technol. 56, 507 (2009)]. The results show general agreement with the experimental results, but significant differences remain to be resolved.

  12. [Atomic force field FFsol for calculation of molecular interactions of in water environment].

    Science.gov (United States)

    Pereiaslavets, L B; Finkel'shtein, A V

    2010-01-01

    Detailed calculations of protein interactions with explicitly considered water takes enormous computer time. The calculation becomes faster if water is considered implicitly (as a continuous media rather than as molecules); however, these calculations are much less precise, unless one uses an additional (and also volumes) computation of the solvent-accessible areas of protein atoms. The aim of our study was to obtain parameters for non-bonded atom-atom interactions for the case when water surrounding is considered implicitly and the solvent-accessible areas are not computed. Since the "in-vacuum" interactions of atoms are obtained from experimental structures of crystals and enthalpies of their sublimation, the "in-water" interactions of atoms must be corrected using solvation free energies of molecules, which can be obtained from the Henry constants. Taken 58 structures of molecular crystals and thermodynamic data on their sublimation and solubility, we obtained parameters for "in-water" attraction and repulsion of atoms typical of protein structures (H, C, N, O, S) in various covalently-bonded states, as well as parameters for electrostatic interactions. All necessary for calculations parameters of covalent interactions have been taken from the ENCAD force field, and partial charges of all atoms of separate molecules of a crystal have been obtained from quantum-mechanical calculations. The sought parameters of the "in-water" van der Waals and electrostatic interactions were optimized so as to achieve the best description of equilibrium crystal structures and their sublimation and solvation at the room temperature. With the optimized parameters, the average error in calculation of the effective cohesion energy of molecules in crystals was less than 10% both in the "in-vacuum" and "in-water" cases. PMID:20586195

  13. Laser-induced atomic adsorption: a mechanism for nanofilm formation

    CERN Document Server

    Martins, Weliton S; Oriá, Marcos; Chevrollier, Martine

    2013-01-01

    We demonstrate and interpret a technique of laser-induced formation of thin metallic films using alkali atoms on the window of a dense-vapour cell. We show that this intriguing photo-stimulated process originates from the adsorption of Cs atoms via the neutralisation of Cs$^+$ ions by substrate electrons. The Cs$^+$ ions are produced via two-photon absorption by excited Cs atoms very close to the surface, which enables the transfer of the laser spatial intensity profile to the film thickness. An initial decrease of the surface work function is required to guarantee Cs$^+$ neutralisation and results in a threshold in the vapour density. This understanding of the film growth mechanism may facilitate the development of new techniques of laser-controlled lithography, starting from thermal vapours.

  14. Statistical mechanics and dynamics of molecular fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Quack, M. (Goettingen Univ. (Germany, F.R.). Inst. fuer Physikalische Chemie)

    1981-05-11

    The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored.

  15. Statistical mechanics and dynamics of molecular fragmentation

    International Nuclear Information System (INIS)

    The foundations of the use of statistical-mechanical equations of motion, in particular the Pauli equation, for the description of intramolecular processes and molecular fragmentation are discussed briefly. Quantum-mechanical trajectories for model systems illustrate how the statistical behaviour may emerge from the dynamical equations of motion. Product state distributions resulting from the fragmentation of strongly coupled, metastable intermediates in chemical-activation experiments can be calculated by using restricted equipartition, which applies as the long-time limit of the Pauli equation. A simple Pauli-equation model is proposed to calculate lifetimes of metastable intermediates. The consequences of the finite rate of intramolecular relaxation processes for the specific rate constants for fragmentation and possible deviations from microcanonical equilibrium are explored. (author)

  16. 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.

  17. Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

    Science.gov (United States)

    Giese, Timothy J; York, Darrin M

    2016-06-14

    A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed. PMID:27171914

  18. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    International Nuclear Information System (INIS)

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample

  19. The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

    Science.gov (United States)

    Wu, X.; Sha, W.

    2008-12-01

    In this paper, we report the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscope (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics (MD) simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.

  20. Molecular inhibitory mechanism of tricin on tyrosinase

    Science.gov (United States)

    Mu, Yan; Li, Lin; Hu, Song-Qing

    2013-04-01

    Tricin was evaluated as a type of tyrosinase inhibitor with good efficacy compared to arbutin. Tricin functioned as a non-competitive inhibitor of tyrosinase, with an equilibrium constant of 2.30 mmol/L. The molecular mechanisms underlying the inhibition of tyrosinase by tricin were investigated by means of circular dichroism spectra, fluorescence quenching and molecular docking. These assays demonstrated that the interactions between tricin and tyrosinase did not change the secondary structure. The interaction of tricin with residues in the hydrophobic pocket of tyrosinase was revealed by fluorescence quenching; the complex was stabilized by hydrophobic associations and hydrogen bonding (with residues Asn80 and Arg267). Docking results implied that the possible inhibitory mechanisms may be attributed to the stereospecific blockade effects of tricin on substrates or products and flexible conformation alterations in the tyrosinase active center caused by weak interactions between tyrosinase and tricin. The application of this type of flavonoid as a tyrosinase inhibitor will lead to significant advances in the field of depigmentation.

  1. International bulletin on atomic and molecular data for fusion. No. 38

    International Nuclear Information System (INIS)

    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

  2. Proceedings of the 2. Latin American Meeting on Atomic, Molecular and Electronic Collisions

    International Nuclear Information System (INIS)

    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.)

  3. International bulletin on atomic and molecular data for fusion. No. 35

    International Nuclear Information System (INIS)

    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

  4. International bulletin on atomic and molecular data for fusion. No. 39

    International Nuclear Information System (INIS)

    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

  5. International Bulletin on Atomic and Molecular Data for Fusion. No. 36

    International Nuclear Information System (INIS)

    The bulletin provides information on atomic and molecular data relevant for fusion research. In Part I the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part II contains all the bibliographic data for both the indexed and non-indexed references (555 references). An author index is included

  6. A Simple Demonstration of Atomic and Molecular Orbitals Using Circular Magnets

    Science.gov (United States)

    Chakraborty, Maharudra; Mukhopadhyay, Subrata; Das, Ranendu Sekhar

    2014-01-01

    A quite simple and inexpensive technique is described here to represent the approximate shapes of atomic orbitals and the molecular orbitals formed by them following the principles of the linear combination of atomic orbitals (LCAO) method. Molecular orbitals of a few simple molecules can also be pictorially represented. Instructors can employ the…

  7. Modeling contact formation between atomic-sized gold tips via molecular dynamics

    International Nuclear Information System (INIS)

    The formation and rupture of atomic-sized contacts is modelled by means of molecular dynamics simulations. Such nano-contacts are realized in scanning tunnelling microscope and mechanically controlled break junction experiments. These instruments routinely measure the conductance across the nano-sized electrodes as they are brought into contact and separated, permitting conductance traces to be recorded that are plots of conductance versus the distance between the electrodes. One interesting feature of the conductance traces is that for some metals and geometric configurations a jump in the value of the conductance is observed right before contact between the electrodes, a phenomenon known as jump-to-contact. This paper considers, from a computational point of view, the dynamics of contact between two gold nano-electrodes. Repeated indentation of the two surfaces on each other is performed in two crystallographic orientations of face-centred cubic gold, namely (001) and (111). Ultimately, the intention is to identify the structures at the atomic level at the moment of first contact between the surfaces, since the value of the conductance is related to the minimum cross-section in the contact region. Conductance values obtained in this way are determined using first principles electronic transport calculations, with atomic configurations taken from the molecular dynamics simulations serving as input structures

  8. Molecular Mechanisms Regulating Macrophage Response to Hypoxia

    Directory of Open Access Journals (Sweden)

    Michal Amit Rahat

    2011-09-01

    Full Text Available Monocytes and Macrophages (Mo/Mϕ exhibit great plasticity, as they can shift between different modes of activation and, driven by their immediate microenvironment, perform divergent functions. These include, among others, patrolling their surroundings and maintaining homeostasis (resident Mo/Mϕ, combating invading pathogens and tumor cells (classically activated or M1 Mo/Mϕ, orchestrating wound healing (alternatively activated or M2 Mo/Mϕ, and restoring homeostasis after an inflammatory response (resolution Mϕ. Hypoxia is an important factor in the Mϕ microenvironment, is prevalent in many physiological and pathological conditions, and is interdependent with the inflammatory response. Although Mo/Mϕ have been studied in hypoxia, the mechanisms by which hypoxia influences the different modes of their activation, and how it regulates the shift between them, remain unclear. Here we review the current knowledge about the molecular mechanisms that mediate this hypoxic regulation of Mϕ activation. Much is known about the hypoxic transcriptional regulatory network, which includes the master regulators HIF-1 and NF-κB, as well as other transcription factors (e.g. AP-1, Erg-1, but we also highlight the role of post-transcriptional and post-translational mechanisms. These mechanisms mediate hypoxic induction of Mϕ pro-angiogenic mediators, suppress M1 Mϕ by post-transcriptionally inhibiting pro-inflammatory mediators, and help shift the classically activated Mϕ into an activation state which approximate the alternatively activated or resolution Mϕ.

  9. Atomic and molecular data for spacecraft re-entry plasmas

    Science.gov (United States)

    Celiberto, R.; Armenise, I.; Cacciatore, M.; Capitelli, M.; Esposito, F.; Gamallo, P.; Janev, R. K.; Laganà, A.; Laporta, V.; Laricchiuta, A.; Lombardi, A.; Rutigliano, M.; Sayós, R.; Tennyson, J.; Wadehra, J. M.

    2016-06-01

    The modeling of atmospheric gas, interacting with the space vehicles in re-entry conditions in planetary exploration missions, requires a large set of scattering data for all those elementary processes occurring in the system. A fundamental aspect of re-entry problems is represented by the strong non-equilibrium conditions met in the atmospheric plasma close to the surface of the thermal shield, where numerous interconnected relaxation processes determine the evolution of the gaseous system towards equilibrium conditions. A central role is played by the vibrational exchanges of energy, so that collisional processes involving vibrationally excited molecules assume a particular importance. In the present paper, theoretical calculations of complete sets of vibrationally state-resolved cross sections and rate coefficients are reviewed, focusing on the relevant classes of collisional processes: resonant and non-resonant electron-impact excitation of molecules, atom–diatom and molecule–molecule collisions as well as gas-surface interaction. In particular, collisional processes involving atomic and molecular species, relevant to Earth (N2, O2, NO), Mars (CO2, CO, N2) and Jupiter (H2, He) atmospheres are considered.

  10. Committee on Atomic and Molecular Sciences: Technical progress report for the period February 1, 1986-January 31, 1987

    International Nuclear Information System (INIS)

    CAMS activities for 1986 dealt with the following areas: (1) Student Guide to AMO Science; (2) International Survey of Atomic and Molecular Science; (3) Update of the Directory of Atomic, Molecular, and Optical Scientists in the United States; (4) Workshop on VUV and Synchrotron Sources; (5) Study of the State of Atomic, Molecular, and Optical Theory; (6) Workshop on the Laser-Atomic Frontier; (7) Report on Heavy-Ion Storage Rings; (8) Review of Computer Needs in Atomic and Molecular Science

  11. Molecular mechanical properties of short-sequence peptide enzyme mimics.

    Science.gov (United States)

    Takahashi, Tsukasa; Vo Ngo, Bao C; Xiao, Leyang; Arya, Gaurav; Heller, Michael J

    2016-03-01

    While considerable attempts have been made to recreate the high turnover rates of enzymes using synthetic enzyme mimics, most have failed and only a few have produced minimal reaction rates that can barely be considered catalytic. One particular approach we have focused on is the use of short-sequence peptides that contain key catalytic groups in close proximity. In this study, we designed six different peptides and tested their ability to mimic the catalytic mechanism of the cysteine proteases. Acetylation and deacylation by Ellman's Reagent trapping experiments showed the importance of having phenylalanine groups surrounding the catalytic sites in order to provide greater proximity between the cysteine, histidine, and aspartate amino acid R-groups. We have also carried out all-atom molecular dynamics simulations to determine the distance between these catalytic groups and the overall mechanical flexibility of the peptides. We found strong correlations between the magnitude of fluctuations in the Cys-His distance, which determines the flexibility and interactions between the cysteine thiol and histidine imidazole groups, and the deacylation rate. We found that, in general, shorter Cys-His distance fluctuations led to a higher deacylation rate constant, implying that greater confinement of the two residues will allow a higher frequency of the acetyl exchange between the cysteine thiol and histidine imidazole R-groups. This may be the key to future design of peptide structures with molecular mechanical properties that lead to viable enzyme mimics. PMID:25921736

  12. Independent analysis of mechanical data from atomic force microscopy

    International Nuclear Information System (INIS)

    Present atomic force microscopes are capable of acquiring large data volumes by point using point force–distance spectroscopic measurements. Even if different trade names and different technical implementations are used, for most of these techniques a force–distance curve in every image pixel is measured, this curve is immediately fitted by some theoretical dependence and results are displayed as a mechanical properties channel (Young modulus, adhesion, etc). Results are processed during the measurement directly in the scanning probe microscopy controller or, after it, by manufacturer provided software. In this paper, we present a software tool for independent numerical processing of such data, including more numerical models for the force–distance curve evaluation and including a simple estimate of uncertainties related to the fitting procedure. This can improve the reliability and the analytical possibilities of mechanical properties mapping methods in an atomic force microscopy. (paper)

  13. Trapping cold molecules and atoms: Simultaneous magnetic deceleration and trapping of cold molecular Oxygen with Lithium atoms

    Science.gov (United States)

    Akerman, Nitzan; Karpov, Michael; Segev, Yair; Bibelink, Natan; Narevicius, Julia; Narevicius, Edvardas

    2016-05-01

    Cooling molecules to the ultra-cold regime remains a major challenge in the growing field of cold molecules. The molecular internal degrees of freedom complicate the effort of direct application of laser cooling. An alternative and general path towards ultra-cold molecules relies on sympathetic cooling via collisions with laser-cooled atoms. Here, we demonstrate the first step towards application of sympathetic cooling by co-trapping of molecular Oxygen with Lithium atoms in a magnetic trap at a temperature of 300 mK. Our experiment begins with a pulsed supersonic beam which is a general source for cold high-flux atomic and molecular beams. Although the supersonic expansion efficiently cools the beam to temperatures below 1K, it also accelerates the beam to high mean velocities. We decelerate a beam of O2 in a moving magnetic trap decelerator from 375 m/s to a stop. We entrained the molecular beam with Li atoms by laser ablation prior to deceleration. The deceleration ends with loading the molecules and atoms into a static quadrupole trap, which is generated by two permanent magnets. We estimate 109 trapped molecules with background limited lifetime of 0.6 Sec. Our achievement enables application of laser cooling on the Li atoms in order to sympathetically cool the O2.

  14. Ion-atom cold collision: Formation of cold molecular ion by radiative processes

    OpenAIRE

    Rakshit, Arpita; Deb, Bimalendu

    2010-01-01

    We discuss theoretically ion-atom collisions at low energy and predict the possibility of formation of cold molecular ion by photoassociation. We present results on radiative homo- and hetero-nuclear atom-ion cold collisions that reveal threshold behaviour of atom-ion systems.

  15. Tunneling Dynamics Between Any Two Multi-atomic-molecular Bose-Einstein Condensates

    Institute of Scientific and Technical Information of China (English)

    CHEN Chang-Yong; GAO Ke-Lin

    2005-01-01

    Tunneling dynamics of multi-atomic molecules between any two multi-atomic molecular Bose-Einstein condensates with Feshbach resonance is investigated. It is indicated that the tunneling in the two Bose-Einstein condensates depends not only on the inter-molecular nonlinear interactions and the initial number of molecule in these condensates, but also on the tunneling coupling between them. It is discovered that besides oscillating tunneling current between the multi-atomic molecular condensates, the nonlinear multi-atomic molecular tunneling dynamics sustains a self-locked population imbalance: a macroscopic quantum self-trapping effect. The influence of de-coherence caused by non-condensate molecule on the tunneling dynamics is studied. It is shown that de-coherence suppresses the multi-atomic molecular tunneling.

  16. International bulletin on atomic and molecular data for fusion. No. 41

    International Nuclear Information System (INIS)

    The Bulletin provides information on atomic and molecular data relevant to fusion research. In Part I, the indexed papers are listed separately for structure and spectra, atomic and molecular collitions and surface interactions. Part II contains all the bibliographic data for both the indexed and non-indexed references. Part III contains the list of evaluated numerical atomic databases which are stored in the IAEA data bank. An author index is included at the end

  17. Methods to extract information on the atomic and molecular states from scientific abstracts

    International Nuclear Information System (INIS)

    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)

  18. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Alocci, Davide, E-mail: alodavide@gmail.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Bernini, Andrea, E-mail: andrea.bernini@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Niccolai, Neri, E-mail: neri.niccolai@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); SienaBioGrafix Srl, via A. Fiorentina 1, 53100 Siena (Italy)

    2013-07-12

    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

  19. Molecular mechanisms of mutagenesis and DNA repair

    International Nuclear Information System (INIS)

    Most organisms including man have evolved ways to handle damage produce in DNA by environmental agents including chemical mutagens and carcinogens. The process of repair of some types of damage is highly regulated in a tissue and cell line-specific fashion and varies from organism to organism. Thus, the ultimate biological effects of the lesions depend not only on the extent of their formation but on the efficiency of their removal as well. The research objectives of this laboratory are to elucidate the mechanism and regulation of repair of damage in DNA produced by simple alkylating mutagens and carcinogens, as well as the mutagenic changes in DNA produced as a result of persistence of unrepaired lesions. Specifically, the current topics of the authors research are (1) to elucidate the enzymatic mechanism of the human repair enzyme, DNA-O6-methylguanine methyltransferase, and to determine the molecular mechanism of its regulation and (2) to study the nature of mutations induced by the presence of alkylated bases and ionizing radiation-damaged bases in DNA using shuttle plasmids that replicate both in human cells and E. coli. The following report on last year's experiments bear upon the first objective

  20. Molecular mechanisms of HIV-1 associated neurodegeneration

    Indian Academy of Sciences (India)

    Hakan Ozdener

    2005-06-01

    Since identification of the human immunodeficiency virus-1 (HIV-1), numerous studies suggest a link between neurological impairments, in particular dementia, with acquired immunodeficiency syndrome (AIDS) with alarming occurrence worldwide. Approximately, 60% of HIV-infected people show some form of neurological impairment, and neuropathological changes are found in 90% of autopsied cases. Approximately 30% of untreated HIV-infected persons may develop dementia. The mechanisms behind these pathological changes are still not understood. Mounting data obtained by in vivo and in vitro experiments suggest that neuronal apoptosis is a major feature of HIV associated dementia (HAD), which can occur in the absence of direct infection of neurons. The major pathway of neuronal apoptosis occurs indirectly through release of neurotoxins by activated cells in the central nervous system (CNS) involving the induction of excitotoxicity and oxidative stress. In addition a direct mechanism induced by viral proteins in the pathogenesis of HAD may also play a role. This review focuses on the molecular mechanisms of HIV-associated dementia and possible therapeutic strategies.

  1. Molecular Mechanisms of Mouse Skin Tumor Promotion

    Energy Technology Data Exchange (ETDEWEB)

    Rundhaug, Joyce E.; Fischer, Susan M., E-mail: smfischer@mdanderson.org [The University of Texas M. D. Anderson Cancer Center, Science Park-Research Division, P.O. Box 389, Smithville, TX 78957 (United States)

    2010-04-13

    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.

  2. Molecular mechanism of TNF signaling and beyond

    Institute of Scientific and Technical Information of China (English)

    Zheng-gang LIU

    2005-01-01

    Tumor necrosis factor (TNF) is a proinflammatory cytokine that plays a critical role in diverse cellular events,including cell proliferation, differentiation and apoptosis. TNF is also involved in many types of diseases. In recent years, the molecular mechanisms of TNF functions have been intensively investigated. Studies from many laboratories have demonstrated that the TNF-mediated diverse biological responses are achieved through activating multiple signaling pathways. Especially the activation of transcription factors NF-κB and AP-1 plays a critical role in mediating these cellular responses. Several proteins, including FADD, the death domain kinase RIP and the TNF receptor associated factor TRAF2 have been identified as the key effectors of TNF signaling. Recently, we found that the effector molecules of TNF signaling, such as RIP and TRAF2, are also involved in other cellular responses. These finding suggests that RIP and TRAF2 serve a broader role than as just an effector of TNF signaling.

  3. Molecular mechanisms involved in intestinal iron absorption

    Institute of Scientific and Technical Information of China (English)

    Paul Sharp; Surjit Kaila Srai

    2007-01-01

    Iron is an essential trace metal in the human diet due to its obligate role in a number of metabolic processes.In the diet, iron is present in a number of different forms, generally described as haem (from haemoglobin and myoglobin in animal tissue) and non-haem iron (including ferric oxides and salts, ferritin and lactoferrin).This review describes the molecular mechanisms that co-ordinate the absorption of iron from the diet and its release into the circulation. While many components of the iron transport pathway have been elucidated, a number of key issues still remain to be resolved. Future work in this area will provide a clearer picture regarding the transcellular flux of iron and its regulation by dietary and humoral factors.

  4. Cellular and molecular mechanisms underlying radiation carcinogenesis

    International Nuclear Information System (INIS)

    When considering and analyzing experimental material concerning cellular aspects of the problem of radiation carcinogenesis, the following conclusions can be made: neoplastic transformation of cells in a culture is caused already by small radiation doses, under the effect of which the level of DNA injury is quite insignificant; the frequency of cell transformation depends on the type of radiation, it is particularly pronounced under the effect of radiations with a high linear energy transfer; a correlation between the processes of postradiation recovery and radiogenic transformation of cells is detected, nonrepairable injures of DNA playing the most important role in radiation carcinogenesis; tumour promoters and anticarcinogenic agens produce a modifying effect on the transformation of irradiated cells. Molecular mechanisms of oncogene activation are thoroughly studied using the model of virus carcinogenesis, the problem of the nature of chemical and, in particular, radiation cell transformation remains scantily investigated

  5. Pilocytic astrocytoma: pathology, molecular mechanisms and markers.

    Science.gov (United States)

    Collins, V Peter; Jones, David T W; Giannini, Caterina

    2015-06-01

    Pilocytic astrocytomas (PAs) were recognized as a discrete clinical entity over 70 years ago. They are relatively benign (WHO grade I) and have, as a group, a 10-year survival of over 90%. Many require merely surgical removal and only very infrequently do they progress to more malignant gliomas. While most show classical morphology, they may present a spectrum of morphological patterns, and there are difficult cases that show similarities to other gliomas, some of which are malignant and require aggressive treatment. Until recently, almost nothing was known about the molecular mechanisms involved in their development. The use of high-throughput sequencing techniques interrogating the whole genome has shown that single abnormalities of the mitogen-activating protein kinase (MAPK) pathway are exclusively found in almost all cases, indicating that PA represents a one-pathway disease. The most common mechanism is a tandem duplication of a ≈2 Mb-fragment of #7q, giving rise to a fusion between two genes, resulting in a transforming fusion protein, consisting of the N-terminus of KIAA1549 and the kinase domain of BRAF. Additional infrequent fusion partners have been identified, along with other abnormalities of the MAP-K pathway, affecting tyrosine kinase growth factor receptors at the cell surface (e.g., FGFR1) as well as BRAF V600E, KRAS, and NF1 mutations among others. However, while the KIAA1549-BRAF fusion occurs in all areas, the incidence of the various other mutations identified differs in PAs that develop in different regions of the brain. Unfortunately, from a diagnostic standpoint, almost all mutations found have been reported in other brain tumor types, although some retain considerable utility. These molecular abnormalities will be reviewed, and the difficulties in their potential use in supporting a diagnosis of PA, when the histopathological findings are equivocal or in the choice of individualized therapy, will be discussed. PMID:25792358

  6. Angular momentum in molecular quantum mechanical integral evaluation

    Science.gov (United States)

    Dunlap, Brett I.

    2005-01-01

    Solid-harmonic derivatives of quantum-mechanical integrals over Gaussian transforms of scalar, or radial, atomic basis functions create angular momentum about each center. Generalized Gaunt coefficients limit the amount of cross differentiation for multi-center integrals to ensure that cross differentiation does not affect the total angular momentum. The generalized Gaunt coefficients satisfy a number of other selection rules, which are exploited in a new computer code for computing forces in analytic density-functional theory based on robust and variational fitting of the Kohn-Sham potential. Two-center exponents are defined for four or more solid-harmonic differentiations of matrix elements. Those differentiations can either build up angular momentum about the centers or give forces on molecular potential-energy surfaces, thus generalized Gaunt coefficients of order greater than the number of centers are considered. These 4- j generalized Gaunt coefficients and two-center exponents are used to compute the first derivatives of all integrals involving all the Gaussian exponents on a triplet of centers at once. First all angular factors are contracted with the corresponding part of the linear-combination-of-atomic-orbitals density matrix. This intermediate quantity is then reused for the nuclear attraction integral and the integrals corresponding to each basis function in the analytic fit of the Kohn-Sham potential in the muffin-tin-like, but analytic, Slater-Roothaan method that allows molecules to dissociate into atoms having any desired energy, including the experimental electronic energy. The energy is stationary in all respects and all forces precisely agree with a previous code in tests on small molecules. During geometry optimization of an icosahedral C 720 fullerene computing these angular factors and transforming them via the 4- j generalized Gaunt coefficient takes more than sixty percent of the total computer time. These same angular factors could be used

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

    International Nuclear Information System (INIS)

    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. Hemolytic mechanism of dioscin proposed by molecular dynamics simulations.

    Science.gov (United States)

    Lin, Fu; Wang, Renxiao

    2010-01-01

    Saponins are a class of compounds containing a triterpenoid or steroid core with some attached carbohydrate modules. Many saponins cause hemolysis. However, the hemolytic mechanism of saponins at the molecular level is not yet fully understood. In an attempt to explore this issue, we have studied dioscin-a saponin with high hemolytic activity-through extensive molecular dynamics (MD) simulations. Firstly, all-atom MD simulations of 8 ns duration were conducted to study the stability of the dioscin-cholesterol complex and the cholesterol-cholesterol complex in water and in decane, respectively. MM-GB/SA computations indicate that the dioscin-cholesterol complex is energetically more favorable than the cholesterol-cholesterol complex in a non-polar environment. Next, several coarse-grained MD simulations of 400 ns duration were conducted to directly observe the distribution of multiple dioscin molecules on a DPPC-POPC-PSM-CHOL lipid bilayer. Our results indicate that dioscin can penetrate into the lipid bilayer, accumulate in the lipid raft micro-domain, and then bind cholesterol. This leads to the destabilization of lipid raft and consequent membrane curvature, which may eventually result in the hemolysis of red cells. This possible mechanism of hemolysis can well explain some experimental observations on hemolysis. PMID:19513766

  9. Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii

    CERN Document Server

    Heyrovska, Raji

    2007-01-01

    The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the bond lengths are close to the sums of the corresponding atomic covalent radii of carbon, nitrogen, oxygen, hydrogen and phosphorus. Thus, the conventional molecular structures have been resolved here, for the first time, into probable atomic structures.

  10. Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

    Science.gov (United States)

    Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

    1993-01-01

    The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

  11. 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.

  12. How hyperglycemia promotes atherosclerosis: molecular mechanisms

    Directory of Open Access Journals (Sweden)

    Rayfield Elliot J

    2002-04-01

    Full Text Available Abstract Both type I and type II diabetes are powerful and independent risk factors for coronary artery disease (CAD, stroke, and peripheral arterial disease. Atherosclerosis accounts for virtually 80% of all deaths among diabetic patients. Prolonged exposure to hyperglycemia is now recognized a major factor in the pathogenesis of atherosclerosis in diabetes. Hyperglycemia induces a large number of alterations at the cellular level of vascular tissue that potentially accelerate the atherosclerotic process. Animal and human studies have elucidated three major mechanisms that encompass most of the pathological alterations observed in the diabetic vasculature: 1 Nonenzymatic glycosylation of proteins and lipids which can interfere with their normal function by disrupting molecular conformation, alter enzymatic activity, reduce degradative capacity, and interfere with receptor recognition. In addition, glycosylated proteins interact with a specific receptor present on all cells relevant to the atherosclerotic process, including monocyte-derived macrophages, endothelial cells, and smooth muscle cells. The interaction of glycosylated proteins with their receptor results in the induction of oxidative stress and proinflammatory responses 2 oxidative stress 3 protein kinase C (PKC activation with subsequent alteration in growth factor expression. Importantly, these mechanisms may be interrelated. For example, hyperglycemia-induced oxidative stress promotes both the formation of advanced glycosylation end products and PKC activation.

  13. Molecular mechanism of phototropin light signaling.

    Science.gov (United States)

    Okajima, Koji

    2016-03-01

    Phototropin (phot) is a blue light (BL) receptor kinase involved in the BL responses of several species, ranging from green algae to higher plants. Phot converts BL signals from the environment into biochemical signals that trigger cellular responses. In phot, the LOV1 and LOV2 domains of the N-terminal region utilize BL for cyclic photoreactions and regulate C-terminal serine/threonine kinase (STK) activity. LOV2-STK peptides are the smallest functional unit of phot and are useful for understanding regulation mechanisms. The combined analysis of spectroscopy and STK activity assay in Arabidopsis phots suggests that the decay speed of the photo-intermediate S390 in LOV2 is one of the factors contributing to light sensitive kinase activity. LOV2 and STK are thought to be adjacent to each other in LOV2-STK with small angle scattering (SAXS). BL irradiation induces LOV2-STK elongation, resulting in LOV2 shifting away from STK. The N- and C-terminal lateral regions of LOV2, A'α-helix, Jα-helix, and A'α/Aβ gap are responsible for the propagation of the BL signal to STK via conformational changes. The comparison between LOV2-STK and full-length phot from Chlamydomonas suggests that LOV1 is directly adjacent to LOV2 in LOV2-STK; therefore, LOV1 may indirectly regulate STK. The molecular mechanism of phot is discussed. PMID:26815763

  14. Molecular View of Protein Crystal Growth: Molecular Interactions, Surface Reconstruction and Growth Mechanism

    Science.gov (United States)

    Nadarajah, Arunan; Li, Huayu; Konnert, John H.; Pusey, Marc L.

    2000-01-01

    Studies of the growth and molecular packing of tetragonal lysozyme crystals suggest that there is an underlying molecular growth mechanism, in addition to the classical one involving screw dislocation/2D) nucleation growth. These crystals are constructed by strongly bonded molecular chains forming helices about the 43 axes. The helices are connected to each other by weaker bonds. Crystal growth proceeds by the formation of these 4(sub 3) helices, which would explain some unexpected observations by earlier investigators, such as bimolecular growth steps on the (110) face. Another consequence of these molecular considerations is that only one of two possible packing arrangements could occur on the crystal faces and that their growth unit was at least a tetramer corresponding to the 4(sub 3) helix. Two new high resolution atomic force microscopy (AFM) techniques were developed to directly confirm these predictions on tetragonal lysozyme crystals. Most earlier investigations of protein crystal growth with AFM were in the low resolution mode which is adequate to investigate the classical growth mechanisms, but cannot resolve molecular features and mechanisms. Employing the first of the newly developed techniques, high resolution AFM images of the (110) face were compared with the theoretically constructed images for the two possible packing arrangements on this face. The prediction that the molecular packing arrangement of these faces corresponded to that for complete 4(sub 3) helices was confirmed in this manner. This investigation also showed the occurrence of surface reconstruction on protein crystals. The molecules on the surface of the (110) face were found to pack closer along the 4(sub 3) axes than those in the interior. The second new AFM technique was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth

  15. 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.

  16. Exploring the electronic and mechanical properties of protein using conducting atomic force microscopy.

    Science.gov (United States)

    Zhao, Jianwei; Davis, Jason J; Sansom, Mark S P; Hung, Andrew

    2004-05-01

    In interfacing man-made electronic components with specifically folded biomacromolecules, the perturbative effects of junction structure on any signal generated should be considered. We report herein on the electron-transfer characteristics of the blue copper metalloprotein, azurin, as characterized at a refined level by conducting atomic force microscopy (C-AFM). Specifically, the modulation of current-voltage (I-V) behavior with compressional force has been examined. In the absence of assignable resonant electron tunneling within the confined bias region, from -1 to 1 V, the I-V behavior was analyzed with a modified Simmons formula. To interpret the variation of tunneling barrier height and barrier length obtained by fitting with the modified Simmons formula, an atom packing density model associated with protein mechanical deformation was proposed and simulated by molecular dynamics. The barrier heights determined at the minimum forces necessary for stable electrical contact correlate reasonably well with those estimated from bulk biophysical (electroanalytical and photochemical) experiments previously reported. At higher forces, the tunnel barrier decreases to fall within the range observed with saturated organic systems. Molecular dynamics simulations revealed changes in secondary structure and atomic density of the protein with respect to compression. At low compression, where transport measurements are made, secondary structure is retained, and atomic packing density is observed to increase linearly with force. These predictions, and those made at higher compression, are consistent with both experimentally observed modulations of tunneling barrier height with applied force and the applicability of the atom packing density model of electron tunneling in proteins to molecular-level analyses. PMID:15113232

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

    International Nuclear Information System (INIS)

    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

  18. International bulletin on atomic and molecular data for fusion. No. 54-55

    International Nuclear Information System (INIS)

    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

  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. Many-body processes in atomic and molecular physics

    International Nuclear Information System (INIS)

    This report discusses the following topics: Dynamics of Multiphoton Excitation in Rydberg Atoms; Nonlinear Schrodinger Equation and Dissipative Quantum Dynamics in Periodic Fields; Density Matrix Formulation of Complex Geometric Phases in Dissipative Systems; and A. C. Stark Shifts of Excited States of Atoms in Strong Fields

  1. Molecular Dynamics Study of Mechanical Behaviour of Screw Dislocation during Cutting with Diamond Tip on Silicon

    International Nuclear Information System (INIS)

    By means of Tersoff and Morse potentials, a three-dimensional molecular dynamics simulation is performed to study atomic force microscopy cutting on silicon monocrystal surface. The interatomic forces between the workpiece and the pin tool and the atoms of workpiece themselves are calculated. A screw dislocation is introduced into workpiece Si. It is found that motion of dislocations does not occur during the atomic force microscopy cutting processing. Simulation results show that the shear stress acting on dislocation is far below the yield strength of Si. (condensed matter: structure, mechanical and thermal properties)

  2. A molecular mechanics approach for analyzing tensile nonlinear deformation behavior of single-walled carbon nanotubes

    Institute of Scientific and Technical Information of China (English)

    Yu Wang; Daining Fang; Ai Kah Soh; Bin Liu

    2007-01-01

    In this paper, by capturing the atomic informa-tion and reflecting the behaviour governed by the nonlin-ear potential function, an analytical molecular mechanics approach is proposed. A constitutive relation for single-walled carbon nanotubes (SWCNT's) is established to describe the nonlinear stress-strain curve of SWCNT's and to predict both the elastic properties and breaking strain of SWCNT's during tensile deformation. An analysis based on the virtual internal bond (VIB) model proposed by P. Zhang et al. is also presented for comparison. The results indicate that the proposed molecular mechanics approach is indeed an acceptable analytical method for analyzing the mechanical behavior of SWCNT's.

  3. Ab initio Mechanism Study on the Reaction of Chlorine Atom with Formic Acid

    Institute of Scientific and Technical Information of China (English)

    于海涛; 付宏刚; 等

    2003-01-01

    The potential energy surface(PES) for the reaction of Cl atom with HCOOH is predicted using ab initio molecular orbital calculation methods at UQCIDS(T,full)6-311++G(3df,2p)//UMP2(full)/6-311+G(d,P) level of theory with zero-point vibrational energy (ZPVE) correction.The calculated results show that the reaction mechanism of Cl atom with formic acid is a C-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom with a 3.73kJ/mol reaction barrier height,leading to the formation of cis-HOCO radical which will reacts with Cl atom or other molecules in such a reaction system.Because the reaction barrier height of O-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom which leads to the formation of HCO2 radical is 67.95kJ/mol,it is a secondary reaction channel in experiment,This is in good agreement with the prediction based on the previous experiments.

  4. International bulletin on atomic and molecular data for fusion. No. 49

    International Nuclear Information System (INIS)

    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'')

  5. Symmetry-derived half-metallicity in atomic and molecular junctions.

    Science.gov (United States)

    Smogunov, Alexander; Dappe, Yannick J

    2015-05-13

    Achieving highly spin-polarized electric currents in atomic-scale junctions is of great importance in the field of nanoelectronics and spintronics. Based on robust symmetry considerations, we propose a mechanism to block completely one of spin conduction channels for a broad class of atomic and molecular junctions bridging two ferromagnetic electrodes. This particular behavior is due to the wave function orthogonality between spin up s-like states in ferromagnetic electrode and available π channels in the junction. As a consequence, the system would ideally yield 100% spin-polarized current, with a junction acting thus as a "half-metallic" conductor. Using ab initio electron transport calculations, we demonstrate this principle on two examples: (i) a short carbon chain and (ii) a π-conjugated molecule (polythiophene) connected either to model semi-infinite Ni wires or to realistic Ni(111) electrodes. It is also predicted that such atomic-scale junctions should lead to very high (ideally, infinite) magneto-resistance ratios since the electric current gets fully blocked if two electrodes have antiparallel magnetic alignment. PMID:25871804

  6. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    Science.gov (United States)

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  7. 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)

    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

  8. Molecular and cellular mechanisms of adipogenesis

    Directory of Open Access Journals (Sweden)

    Aleksander Dmitrievich Egorov

    2015-03-01

    Full Text Available The main components of metabolic syndrome include insulin resistance, hypertriglyceridemia and arterial hypertension. Obesity is the cause of metabolic syndrome, mainly as a consequence of the endocrine function of adipose tissue. The volume of adipose tissue depends on the size of individual adipocytes and on their number. The number of adipocytes increases as a result of enhanced adipocyte differentiation. The transcriptional cascade that regulates this differentiation has been well studied. The major adipogenic transcription factor peroxisome proliferator-activated receptor gamma is a ligand-activated nuclear receptor with essential roles in adipogenesis. Its ligands are used to treat metabolic syndrome and type 2 diabetes mellitus. The present article describes the basic molecular and cellular mechanisms of adipogenesis and discusses the impact of insulin, glucocorticoids, cyclic adenosine monophosphate-activating agents, nuclear receptors and transcription factors on the process of adipogenesis. New regulatory regions of the genome that are capable of binding multiple transcription factors are described, and the most promising drug targets for the treatment of metabolic syndrome and obesity, including the homeodomain proteins Pbx1 and Prep1, are discussed.

  9. Molecular mechanisms of radiation onco-genesis

    International Nuclear Information System (INIS)

    Induction of cancer is the most important somatic effect of radiation at dose level below 1 Gy (100 rad). Most of the data used to derive risk estimates for low-dose levels are obtained from exposures occurring at dose levels of 0.1 Gy (10 Rad) or above. Benign or malignant tumour induction, is viewed as a probable function of the dose received. This is known as a stochastic effect. When the radiation dose increases the probability of the effect is increased, but there is no effect on the severity. In order to allow that future extrapolation of high-dose epidemiological data may be made with confidence, it is important that a much more detailed picture be gained of the cellular and molecular processes that mediate oncogenic changes in mammalian cells. Many studies have been done in understanding the mechanisms of radiation onco-genesis Today we are just on the frontier of what is a fast-moving and complex research field. (author)

  10. Cellular and molecular mechanisms in liver fibrogenesis.

    Science.gov (United States)

    Novo, Erica; Cannito, Stefania; Paternostro, Claudia; Bocca, Claudia; Miglietta, Antonella; Parola, Maurizio

    2014-04-15

    Liver fibrogenesis is a dynamic and highly integrated molecular, tissue and cellular process, potentially reversible, that drives the progression of chronic liver diseases (CLD) towards liver cirrhosis and hepatic failure. Hepatic myofibroblasts (MFs), the pro-fibrogenic effector cells, originate mainly from activation of hepatic stellate cells and portal fibroblasts being characterized by a proliferative and survival attitude. MFs also contract in response to vasoactive agents, sustain angiogenesis and recruit and modulate activity of cells of innate or adaptive immunity. Chronic activation of wound healing and oxidative stress as well as derangement of epithelial-mesenchymal interactions are "major" pro-fibrogenic mechanisms, whatever the etiology. However, literature has outlined a complex network of pro-fibrogenic factors and mediators proposed to modulate CLD progression, with some of them being at present highly debated in the field, including the role of epithelial to mesenchymal transition and Hedgehog signaling pathways. Hypoxia and angiogenesis as well as inflammasomes are recently emerged as ubiquitous pro-inflammatory and pro-fibrogenic determinants whereas adipokines are mostly involved in CLD related to metabolic disturbances (metabolic syndrome and/or obesity and type 2 diabetes). Finally, autophagy as well as natural killer and natural killer-T cells have been recently proposed to significantly affect fibrogenic CLD progression. PMID:24631571

  11. Molecular Mechanisms Underlying Psychological Stress and Cancer.

    Science.gov (United States)

    Shin, Kyeong Jin; Lee, Yu Jin; Yang, Yong Ryoul; Park, Seorim; Suh, Pann-Ghill; Follo, Matilde Yung; Cocco, Lucio; Ryu, Sung Ho

    2016-01-01

    Psychological stress is an emotion experienced when people are under mental pressure or encounter unexpected problems. Extreme or repetitive stress increases the risk of developing human disease, including cardiovascular disease (CVD), immune diseases, mental disorders, and cancer. Several studies have shown an association between psychological stress and cancer growth and metastasis in animal models and case studies of cancer patients. Stress induces the secretion of stress-related mediators, such as catecholamine, cortisol, and oxytocin, via the activation of the hypothalamic-pituitary-adrenocortical (HPA) axis or the sympathetic nervous system (SNS). These stress-related hormones and neurotransmitters adversely affect stress-induced tumor progression and cancer therapy. Catecholamine is the primary factor that influences tumor progression. It can regulate diverse cellular signaling pathways through adrenergic receptors (ADRs), which are expressed by several types of cancer cells. Activated ADRs enhance the proliferation and invasion abilities of cancer cells, alter cell activity in the tumor microenvironment, and regulate the interaction between cancer and its microenvironment to promote tumor progression. Additionally, other stress mediators, such as glucocorticoids and oxytocin, and their cognate receptors are involved in stress-induced cancer growth and metastasis. Here, we will review how each receptor-mediated signal cascade contributes to tumor initiation and progression and discuss how we can use these molecular mechanisms for cancer therapy. PMID:26916018

  12. Molecular and genetic mechanisms of environmental mutagens

    International Nuclear Information System (INIS)

    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

  13. Casimir effects in atomic, molecular, and optical physics

    CERN Document Server

    Babb, James F

    2010-01-01

    The long-range interaction between two atoms and the long-range interaction between an ion and an electron are compared at small and large intersystem separations. The vacuum dressed atom formalism is applied and found to provide a framework for interpretation of the similarities between the two cases. The van der Waals forces or Casimir-Polder potentials are used to obtain insight into relativistic and higher multipolar terms.

  14. Experimental comparison of the critical ionization velocity in atomic and molecular gases

    International Nuclear Information System (INIS)

    The critical ionization velocity usub(c) of Ne, Kr, Xe, Cl2, O2, CO, CO2, NH3 and H2O 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

  15. Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling

    Energy Technology Data Exchange (ETDEWEB)

    Tawara, H. [ed.

    1997-01-01

    This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)

  16. Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling

    International Nuclear Information System (INIS)

    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.)

  17. A molecular mechanical model for N-heterocyclic carbenes.

    Science.gov (United States)

    Gehrke, Sascha; Hollóczki, Oldamur

    2016-08-10

    In this work we present a set of force fields for nine synthetically relevant and/or structurally interesting N-heterocyclic carbenes, including imidazol-, thiazol-, triazol-, imidazolidin-, and pyridine-ylidenes. The bonding parameters were calculated by using a series of geometry optimizations by ab initio methods. For fitting the non-bonding interactions, a water molecule was employed as a probe. The interaction energy between the carbene and the probe molecule was sampled along two coordinates for each carbene, representing the interaction through the lone pair, or the π system of the molecule. The corresponding reference interaction energies were obtained by CCSD(T)/CBS calculations. To describe the direction dependence of the intermolecular potential energy, an extra, massless Coulombic interaction site was included for all carbenes, which represents the lone pair of the divalent carbon atom. The resulting fitted carbene force field (CaFF) showed a robust behavior regarding probe molecule, as changing the molecular mechanical water model, or employing, instead, an OPLS methanol molecule did not introduce significant deviations in the potential energies. The obtained CaFF models are easy to merge with standard OPLS or AMBER force fields, therefore the molecular simulations of a large number of N-heterocyclic carbenes becomes available. PMID:27426687

  18. Molecular mechanisms of deformation and failure in glassy materials

    Science.gov (United States)

    Rottler, Joerg

    2004-03-01

    Understanding the molecular origins of macroscopic mechanical properties is a fundamental scientific challenge. Fracture of both amorphous and crystalline materials involves many length scales reaching from the continuum to atomic level processes near a crack tip. Using molecular simulations of simple models for amorphous glassy materials, we first study elastoplastic deformation and discuss the nature of the shear yield stress and its dependence on loading conditions, strain rate and temperature. We then focus on the deformation of glassy polymeric systems into crazes at large strains. In the craze, polymers ( 0.5 nm diameter) are bundled into an intricate network of 10 nm diameter fibrils that extends 10 micrometers on either side of a mm crack tip. Analysis of local geometry and stresses provide insight into the real-space nature of the entanglements that control craze formation as well as melt dynamics. Crazes are also shown to share many features with jammed systems such as granular media and foams, but are unique in jamming under a tensile load. This allows explanations for the exponential force distribution in jammed systems to be tested. The force distribution strongly influences the ultimate breakdown of the craze fibrils either through disentanglement or chain scission. We conclude by quantifying the contribution of crazing to the unusually large fracture energy of glassy polymers.

  19. Single DNA molecular manipulation with atomic force microscopy

    International Nuclear Information System (INIS)

    Nanomanipulation of DNA molecules or other biomolecules to form artificial patterns or structures at nanometer scale has potential applications in the construction of molecular devices in future industries. It may also lead to new insights into the interesting properties and behavior of this fantastic nature-selected molecule at the single-molecular level. Here we present a special method based on the combination of macroscopic 'molecular combing' and microscopic 'molecular cutting' to manipulate DNA molecules and form complex patterns at nanometer scale on solid surfaces. A possible strategy for ordered DNA sequencing based on this nanomanipulation technique has also been proposed. (authors)

  20. Single DNA molecular manipulation with atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    L(U) Jun-Hong; WU Shi-Ying; ZHANG Yi; HU Jun; LI Min-Qian

    2004-01-01

    Nanomanipulation of DNA molecules or other biomolecules to form artificial patterns or structures at nanometer scale has potential applications in the construction of molecular devices in future industries. It may also lead to new insights into the interesting properties and behavior of this fantastic nature-selected molecule at the single-molecular level. Here we present a special method based on the combination of macroscopic "molecular combing" and microscopic "molecular cutting" to manipulate DNA molecules and form complex patterns at nanometer scale on solid surfaces. A possible strategy for ordered DNA sequencing based on this nanomanipulation technique has also been proposed.

  1. Chemisorption of atomic and molecular oxygen on Au and Ag cluster anions : discrimination of different isomers

    OpenAIRE

    Kim, Young Dok; Ganteför, Gerd; Sun, Qiang; Jena, Purusottam

    2004-01-01

    Structures of coinage metal clusters reacted with atomic and molecular oxygen were studied using Ultraviolet Photoelectron Spectroscopy and Density Functional Theory calculations. We show that O2 partially dissociates on Ag-2, and this dissociative chemisorption is a kinetically hindered step. For Au4O-2, in addition to the previously observed molecularly adsorbed oxygen, we are now able to synthesize a second isomer using atomic oxygen reagents, in which oxygen adsorbs dissociatively. We dem...

  2. International bulletin on atomic and molecular data for fusion. No. 61

    International Nuclear Information System (INIS)

    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. Molecular dynamics simulation of gaseous atomic hydrogen interactions with hydrocarbon grains

    OpenAIRE

    Papoular, Renaud

    2004-01-01

    Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities are determined by multiple numerical experiments, as a function of initial velocity of gas atoms. The equilibrium hydrogen coverage of free grains is then derived. These data can be used in calculations of material and energy balance as well as rates of hy...

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

    International Nuclear Information System (INIS)

    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 year 1979 for all the publications on controlled fusion and plasma physics. A short description of the Programme of the IAEA Atomic and Molecular Data Unit is outlined

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

    International Nuclear Information System (INIS)

    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)

  6. 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.)

  7. International bulletin on atomic and molecular data for fusion. No. 25

    International Nuclear Information System (INIS)

    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)

  8. Atomic and global mechanical properties of systems described by the Stillinger–Weber potential

    Science.gov (United States)

    Voyiatzis, Evangelos; Böhm, Michael C.

    2016-08-01

    Analytical expressions for the stress and elasticity tensors of materials, in which the interactions are described by the Stillinger–Weber potential, are derived in the context of the stress fluctuation formalism. The derived formulas can be used both in Monte Carlo and molecular dynamics simulations. As an example of possible applications, they are employed to calculate the influence of the temperature and system size on the mechanical properties of crystalline cubic boron nitride. The system has been studied by molecular dynamics simulations. The computed mechanical properties are in good agreement with available experimental data and first principle calculations. In the studied crystalline cubic boron nitride system, the employed formalism is of higher accuracy than the ‘small-strain’ non-equilibrium method. The dominant contributions to the elastic constants stem from the Born and stress fluctuation terms. An increase in the system size reduces the statistical uncertainties in the computation of the mechanical properties. A rise of the temperature leads to a slight increase in the observed uncertainties. The derived expressions for the stress and elasticity tensors are further decomposed into sums of atomic level stress and atomic level elasticity tensors. The developed factorization enables us (i) to quantify the contribution of the various chemical groups, in the case under consideration of the different atoms, to the observed mechanical properties and (ii) to determine the elastic constants with reduced computational uncertainties. The reason is that the exact values of some terms of the proposed factorization can be determined theoretically beforehand. Thus, they can be substituted in the derived formulas leading to an enhanced convergence.

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

    International Nuclear Information System (INIS)

    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)

  10. 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.

  11. Physiology and molecular mechanism of glucocorticoid action

    Directory of Open Access Journals (Sweden)

    Andrzej Nagalski

    2010-03-01

    Full Text Available Endogenous glucocorticoids (GCs are secreted into the systemic circulation from the adrenal cortex. This release is under the control of the circadian clock and can be enhanced at any time in response to a stressor. The levels of circulating GC are regulated systemically by the hypothalamo-pituitary-adrenal axis and locally by access to target cells and pre-receptor metabolism by 11β-hydroxysteroids dehydrogenase enzymes. GCs mediate their genomic action by binding to two different ligand-inducible transcription factors: high-affinity mineralocorticoid receptor (MR and 10-fold lower affinity glucocorticoid receptors (GRs. Responses to GCs vary among individuals, cells, and tissues. The diversity and specificity in the steroid hormone’s response in the cell is controlled at different levels, including receptor translocation, interaction with specific transcription factors and coregulators, and the regulation of receptor protein levels by microRNA. Moreover, multiple GR isoforms are generated from one single GR gene by alternative splicing and alternative translation initiation. These isoforms all have unique tissue distribution patterns and transcriptional regulatory profiles. Furthermore, each is subjected to various post-translational modifications that affect receptor function. Deciphering the molecular mechanisms of GC action is further complicated by the realization that GCs can induce rapid, non-genomic effects within the cytoplasm. A tight regulation of GC secretion and their cell-specific activity is essential for proper organism function. This is particularly seen under conditions of GC deficiency or excess, as in Addison’s disease and Cushing’s syndrome, respectively.

  12. Atomic Study on Some Problems in Nanometric Cutting Mechanism

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    An investigation of some problems such as chip formation and surface generation in nanometric cutting mechanism based on molecular dynamics(MD) simulation is presented.It shows that chip formation is similar to that observed in macro-scale cutting.The movement of some micro-dislocation is the main cause of formation of chip and surface.Surface generation is notably affected by very small cutting force vibration.The highest stress appears in tool cutting edge,and it may cause wear,so it is necessary to build a MD model of tool wear.

  13. Applications of Quantum Theory of Atomic and Molecular Scattering to Problems in Hypersonic Flow

    Science.gov (United States)

    Malik, F. Bary

    1995-01-01

    The general status of a grant to investigate the applications of quantum theory in atomic and molecular scattering problems in hypersonic flow is summarized. Abstracts of five articles and eleven full-length articles published or submitted for publication are included as attachments. The following topics are addressed in these articles: fragmentation of heavy ions (HZE particles); parameterization of absorption cross sections; light ion transport; emission of light fragments as an indicator of equilibrated populations; quantum mechanical, optical model methods for calculating cross sections for particle fragmentation by hydrogen; evaluation of NUCFRG2, the semi-empirical nuclear fragmentation database; investigation of the single- and double-ionization of He by proton and anti-proton collisions; Bose-Einstein condensation of nuclei; and a liquid drop model in HZE particle fragmentation by hydrogen.

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

    International Nuclear Information System (INIS)

    Alfven's critical ionization velocity (CIV) is a multi-step 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, and help explain the low energy threshold as well as the fast time scale in the onset of CIV. For a sustaining CIV to occur, an energy requirement and Townsend's criterion have to be satisfied. The kinetic energies of the neutrals are transformed to plasma wave energies via beam-plasma instabilities, and the plasma waves heat the electrons resulting in a tail formation. A parametric domain of beam angle and neutral densities satisfying Townsend's criterion is presented

  15. Modeling the molecular mechanism of the perception of smell

    OpenAIRE

    March, Claire de

    2015-01-01

    This research project is focused on the link between chemical structures of odorant molecules and their interactions with odorant receptors expressed in olfactory neurons. This basic research is of primary importance for building a physiologically-inspired “computational nose” that reproduces the function of the 400 types of odorant receptors involved in the perception of smells. Here, each odorant receptor is represented as a molecular system, reproduced atom per atom in a computational mode...

  16. Molecular mechanisms in radiation carcinogenesis: introduction

    International Nuclear Information System (INIS)

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

    International Nuclear Information System (INIS)

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

    International Nuclear Information System (INIS)

    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

  19. 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.

  20. New results in the theory of muonic atom formation in molecular hydrogen

    International Nuclear Information System (INIS)

    Muonic atom formation in molecular hydrogen proceeds in two stages. In the first stage, the mu-molecular complex (abμe)* is formed due to Coulomb capture of a muon by a hydrogen molecule (abee), and, in the second stage, the decay of the complex leads to exotic-atom formation. We consider various channels for the decay of the complex. The main competition channels are direct dissociation and Auger decay. The primary distribution of muonic atoms over quantum states and kinetic energy has been obtained taking into account the competition of the decay channels. (orig.)

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

    International Nuclear Information System (INIS)

    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

  2. Weak links between fast mobility and local structure in molecular and atomic liquids

    CERN Document Server

    Bernini, S; Leporini, D

    2016-01-01

    We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable We investigate by Molecular-Dynamics simulations the fast mobility - the rattling amplitude of the particles temporarily trapped by the cage of the neighbors - in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is characteristic of small $n$-alkanes and $n$-alcohols. Possible links between the fast mobility and ...

  3. Structure of the Alkali-metal-atom-Strontium molecular ions: towards photoassociation and formation of cold molecular ions

    OpenAIRE

    Aymar, Mireille; Guérout, Romain; Dulieu, Olivier

    2011-01-01

    The potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkali-metal atom and a Strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective two-electron systems and are treated using effective core potentials including core polarization, large gaussian basis sets, and full configuration interaction. In the perspective of upcoming experiments aiming at merging ...

  4. 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. PMID:27352028

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

    Science.gov (United States)

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

    2016-08-01

    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 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.

  6. Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties

    OpenAIRE

    Riley, Kevin E.; Op’t Holt, Bryan T.; Merz, Kenneth M.

    2007-01-01

    The reliable prediction of molecular properties is a vital task of computational chemistry. In recent years, density functional theory (DFT) has become a popular method for calculating molecular properties for a vast array of systems varying in size from small organic molecules to large biological compounds such as proteins. In this work we assess the ability of many DFT methods to accurately determine atomic and molecular properties for small molecules containing elements commonly found in p...

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

    International Nuclear Information System (INIS)

    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)

  8. First quantum mechanics/molecular mechanics studies of the inhibition mechanism of cruzain by peptidyl halomethyl ketones.

    Science.gov (United States)

    Arafet, Kemel; Ferrer, Silvia; Moliner, Vicent

    2015-06-01

    Cruzain is a primary cysteine protease expressed by the protozoan parasite Trypanosoma cruzi during Chagas disease infection, and thus, the development of inhibitors of this protein is a promising target for designing an effective therapy against the disease. In this paper, the mechanism of inhibition of cruzain by two different irreversible peptidyl halomethyl ketones (PHK) inhibitors has been studied by means of hybrid quantum mechanics/molecular mechanics-molecular dynamics (MD) simulations to obtain a complete representation of the possible free energy reaction paths. These have been traced on free energy surfaces in terms of the potential of mean force computed at AM1d/MM and DFT/MM levels of theory. An analysis of the possible reaction mechanisms of the inhibition process has been performed showing that the nucleophilic attack of an active site cysteine, Cys25, on a carbon atom of the inhibitor and the cleavage of the halogen-carbon bond take place in a single step. PClK appears to be much more favorable than PFK from a kinetic point of view. This result would be in agreement with experimental studies in other papain-like enzymes. A deeper analysis of the results suggests that the origin of the differences between PClK and PFK can be the different stabilizing interactions established between the inhibitors and the residues of the active site of the protein. Any attempt to explore the viability of the inhibition process through a stepwise mechanism involving the formation of a thiohemiketal intermediate and a three-membered sulfonium intermediate has been unsuccessful. Nevertheless, a mechanism through a protonated thiohemiketal, with participation of His159 as a proton donor, appears to be feasible despite showing higher free energy barriers. Our results suggest that PClK can be used as a starting point to develop a proper inhibitor of cruzain. PMID:25965914

  9. 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)

    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 SO2 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

  10. 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

  11. Perfect Precision Detecting Probability Of An Atom Via Sgc Mechanism

    Science.gov (United States)

    Hamedi, H. R.

    2015-06-01

    This letter investigates a scheme of high efficient two-dimensional (2D) atom localization via scanning probe absorption in a Y-type four-level atomic scheme with two orthogonal standing waves. It is shown that because of the position dependent atom-field interaction, the spatial probability distribution of the atom can be directly determined via monitoring the probe absorption and gain spectra. The impact of different controlling parameters of the system on 2D localization is studied. We find that owning the effect of spontaneously generated coherence (SGC), the atom can be localized at a particular position and the maximal probability of detecting the atom within the sub-wavelength domain of the two orthogonal standing waves reaches to hundred percent. Phase controlling of position dependent probe absorption is then discussed. The presented scheme may be helpful in laser cooling or atom nanolithography via high precision and high resolution atom localization.

  12. Local Mechanical Properties by Atomic Force Microscopy Nanoindentations

    Science.gov (United States)

    Tranchida, Davide; Piccarolo, Stefano

    The analysis of mechanical properties on a nanometer scale is a useful tool for combining information concerning texture organization obtained by microscopy with the properties of individual components. Moreover, this technique promotes the understanding of the hierarchical arrangement in complex natural materials as well in the case of simpler morphologies arising from industrial processes. Atomic Force Microscopy (AFM) can bridge morphological information, obtained with outstanding resolution, to local mechanical properties. When performing an AFM nanoindentation, the rough force curve, i.e., the plot of the voltage output from the photodiode vs. the voltage applied to the piezo-scanner, can be translated into a curve of the applied load vs. the penetration depth after a series of preliminary determinations and calibrations. However, the analysis of the unloading portion of the force curves collected for polymers does not lead to a correct evaluation of Young's modulus. The high slope of the unloading curves is not linked to an elastic behavior, as would be expected, but rather to a viscoelastic effect. This can be argued on the basis that the unloading curves are superimposed on the loading curves in the case of an ideal elastic behavior, as for rubbers, or generally in the case of materials with very short relaxation times. In contrast, when the relaxation time of the sample is close to or even much larger than the indentation time scale, very high slopes are recorded.

  13. Reasoning with Atomic-Scale Molecular Dynamic Models

    Science.gov (United States)

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

    The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

  14. Simultaneous melting of shell and core atoms, a molecular dynamics study of lithium–copper nanoalloys

    International Nuclear Information System (INIS)

    Melting of nanoalloys originates from the alloy surface and gradually propagates into the interior region. The thermal stability of Li cores and Cu shells nanoalloy with size of 3.5 nm is studied through molecular dynamics and embedded atom method with the use of potential energy, Lindemann index, and radial distribution function. Results show that the shell and core Li atoms are melted in two steps: first, some Li atoms in the core migrate to the nanoalloy surface and maintain a typical solid state despite that the system temperature is higher than the bulk melting point of Li because of Li solidification in the solid–liquid interface; second, the shell and core Li atoms are simultaneously melted at high temperatures. A comparative study of Li@Cu nanoalloys with different Li atomic numbers shows that thermal stability is enhanced with the decreasing number of Li atoms within the nanoalloys because of weak binding for Cu thin shells

  15. Molecular Dynamics Study on the Diffusion Properties of Hydrogen Atoms in Bulk Tungsten

    International Nuclear Information System (INIS)

    Molecular dynamics simulations were performed to study the diffusion behavior of hydrogen atoms in body-centered cubic(bcc) tungsten(W). The energy distribution of a single hydrogen atom in the (001) plane of tungsten lattice was computed. The values of diffusion barriers agree well with other theoretical and experimental results. The interaction between an H atom and a vacancy was simulated, which shows evidence of strong binding effect. The temperature effect on the diffusion behavior of hydrogen atoms was investigated. The critical temperature for an H atom to diffuse in bulk W with and without vacancies were calculated to be 950 K and 450 K, respectively, which is supported by several experimental results. In addition, the diffusion coefficient of hydrogen atoms in tungsten was evaluated and analyzed

  16. Spatial decomposition of molecular ions within 3D atom probe reconstructions

    Energy Technology Data Exchange (ETDEWEB)

    Breen, Andrew [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, NSW 2006 (Australia); Australian Centre for Microscopy and Microanalysis, Madsen Building F09, The University of Sydney, NSW 2006 (Australia); Moody, Michael P. [Department of Materials, University of Oxford, Parks Road, OX13PH, Oxford (United Kingdom); Gault, Baptiste [Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ont. L8S4L8 (Canada); Ceguerra, Anna V. [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, NSW 2006 (Australia); Australian Centre for Microscopy and Microanalysis, Madsen Building F09, The University of Sydney, NSW 2006 (Australia); Xie, Kelvin Y. [Johns Hopkins University, Department of Mechanical Engineering, Baltimore, MD 21218 (United States); Du, Sichao [Australian Centre for Microscopy and Microanalysis, Madsen Building F09, The University of Sydney, NSW 2006 (Australia); School of Physics, The University of Sydney, NSW 2006 (Australia); Ringer, Simon P., E-mail: simon.ringer@sydney.edu.au [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, NSW 2006 (Australia); Australian Centre for Microscopy and Microanalysis, Madsen Building F09, The University of Sydney, NSW 2006 (Australia)

    2013-09-15

    Two methods for separating the constituent atoms of molecular ions within atom probe tomography reconstructions are presented. The Gaussian Separation Method efficiently deconvolutes molecular ions containing two constituent atoms and is tested on simulated data before being applied to an experimental HSLA steel dataset containing NbN. The Delaunay Separation Method extends separation to larger complex ions and is also tested on simulated data before being applied to an experimental GaAs dataset containing many large (>3 atoms) complex ions. First nearest neighbour (1NN) distributions and images of the reconstruction before and after the separations are used to show the effect of the algorithms and their validity and practicality are also discussed. - Highlights: ► The need to deconvolute molecular ions within atom probe data is discussed. ► Two algorithms to separate the constituent atoms of molecular ions are proposed. ► The algorithms developed are tested on simulated and experimental data. ► Nearest neighbour distributions are used to highlight the improvements.

  17. Spatial decomposition of molecular ions within 3D atom probe reconstructions

    International Nuclear Information System (INIS)

    Two methods for separating the constituent atoms of molecular ions within atom probe tomography reconstructions are presented. The Gaussian Separation Method efficiently deconvolutes molecular ions containing two constituent atoms and is tested on simulated data before being applied to an experimental HSLA steel dataset containing NbN. The Delaunay Separation Method extends separation to larger complex ions and is also tested on simulated data before being applied to an experimental GaAs dataset containing many large (>3 atoms) complex ions. First nearest neighbour (1NN) distributions and images of the reconstruction before and after the separations are used to show the effect of the algorithms and their validity and practicality are also discussed. - Highlights: ► The need to deconvolute molecular ions within atom probe data is discussed. ► Two algorithms to separate the constituent atoms of molecular ions are proposed. ► The algorithms developed are tested on simulated and experimental data. ► Nearest neighbour distributions are used to highlight the improvements

  18. Molecular and atomic gas along and across the main sequence of star-forming galaxies

    CERN Document Server

    Saintonge, A; Cortese, L; Genzel, R; Giovanelli, R; Haynes, M P; Janowiecki, S; Kramer, C; Lutz, K A; Schiminovich, D; Tacconi, L J; Wuyts, S; Accurso, G

    2016-01-01

    We use spectra from the ALFALFA, GASS and COLD GASS surveys to quantify variations in the mean atomic and molecular gas mass fractions throughout the SFR-M* plane and along the main sequence (MS) of star-forming galaxies. Although galaxies well below the MS tend to be undetected in the Arecibo and IRAM observations, reliable mean atomic and molecular gas fractions can be obtained through a spectral stacking technique. We find that the position of galaxies in the SFR-M* plane can be explained mostly by their global cold gas reservoirs as observed in the HI line, with in addition systematic variations in the molecular-to-atomic ratio and star formation efficiency. When looking at galaxies within +/-0.4 dex of the MS, we find that as stellar mass increases, both atomic and molecular gas mass fractions decrease, stellar bulges become more prominent, and the mean stellar ages increase. Both star formation efficiency and molecular-to-atomic ratios vary little for massive main sequence galaxies, indicating that the ...

  19. 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.

  20. Growth mechanism, electronic spectral investigation and molecular orbital studies of L-prolinium phosphate.

    Science.gov (United States)

    Liu, Xiaojing; Sun, Xin; Xu, Xijin; Sun, Ping

    2015-11-01

    By using atomic force microscopy, birth and spread has proved to be the primary growth mechanism for L-prolinium phosphate (LPP). The phenomenon of newly formed islands expanding to the edge of the preceding terrace was observed. The optimized molecular structure and the molecular properties were calculated by density functional theory method. Natural bond orbital analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of LPP leading to high NLO activity. Molecular electrostatic potential, frontier molecular orbital analysis and thermodynamic properties were investigated to get a better insight of the molecular properties. Global and local reactivity descriptors were computed to predict the reactivity and reactive sites on the molecules. Non-linear optical (NLO) properties such as the total dipole moment (μ) and first order hyperopolarizability (β) were also calculated to predict NLO behavior. PMID:26067937

  1. Analysis of Adhesive Characteristics of Asphalt Based on Atomic Force Microscopy and Molecular Dynamics Simulation.

    Science.gov (United States)

    Xu, Meng; Yi, Junyan; Feng, Decheng; Huang, Yudong; Wang, Dongsheng

    2016-05-18

    Asphalt binder is a very important building material in infrastructure construction; it is commonly mixed with mineral aggregate and used to produce asphalt concrete. Owing to the large differences in physical and chemical properties between asphalt and aggregate, adhesive bonds play an important role in determining the performance of asphalt concrete. Although many types of adhesive bonding mechanisms have been proposed to explain the interaction forces between asphalt binder and mineral aggregate, few have been confirmed and characterized. In comparison with chemical interactions, physical adsorption has been considered to play a more important role in adhesive bonding between asphalt and mineral aggregate. In this study, the silicon tip of an atomic force microscope was used to represent silicate minerals in aggregate, and a nanoscale analysis of the characteristics of adhesive bonding between asphalt binder and the silicon tip was conducted via an atomic force microscopy (AFM) test and molecular dynamics (MD) simulations. The results of the measurements and simulations could help in better understanding of the bonding and debonding procedures in asphalt-aggregate mixtures during hot mixing and under traffic loading. MD simulations on a single molecule of a component of asphalt and monocrystalline silicon demonstrate that molecules with a higher atomic density and planar structure, such as three types of asphaltene molecules, can provide greater adhesive strength. However, regarding the real components of asphalt binder, both the MD simulations and AFM test indicate that the colloidal structural behavior of asphalt also has a large influence on the adhesion behavior between asphalt and silicon. A schematic model of the interaction between asphalt and silicon is presented, which can explain the effect of aging on the adhesion behavior of asphalt. PMID:27115043

  2. Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy.

    Science.gov (United States)

    Suzuki, Yuki; Higuchi, Yuji; Hizume, Kohji; Yokokawa, Masatoshi; Yoshimura, Shige H; Yoshikawa, Kenichi; Takeyasu, Kunio

    2010-05-01

    Nucleosome is a fundamental structural unit of chromatin, and the exposure from or occlusion into chromatin of genomic DNA is closely related to the regulation of gene expression. In this study, we analyzed the molecular dynamics of poly-nucleosomal arrays in solution by fast-scanning atomic force microscopy (AFM) to obtain a visual glimpse of nucleosome dynamics on chromatin fiber at single molecule level. The influence of the high-speed scanning probe on nucleosome dynamics can be neglected since bending elastic energy of DNA molecule showed similar probability distributions at different scan rates. In the sequential images of poly-nucleosomal arrays, the sliding of the nucleosome core particle and the dissociation of histone particle were visualized. The sliding showed limited fluctuation within approximately 50nm along the DNA strand. The histone dissociation occurs by at least two distinct ways: a dissociation of histone octamer or sequential dissociations of tetramers. These observations help us to develop the molecular mechanisms of nucleosome dynamics and also demonstrate the ability of fast-scanning AFM for the analysis of dynamic protein-DNA interaction in sub-seconds time scale. PMID:20236766

  3. TOPICAL REVIEW: Polarization effects in molecular mechanical force fields

    Science.gov (United States)

    Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei

    2009-08-01

    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.

  4. Quantum Control of Atomic and Molecular Translational Motion

    Energy Technology Data Exchange (ETDEWEB)

    Raizen, M.G.; Fink, M.

    2005-08-25

    Our research program focuses on the development of a method to cool atoms and molecules of any choice as long as they have a stable gaseous phase. Our approach starts with a very cold supersonic beam of He seeded with the molecules of choice. The internal temperature can reach 1 milliKelvin or less. The high center of mass velocity of the particles forming the beam will be reduced by elastically scattering the atoms/molecules from a very cold single crystal surface (20-40K), which moves in the beam direction. This will enable the continuous control of the mean velocity over a large range, after scattering, down to a few tens of m/s or even below as the crystal surface's velocity approaches v/2 of the impacting particles. We will use the decelerated particles as a source for a white-fringe matter-wave interferometer, where one reflector is a very cold surface of interest. The interference pattern will reveal the real part (via integral intensities) and the imaginary part (via phase shifts) of the scattering cross sections. This is particularly interesting for H{sub 2} and resonance structures. This interferometer set-up follows closely Prichard's arrangement.

  5. 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. PMID:26592414

  6. Cellular and molecular mechanisms underlying muscular dystrophy

    OpenAIRE

    Rahimov, Fedik; Kunkel, Louis M

    2013-01-01

    The muscular dystrophies are a group of heterogeneous genetic diseases characterized by progressive degeneration and weakness of skeletal muscle. Since the discovery of the first muscular dystrophy gene encoding dystrophin, a large number of genes have been identified that are involved in various muscle-wasting and neuromuscular disorders. Human genetic studies complemented by animal model systems have substantially contributed to our understanding of the molecular pathomechanisms underlying ...

  7. Graph of atomic orbitals and the molecular structure-descriptors based on it

    Directory of Open Access Journals (Sweden)

    ANDREY A. TOROPOV

    2005-04-01

    Full Text Available The graph of atomic orbitals (GAO is a novel type of molecular graph, recently proposed by one of the authors. Various molecular structure-descriptors computed for GAO are compared with their analogs computed for ordinary molecular graphs. The quality of these structure-descriptors was tested for correlation with the normal boiling points of alkanes and cycloalkanes. In all the studied cases, the results based on GAO are similar to, and usually slightly better than, those obtained by means of ordinary molecular graps.

  8. Effects of Contact Atomic Structure on Electronic Transport in Molecular Junction

    International Nuclear Information System (INIS)

    Based on nonequilibrium Green's function and first-principles calculations, we investigate the change in molecular conductance caused by different adsorption sites with the presence of additional Au atom around the metal-molecule contact in the system that benzene sandwiched between two Au(111) leads. The motivation is the variable situations that may arise in break junction experiments. Numerical results show that the enhancement of conductance induced by the presence of additional Au is dependent on the adsorption sites of anchoring atom. When molecule is located on top site with the presence of additional Au atoms, it can increase molecular conductance remarkably and present negative differential resistance under applied bias which cannot be found in bridge and hollow sites. Furthermore, the effects of different distance between additional Au and sulfur atoms in these three adsorption sites are also discussed. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  9. The ratio of molecular to atomic gas in infrared luminous galaxies

    International Nuclear Information System (INIS)

    In infrared luminous galaxies the ratio of the CO(1 - 0) to H I integrated fluxes increases with the far-infrared excess, f(fir)/f(b). All infrared active galaxies with f(fir)/f(b) greater than 2 have molecular to atomic gas mass fractions greater than 0.5. Among the galaxies with the higher infrared excesses there are systems with strikingly small atomic mass fractions, where less than 15 percent of the total mass of interstellar gas is in atomic form. The optical morphology of luminous infrared galaxies indicates that the majority, if not all, of these objects are interacting systems. These observations suggest that the overall mass fraction of molecular to atomic gas, and the infrared luminosities per nucleon of interstellar gas are enhanced during galaxy-galaxy interactions. 18 refs

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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 concomitantly the determination of the heavy atom substructure. This is customarily done by direct methods or Patterson......-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...

  11. Spatial decomposition of molecular ions within 3D atom probe reconstructions.

    Science.gov (United States)

    Breen, Andrew; Moody, Michael P; Gault, Baptiste; Ceguerra, Anna V; Xie, Kelvin Y; Du, Sichao; Ringer, Simon P

    2013-09-01

    Two methods for separating the constituent atoms of molecular ions within atom probe tomography reconstructions are presented. The Gaussian Separation Method efficiently deconvolutes molecular ions containing two constituent atoms and is tested on simulated data before being applied to an experimental HSLA steel dataset containing NbN. The Delaunay Separation Method extends separation to larger complex ions and is also tested on simulated data before being applied to an experimental GaAs dataset containing many large (>3 atoms) complex ions. First nearest neighbour (1NN) distributions and images of the reconstruction before and after the separations are used to show the effect of the algorithms and their validity and practicality are also discussed. PMID:23522847

  12. The geometry of C_60: a rigorous approach via Molecular Mechanics

    OpenAIRE

    Friedrich, Manuel; Piovano, Paolo; Stefanelli, Ulisse

    2016-01-01

    Molecular Mechanics describes molecules as particle configurations interacting via classical potentials. These {\\it configurational energies} usually consist of the sum of different phenomenological terms which are tailored to the description of specific bonding geometries. This approach is followed here to model the fullerene $C_{60}$, an allotrope of carbon corresponding to a specific hollow spherical structure of sixty atoms. We rigorously address different modeling options and advance a s...

  13. International bulletin on atomic and molecular data for fusion. No. 21

    International Nuclear Information System (INIS)

    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 (Electron Loss and Capture Cross Sections for C atoms in He, Calculations of Electron Impact Ionization Cross Sections). The document contains a list of references covering the years 1980, 1981 and 1982 for publications on fusion and plasma physics

  14. Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation

    OpenAIRE

    Yasushi Shibuta; Kanae Oguchi; Tomohiro Takaki; Munekazu Ohno

    2015-01-01

    Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This...

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

    International Nuclear Information System (INIS)

    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

  16. Micro-mechanical oscillator ground state cooling via intracavity optical atomic excitations

    CERN Document Server

    Genes, C; Vitali, D

    2009-01-01

    We predict ground state cooling of a micro-mechanical oscillator, i.e. a vibrating end-mirror of an optical cavity, by resonant coupling of mirror vibrations to a narrow internal optical transition of an ensemble of two level systems. The particles represented by a collective mesoscopic spin model implement, together with the cavity, an efficient, frequency tailorable zero temperature loss channel which can be turned to a gain channel of pump. As opposed to the case of resolved-sideband cavity cooling requiring a small cavity linewidth, one can work here with low finesses and very small cavity volumes to enhance the light mirror and light atom coupling. The tailored loss and gain channels provide for efficient removal of vibrational quanta and suppress reheating. In a simple physical picture of sideband cooling, the atoms shape the cavity profile to enhance/inhibit scattering into higher/lower energy sidebands. The method should be applicable to other cavity based cooling schemes for atomic and molecular gase...

  17. Molecular mechanics applied to single-walled carbon nanotubes

    Directory of Open Access Journals (Sweden)

    Antonio Ferreira Ávila

    2008-09-01

    Full Text Available Single-walled carbon nanotubes, with stiffness of 1.0 TPa and strength of 60 GPa, are a natural choice for high strength materials. A problem, however, arises when experimental data are compiled. The large variability of experimental data leads to the development of numerical models denominated molecular mechanics, which is a "symbiotic" association of molecular dynamics and solid mechanics. This paper deals with molecular mechanics simulations of single-walled carbon nanotubes. To be able to evaluate the molecular mechanics model, the three major carbon nanotube configurations (armchair, zigzag and chiral were simulated. It was proven that the carbon nanotube configuration has influence on stiffness. By varying the radius, hence the curvature, the Young's modulus changed from 0.95 TPa to 5.5 TPa, and the Poisson's ratio ranged from 0.15 to 0.29. The numerical simulations were in good agreement with those presented in the literature.

  18. Symposium on molecular and cellular mechanisms of mutagenesis

    International Nuclear Information System (INIS)

    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

  19. 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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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)

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

    International Nuclear Information System (INIS)

    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)

  3. Channel cracks in atomic-layer and molecular-layer deposited multilayer thin film coatings

    International Nuclear Information System (INIS)

    Metal oxide thin film coatings produced by atomic layer deposition have been shown to be an effective permeation barrier. The primary failure mode of such coatings under tensile loads is the propagation of channel cracks that penetrate vertically into the coating films. Recently, multi-layer structures that combine the metal oxide material with relatively soft polymeric layers produced by molecular layer deposition have been proposed to create composite thin films with desired properties, including potentially enhanced resistance to fracture. In this paper, we study the effects of layer geometry and material properties on the critical strain for channel crack propagation in the multi-layer composite films. Using finite element simulations and a thin-film fracture mechanics formalism, we show that if the fracture energy of the polymeric layer is lower than that of the metal oxide layer, the channel crack tends to penetrate through the entire composite film, and dividing the metal oxide and polymeric materials into thinner layers leads to a smaller critical strain. However, if the fracture energy of the polymeric material is high so that cracks only run through the metal oxide layers, more layers can result in a larger critical strain. For intermediate fracture energy of the polymer material, we developed a design map that identifies the optimal structure for given fracture energies and thicknesses of the metal oxide and polymeric layers. These results can facilitate the design of mechanically robust permeation barriers, an important component for the development of flexible electronics.

  4. Applications of quantum and classical connections in modeling atomic, molecular and electrodynamic systems

    CERN Document Server

    Popa, Alexandru

    2013-01-01

    Applications of Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamical Systems is a reference on the new field of relativistic optics, examining topics related to relativistic interactions between very intense laser beams and particles. Based on 30 years of research, this unique book connects the properties of quantum equations to corresponding classical equations used to calculate the energetic values and the symmetry properties of atomic, molecular and electrodynamical systems. In addition, it examines applications for these methods, and for the calculation of

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

    International Nuclear Information System (INIS)

    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 C3+, F23+, Mo39+ and W71+ calculated in the relativistic Coulomb-Born approximation are presented

  6. Molecular mechanisms of epithelial host defense in the airways

    OpenAIRE

    Vos, Joost Bastiaan

    2007-01-01

    Airway epithelial cells are indispensable for the host defense system in the lungs. Various strategies by which epithelial cells protect the lungs against inhaled pathogens have been described. In spite of that, the molecular mechanisms by which epithelial cells initiate and control the host defense response have not been explored systematically. In this thesis, the molecular mechanisms underlying the initiation and regulation of the early epithelial host defense response in the airways were ...

  7. 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

  8. An investigation of a possible molecular effect in ion atom collision using a gaseous argon target

    International Nuclear Information System (INIS)

    The present work deals with an investigation of the molecular effect, which is defined as the difference in experimental results using isotachic atomic ion and molecular ion beams in ion atom collisions. Previous studies have dealt almost exclusively with total cross section measurements. This thesis explores the idea that the molecular effect may be more pronounced in the differential ionization probability of the target atoms. Also, a gaseous argon target of sufficiently low density was used in order to ensure that the two correlated protons in the H+2 beam did not interact with two adjacent target atoms simultaneously. The author reports that, contrary to the expectations noted above, the molecular effect in the K shell differential ionization probability of argon for scattering angles up to 90 degrees appears to be no more than the molecular effect in the total ionization probability. The uncertainty in the results is statistical in nature and can be improved upon by running the experiment for a longer duration of time

  9. A theoretical molecular orbital approach to the adsorption and absorption of atomic hydrogen on Ni(111)

    Energy Technology Data Exchange (ETDEWEB)

    Ferullo, R.M. (Planta Piloto de Ingenieria Quimica (UNS-CONICET), Bahia Blanca (Argentina)); Castellani, N.J. (Planta Piloto de Ingenieria Quimica (UNS-CONICET), Bahia Blanca (Argentina))

    1993-02-19

    A semiempirical molecular orbital approach to the H-Ni interaction for a hydrogen atom adsorbed on the (111) surface or immersed in the bulk of Ni is given. The results show that the chemisorptive surface sites are more stable than the subsurface interstitials and that the bulk octahedral sites are more stable than the tetrahedral sites, in agreement with earlier models. The repulsive influence on hydrogen atom adsorption due to other hydrogen atoms residing in the nearer subsurface interstitials is also considered and discussed in terms of electronic arguments. (orig.)

  10. Process of Energetic Carbon Atom Deposition on Si (001) Substrate by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    于威; 滕晓云; 李晓苇; 傅广生

    2002-01-01

    The process of energetic C atom deposition on Si (001)-(2×1) is studied by the molecular dynamics method using the semi-empirical many-bond Tersoff potential. It is found that the incident energy of the carbon atom has an important effect on the collision process and its diffusion process on the substrate. Most of the incident energy of the carbon atom is transferred to the substrate atoms within the initial two vibration periods of substrate atoms and its value increases with the incident energy. The spreading distance and penetration depth of the incident atom increasing with the incident energy are also identified. The simulated results imply that an important effect of energy of incident carbon on the film growth at Iow substrate temperature provides activation energy for silicon carbide formation through the vibration enhancement of local substrate atoms. In addition, suppressing carbon atom inhomogeneous collection and dispensing with the silicon diffusion process may be effectively promoted by the spreading and penetration of the energetic carbon atom in the silicon substrate.

  11. Ab initio investigation of the adsorption of atomic and molecular hydrogen on AlN nanotubes

    International Nuclear Information System (INIS)

    Highlights: • The adsorption characteristics of hydrogen inside the zigzag and armchair AlN nanotubes are explored. • The AlN nanotubes can store hydrogen up to 8.89 wt% with the average binding energies of 0.2–0.4 eV/H-2. - Abstract: The adsorption of atomic and molecular hydrogen on zigzag and armchair AlN nanotubes is investigated within the ab initio density functional theory. The adsorption configurations are magnetic when the H atom is adsorbed on the Al atom and the center of a hexagon. The total magnetic moment is 1.00 μB which comes from the H atom and the nearest neighbor N atoms. The barrier height of various adsorption configurations is very low, indicating that the adsorbed H atom can easily transform into other forms. The adsorption energies of hydrogen atoms to the zigzag and armchair AlN nanotubes are calculated at 25%, 50%, 75%, 100%, 133%, and 200% coverages, the most favorable adsorption configurations are 100% hydrogen coverages. The adsorption configuration of hydrogen molecule adsorbed on the Al atom is the most energetically favorable. Each Al atom is capable of binding one hydrogen molecule, corresponding to the hydrogen gravimetric density to 8.89 wt%. Our theoretical study demonstrates that AlN nanotube can be a potential candidate for the hydrogen storage materials

  12. Picosecond multiphoton ionization of atomic and molecular clusters

    International Nuclear Information System (INIS)

    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. Crossed-molecular-beams reactive scattering of oxygen atoms

    International Nuclear Information System (INIS)

    The reactions of O(3P) with six prototypical unsaturated hydrocarbons, and the reaction of O(1D) 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(3P)-unsaturated hydrocarbon chemistry is dominated by single bond cleavages, leading to radical products exclusively

  14. Molecular and cellular mechanisms of cadmium carcinogenesis

    International Nuclear Information System (INIS)

    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. Cd2+ 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

  15. Molecular mechanisms of carcinogenesis by vinyl chloride.

    Science.gov (United States)

    Dogliotti, Eugenia

    2006-01-01

    In 1974 vinyl chloride (VC), a gas used in the plastics industry, was shown to be a human carcinogen, inducing a very rare type of tumor, angiosarcoma of the liver. The same type of tumor was induced in rodents exposed to VC thus providing an excellent model for mechanistic studies. Here, we review the numerous studies on the mechanism of action of VC with particular emphasis on the DNA products induced by this strong alkylating agent. In particular, the genotoxicity, repair mechanisms, in vivo formation and tumor mutation spectra by etheno-adducts will be analysed and possible approaches for future research suggested. PMID:17033136

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

    International Nuclear Information System (INIS)

    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

  17. Cold atomic and molecular collisions: approaching the universal loss regime

    CERN Document Server

    Frye, Matthew D; Hutson, Jeremy M

    2014-01-01

    We investigate the behaviour of single-channel theoretical models of cold and ultracold collisions that take account of inelastic and reactive processes using a single parameter to represent short-range loss. We present plots of the resulting energy-dependence of elastic and inelastic cross sections over the full parameter space of loss parameters and short-range phase shifts. We then test the single-channel model by comparing it with the results of coupled-channel calculations of rotationally inelastic collisions between LiH molecules and Li atoms. We find that the single-channel model becomes increasingly accurate as the initial LiH rotational quantum number increases, with a corresponding increase in the number of open loss channels. The results suggest that coupled-channel calculations at very low energy (in the s-wave regime) could in some cases be used to estimate a loss parameter and then to predict the range of possible loss rates at higher energy, without the need for an explicit partial-wave sum.

  18. Spatially Resolved Atomic and Molecular Spectroscopy in Microelectronics Processing Plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Hebner, G.A.

    1998-10-14

    Plasma processing of microelectronic materials is strongly dependent on the generation and control of neutral radial and ion species generated in a plasma. For example, process uniformity across a #er is drken by a combination of plasma charged particle and neutral uniformity. Due to extensive rexarch and engineering the current generation of commercial plasma reactors can generate very radially uniform ion distributions, usually better than ~ 2 perwnt as determined by ion saturation measurements. Due in part to the difficulty associated with determining the neutral radial distributions, control of the neutral radical uniformity is less well developed. This abstract will review our recent measurements of the spatial distribution of severaI important atomic and molecukw species in inductively coupled plasmas through C12 / BCIJ / Ar containing gas mixtures. Measured species include the ground state Cl and BC1 densities as well as the metastable argon density. The fbeus of this review will be on the experimental techniques and results. In addition to assisting in the development of a fbndarnental understanding of the important pkunna physics, these measurements have been used to benchmark multi dimensional plasma discharge codes.

  19. Direct detection of atomic ions from molecular photofragmentation during nonresonant multiphoton ionization of sputtered species

    International Nuclear Information System (INIS)

    The photoionization of sputtered Cu, Al, and Ru atoms and dimers was investigated by measuring velocity distributions using both resonant and nonresonant photoionization. Nonresonant ionization produced an atomic distribution that peaked at the same velocity as the respective dimer distribution, indicating that virtually all the nonresonant atomic ion signal is from photofragmented dimers. Various mechanisms of dimer photofragmentation are discussed. Domination of the atomic photoion channel by molecule fragmentation appears to be a general phenomenon that must be accounted for in all gas-phase multiphoton nonresonant ionization experiments at easily achievable laser power densities (≤ 109 W/cm2)

  20. First direct observation of hyperfine effects in muonic deuterium: Atomic hyperfine transition and resonant molecular formation

    International Nuclear Information System (INIS)

    Negative muons in hydrogen induce a rich phenomenology of mesoatomic and mesomolecular processes. On one hand the study of these reactions is of basic interest, because they are rare examples of 3 body Coulomb interactions among particles with comparable masses. On the other hand, the detailed understanding of these processes is essential for the interpretation of results concerning weak interaction. In this work a resonant formation process of the dμd mesomolecule from the upper F = 3/2 state of the μd atom was discovered, while detecting neutrons from muoncatalyzed fusion dμd→He3 + n + μ in cold deuterium gas. Since the molecular formation rates from the two hyperfine states (F = 1/2 and F = 3/2) are found to differ by nearly two orders of magnitude, it was possible for the first time to directly observe the lifetime of the F = 3/2 state. This yields the first accurate experimental value for the hyperfine transition rate lambda sub(d) = 42.6 (1.7) X 106 xs-1. Together with our experiment on fusion gammas in 1H/2H liquid mixtures this result gives the long missed knowledge about the μd hyperfine population in 1H and 1H/2H mixtures (at least at low temperatures). Using this information the two existing experiments on nuclear muoncapture in deuterium were reanalyzed leading to a striking discrepancy between the two experimental values. In addition, these results imply valuable insight into the three body Coulomb problem. The precision of the measured transition rate exceeds all previous experimental data on low energy scattering of μd atoms by one order of magnitude. The strong enhancement of the F = 3/2 molecular formation rate could be explained by a resonance mechanism occurring at low temperatures. These findings give rise to significant corrections to the published molecular formation rates and open new experimental possibilities for even more stringent tests of Coulomb three body calculations. (author)

  1. Formation of molecular ions by radiative association of cold trapped atoms and ions

    OpenAIRE

    Silva Jr, Humberto Da; Raoult, Maurice; Aymar, Mireille; Dulieu, Olivier

    2015-01-01

    Radiative emission during cold collisions between trapped laser-cooled Rb atoms and alkaline-earth ions (Ca$^+$, Sr$^+$, Ba$^+$) and Yb$^+$, and between Li and Yb$^+$, are studied theoretically, using accurate effective-core-potential based quantum chemistry calculations of potential energy curves and transition dipole moments of the related molecular ions. Radiative association of molecular ions is predicted to occur for all systems with a cross section two to ten times larger than the radia...

  2. Cold collisions of polyatomic molecular radicals with S-state atoms in a magnetic field: An ab initio study of He + CH2(X) collisions

    OpenAIRE

    Tscherbul, T.V.; Grinev, T. A.; Yu, H.-G.; Dalgarno, A.; Klos, Jacek; Ma, Lifang; Alexander, Millard H.

    2012-01-01

    We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wavefunction. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calc...

  3. 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.

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

    International Nuclear Information System (INIS)

    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 Cu64Zr36 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

  5. Molecular mechanisms of alternative estrogen receptor signaling

    OpenAIRE

    Björnström, Linda

    2003-01-01

    Estrogen is a key regulator of growth, differentiation and function in a broad range of target tissues, including the male and female reproductive tracts, mammary gland, bone, brain and the cardiovascular system. The biological effects of estrogen are mediated through estrogen receptor a (ERalpha) and estrogen receptor beta (ERbeta), which belong to a large superfamily of nuclear receptors that act as ligand-activated transcription factors. The classical mechanism of ER acti...

  6. Molecular Mechanisms of Green Tea Polyphenols

    OpenAIRE

    Dou, Q. Ping

    2009-01-01

    Tea, next to water, is the most popular beverage in the world. It has been suggested that tea consumption has the cancer-preventive effects. Epidemiological studies have indicated decreased cancer occurrence in people who regularly drink green tea. Research has also discovered numerous mechanisms of action to explain the biological effects of tea. The most abundant and popular compound studied in tea research is (−)-epigallocatechin-3-gallate or (−)-EGCG, which is a powerful antioxidant and c...

  7. Molecular Mechanisms of Sleep and Mood

    OpenAIRE

    Lagus, Markus

    2013-01-01

    BACKGROUND Sleep disturbances and mood alterations are highly interrelated. The majority of patients suffering from depression report a reduced sleep quality. Inversely, people with sleep complaints are at elevated risk to develop depression. The complex regulation of these phenomena involves several brain areas and mechanisms. The susceptibility to change in this system is influenced by several factors, such as age and stressful lifestyle that are considered in this study. HYPOTHESIS The hyp...

  8. Molecular mechanisms of bone formation in spondyloarthritis.

    Science.gov (United States)

    González-Chávez, Susana Aideé; Quiñonez-Flores, Celia María; Pacheco-Tena, César

    2016-07-01

    Spondyloarthritis comprise a group of inflammatory rheumatic diseases characterized by its association to HLA-B27 and the presence of arthritis and enthesitis. The pathogenesis involves both an inflammatory process and new bone formation, which eventually lead to ankylosis of the spine. To date, the intrinsic mechanisms of the pathogenic process have not been fully elucidated, and our progress is remarkable in the identification of therapeutic targets to achieve the control of the inflammatory process, yet our ability to inhibit the excessive bone formation is still insufficient. The study of new bone formation in spondyloarthritis has been mostly conducted in animal models of the disease and only few experiments have been done using human biopsies. The deregulation and overexpression of molecules involved in the osteogenesis process have been observed in bone cells, mesenchymal cells, and fibroblasts. The signaling associated to the excessive bone formation is congruent with those involved in the physiological processes of bone remodeling. Bone morphogenetic proteins and Wnt pathways have been found deregulated in this disease; however, the cause for uncontrolled stimulation remains unknown. Mechanical stress appears to play an important role in the pathological osteogenesis process; nevertheless, the association of other important factors, such as the presence of HLA-B27 and environmental factors, remains uncertain. The present review summarizes the experimental findings that describe the signaling pathways involved in the new bone formation process in spondyloarthritis in animal models and in human biopsies. The role of mechanical stress as the trigger of these pathways is also reviewed. PMID:26838262

  9. 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.

  10. Molecular mechanisms for tumour resistance to chemotherapy.

    Science.gov (United States)

    Pan, Shu-Ting; Li, Zhi-Ling; He, Zhi-Xu; Qiu, Jia-Xuan; Zhou, Shu-Feng

    2016-08-01

    Chemotherapy is one of the prevailing methods used to treat malignant tumours, but the outcome and prognosis of tumour patients are not optimistic. Cancer cells gradually generate resistance to almost all chemotherapeutic drugs via a variety of distinct mechanisms and pathways. Chemotherapeutic resistance, either intrinsic or acquired, is caused and sustained by reduced drug accumulation and increased drug export, alterations in drug targets and signalling transduction molecules, increased repair of drug-induced DNA damage, and evasion of apoptosis. In order to better understand the mechanisms of chemoresistance, this review highlights our current knowledge of the role of altered drug metabolism and transport and deregulation of apoptosis and autophagy in the development of tumour chemoresistance. Reduced intracellular activation of prodrugs (e.g. thiotepa and tegafur) or enhanced drug inactivation by Phase I and II enzymes contributes to the development of chemoresistance. Both primary and acquired resistance can be caused by alterations in the transport of anticancer drugs which is mediated by a variety of drug transporters such as P-glycoprotein (P-gp), multidrug resistance associated proteins, and breast cancer resistance protein. Presently there is a line of evidence indicating that deregulation of programmed cell death including apoptosis and autophagy is also an important mechanism for tumour resistance to anticancer drugs. Reversal of chemoresistance is likely via pharmacological and biological approaches. Further studies are warranted to grasp the full picture of how each type of cancer cells develop resistance to anticancer drugs and to identify novel strategies to overcome it. PMID:27097837

  11. 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

    , 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 that the results measured in a nanocontact experiment depend significantly on the elastic stiffness of the experimental apparatus. For a soft setup, some of the atomic rearrangements might not be detected, whereas others are amplified....

  12. Effect of hydrogen on degradation mechanism of zirconium: A molecular dynamics study

    Science.gov (United States)

    Chakraborty, Poulami; Moitra, Amitava; Saha-Dasgupta, Tanusri

    2015-11-01

    Using large scale molecular dynamics simulation, we investigate the deleterious effect of hydrogen in Zr. We consider both dilute and concentrated limit of H. In the dilute and concentrated H limits, we study the effect of 1-5 atomic percentage of hydrogen, and that of ε-ZrH2 precipitate having 5-10 nm diameters, respectively. From the stress-strain curves and micro-structure analysis at different strain values, we characterize the deformation behavior and correlate our result with previously reported mechanisms. We show hydrogen atoms in dilute limit help in dislocation multiplication, following the hydrogen-enhanced localized plasticity mechanism. In the concentrated limit, on the other hand, dislocations and cracks nucleate from precipitate-matrix interface, indicating the decohesion mechanism as primary method for Zr degradation. These findings are corroborated with a nucleation and growth model as expressed in Kolmogorov-Johnson-Mehl-Avrami equation.

  13. Molecular Mechanisms of Circadian Regulation During Spaceflight

    Science.gov (United States)

    Zanello, Susana; Boyle, Richard

    2011-01-01

    Disruption of the regular environmental circadian cues in addition to stringent and demanding operational schedules are two main factors that undoubtedly impact sleep patterns and vigilant performance in the astronaut crews during spaceflight. Most research is focused on the behavioral aspects of the risk of circadian desynchronization, characterized by fatigue and health and performance decrement. A common countermeasure for circadian re-entrainment utilizes blue-green light to entrain the circadian clock and mitigate this risk. However, an effective countermeasure targeting the photoreceptor system requires that the basic circadian molecular machinery remains intact during spaceflight. The molecular clock consists of sets of proteins that perform different functions within the clock machinery: circadian oscillators (genes whose expression levels cycle during the day, keep the pass of cellular time and regulate downstream effector genes), the effector or output genes (those which impact the physiology of the tissue or organism), and the input genes (responsible for sensing the environmental cues that allow circadian entrainment). The main environmental cue is light. As opposed to the known photoreceptors (rods and cones), the non-visual light stimulus is received by a subset of the population of retinal ganglion cells called intrinsically photosensitive retinal ganglion cells (ipRGC) that express melanopsin (opsin 4 -Opn4-) as the photoreceptor. We hypothesize that spaceflight may affect ipRGC and melanopsin expression, which may be a contributing cause of circadian disruption during spaceflight. To answer this question, eyes from albino Balb/cJ mice aboard STS-133 were collected for histological analysis and gene expression profiling of the retina at 1 and 7 days after landing. Both vivarium and AEM (animal enclosure module) mice were used as ground controls. Opn4 expression was analyzed by real time RT/qPCR and retinal sections were stained for Opn4

  14. Advances in metallomics by atomic and molecular spectrometry

    International Nuclear Information System (INIS)

    Complete text of publication follows. The scope of research in the field of elemental speciation has considerably evolved during the last decade. The analysis of specific metal-containing contaminants reached the maturity and has given way to the development of analytical methods to describe interactions of metals with biomolecules which are constituents of the genome, proteome, metabolome and other -omes in a cell, tissue or organism. The entirety of metal-biomolecule species has been termed the 'metallome' which gave rise to an emerging discipline: metallomics. Advances of trace element analysis in life sciences resulted in the proliferation of new terms related to the description of metal-interactions with biomolecules, such as, e.g. ionome, metalloproteome, metallogenome, metallometabolome, heteroatom-tagged proteome, single element proteomes (e.g., selenoproteome) and the corresponding -omics. The analytical chemistry challenges in the area metallomics include the detection, quantification, identification and characterization of complexes of metals (metalloids) at trace levels in an environment rich in biomolecules often having similar physicochemical properties. In the past, the only way to access to this information was modelling using stability constants. Today, hyphenated techniques based on the coupling of a high resolution separation technique with sensitive elemental (ICP MS) and molecular (ES MS/MS) mass spectrometry offer the possibility of high-throughput acquisition of metallomics information in many biological systems. The lecture discusses advances in analytical techniques in the field of metallomics. Particular attention will be to developments in multidimensional nanoHPLC with the parallel ICP MS and ESI MS detection and the sensitive spotting of heteroelement-containing proteins in 2D gels, accompanied by advances in MALDI TOF MS. Potential for medical research (e.g., characterization for selenoproteins as new biomarkers of clinical utility

  15. Coupled atomic-molecular condensates in a double-well potential: decaying molecular oscillations

    CERN Document Server

    Jing, H; Zhan, M; Gu, Sihong; Jing, Hui; Zhan, Mingsheng

    2005-01-01

    We present a four-mode model that describes coherent photo-association (PA) in a double-well Bose-Einstein condensate, focusing on the $average$ molecular populations in certain parameters. Our numerical results predict an interesting strong-damping effect of molecular oscillations by controlling the particle tunnellings and PA light strength, which may provide a promising way for creating a stable molecular condensate via coherent PA in a magnetic double-well potential.

  16. VAMDC as a Resource for Atomic and Molecular Data and the New Release of VALD

    CERN Document Server

    Kupka, F

    2012-01-01

    The Virtual Atomic and Molecular Data Centre (VAMDC) (M.L. Dubernet et al. 2010, JQSRT 111, 2151) is an EU-FP7 e-infrastructure project devoted to building a common electronic infrastructure for the exchange and distribution of atomic and molecular data. It involves two dozen teams from six EU member states (Austria, France, Germany, Italy, Sweden, United Kingdom) as well as Russia, Serbia, and Venezuela. Within VAMDC scientists from many different disciplines in atomic and molecular physics collaborate with users of their data and also with scientists and engineers from the information and communication technology community. In this presentation an overview of the current status of VAMDC and its capabilities will be provided. In the second part of the presentation I will focus on one of the databases which have become part of the VAMDC platform, the Vienna Atomic Line Data Base (VALD). VALD has developed into a well-known resource of atomic data for spectroscopy particularly in astrophysics. A new release, V...

  17. Photoionization of ions and the general program in atomic and molecular physics at Daresbury

    International Nuclear Information System (INIS)

    The current program in Atomic and Molecular Science is focused on photoionization of atoms and small molecules. On the atomic side, experiments on the double ionization of helium were completed recently, verifying the Wannier threshold law for double photoionization. Also, the angular distribution of the electrons has just been measured, and these results show a marked divergence form theoretical expectations. Other experiments include fluorescence polarization measurements for the atomic ions calcium and strontium, which, when combined with photoelectron angular distribution measurements, form the complete photoionization experiment. A sizeable part of the program is devoted to studying molecular fragmentation. The triple coincidence technique, in which the two fragment ions are detected in coincidence with the photoelectron after the parent molecule has been doubly ionized, was developed at Daresbury, and experiments in this area continue with the addition of fluorescence measurements. Looking to the future, the atomic and molecular science program at Daresbury will move closer to applied science areas, with metal clusters and transient species becoming more prominent. Much of this work will require a source with two to three orders of magnitude advantage in photon intensity over the SRS, and a design study is presently under way for a VUV/Soft X-ray source to meet these requirements

  18. Plant regeneration: cellular origins and molecular mechanisms.

    Science.gov (United States)

    Ikeuchi, Momoko; Ogawa, Yoichi; Iwase, Akira; Sugimoto, Keiko

    2016-05-01

    Compared with animals, plants generally possess a high degree of developmental plasticity and display various types of tissue or organ regeneration. This regenerative capacity can be enhanced by exogenously supplied plant hormones in vitro, wherein the balance between auxin and cytokinin determines the developmental fate of regenerating organs. Accumulating evidence suggests that some forms of plant regeneration involve reprogramming of differentiated somatic cells, whereas others are induced through the activation of relatively undifferentiated cells in somatic tissues. We summarize the current understanding of how plants control various types of regeneration and discuss how developmental and environmental constraints influence these regulatory mechanisms. PMID:27143753

  19. Direct visualization of triplex DNA molecular dynamics by fluorescence resonance energy transfer and atomic force microscopy measurements

    Science.gov (United States)

    Chang, Chia-Ching; Lin, Po-Yen; Chen, Yen-Fu; Chang, Chia-Seng; Kan, Lou-Sing

    2007-11-01

    We have detected the dynamics of 17-mer DNA triplex dissociation mechanism at the molecular level. Fluorescence resonance energy transfer (FRET) was used as an indicator of intermolecular interaction in nanometer range, whereas atomic force microscopy (AFM) was employed to address single molecule with sub-angstrom precision. The maximum rupture force of DNA triplex was found at pH 4.65, consistent with macroscopic observations. These results indicated that the FRET together with an AFM detection system could be used to reveal the DNA triplex interaction in nanometer scale unambiguously.

  20. Dislocation emission at the Silicon/Silicon nitride interface: A million atom molecular dynamics simulation on parallel computers

    Science.gov (United States)

    Bachlechner; Omeltchenko; Nakano; Kalia; Vashishta; Ebbsjo; Madhukar

    2000-01-10

    Mechanical behavior of the Si(111)/Si(3)N4(0001) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the (1; 1;1) plane of the silicon substrate with a speed of 500 (+/-100) m/s. Time evolution of the dislocation emission and nature of defects is studied. PMID:11015901

  1. Dislocation Emission at the Silicon/Silicon Nitride Interface: A Million Atom Molecular Dynamics Simulation on Parallel Computers

    International Nuclear Information System (INIS)

    Mechanical behavior of the Si(111)/Si3N4 (0001) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the (1 11) plane of the silicon substrate with a speed of 500 (±100) m/s . Time evolution of the dislocation emission and nature of defects is studied. (c) 2000 The American Physical Society

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

    International Nuclear Information System (INIS)

    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

  3. Crossed molecular beam study of H and D atom reactions with NO2

    International Nuclear Information System (INIS)

    The experimental details and results of molecular beam studies of the reactions of H and D atoms with NO2 (with an observed isotope effect of the differential cross section) with much improved sensitivity and resolution, in good agreement with earlier results of the authors, are briefly summerized. (HK)

  4. Atomic and molecular gas in the merger galaxy NGC 1316 (Fornax A) and its environment

    NARCIS (Netherlands)

    Horellou, C; Black, JH; van Gorkom, JH; Combes, F; van der Hulst, JM; Charmandaris, [No Value

    2001-01-01

    We present and interpret observations of atomic and molecular gas toward the southern elliptical galaxy NGC 1316 (Fornax A), a strong double-lobe radio source with a disturbed optical morphology that includes numerous shells and loops. The (CO)-C-12(1-0), (CO)-C-12(2-1), and Hi observations were mad

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

  7. Time-dependent electron interference prior to ionization in the hydrogen atom and hydrogen molecular ion

    OpenAIRE

    de la Calle Negro, A.; Dundas, D.; Taylor, K. T.

    2014-01-01

    We investigate electron dynamics in the hydrogen atom and the hydrogen molecular ion when exposed to long wavelength laser pulses yet having intensity insufficient to ionize the system. We find that the field is still able to drive the electron, leading to time-dependent interference effects.

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

  10. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    Science.gov (United States)

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases. PMID:27071540

  11. Molecular dynamics study of mechanical properties of carbon nanotube reinforced aluminum composites

    Science.gov (United States)

    Srivastava, Ashish Kumar; Mokhalingam, A.; Singh, Akhileshwar; Kumar, Dinesh

    2016-05-01

    Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for the interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young's modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young's modulus of the Al matrix up to 77 % as compared to pure Al.

  12. Atomic and molecular processes generated by linearly polarized few-cycle laser pulses

    International Nuclear Information System (INIS)

    S-matrix theory is used to analyze different atomic and molecular processes in a linearly polarized few-cycle laser field. The energy spectra of high-order above-threshold ionization (HATI) are presented. Electron-atom potential scattering assisted by a few-cycle laser pulse is also analyzed. It is shown that the plateau structures in the energy spectra of the electron-atom potential scattering are dependent on the carrier-envelope phase (CEP) of the laser pulse, so that the cutoff positions of the plateaus can be controlled by changing the CEP. Regarding our analysis of the molecular HATI process, the angle-resolved spectra, obtained by different theoretical approaches, are also presented. (paper)

  13. Interaction of Atomic and Molecular Hydrogen with Tholin Surfaces at Low Temperatures

    CERN Document Server

    Li, Ling; Vidali, Gianfranco; Frank, Yechiel; Lohmar, Ingo; Perets, Hagai B; Biham, Ofer; 10.1021/jp104944y

    2010-01-01

    We study the interaction of atomic and molecular hydrogen with a surface of tholin, a man-made polymer considered to be an analogue of aerosol particles present in Titan's atmosphere, using thermal programmed desorption at low temperatures below 30 K. The results are fitted and analyzed using a fine-grained rate equation model that describes the diffusion, reaction and desorption processes. We obtain the energy barriers for diffusion and desorption of atomic and molecular hydrogen. These barriers are found to be in the range of 30 to 60 meV, indicating that atom/molecule-surface interactions in this temperature range are dominated by weak adsorption forces. The implications of these results for the understanding of the atmospheric chemistry of Titan are discussed.

  14. 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

  15. 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

  16. Photodynamic therapy: Biophysical mechanisms and molecular responses

    Science.gov (United States)

    Mitra, Soumya

    In photodynamic therapy (PDT), photochemical reactions induced by optical activation of sensitizer molecules cause destruction of the target tissue. In this thesis we present results of several related studies, which investigated the influence of photophysical properties and photobleaching mechanisms of sensitizers and oxygen-dependent tissue optical properties on PDT treatment efficacy. The bleaching mechanism of the sensitizer meso-tetra hydroxyphenyl chlorin (mTHPC) is examined indirectly using measurements of photochemical oxygen consumption during PDT irradiation of multicell tumor spheroids. Analysis of the results with a theoretical model of oxygen diffusion that incorporates the effects of sensitizer photobleaching shows that mTHPC is degraded via a singlet-oxygen (1O2)-mediated bleaching process. The analysis allows us to extract photophysical parameters of mTHPC which are used to account for its enhanced clinical photodynamic potency in comparison to that of Photofrin. Evaluation of the spatially-resolved fluorescence in confocal optical sections of intact spheroids during PDT irradiation allows for the direct experimental verification of mTHPC's 1O2-mediated bleaching mechanism. The technique is also used to investigate the complex bleaching kinetics of Photofrin. The results allow us to successfully reconcile apparently contradictory experimental observations and to confirm the predictions of a new theoretical model in which both 1O2 and excited triplet sensitizer molecules are allowed to contribute to photobleaching. Based on studies performed in tissue-simulating erythrocyte phantoms and in a murine tumor model in vivo, we present clinically relevant results which indicate that a shift toward increased hemoglobin-oxygen saturation due to improved tissue oxygenation reduces PDT treatment beam attenuation and may allow for more effective treatment of deeper lesions. Finally, we investigate the induction of the stress protein, heat shock protein 70 (HSP

  17. Understanding molecular mechanism of higher plant plasticity under abiotic stress.

    Science.gov (United States)

    Shao, Hong-Bo; Guo, Qing-Jie; Chu, Li-Ye; Zhao, Xi-Ning; Su, Zhong-Liang; Hu, Ya-Chen; Cheng, Jiang-Feng

    2007-01-15

    Higher plants play the most important role in keeping a stable environment on the earth, which regulate global circumstances in many ways in terms of different levels (molecular, individual, community, and so on), but the nature of the mechanism is gene expression and control temporally and spatially at the molecular level. In persistently changing environment, there are many adverse stress conditions such as cold, drought, salinity and UV-B (280-320 mm), which influence plant growth and crop production greatly. Plants differ from animals in many aspects, but the important may be that plants are more easily influenced by environment than animals. Plants have a series of fine mechanisms for responding to environmental changes, which has been established during their long-period evolution and artificial domestication. These mechanisms are involved in many aspects of anatomy, physiology, biochemistry, genetics, development, evolution and molecular biology, in which the adaptive machinery related to molecular biology is the most important. The elucidation of it will extremely and purposefully promote the sustainable utilization of plant resources and make the best use of its current potential under different scales. This molecular mechanism at least include environmental signal recognition (input), signal transduction (many cascade biochemical reactions are involved in this process), signal output, signal responses and phenotype realization, which is a multi-dimensional network system and contain many levels of gene expression and regulation. We will focus on the molecular adaptive machinery of higher plant plasticity under abiotic stresses. PMID:16914294

  18. Molecular imaging in neuroendocrine tumors : Molecular uptake mechanisms and clinical results

    NARCIS (Netherlands)

    Koopmans, Klaas P.; Neels, Oliver N.; Kema, Ido P.; Elsinga, Philip H.; Links, Thera P.; de Vries, Elisabeth G. E.; Jager, Pieter L.

    2009-01-01

    Neuroendocrine tumors can originate almost everywhere in the body and consist of a great variety of subtypes. This paper focuses on molecular imaging methods using nuclear medicine techniques in neuroendocrine tumors, coupling molecular uptake mechanisms of radiotracers with clinical results. A non-

  19. Research on the molecular scale material removal mechanism in chemical mechanical polishing

    Institute of Scientific and Technical Information of China (English)

    WANG YongGuang; ZHAO YongWu

    2008-01-01

    This paper investigates a novel molecular scale material removal mechanism in chemical mechanical polishing (CMP) by incorporating the order-of-magnitude calculations,particle adhesion force,defect of wafer,thickness of newly formed oxidizedlayer,and large deformation of pad/particle not discussed by previous analysis.The theoretical analysis and experimental data show that the indentation depth,scratching depth and polishing surface roughness are on the order of molecular scale or less.There.fore,this novel mechanism has gained the support from wide order-of- magnitude calculations and experimental data.In addition,with the decrease in the particle size,the molecular scale removal mechanism is plausibly one of the most promising removal mechanisms to clarify the CMP polishing process.The results are useful to substantiating the molecular-scale mechanism of the CMP material removal in addition to its underlying theoretical foundation.

  20. Correlation of interfacial bonding mechanism and equilibrium conductance of molecular junctions

    OpenAIRE

    Ning, Zhanyu; Qiao, Jingsi; Ji, Wei; Guo, Hong

    2009-01-01

    We report theoretical investigations on the role of interfacial bonding mechanism and its resulting structures to quantum transport in molecular wires. Two bonding mechanisms for the Au-S bond in an Au(111)/1,4-benzenedithiol(BDT)/Au(111) junction were identified by ab initio calculation, confirmed by a recent experiment, which, we showed, critically control charge conduction. It was found, for Au/ BDT/Au junctions, the hydrogen atom, bound by a dative bond to the Sulfur, is energetically non...

  1. 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.

  2. 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.

  3. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations.

    Science.gov (United States)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano; Lindorff-Larsen, Kresten; Cerminara, Michele; Santiveri, Clara M; Shaw, David E; de Alba, Eva; Muñoz, Victor

    2015-05-27

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue-residue couplings associated with cooperative folding emerges. Such thermodynamic residue-residue couplings appear to be linked to the order of mechanistically significant events that take place during the folding process. Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins. PMID:25924808

  4. Molecular mechanisms of LRRK2 regulation

    Science.gov (United States)

    Webber, Philip Jeffrey

    Non-synonymous mutations in LRRK2 are the most common known cause of familial and sporadic Parkinson's disease (PD). The dominant inheritance of these mutations in familial PD suggests a gain-of-function mechanism. Increased kinase activity observed in the most common PD associated LRRK2 mutation G2019S suggests that kinase activity is central to disease. However, not all mutations associated with disease are reported to alter kinase activity and controversy exists in the literature about the effects of mutations appearing in the GTPase domain on kinase activity. The studies conducted as a part of this work aim to characterize the mechanisms that regulate LRRK2 kinase activity and the effects of mutations on enzymatic activity of LRRK2 protein. LRRK2 is a large protein with multiple predicted functional domains including two enzymatic domains in the same protein, the small ras-like GTPase domain and a serine-threonine protein kinase domain. Previous studies indicate that LRRK2 kinase is dependent on a functional GTPase domain and binding to GTP is required for kinase activity. Recent work detailed in this dissertation indicates a complex and reciprocal relationship between kinase and GTPase domains. LRRK2 kinase activity is dependent on adapting a homo-dimer that is augmented by PD mutations that increase LRRK2 kinase activity. Activated LRRK2 autophosphorylates the GTPase and c-terminus of Ras (COR) domains robustly. Phosphorylation of these domains is required for normal activity, as preventing autophosphorylation of these sites drastically lowers kinase activity and GTP binding while phosphorylation maintains baseline activity while still reducing GTP binding. Furthermore, we have developed antibodies specific to autophosphorylation residues that track with LRRK2 kinase activity in vitro. While no measurable activity was detected from treated LRRK2 in vivo, LRRK2 protein purified from brain tissue treated with inflammatory stimuli such as LPS, which increases

  5. A molecular dynamics study of impurity atoms in a host lattice

    International Nuclear Information System (INIS)

    Full text: A single impurity atom was placed in an otherwise perfect host FCC lattice and the dynamical behaviour of the lattice and impurity were followed by use of the Molecular Dynamics (MD) technique. It was found that an impurity atom of relative diameter 1.06 has a significant effect on the behaviour of the mean square displacement and velocity autocorrelation function of the host lattice and, hence, on diffusive behaviour. If the relative diameter of the impurity was made as large as 1.12 then much larger effects were seen. In fact, under some conditions the lattice was amorphized and could not be annealed, to return to a perfect lattice by replacement of the impurity atom by a host lattice atom

  6. Electron capture by slow highly-charged neon and argon ions from molecular and atomic hydrogen

    International Nuclear Information System (INIS)

    Electron capture cross sections for low velocity (106-107 cm/s) highly charged Ne/sup q+/ (2 less than or equal to q less than or equal to 7) and Ar/sup q+/ (2 less than or equal to q less than or equal to 10) projectiles incident on molecular and atomic hydrogen targets have been measured. A recoil ion source that uses the collisions of fast heavy (1 MeV/amu) ions with target gas atoms was utilized to produce slow highly charged ions. Atomic hydrogen was produced by dissociating hydrogen molecules in a thermal oven. Measurements and analysis of the data for the atomic hydrogen oven target are discussed in detail. The measured absolute cross sections were compared with the published data and the predictions of theoretical models

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    -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......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...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    in the determination of a membrane protein structure, the CopA Cu+-ATPase, when other methods had failed to resolve the heavy atom substructure. MRPM is particularly suited for proteins undergoing large conformational changes where multiple search models should be generated, and it enables the identification of weak......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 concomitantly the determination of the heavy atom substructure. This is customarily done by direct methods or Patterson......-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...

  9. Mapping hydrophobicity on the protein molecular surface at atom-level resolution.

    Directory of Open Access Journals (Sweden)

    Dan V Nicolau

    Full Text Available 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

  10. Atoms

    Institute of Scientific and Technical Information of China (English)

    刘洪毓

    2007-01-01

    Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what

  11. Molecular mechanisms of asymmetric RAF dimer activation.

    Science.gov (United States)

    Jambrina, Pablo G; Bohuszewicz, Olga; Buchete, Nicolae-Viorel; Kolch, Walter; Rosta, Edina

    2014-08-01

    Protein phosphorylation is one of the most common post-translational modifications in cell regulatory mechanisms. Dimerization plays also a crucial role in the kinase activity of many kinases, including RAF, CDK2 (cyclin-dependent kinase 2) and EGFR (epidermal growth factor receptor), with heterodimers often being the most active forms. However, the structural and mechanistic details of how phosphorylation affects the activity of homo- and hetero-dimers are largely unknown. Experimentally, synthesizing protein samples with fully specified and homogeneous phosphorylation states remains a challenge for structural biology and biochemical studies. Typically, multiple changes in phosphorylation lead to activation of the same protein, which makes structural determination methods particularly difficult. It is also not well understood how the occurrence of phosphorylation and dimerization processes synergize to affect kinase activities. In the present article, we review available structural data and discuss how MD simulations can be used to model conformational transitions of RAF kinase dimers, in both their phosphorylated and unphosphorylated forms. PMID:25109958

  12. Molecular mechanisms of alcohol associated pancreatitis

    Institute of Scientific and Technical Information of China (English)

    Dahn; L; Clemens; Mark; A; Wells; Katrina; J; Schneider; Shailender; Singh

    2014-01-01

    Alcohol abuse is commonly associated with the development of both acute and chronic pancreatitis. Despite this close association, the fact that only a small percentage of human beings who abuse alcohol develop pancreatitis indicates that alcohol abuse alone is not sufficient to initiate clinical pancreatitis. This contention is further supported by the fact that administration of ethanol to experimental animals does not cause pancreatitis. Because of these findings, it is widely believed that ethanol sensitizes the pancreas to injury and additional factors trigger the development of overt pancreatitis. How ethanol sensitizes the pancreas to pancreatitis is not entirely known. Numerous studies have demonstrated that ethanol and its metabolites have a number of deleterious effects on acinar cells. Important acinar cells properties that are affected by ethanol include: calcium signaling, secretion of zymogens, autophagy, cellular regeneration, the unfolded protein response, and mitochondrial membrane integrity. In addition to the actions of ethanol on acinar cells, it is apparent that ethanol also affects pancreatic stellatecells. Pancreatic stellate cells have a critical role in normal tissue repair and the pathologic fibrotic response. Given that ethanol and its metabolites affect so many pancreatic functions, and that all of these effects occur simultaneously, it is likely that none of these effects is "THE" effect. Instead, it is most likely that the cumulative effect of ethanol on the pancreas predisposes the organ to pancreatitis. The focus of this article is to highlight some of the important mechanisms by which ethanol alters pancreatic functions and may predispose the pancreas to disease.

  13. Molecular mechanisms of radioresistance: applications for head and neck cancer

    International Nuclear Information System (INIS)

    A significant part of head and neck cancers is clinically radioresistant. The mechanisms of acquired or intrinsic radioresistance of head and neck tumors are still unclear. More recently molecular research focused on alterations in cell cycle control and resistance to programmed cell death in tumor cells as possible mechanisms of radioresistance. Some molecular targets of radiosensitivity or radioresistance (e.g. specific oncogenes or tumor suppressor genes) are known in specific tumor cells or tumor model systems. Such key targets for head and neck cancer cells are also emerging in in vitro studies. However, it is unclear so far if the modification of such molecular targets in vivo leads to an increased tumor selective radiosensitivity. Nevertheless, selected molecular targets could be potential novel tools for modifying radiosensitivity through gene therapy in patients with radioresistant head and neck cancers. (orig.)

  14. Mechanical feedback in the molecular ISM of luminous IR galaxies

    OpenAIRE

    Loenen, A. F.; Spaans, M.; Baan, W. A.; Meijerink, R

    2008-01-01

    Aims: Molecular emission lines originating in the nuclei of luminous infra-red galaxies are used to determine the physical properties of the nuclear ISM in these systems. Methods: A large observational database of molecular emission lines is compared with model predictions that include heating by UV and X-ray radiation, mechanical heating, and the effects of cosmic rays. Results: The observed line ratios and model predictions imply a separation of the observedsystems into three groups: XDRs, ...

  15. Lactobacilli as multifaceted probiotics with poorly disclosed molecular mechanisms

    OpenAIRE

    Turpin, Williams; Humblot, Christèle; M. Thomas; Guyot, Jean-Pierre

    2010-01-01

    Lactic acid bacteria and more particularly lactobacilli have been used for the production of fermented foods for centuries. Several lactobacilli have been recognized as probiotics due to their wide range of health-promoting effects in humans. However, little is known about the molecular mechanisms underpinning their probiotic functions. Here we reviewed the main beneficial effects of lactobacilli and discussed, when the information is available, the molecular machinery involved in their probi...

  16. SUP-VAMDC: Uniting the International Atomic and Molecular Data Community

    International Nuclear Information System (INIS)

    atomic and molecular data that will underpin the development of the scientific knowledge base that will be required to meet (and overcome) the great scientific challenges of the early 21st century (e.g climate change, space exploration, human health and. crucially, the continued technological advances that will drive the global economy). SUP-VAMDC will therefore develop a strategy that will allow A+M databases/data centres (especially those outside the EU) to adapt their pre-existing structures to those fashioned by the VAMDC e-infrastructure whilst providing the mechanisms and tools for new data centres/databases to be developed such that they are immediately compatible with the recently developed VAMDC platform extending their reach and thence facilitating the adoption of such data centres/databases amongst a wider range of user communities spanning across academia, higher education, citizens and industry. Furthermore SUP-VAMDC will explore both the necessity for, and practicality of, an open e-infrastructure - Open VAMDC - that will takes a product based on e-science technology and primarly used by its established users, and transforms it into a worldwide product shared across communities from academia to citizens, with the inherent opportunities for training and exploitation that such a product brings. (author)

  17. 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.

  18. 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.

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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 H2+ 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.)

  3. GROUP-2, Atomic and Molecular Lattice Vibrations, Group Theory and Symmetry

    International Nuclear Information System (INIS)

    1 - Description of problem or function: This program calculates the symmetry properties of lattice vibrations either for atomic crystals or for external modes of molecular crystals and generates the irreducible multiplier representations (IMR's) including the effects of time reversal invariance (TRI) on the symmetry coordinates. 2 - Method of solution: The invariance of the dynamical matrix under unitary transformations by matrices in a reducible multiplier representation of the time reversal invariant point group of the wave vector leads to a formula for the symmetry-reduction of the dynamical matrix. The projection operator method is used to construct the symmetry coordinates. The projection operator is dependent on the reducible multiplier representation used and the IMR's of the group of the wave vector. These IMR's are generated in the program by the method of orbitals from the representations of cyclic subgroups of the group of the wave vector which in turn are constructed from the roots of unity. The symmetry coordinate vectors form a matrix, which transforms the symmetry-reduced dynamical matrix into block-diagonalized form. 3 - Restrictions on the complexity of the problem: The program is dimensioned for up to 30 degrees of freedom per unit cell. This may be 10 atoms or 5 molecular units per unit cell or some combination of atoms and molecular units. Each atom has 3 degrees of freedom, and each molecular unit has 6. By changing a dimension statement, up to 60 degrees of freedom per unit cell may be considered. Because of the use of random numbers instead of algebraic techniques, the symmetry reduction will be incomplete for crystals of the D3 or C3 point groups. This same problem sometimes occurs for other crystals with a large number of atoms per unit cell

  4. Molecular mechanics work station for protein conformational studies

    International Nuclear Information System (INIS)

    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

  5. Kinetic pathways leading to layer-by-layer growth from hyperthermal atoms: A multibillion time step molecular dynamics study

    International Nuclear Information System (INIS)

    We employ multibillion time step embedded-atom molecular dynamics simulations to investigate the homoepitaxial growth of Pt(111) from hyperthermal Pt atoms (EPt=0.2-50 eV) using deposition fluxes approaching experimental conditions. Calculated antiphase diffraction intensity oscillations, based on adatom coverages as a function of time, reveal a transition from a three-dimensional multilayer growth mode with EPtPt≥20 eV. We isolate the effects of irradiation-induced processes and thermally activated mass transport during deposition in order to identify the mechanisms responsible for promoting layer-by-layer growth. Direct evidence is provided to show that the observed transition in growth modes is primarily due to irradiation-induced processes which occur during the 10 ps following the arrival of each hyperthermal atom. The kinetic pathways leading to the transition involve both enhanced intralayer and interlayer adatom transport, direct incorporation of energetic atoms into clusters, and cluster disruption leading to increased terrace supersaturation

  6. Atomic-Scale Variations of the Mechanical Response of 2D Materials Detected by Noncontact Atomic Force Microscopy

    Science.gov (United States)

    de la Torre, B.; Ellner, M.; Pou, P.; Nicoara, N.; Pérez, Rubén; Gómez-Rodríguez, J. M.

    2016-06-01

    We show that noncontact atomic force microscopy (AFM) is sensitive to the local stiffness in the atomic-scale limit on weakly coupled 2D materials, as graphene on metals. Our large amplitude AFM topography and dissipation images under ultrahigh vacuum and low temperature resolve the atomic and moiré patterns in graphene on Pt(111), despite its extremely low geometric corrugation. The imaging mechanisms are identified with a multiscale model based on density-functional theory calculations, where the energy cost of global and local deformations of graphene competes with short-range chemical and long-range van der Waals interactions. Atomic contrast is related with short-range tip-sample interactions, while the dissipation can be understood in terms of global deformations in the weakly coupled graphene layer. Remarkably, the observed moiré modulation is linked with the subtle variations of the local interplanar graphene-substrate interaction, opening a new route to explore the local mechanical properties of 2D materials at the atomic scale.

  7. Molecular intrinsic characteristic contours of small organic molecules containing oxygen atom

    Institute of Scientific and Technical Information of China (English)

    GONG Lidong; ZHAO Dongxia; YANG Zhongzhi

    2003-01-01

    By utilizing the classical turning point of the electron movement, we have defined and computed the molecular intrinsic characteristic contour (MICC) via the combination of the ab initio quantum chemistry computational method with the ionization potential measured by photoelectron spectroscopy experiment. In this paper, we calculated the MICCs of several small organic molecules containing oxygen atom for the first time. The three-dimensional pictures have been drawn, by performing a large number of calculations. The analysis on some characterized cross-sections of the MICC can provide atomic spatial changing information in the process of forming a molecule.

  8. Atomic and molecular sciences. Progress report No. 9, April 1, 1982-March 31, 1983

    International Nuclear Information System (INIS)

    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 three principal areas: (A) gaseous electronics, (B) reactions in a flowing helium afterglow, and (C) spin-polarized beams and spin-polarimetry

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

    International Nuclear Information System (INIS)

    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

  10. Electronic Friction-Based Vibrational Lifetimes of Molecular Adsorbates: Beyond the Independent-Atom Approximation.

    Science.gov (United States)

    Rittmeyer, Simon P; Meyer, Jörg; Juaristi, J Iñaki; Reuter, Karsten

    2015-07-24

    We assess the accuracy of vibrational damping rates of diatomic adsorbates on metal surfaces as calculated within the local-density friction approximation (LDFA). An atoms-in-molecules (AIM) type charge partitioning scheme accounts for intramolecular contributions and overcomes the systematic underestimation of the nonadiabatic losses obtained within the prevalent independent-atom approximation. The quantitative agreement obtained with theoretical and experimental benchmark data suggests the LDFA-AIM scheme as an efficient and reliable approach to account for electronic dissipation in ab initio molecular dynamics simulations of surface chemical reactions. PMID:26252696

  11. 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

  12. Formation of molecular ions by radiative association of cold trapped atoms and ions

    Science.gov (United States)

    Dulieu, Olivier; da Silva, Humberto, Jr.; Aymar, Mireille; Raoult, Maurice

    2015-05-01

    Radiative emission during cold collisions between trapped laser-cooled Rb atoms and alkaline-earth ions (Ca+ , Sr+ , Ba+) and Yb+ are studied theoretically, using accurate effective-core-potential based quantum chemistry calculations of potential energy curves and transition dipole moments of the related molecular ions. Radiative association of molecular ions is predicted to occur for all systems with a cross section two to ten times larger than the radiative charge transfer one. Partial and total rate constants are also calculated and compared to available experiments. Narrow shape resonances are expected, which could be detectable at low temperature with an experimental resolution at the limit of the present standards. Vibrational distributions show that the final molecular ions are not created in their ground state level. Supported by the Marie-Curie ITN ``COMIQ: Cold Molecular Ions at the Quantum limit'' of the EU (#607491).

  13. A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data

    CERN Document Server

    Eckl, Bernhard; Hasse, Hans

    2009-01-01

    A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...

  14. Molecular Mechanisms Controlling the Early Mouse Embryo Development

    Directory of Open Access Journals (Sweden)

    Alexandra Ivan

    2010-05-01

    Full Text Available Few are known about the molecular mechanism controlling the early embryo development. The reduce dimension of the embryos, only a few μm, the small quantities of proteins synthesized and the artificial environment influence makes difficult to decode the mechanisms controlling early embryonic stages of development. Although, in the last few years many genes have been showed to be active in the early embryonic stages of development, only a few have been characterized and found to be implicated in the molecular mechanism responsible of preimplantational embryos development. Ped gene (Preimplantational embryo development is considered to be involved in regulation of embryonic cleavage division and subsequent embryo survival. This review presents, based on a rich documentation, the main mechanisms involved in early embryo development.

  15. Atomic nitrogen: a parameter study of a micro-scale atmospheric pressure plasma jet by means of molecular beam mass spectrometry

    International Nuclear Information System (INIS)

    Absolute atomic nitrogen densities (N) in the effluent of a micro-scale atmospheric pressure plasma jet (µ-APPJ) operated in He with small admixtures of molecular nitrogen (N2) are measured by means of molecular beam mass spectrometry. Focusing on changes of the external plasma parameters, the dependency of the atomic nitrogen density on the admixture of molecular nitrogen to the plasma, the variation of applied electrode voltage and the variation of distance between the jet nozzle and the sampling orifice of the mass spectrometer are analysed. When varying the N2 admixture, a maximum density of atomic nitrogen of approximately 1.5  ×  1014 cm−3 (∼6 ppm) is reached at about 0.25% N2 admixture. Moreover, the N density increases approximately linearly with the applied voltage. Both results are comparable to atomic oxygen (O) behaviour of the µ-APPJ operated at equal plasma conditions except for admixing molecular O2 instead of nitrogen (Ellerweg et al 2010 New J. Phys. 12 013021). The N density decreases continuously with increasing distance, but the decrease is slower than in the case of O atoms in He/O2 plasma. N atoms with a density of 2.0  ×  1013 cm−3 (∼0.8 ppm) are still detected at 40 mm distance from the jet nozzle in controlled He/N2 atmosphere. The simple fluid simulation of N diffusion does not reproduce the measured densities of N. Nevertheless, a simulation taking into account atomic nitrogen reactions with gas impurities are able to reproduce the measured data, indicating that these reactions are an important loss mechanism of N atoms. The presented results are relevant for the future investigation of interactions of reactive nitrogen species with biological substrates. (paper)

  16. Ultra High Molecular Weight Polyethylene: Mechanics, Morphology, and Clinical Behavior

    OpenAIRE

    Sobieraj, MC; Rimnac, CM

    2008-01-01

    Ultra high molecular weight polyethylene (UHMWPE) is a semicrystalline polymer that has been used for over four decades as a bearing surface in total joint replacements. The mechanical properties and wear properties of UHMWPE are of interest with respect to the in vivo performance of UHMWPE joint replacement components. The mechanical properties of the polymer are dependent on both its crystalline and amorphous phases. Altering either phase (i.e., changing overall crystallinity, crystalline m...

  17. Molecular mechanisms of experience-dependent plasticity in visual cortex

    OpenAIRE

    Tropea, Daniela; Van Wart, Audra; Sur, Mriganka

    2008-01-01

    A remarkable amount of our current knowledge of mechanisms underlying experience-dependent plasticity during cortical development comes from study of the mammalian visual cortex. Recent advances in high-resolution cellular imaging, combined with genetic manipulations in mice, novel fluorescent recombinant probes, and large-scale screens of gene expression, have revealed multiple molecular mechanisms that underlie structural and functional plasticity in visual cortex. We situate these mechanis...

  18. Rotational spectra of N$_2^+$: An advanced undergraduate laboratory in atomic and molecular spectroscopy

    CERN Document Server

    Bayram, S B; Arndt, P T

    2015-01-01

    We describe an inexpensive instructional experiment that demonstrates the rotational energy levels of diatomic nitrogen, using the emission band spectrum of molecular nitrogen ionized by various processes in a commercial AC capillary discharge tube. The simple setup and analytical procedure is introduced as part of a sequence of educational experiments employed by a course of advanced atomic and molecular spectroscopy, where the study of rotational spectra is combined with the analysis of vibrational characteristics for a multifaceted picture of the quantum states of diatomic molecules.

  19. Resveratrol and Calcium Signaling: Molecular Mechanisms and Clinical Relevance

    Directory of Open Access Journals (Sweden)

    Audrey E. McCalley

    2014-06-01

    Full Text Available Resveratrol is a naturally occurring compound contributing to cellular defense mechanisms in plants. Its use as a nutritional component and/or supplement in a number of diseases, disorders, and syndromes such as chronic diseases of the central nervous system, cancer, inflammatory diseases, diabetes, and cardiovascular diseases has prompted great interest in the underlying molecular mechanisms of action. The present review focuses on resveratrol, specifically its isomer trans-resveratrol, and its effects on intracellular calcium signaling mechanisms. As resveratrol’s mechanisms of action are likely pleiotropic, its effects and interactions with key signaling proteins controlling cellular calcium homeostasis are reviewed and discussed. The clinical relevance of resveratrol’s actions on excitable cells, transformed or cancer cells, immune cells and retinal pigment epithelial cells are contrasted with a review of the molecular mechanisms affecting calcium signaling proteins on the plasma membrane, cytoplasm, endoplasmic reticulum, and mitochondria. The present review emphasizes the correlation between molecular mechanisms of action that have recently been identified for resveratrol and their clinical implications.

  20. Molecular and Atomic Excitation Stratification in the Outflow of the Planetary Nebula M27

    CERN Document Server

    McCandliss, S R; Lupu, R E; Burgh, E B; Sembach, K; Kruk, J; Andersson, B G; Feldman, P D; Candliss, Stephan R. Mc; France, Kevin; Lupu, Roxana E.; Burgh, Eric B.; Sembach, Kenneth; Kruk, Jeffrey; Feldman, Paul D.

    2007-01-01

    High resolution spectroscopy with FUSE and STIS of atomic and molecular velocity stratification in the nebular outflow of M27 challenge models for the abundance kinematics in planetary nebulae. The simple picture of a very high speed (~ 1000 km/s), high ionization, radiation driven stellar wind surrounded by a slower (~ 10 km/s) mostly molecular outflow, with low ionization and neutral atomic species residing at the wind interaction interface, is not supported... We find ...there is a fast (33 -- 65 km/s) low ionization zone, surrounding a slower ( H_2^+ + e -> H(1s) + H (nl)), which ultimately produces fluorescence of Ha and Lya. In the optically thin limit at the inferred radius of the velocity transition we find dissociation of H_2 by stellar Lyc photons is an order of magnitude more efficient than spontaneous dissociation by far-UV photons. We suggest that the importance of this H_2 destruction process in HII regions has been overlooked.

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

    International Nuclear Information System (INIS)

    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

  2. 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.

  3. Assessment of atomic and molecular data priorities. Summary report of an IAEA technical meeting

    International Nuclear Information System (INIS)

    The interaction of plasma particles with surfaces will be a vital aspect of the ITER machine and other future fusion devices. The Atomic and Molecular Data Subcommittee of the International Fusion Research Council had recommended that the Atomic and Molecular Data Unit hold a Technical Meeting (TM) to assess the current data priorities in this area. Accordingly, eleven international experts on particle-surface interactions participated in a TM at IAEA Headquarters, Vienna, on 4, 5 December 2006 to assess the data priorities. After a review of the current state of understanding on particle-surface processes involving various proposed materials under different conditions, a list of specific data needs for fusion-related materials was formulated. Areas in which a meaningful CRP could be established were also defined. The discussions, conclusions and recommendations of the TM are briefly described in this report. (author)

  4. Molecular mechanism of adaptive response to low dose radiation

    International Nuclear Information System (INIS)

    Adaptive response is a term used to describe the ability of a low, priming dose of ionizing radiation to modify the effects of a subsequent higher, challenge dose. Molecular mechanism of adaptive response to low dose radiation is involved in signal transduction pathway, reactive oxygen species, DNA damage repair

  5. Dissection of molecular mechanisms underlying speech and language disorders

    OpenAIRE

    Fisher, S

    2005-01-01

    Developmental disorders affecting speech and language are highly heritable, but very little is currently understood about the neuromolecular mechanisms that underlie these traits. Integration of data from diverse research areas, including linguistics, neuropsychology, neuroimaging, genetics, molecular neuroscience, developmental biology, and evolutionary anthropology, is becoming essential for unraveling the relevant pathways. Recent studies of the FOXP2 gene provide a case in point. Mutation...

  6. Rapid Molecular Cloud and Star Formation: Mechanisms and Movies

    CERN Document Server

    Heitsch, Fabian

    2008-01-01

    We demonstrate that the observationally inferred rapid onset of star formation after parental molecular clouds have assembled can be achieved by flow-driven cloud formation of atomic gas, using our previous three-dimensional numerical simulations. We post-process these simulations to approximate CO formation, which allows us to investigate the times at which CO becomes abundant relative to the onset of cloud collapse. We find that global gravity in a finite cloud has two crucial effects on cloud evolution. (a) Lateral collapse (perpendicular to the flows sweeping up the cloud) leads to rapidly increasing column densities above the accumulation from the one-dimensional flow. This in turn allows fast formation of CO, allowing the molecular cloud to ``appear'' rapidly. (b) Global gravity is required to drive the dense gas to the high pressures necessary to form solar-mass cores, in support of recent analytical models of cloud fragmentation. While the clouds still appear ``supersonically turbulent'', this turbule...

  7. Atomic and molecular physics and data activities for astrophysics at Oak Ridge National Laboratory

    International Nuclear Information System (INIS)

    The atomic astrophysics group at ORNL produces, collects, evaluates, and disseminates atomic and molecular data relevant to astrophysics and actively models various astrophysical environments utilizing this information. With the advent of the World Wide Web, these data are also being placed on-line to facilitate their use by end-users. In this brief report, the group's recent activities in data production and in modeling are highlighted. For example, the authors describe recent calculations of elastic and transport cross sections relevant to ionospheric and heliospheric studies, charge transfer between metal ions and metal atoms and novel supernova nebular spectra modeling, ion-molecule collision data relevant to planetary atmospheres and comets, and data for early universe modeling

  8. Hybrid inorganic–organic superlattice structures with atomic layer deposition/molecular layer deposition

    OpenAIRE

    Tynell, Tommi; Yamauchi, Hisao; Karppinen, Maarit

    2014-01-01

    A combination of the atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques is successfully employed to fabricate thin films incorporating superlattice structures that consist of single layers of organic molecules between thicker layers of ZnO. Diethyl zinc and water are used as precursors for the deposition of ZnO by ALD, while three different organic precursors are investigated for the MLD part: hydroquinone, 4-aminophenol and 4,4′-oxydianiline. The successful superla...

  9. IAEA advisory group meeting on atomic and molecular data for fusion plasma impurities

    International Nuclear Information System (INIS)

    This Summary Report briefly summarizes the proceedings, conclusions and recommendations of the IAEA Advisory Group Meeting on ''Atomic and Molecular Data for Fusion Plasma Impurities'', held at the IAEA Headquarters in Vienna on 25-27 September 1991. The reports of the two Meeting Working Groups regarding the data status and needs for spectroscopic and collisional data on plasma impurities are also included. Refs, figs and tabs

  10. Molecular-dynamics simulations of atomic ionization by strong laser fields

    OpenAIRE

    Wasson, D. A.; Koonin, S. E.

    1989-01-01

    We use molecular-dynamics simulations to study the competition between sequential and collective ionization in low-Z atoms by strong laser fields. The model shows sequential ionization at low fields, changing to collective ionization at large fields. The field strength at which this occurs is lower for higher frequencies. We also study the ionization as a function of pulse length and find that collective ionization is favored for shorter pulses.

  11. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    OpenAIRE

    Andrzej Koliński; Maksim Kouza; Dominik Gront; Sebastian Kmiecik; Jacek Wabik

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combi...

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

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

    2005-01-01

    Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between...... the full nonequilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including nonequilibrium heating and provide...

  13. Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics.

    Science.gov (United States)

    Widdifield, Cory M; Robson, Harry; Hodgkinson, Paul

    2016-05-10

    The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples. While the structures differ in the placement of one H atom, using this approach, we verify one of the structures in the Cambridge Structural Database using quantitative tools, while establishing that the other structure does not meet the verification criteria. PMID:27115483

  14. Intense Electron Beams from GaAs Photocathodes as a Tool for Molecular and Atomic Physics

    OpenAIRE

    Krantz, C.

    2009-01-01

    We present cesium-coated GaAs photocathodes as reliable sources of intense, quasi-monoenergetic electron beams in atomic and molecular physics experiments. In long-time operation of the Electron Target of the ion storage ring TSR in Heidelberg, cold electron beams could be realised at steadily improving intensity and reliability. Minimisation of processes degrading the quantum efficiency allowed to increase the extractable current to more than 1mA at stable cathode lifetimes of 24 h or more. ...

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

    International Nuclear Information System (INIS)

    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)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

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

    International Nuclear Information System (INIS)

    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

  18. Atomic and molecular hydrogen in the circumstellar envelopes of late-type stars

    Science.gov (United States)

    Glassgold, A. E.; Huggins, P. J.

    1983-01-01

    The distribution of atomic and molecular hydrogen in the expanding circumstellar envelopes of cool evolved stars is discussed. The main concern is to evaluate the effects of photodestruction of H2 by galactic UV radiation, including shielding of the radiation by H2 itself and by dust in the envelope. One of the most important parameters is the H/H2 ratio which is frozen out in the upper atmosphere of the star. For stars with photospheric temperatures greater than about 2500 K, atmospheric models suggest that the outflowing hydrogen is mainly atomic, whereas cooler stars should be substantially molecular. In the latter case, photodissociation of H2 and heavy molecules contribute to the atomic hydrogen content of the outer envelope. The presented estimates indicate that atomic hydrogen is almost at the limit of detection in the C-rich star IRC + 10216, and may be detectable in warmer stars. Failure to detect it would have important implications for the general understanding of circumstellar envelopes.

  19. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.

    Science.gov (United States)

    Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

    2011-06-15

    We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ∼15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ∼1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction. PMID:21539371

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

    International Nuclear Information System (INIS)

    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 Al3, resulted in production of similar concentration of vacancy defects. However, a drastic increase in vacancy defects is observed due to Al4 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